[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/15082975/LIHC-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/LIHC-TP/15089885/transformed.cor.cli.txt"

nPatients in clinical file=363, in cluster file=370, common to both=357
[1]  62 357
[1] "AMP PEAK  1(1P22.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  1(1P22.3) MUTATED AMP PEAK  1(1P22.3) WILD-TYPE 
                           85                           272 
  AMP PEAK  1(1P22.3) MUTATED AMP PEAK  1(1P22.3) WILD-TYPE 
                           85                           272 
[1] "AMP PEAK  2(1Q22) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  2(1Q22) MUTATED AMP PEAK  2(1Q22) WILD-TYPE 
                        272                          85 
  AMP PEAK  2(1Q22) MUTATED AMP PEAK  2(1Q22) WILD-TYPE 
                        272                          85 
[1] "AMP PEAK  3(1Q42.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  3(1Q42.3) MUTATED AMP PEAK  3(1Q42.3) WILD-TYPE 
                          261                            96 
  AMP PEAK  3(1Q42.3) MUTATED AMP PEAK  3(1Q42.3) WILD-TYPE 
                          261                            96 
[1] "AMP PEAK  4(2P24.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  4(2P24.1) MUTATED AMP PEAK  4(2P24.1) WILD-TYPE 
                           64                           293 
  AMP PEAK  4(2P24.1) MUTATED AMP PEAK  4(2P24.1) WILD-TYPE 
                           64                           293 
[1] "AMP PEAK  5(2Q33.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  5(2Q33.1) MUTATED AMP PEAK  5(2Q33.1) WILD-TYPE 
                           62                           295 
  AMP PEAK  5(2Q33.1) MUTATED AMP PEAK  5(2Q33.1) WILD-TYPE 
                           62                           295 
[1] "AMP PEAK  6(3Q26.31) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  6(3Q26.31) MUTATED AMP PEAK  6(3Q26.31) WILD-TYPE 
                            74                            283 
  AMP PEAK  6(3Q26.31) MUTATED AMP PEAK  6(3Q26.31) WILD-TYPE 
                            74                            283 
[1] "AMP PEAK  7(4P14) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  7(4P14) MUTATED AMP PEAK  7(4P14) WILD-TYPE 
                         52                         305 
  AMP PEAK  7(4P14) MUTATED AMP PEAK  7(4P14) WILD-TYPE 
                         52                         305 
[1] "AMP PEAK  8(5P15.33) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  8(5P15.33) MUTATED AMP PEAK  8(5P15.33) WILD-TYPE 
                           158                            199 
  AMP PEAK  8(5P15.33) MUTATED AMP PEAK  8(5P15.33) WILD-TYPE 
                           158                            199 
[1] "AMP PEAK  9(5Q35.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  9(5Q35.3) MUTATED AMP PEAK  9(5Q35.3) WILD-TYPE 
                          131                           226 
  AMP PEAK  9(5Q35.3) MUTATED AMP PEAK  9(5Q35.3) WILD-TYPE 
                          131                           226 
[1] "AMP PEAK 10(6P25.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 10(6P25.2) MUTATED AMP PEAK 10(6P25.2) WILD-TYPE 
                          150                           207 
  AMP PEAK 10(6P25.2) MUTATED AMP PEAK 10(6P25.2) WILD-TYPE 
                          150                           207 
[1] "AMP PEAK 11(6P21.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 11(6P21.1) MUTATED AMP PEAK 11(6P21.1) WILD-TYPE 
                          151                           206 
  AMP PEAK 11(6P21.1) MUTATED AMP PEAK 11(6P21.1) WILD-TYPE 
                          151                           206 
[1] "AMP PEAK 12(6Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 12(6Q12) MUTATED AMP PEAK 12(6Q12) WILD-TYPE 
                        102                         255 
  AMP PEAK 12(6Q12) MUTATED AMP PEAK 12(6Q12) WILD-TYPE 
                        102                         255 
[1] "AMP PEAK 13(6Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 13(6Q12) MUTATED AMP PEAK 13(6Q12) WILD-TYPE 
                         78                         279 
  AMP PEAK 13(6Q12) MUTATED AMP PEAK 13(6Q12) WILD-TYPE 
                         78                         279 
[1] "AMP PEAK 14(7Q31.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 14(7Q31.2) MUTATED AMP PEAK 14(7Q31.2) WILD-TYPE 
                          115                           242 
  AMP PEAK 14(7Q31.2) MUTATED AMP PEAK 14(7Q31.2) WILD-TYPE 
                          115                           242 
[1] "AMP PEAK 15(8Q13.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 15(8Q13.3) MUTATED AMP PEAK 15(8Q13.3) WILD-TYPE 
                          200                           157 
  AMP PEAK 15(8Q13.3) MUTATED AMP PEAK 15(8Q13.3) WILD-TYPE 
                          200                           157 
[1] "AMP PEAK 16(8Q24.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 16(8Q24.21) MUTATED AMP PEAK 16(8Q24.21) WILD-TYPE 
                           224                            133 
  AMP PEAK 16(8Q24.21) MUTATED AMP PEAK 16(8Q24.21) WILD-TYPE 
                           224                            133 
[1] "AMP PEAK 17(9Q34.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 17(9Q34.2) MUTATED AMP PEAK 17(9Q34.2) WILD-TYPE 
                           44                           313 
  AMP PEAK 17(9Q34.2) MUTATED AMP PEAK 17(9Q34.2) WILD-TYPE 
                           44                           313 
[1] "AMP PEAK 18(11Q13.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 18(11Q13.3) MUTATED AMP PEAK 18(11Q13.3) WILD-TYPE 
                            56                            301 
  AMP PEAK 18(11Q13.3) MUTATED AMP PEAK 18(11Q13.3) WILD-TYPE 
                            56                            301 
[1] "AMP PEAK 19(13Q32.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 19(13Q32.3) MUTATED AMP PEAK 19(13Q32.3) WILD-TYPE 
                            63                            294 
  AMP PEAK 19(13Q32.3) MUTATED AMP PEAK 19(13Q32.3) WILD-TYPE 
                            63                            294 
[1] "AMP PEAK 20(13Q33.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 20(13Q33.3) MUTATED AMP PEAK 20(13Q33.3) WILD-TYPE 
                            64                            293 
  AMP PEAK 20(13Q33.3) MUTATED AMP PEAK 20(13Q33.3) WILD-TYPE 
                            64                            293 
[1] "AMP PEAK 21(15Q26.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 21(15Q26.3) MUTATED AMP PEAK 21(15Q26.3) WILD-TYPE 
                            53                            304 
  AMP PEAK 21(15Q26.3) MUTATED AMP PEAK 21(15Q26.3) WILD-TYPE 
                            53                            304 
[1] "AMP PEAK 22(17P11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 22(17P11.2) MUTATED AMP PEAK 22(17P11.2) WILD-TYPE 
                            46                            311 
  AMP PEAK 22(17P11.2) MUTATED AMP PEAK 22(17P11.2) WILD-TYPE 
                            46                            311 
[1] "AMP PEAK 23(17Q25.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 23(17Q25.3) MUTATED AMP PEAK 23(17Q25.3) WILD-TYPE 
                           141                            216 
  AMP PEAK 23(17Q25.3) MUTATED AMP PEAK 23(17Q25.3) WILD-TYPE 
                           141                            216 
[1] "AMP PEAK 24(19P13.12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 24(19P13.12) MUTATED AMP PEAK 24(19P13.12) WILD-TYPE 
                             66                             291 
  AMP PEAK 24(19P13.12) MUTATED AMP PEAK 24(19P13.12) WILD-TYPE 
                             66                             291 
[1] "AMP PEAK 25(19Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 25(19Q12) MUTATED AMP PEAK 25(19Q12) WILD-TYPE 
                          75                          282 
  AMP PEAK 25(19Q12) MUTATED AMP PEAK 25(19Q12) WILD-TYPE 
                          75                          282 
[1] "AMP PEAK 26(19Q13.11) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 26(19Q13.11) MUTATED AMP PEAK 26(19Q13.11) WILD-TYPE 
                             87                             270 
  AMP PEAK 26(19Q13.11) MUTATED AMP PEAK 26(19Q13.11) WILD-TYPE 
                             87                             270 
[1] "AMP PEAK 27(20Q13.13) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 27(20Q13.13) MUTATED AMP PEAK 27(20Q13.13) WILD-TYPE 
                            118                             239 
  AMP PEAK 27(20Q13.13) MUTATED AMP PEAK 27(20Q13.13) WILD-TYPE 
                            118                             239 
[1] "AMP PEAK 28(20Q13.33) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 28(20Q13.33) MUTATED AMP PEAK 28(20Q13.33) WILD-TYPE 
                            123                             234 
  AMP PEAK 28(20Q13.33) MUTATED AMP PEAK 28(20Q13.33) WILD-TYPE 
                            123                             234 
[1] "AMP PEAK 29(XQ28) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 29(XQ28) MUTATED AMP PEAK 29(XQ28) WILD-TYPE 
                         83                         274 
  AMP PEAK 29(XQ28) MUTATED AMP PEAK 29(XQ28) WILD-TYPE 
                         83                         274 
[1] "DEL PEAK  1(1P36.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                           159                            198 
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                           159                            198 
[1] "DEL PEAK  2(1P36.11) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  2(1P36.11) MUTATED DEL PEAK  2(1P36.11) WILD-TYPE 
                           139                            218 
  DEL PEAK  2(1P36.11) MUTATED DEL PEAK  2(1P36.11) WILD-TYPE 
                           139                            218 
[1] "DEL PEAK  3(2Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                           51                           306 
  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                           51                           306 
[1] "DEL PEAK  4(2Q37.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                           60                           297 
  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                           60                           297 
[1] "DEL PEAK  5(3P13) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  5(3P13) MUTATED DEL PEAK  5(3P13) WILD-TYPE 
                         69                         288 
  DEL PEAK  5(3P13) MUTATED DEL PEAK  5(3P13) WILD-TYPE 
                         69                         288 
[1] "DEL PEAK  6(4P16.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  6(4P16.3) MUTATED DEL PEAK  6(4P16.3) WILD-TYPE 
                           80                           277 
  DEL PEAK  6(4P16.3) MUTATED DEL PEAK  6(4P16.3) WILD-TYPE 
                           80                           277 
[1] "DEL PEAK  7(4Q21.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  7(4Q21.3) MUTATED DEL PEAK  7(4Q21.3) WILD-TYPE 
                          165                           192 
  DEL PEAK  7(4Q21.3) MUTATED DEL PEAK  7(4Q21.3) WILD-TYPE 
                          165                           192 
[1] "DEL PEAK  8(4Q22.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  8(4Q22.3) MUTATED DEL PEAK  8(4Q22.3) WILD-TYPE 
                          166                           191 
  DEL PEAK  8(4Q22.3) MUTATED DEL PEAK  8(4Q22.3) WILD-TYPE 
                          166                           191 
[1] "DEL PEAK  9(4Q35.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  9(4Q35.1) MUTATED DEL PEAK  9(4Q35.1) WILD-TYPE 
                          168                           189 
  DEL PEAK  9(4Q35.1) MUTATED DEL PEAK  9(4Q35.1) WILD-TYPE 
                          168                           189 
[1] "DEL PEAK 10(6Q27) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 10(6Q27) MUTATED DEL PEAK 10(6Q27) WILD-TYPE 
                        133                         224 
  DEL PEAK 10(6Q27) MUTATED DEL PEAK 10(6Q27) WILD-TYPE 
                        133                         224 
[1] "DEL PEAK 11(8P23.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 11(8P23.2) MUTATED DEL PEAK 11(8P23.2) WILD-TYPE 
                          240                           117 
  DEL PEAK 11(8P23.2) MUTATED DEL PEAK 11(8P23.2) WILD-TYPE 
                          240                           117 
[1] "DEL PEAK 12(8P12) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 12(8P12) MUTATED DEL PEAK 12(8P12) WILD-TYPE 
                        234                         123 
  DEL PEAK 12(8P12) MUTATED DEL PEAK 12(8P12) WILD-TYPE 
                        234                         123 
[1] "DEL PEAK 13(9P21.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 13(9P21.3) MUTATED DEL PEAK 13(9P21.3) WILD-TYPE 
                          146                           211 
  DEL PEAK 13(9P21.3) MUTATED DEL PEAK 13(9P21.3) WILD-TYPE 
                          146                           211 
[1] "DEL PEAK 14(9Q31.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 14(9Q31.3) MUTATED DEL PEAK 14(9Q31.3) WILD-TYPE 
                          116                           241 
  DEL PEAK 14(9Q31.3) MUTATED DEL PEAK 14(9Q31.3) WILD-TYPE 
                          116                           241 
[1] "DEL PEAK 15(10Q23.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 15(10Q23.31) MUTATED DEL PEAK 15(10Q23.31) WILD-TYPE 
                             95                             262 
  DEL PEAK 15(10Q23.31) MUTATED DEL PEAK 15(10Q23.31) WILD-TYPE 
                             95                             262 
[1] "DEL PEAK 16(10Q26.13) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 16(10Q26.13) MUTATED DEL PEAK 16(10Q26.13) WILD-TYPE 
                            102                             255 
  DEL PEAK 16(10Q26.13) MUTATED DEL PEAK 16(10Q26.13) WILD-TYPE 
                            102                             255 
[1] "DEL PEAK 17(11Q14.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 17(11Q14.1) MUTATED DEL PEAK 17(11Q14.1) WILD-TYPE 
                            72                            285 
  DEL PEAK 17(11Q14.1) MUTATED DEL PEAK 17(11Q14.1) WILD-TYPE 
                            72                            285 
[1] "DEL PEAK 18(11Q24.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 18(11Q24.2) MUTATED DEL PEAK 18(11Q24.2) WILD-TYPE 
                            90                            267 
  DEL PEAK 18(11Q24.2) MUTATED DEL PEAK 18(11Q24.2) WILD-TYPE 
                            90                            267 
[1] "DEL PEAK 19(12P12.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 19(12P12.1) MUTATED DEL PEAK 19(12P12.1) WILD-TYPE 
                            73                            284 
  DEL PEAK 19(12P12.1) MUTATED DEL PEAK 19(12P12.1) WILD-TYPE 
                            73                            284 
[1] "DEL PEAK 20(12Q24.33) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 20(12Q24.33) MUTATED DEL PEAK 20(12Q24.33) WILD-TYPE 
                             54                             303 
  DEL PEAK 20(12Q24.33) MUTATED DEL PEAK 20(12Q24.33) WILD-TYPE 
                             54                             303 
[1] "DEL PEAK 21(13Q14.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 21(13Q14.2) MUTATED DEL PEAK 21(13Q14.2) WILD-TYPE 
                           169                            188 
  DEL PEAK 21(13Q14.2) MUTATED DEL PEAK 21(13Q14.2) WILD-TYPE 
                           169                            188 
[1] "DEL PEAK 22(14Q23.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 22(14Q23.3) MUTATED DEL PEAK 22(14Q23.3) WILD-TYPE 
                           126                            231 
  DEL PEAK 22(14Q23.3) MUTATED DEL PEAK 22(14Q23.3) WILD-TYPE 
                           126                            231 
[1] "DEL PEAK 23(14Q32.33) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 23(14Q32.33) MUTATED DEL PEAK 23(14Q32.33) WILD-TYPE 
                            129                             228 
  DEL PEAK 23(14Q32.33) MUTATED DEL PEAK 23(14Q32.33) WILD-TYPE 
                            129                             228 
[1] "DEL PEAK 24(15Q26.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 24(15Q26.3) MUTATED DEL PEAK 24(15Q26.3) WILD-TYPE 
                            75                            282 
  DEL PEAK 24(15Q26.3) MUTATED DEL PEAK 24(15Q26.3) WILD-TYPE 
                            75                            282 
[1] "DEL PEAK 25(16Q23.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 25(16Q23.1) MUTATED DEL PEAK 25(16Q23.1) WILD-TYPE 
                           159                            198 
  DEL PEAK 25(16Q23.1) MUTATED DEL PEAK 25(16Q23.1) WILD-TYPE 
                           159                            198 
[1] "DEL PEAK 26(17P13.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 26(17P13.1) MUTATED DEL PEAK 26(17P13.1) WILD-TYPE 
                           217                            140 
  DEL PEAK 26(17P13.1) MUTATED DEL PEAK 26(17P13.1) WILD-TYPE 
                           217                            140 
[1] "DEL PEAK 27(17P11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 27(17P11.2) MUTATED DEL PEAK 27(17P11.2) WILD-TYPE 
                           186                            171 
  DEL PEAK 27(17P11.2) MUTATED DEL PEAK 27(17P11.2) WILD-TYPE 
                           186                            171 
[1] "DEL PEAK 28(18Q21.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 28(18Q21.2) MUTATED DEL PEAK 28(18Q21.2) WILD-TYPE 
                            88                            269 
  DEL PEAK 28(18Q21.2) MUTATED DEL PEAK 28(18Q21.2) WILD-TYPE 
                            88                            269 
[1] "DEL PEAK 29(19P13.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 29(19P13.3) MUTATED DEL PEAK 29(19P13.3) WILD-TYPE 
                            84                            273 
  DEL PEAK 29(19P13.3) MUTATED DEL PEAK 29(19P13.3) WILD-TYPE 
                            84                            273 
[1] "DEL PEAK 30(20P12.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 30(20P12.1) MUTATED DEL PEAK 30(20P12.1) WILD-TYPE 
                            27                            330 
  DEL PEAK 30(20P12.1) MUTATED DEL PEAK 30(20P12.1) WILD-TYPE 
                            27                            330 
[1] "DEL PEAK 31(22Q12.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 31(22Q12.1) MUTATED DEL PEAK 31(22Q12.1) WILD-TYPE 
                            75                            282 
  DEL PEAK 31(22Q12.1) MUTATED DEL PEAK 31(22Q12.1) WILD-TYPE 
                            75                            282 
[1] "DEL PEAK 32(22Q13.32) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 32(22Q13.32) MUTATED DEL PEAK 32(22Q13.32) WILD-TYPE 
                             79                             278 
  DEL PEAK 32(22Q13.32) MUTATED DEL PEAK 32(22Q13.32) WILD-TYPE 
                             79                             278 
[1] "DEL PEAK 33(XQ26.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 33(XQ26.2) MUTATED DEL PEAK 33(XQ26.2) WILD-TYPE 
                           65                           292 
  DEL PEAK 33(XQ26.2) MUTATED DEL PEAK 33(XQ26.2) WILD-TYPE 
                           65                           292 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                        
 [2] "VITAL_STATUS"                          
 [3] "DAYS_TO_DEATH"                         
 [4] "DAYS_TO_LAST_FOLLOWUP"                 
 [5] "PRIMARY_SITE_OF_DISEASE"               
 [6] "NEOPLASM_DISEASESTAGE"                 
 [7] "PATHOLOGY_T_STAGE"                     
 [8] "PATHOLOGY_N_STAGE"                     
 [9] "PATHOLOGY_M_STAGE"                     
[10] "DCC_UPLOAD_DATE"                       
[11] "GENDER"                                
[12] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"  
[13] "DAYS_TO_LAST_KNOWN_ALIVE"              
[14] "RADIATION_THERAPY"                     
[15] "HISTOLOGICAL_TYPE"                     
[16] "RADIATIONS_RADIATION_REGIMENINDICATION"
[17] "COMPLETENESS_OF_RESECTION"             
[18] "RACE"                                  
[19] "ETHNICITY"                             
[20] "BATCH_NUMBER"                          

Input Data has 20 rows and 357 columns.

[1] "Batch" "20"   
[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=61,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=104,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 4:'DAYS_TO_LAST_FOLLOWUP':	nDistinctValues=223,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'PRIMARY_SITE_OF_DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PRIMARY_SITE_OF_DISEASE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'NEOPLASM_DISEASESTAGE':	nDistinctValues=9,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY_T_STAGE':	nDistinctValues=10,	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:'DCC_UPLOAD_DATE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 11:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=19,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 13:'DAYS_TO_LAST_KNOWN_ALIVE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "DAYS_TO_LAST_KNOWN_ALIVE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 14:'RADIATION_THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATION_THERAPY is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
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.
[1] "RADIATIONS_RADIATION_REGIMENINDICATION is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
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=22,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] NA
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "PATHOLOGY_T_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_N_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_M_STAGE is converted to rank data using modified categoies"
[1] "****** SUMMARY ***** "
Output Data has 357 columns, 1 survival variables, and 10 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
 [1] "YEARS_TO_BIRTH"            "NEOPLASM_DISEASESTAGE"    
 [3] "PATHOLOGY_T_STAGE"         "PATHOLOGY_N_STAGE"        
 [5] "PATHOLOGY_M_STAGE"         "GENDER"                   
 [7] "HISTOLOGICAL_TYPE"         "COMPLETENESS_OF_RESECTION"
 [9] "RACE"                      "ETHNICITY"                
YEARS_TO_BIRTH, nv=61, 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 
  1 178  91  73  12 
[1] "table(vv)"
vv
T0+T1    T2    T3    T4 
  179    91    73    12 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T0  T1  T2  T3  T4 
  1 178  91  73  12 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


T0+T1    T2    T3    T4 
  179    91    73    12 
PATHOLOGY_N_STAGE, nv=2, binary=FALSE, numeric=TRUE
PATHOLOGY_M_STAGE, nv=2, binary=FALSE, numeric=TRUE
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    50  26
  AMP PEAK  1(1P22.3) WILD-TYPE 175  83
  AMP PEAK  1(1P22.3) MUTATED AMP PEAK  1(1P22.3) WILD-TYPE 
                           76                           258 
  AMP PEAK  1(1P22.3) MUTATED AMP PEAK  1(1P22.3) WILD-TYPE 
                           26                            83 
$`AMP PEAK  1(1P22.3) MUTATED`
TCGA-2Y-A9GX TCGA-2Y-A9GZ TCGA-2Y-A9H2 TCGA-5C-A9VH TCGA-5R-AA1C TCGA-BC-A10Q 
       80.28        27.88        56.91        10.59        11.97        37.32 
TCGA-BC-A10S TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A8YO 
       46.78        27.52         2.99        44.42        13.84        18.48 
TCGA-BW-A5NO TCGA-CC-5261 TCGA-CC-5263 TCGA-CC-A3MB TCGA-DD-A113 TCGA-DD-A114 
        0.66         3.19         4.24         0.10        79.73        37.78 
TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11C TCGA-DD-A1EH TCGA-DD-A1EJ TCGA-DD-A39X 
        7.33         2.60        21.76        49.15        33.04        55.69 
TCGA-DD-A39Y TCGA-DD-A3A1 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NJ TCGA-DD-A73G 
        5.62         7.66        13.78        30.61        30.51       114.35 
TCGA-DD-AAC8 TCGA-DD-AACB TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACN 
        0.53        76.41         6.41        53.19        69.11        42.81 
TCGA-DD-AACO TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AAD0 TCGA-DD-AADD TCGA-DD-AADF 
       61.68        59.31        51.35         4.50        40.47         3.78 
TCGA-DD-AADI TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADR TCGA-DD-AADW TCGA-DD-AADY 
       35.67        20.91         0.39        66.67        19.30        18.25 
TCGA-DD-AAE0 TCGA-DD-AAE7 TCGA-DD-AAEG TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 
       18.25        21.17        23.64        64.77        62.47        66.25 
TCGA-DD-AAW1 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A7PY TCGA-ED-A7XO TCGA-ED-A8O5 
       65.39        13.41        12.69        12.82        14.04        13.35 
TCGA-EP-A2KB TCGA-FV-A496 TCGA-FV-A4ZP TCGA-G3-A25S TCGA-G3-A25W TCGA-G3-A3CK 
       19.59         0.33        81.73        13.68        30.74        19.23 
TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A7M6 TCGA-G3-A7M9 TCGA-G3-AAV1 TCGA-KR-A7K2 
       25.25        22.95        12.03         1.84        11.80        11.84 
TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MF TCGA-UB-AA0U 
       19.76        16.44         7.04        10.75 

$`AMP PEAK  1(1P22.3) WILD-TYPE`
TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GV TCGA-2Y-A9GW TCGA-2Y-A9GY 
       23.80        53.39        63.75        83.24        41.79        24.89 
TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H3 TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H6 
      120.82        40.41        41.33        47.74        18.25        11.74 
TCGA-2Y-A9H7 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 
       37.25        20.81        14.99         1.18         8.55        13.02 
TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-AAPD TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4072 
        8.61        10.78         0.66        11.08         1.51        48.99 
TCGA-BC-4073 TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z 
       27.91        10.13        27.52        25.32        23.34         1.12 
TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H 
       69.57         5.03         0.26        22.36        17.98        14.60 
TCGA-BC-A69I TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BD-A3ER TCGA-CC-5258 TCGA-CC-5260 
       12.72        44.81        13.45        36.66         0.07         2.86 
TCGA-CC-5262 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MC TCGA-DD-A115 
        3.39         3.32         0.10         0.07         0.13        83.57 
TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A11B TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA 
       53.33       113.00         0.46        51.29        90.71        79.40 
TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG 
       66.31        19.79        75.65        11.47        12.95        45.11 
TCGA-DD-A1EI TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39Z 
        6.02        18.35        13.64        21.14        27.19        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-A4NB TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH 
        0.36        33.14        32.52        90.28        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-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B 
       12.26         0.30        80.75        78.84        23.93         9.30 
TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-AA3A TCGA-DD-AAC9 
       23.05        22.78         1.45        35.67        13.48        11.41 
TCGA-DD-AACA TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG 
       75.65        55.40        12.53        63.48        12.00        15.42 
TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACU 
        0.30         3.52        58.16        13.64        14.20        51.52 
TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD1 
       50.33        46.82         5.59        47.67         5.62        18.54 
TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA 
       21.63        42.58        44.22        22.09        40.08        40.54 
TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADE TCGA-DD-AADG TCGA-DD-AADJ TCGA-DD-AADK 
       40.83        13.97        39.52        37.64        35.05        34.49 
TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADS TCGA-DD-AADU 
       29.52        14.89        15.06        14.33        15.58        18.21 
TCGA-DD-AADV TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 
       18.87        18.15        20.98        18.61        19.99         4.64 
TCGA-DD-AAE8 TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE 
       21.83        23.74        18.90        15.72        25.08        16.37 
TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR 
       25.78        50.33        35.08        79.07        89.69        82.62 
TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAW2 TCGA-DD-AAW3 
       59.93        72.39        76.18        56.48        49.48        53.69 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PZ 
       15.85        13.91        13.35         9.73         0.20         0.20 
TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S 
       13.15        13.41         1.84         0.20        18.74        19.99 
TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT 
       20.61         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 
       60.89        23.97        19.10        27.88         8.12         6.38 
TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V 
       12.03         0.03         0.39        51.06        53.79        28.27 
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-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-AAUZ 
       19.53        20.42        17.10         7.76         5.98        11.24 
TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 
        8.55         9.70         9.17         0.89         8.75         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         2.99        37.91        20.75 
TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-KR-A7K8 
       17.06        16.83         3.72         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        13.97        12.03         9.57        16.67        18.38 
TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF 
       12.85        20.71         0.62        10.85        58.88        19.92 
TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF 
       17.69        21.01         3.09        21.04        19.33        19.04 
TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-T1-A6J8 TCGA-UB-A7MA TCGA-UB-A7MD 
       15.39        15.52        24.13         0.76        17.59         1.71 
TCGA-UB-A7ME TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA46 
       15.98        10.32        11.34         0.99        12.99        24.85 
TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 
       13.55        35.77        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        40.80        79.30        11.21 

  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 
                       114.35                        120.82 
  AMP PEAK  1(1P22.3) MUTATED AMP PEAK  1(1P22.3) WILD-TYPE 
                       19.675                        18.970 
[1] "0.1 - 114.3 (19.7)" "0.0 - 120.8 (19.0)"
[1] "hr=" "1"  
D1V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IIIA
  AMP PEAK  1(1P22.3) MUTATED        34       18         1         18
  AMP PEAK  1(1P22.3) WILD-TYPE     134       66         2         41
                               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          4          4        1         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                             34                           134
  STAGE II                            18                            66
  STAGE III                            1                             2
  STAGE IIIA                          18                            41
  STAGE IIIB                           4                             4
  STAGE IIIC                           3                             4
  STAGE IV                             2                             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  1(1P22.3) MUTATED      35  21  24   5
  AMP PEAK  1(1P22.3) WILD-TYPE   144  70  49   7
D1V4, multiclass
       clus
vv      AMP PEAK  1(1P22.3) MUTATED AMP PEAK  1(1P22.3) WILD-TYPE
  T0+T1                          35                           144
  T2                             21                            70
  T3                             24                            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"
D1V5, binary
                               cls
clus                              0   1
  AMP PEAK  1(1P22.3) MUTATED    61   1
  AMP PEAK  1(1P22.3) WILD-TYPE 188   2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1P22.3) MUTATED     61    1
  AMP PEAK  1(1P22.3) WILD-TYPE  188    2
   clus
vv  AMP PEAK  1(1P22.3) MUTATED AMP PEAK  1(1P22.3) WILD-TYPE
  0                          61                           188
  1                           1                             2
[1] 2 2
[1] FALSE
D1V6, binary
                               cls
clus                              0   1
  AMP PEAK  1(1P22.3) MUTATED    66   3
  AMP PEAK  1(1P22.3) WILD-TYPE 194   1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1P22.3) MUTATED     66    3
  AMP PEAK  1(1P22.3) WILD-TYPE  194    1
   clus
vv  AMP PEAK  1(1P22.3) MUTATED AMP PEAK  1(1P22.3) WILD-TYPE
  0                          66                           194
  1                           3                             1
[1] 2 2
[1] FALSE
D1V7, binary
                               cls
clus                              0   1
  AMP PEAK  1(1P22.3) MUTATED    30  55
  AMP PEAK  1(1P22.3) WILD-TYPE  83 189
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1P22.3) MUTATED     30   55
  AMP PEAK  1(1P22.3) WILD-TYPE   83  189
        clus
vv       AMP PEAK  1(1P22.3) MUTATED AMP PEAK  1(1P22.3) WILD-TYPE
  FEMALE                          30                            83
  MALE                            55                           189
[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                         84
  AMP PEAK  1(1P22.3) WILD-TYPE                      264
                               vv
clus                            HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK  1(1P22.3) MUTATED                                  1
  AMP PEAK  1(1P22.3) WILD-TYPE                                6
D1V8, multiclass
                                  clus
vv                                 AMP PEAK  1(1P22.3) MUTATED
  FIBROLAMELLAR CARCINOMA                                    0
  HEPATOCELLULAR CARCINOMA                                  84
  HEPATOCHOLANGIOCARCINOMA (MIXED)                           1
                                  clus
vv                                 AMP PEAK  1(1P22.3) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                      2
  HEPATOCELLULAR CARCINOMA                                   264
  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  1(1P22.3) MUTATED    71   7   1   6
  AMP PEAK  1(1P22.3) WILD-TYPE 244   8   0  13
D1V9, multiclass
    clus
vv   AMP PEAK  1(1P22.3) MUTATED AMP PEAK  1(1P22.3) WILD-TYPE
  R0                          71                           244
  R1                           7                             8
  R2                           1                             0
  RX                           6                            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  1(1P22.3) MUTATED                                  0    46
  AMP PEAK  1(1P22.3) WILD-TYPE                                1   110
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  1(1P22.3) MUTATED                           3    34
  AMP PEAK  1(1P22.3) WILD-TYPE                        14   139
D1V10, multiclass
                                  clus
vv                                 AMP PEAK  1(1P22.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                     46
  BLACK OR AFRICAN AMERICAN                                  3
  WHITE                                                     34
                                  clus
vv                                 AMP PEAK  1(1P22.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                      110
  BLACK OR AFRICAN AMERICAN                                   14
  WHITE                                                      139
[1] 4 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     1  79
  AMP PEAK  1(1P22.3) WILD-TYPE  10 250
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1P22.3) MUTATED      1   79
  AMP PEAK  1(1P22.3) WILD-TYPE   10  250
                        clus
vv                       AMP PEAK  1(1P22.3) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          79
                        clus
vv                       AMP PEAK  1(1P22.3) WILD-TYPE
  HISPANIC OR LATINO                                10
  NOT HISPANIC OR LATINO                           250
[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   170  85
  AMP PEAK  2(1Q22) WILD-TYPE  55  24
  AMP PEAK  2(1Q22) MUTATED AMP PEAK  2(1Q22) WILD-TYPE 
                        255                          79 
  AMP PEAK  2(1Q22) MUTATED AMP PEAK  2(1Q22) WILD-TYPE 
                         85                          24 
$`AMP PEAK  2(1Q22) MUTATED`
TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H0 
       63.75        41.79        80.28        24.89        27.88       120.82 
TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H5 TCGA-2Y-A9H6 TCGA-2Y-A9H7 
       40.41        56.91        41.33        18.25        11.74        37.25 
TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-5C-A9VG 
       20.81        14.99         1.18         8.55        13.02        10.78 
TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T 
       10.59         0.66        11.97        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        17.98        14.60        12.72        18.48 
TCGA-BD-A3ER TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 
       36.66         0.66         0.07         3.19         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        11.47        12.95 
TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V 
       45.11        49.15        33.04        18.35        13.64        21.14 
TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 
       27.19        55.69         5.62        19.76        25.81         7.66 
TCGA-DD-A3A3 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NF TCGA-DD-A4NH 
       17.59        13.78         0.36        30.61        30.97        30.15 
TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NR 
       26.83        30.51        39.78        29.56        73.81         0.30 
TCGA-DD-A4NV TCGA-DD-A73B TCGA-DD-A73D TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A 
       78.84         9.30        22.78        35.67       114.35        13.48 
TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACE TCGA-DD-AACF 
        0.53        11.41        76.41        55.40        63.48        12.00 
TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN 
        6.41        53.19        69.11         3.52        58.16        42.81 
TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACU 
       61.68        13.64        14.20        59.31        51.35        51.52 
TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD0 
       50.33        46.82         5.59        47.67         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        42.58        44.22        40.08        40.54 
TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ 
       13.97        40.47         3.78        37.64        35.67        35.05 
TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADR 
       34.49        20.91         0.39        14.89        15.06        66.67 
TCGA-DD-AADU TCGA-DD-AADV TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 
       18.21        18.87        19.30        18.25        18.25        18.15 
TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAE9 
       18.61        19.99         4.64        21.17        21.83        23.74 
TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAEK 
       18.90        15.72        25.08        23.64        25.78        35.08 
TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVW TCGA-DD-AAVY 
       79.07        89.69        82.62        59.93        76.18        64.77 
TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 
       62.47        66.25        65.39        49.48        53.69        13.41 
TCGA-ED-A4XI TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO 
       12.69        13.35         9.73        12.82         0.20        14.04 
TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-EP-A12J TCGA-EP-A26S 
       13.15        13.41        13.35         1.84        18.74        19.99 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HT 
       20.61        19.59         0.62         9.96        11.93        14.40 
TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I1 TCGA-FV-A3R3 TCGA-FV-A495 
       60.89        23.97        19.10         8.12        12.03         0.03 
TCGA-FV-A496 TCGA-FV-A4ZP TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25W TCGA-G3-A25X 
        0.33        81.73        13.68        53.79        30.74        58.49 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI 
       14.86        21.53        22.13        19.53        19.23        25.25 
TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M9 TCGA-G3-AAUZ 
       20.42        17.10         7.76        12.03         1.84        11.24 
TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 
        8.55        11.80         9.70         9.17         0.89         8.75 
TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A6G5 
        2.14         3.02         1.02         2.99        37.91        16.83 
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        13.97 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-NI-A8LF 
        9.57        16.67        18.38        12.85        20.71        19.92 
TCGA-O8-A75V TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 
       17.69         3.09        21.04        15.39        15.52        24.13 
TCGA-T1-A6J8 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME 
        0.76        17.59        19.76        16.44         1.71        15.98 
TCGA-UB-A7MF TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-YA-A8S7 
        7.04        10.75        11.34         0.99        12.99        13.55 
TCGA-ZP-A9CV TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZP-A9D4 
       35.77        23.21        23.57         0.69        24.43        12.99 
TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CG 
       45.57        40.80        11.21 

$`AMP PEAK  2(1Q22) WILD-TYPE`
TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GV TCGA-2Y-A9H4 TCGA-4R-AA8I TCGA-5R-AA1D 
       23.80        53.39        83.24        47.74         8.61        11.08 
TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10S TCGA-BC-A10X TCGA-BC-A110 
        1.51        48.99        27.91        46.78        25.32        69.57 
TCGA-BC-A3KF TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-CC-5260 TCGA-CC-A3M9 TCGA-DD-A116 
        0.26        44.81        13.45         2.86         0.10        53.33 
TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EI TCGA-DD-A3A2 TCGA-DD-A3A4 TCGA-DD-A3A5 
       19.79        75.65         6.02        70.06        20.12       102.74 
TCGA-DD-A3A6 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NL TCGA-DD-A4NP 
      107.11        33.14        32.52        90.28        56.25       108.76 
TCGA-DD-A4NQ TCGA-DD-A4NS TCGA-DD-A73A TCGA-DD-A73C TCGA-DD-A73E TCGA-DD-AACA 
       12.26        80.75        23.93        23.05         1.45        75.65 
TCGA-DD-AACD TCGA-DD-AACG TCGA-DD-AACK TCGA-DD-AAD6 TCGA-DD-AADB TCGA-DD-AADE 
       12.53        15.42         0.30        22.09        40.83        39.52 
TCGA-DD-AADN TCGA-DD-AADQ TCGA-DD-AADS TCGA-DD-AAE2 TCGA-DD-AAEE TCGA-DD-AAEI 
       29.52        14.33        15.58        20.98        16.37        50.33 
TCGA-DD-AAVU TCGA-DD-AAVX TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A7PX TCGA-ED-A97K 
       72.39        56.48        15.85        13.91         0.20         0.20 
TCGA-ES-A2HS TCGA-FV-A3I0 TCGA-FV-A3R2 TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25V 
       22.85        27.88         6.38         0.39        51.06        28.27 
TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A5SJ TCGA-G3-A7M7 TCGA-GJ-A9DB TCGA-K7-A5RF 
       25.64         5.92        22.95         5.98         2.20        20.75 
TCGA-K7-A5RG TCGA-K7-AAU7 TCGA-LG-A9QD TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 
       17.06         3.72        12.03         0.62        10.85        58.88 
TCGA-PD-A5DF TCGA-RC-A7SB TCGA-RC-A7SF TCGA-UB-AA0V TCGA-WX-AA46 TCGA-ZP-A9CY 
       21.01        19.33        19.04        10.32        24.85        25.71 
TCGA-ZS-A9CF 
       79.30 

  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 
                     120.82                      108.76 
  AMP PEAK  2(1Q22) MUTATED AMP PEAK  2(1Q22) WILD-TYPE 
                      18.48                       22.85 
[1] "0.0 - 120.8 (18.5)" "0.1 - 108.8 (22.9)"
[1] "hr=" "1.3"
D2V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  2(1Q22) MUTATED       125       67         2         43          7
  AMP PEAK  2(1Q22) WILD-TYPE      43       17         1         16          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        1         0         0
D2V3, multiclass
            clus
vv           AMP PEAK  2(1Q22) MUTATED AMP PEAK  2(1Q22) WILD-TYPE
  STAGE I                          125                          43
  STAGE II                          67                          17
  STAGE III                          2                           1
  STAGE IIIA                        43                          16
  STAGE IIIB                         7                           1
  STAGE IIIC                         5                           2
  STAGE IV                           2                           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
  AMP PEAK  2(1Q22) MUTATED     134  71  55  10
  AMP PEAK  2(1Q22) WILD-TYPE    45  20  18   2
D2V4, multiclass
       clus
vv      AMP PEAK  2(1Q22) MUTATED AMP PEAK  2(1Q22) WILD-TYPE
  T0+T1                       134                          45
  T2                           71                          20
  T3                           55                          18
  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   193   2
  AMP PEAK  2(1Q22) WILD-TYPE  56   1
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  2(1Q22) MUTATED    193    2
  AMP PEAK  2(1Q22) WILD-TYPE   56    1
   clus
vv  AMP PEAK  2(1Q22) MUTATED AMP PEAK  2(1Q22) WILD-TYPE
  0                       193                          56
  1                         2                           1
[1] 2 2
[1] FALSE
D2V6, binary
                             cls
clus                            0   1
  AMP PEAK  2(1Q22) MUTATED   202   4
  AMP PEAK  2(1Q22) WILD-TYPE  58   0
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  2(1Q22) MUTATED    202    4
  AMP PEAK  2(1Q22) WILD-TYPE   58    0
   clus
vv  AMP PEAK  2(1Q22) MUTATED AMP PEAK  2(1Q22) WILD-TYPE
  0                       202                          58
  1                         4                           0
[1] 2 2
[1] FALSE
D2V7, binary
                             cls
clus                            0   1
  AMP PEAK  2(1Q22) MUTATED    89 183
  AMP PEAK  2(1Q22) WILD-TYPE  24  61
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  2(1Q22) MUTATED     89  183
  AMP PEAK  2(1Q22) WILD-TYPE   24   61
        clus
vv       AMP PEAK  2(1Q22) MUTATED AMP PEAK  2(1Q22) WILD-TYPE
  FEMALE                        89                          24
  MALE                         183                          61
[1] 2 2
[1] FALSE
                             vv
clus                          FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  AMP PEAK  2(1Q22) MUTATED                         0                      268
  AMP PEAK  2(1Q22) WILD-TYPE                       2                       80
                             vv
clus                          HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK  2(1Q22) MUTATED                                  4
  AMP PEAK  2(1Q22) WILD-TYPE                                3
D2V8, multiclass
                                  clus
vv                                 AMP PEAK  2(1Q22) MUTATED
  FIBROLAMELLAR CARCINOMA                                  0
  HEPATOCELLULAR CARCINOMA                               268
  HEPATOCHOLANGIOCARCINOMA (MIXED)                         4
                                  clus
vv                                 AMP PEAK  2(1Q22) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                    2
  HEPATOCELLULAR CARCINOMA                                  80
  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  2(1Q22) MUTATED   238  13   1  15
  AMP PEAK  2(1Q22) WILD-TYPE  77   2   0   4
D2V9, multiclass
    clus
vv   AMP PEAK  2(1Q22) MUTATED AMP PEAK  2(1Q22) WILD-TYPE
  R0                       238                          77
  R1                        13                           2
  R2                         1                           0
  RX                        15                           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
  AMP PEAK  2(1Q22) MUTATED                                  1   125
  AMP PEAK  2(1Q22) WILD-TYPE                                0    31
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  2(1Q22) MUTATED                          13   123
  AMP PEAK  2(1Q22) WILD-TYPE                         4    50
D2V10, multiclass
                                  clus
vv                                 AMP PEAK  2(1Q22) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         1
  ASIAN                                                  125
  BLACK OR AFRICAN AMERICAN                               13
  WHITE                                                  123
                                  clus
vv                                 AMP PEAK  2(1Q22) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                     31
  BLACK OR AFRICAN AMERICAN                                  4
  WHITE                                                     50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V11, binary
                             cls
clus                            0   1
  AMP PEAK  2(1Q22) MUTATED     8 250
  AMP PEAK  2(1Q22) WILD-TYPE   3  79
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  2(1Q22) MUTATED      8  250
  AMP PEAK  2(1Q22) WILD-TYPE    3   79
                        clus
vv                       AMP PEAK  2(1Q22) MUTATED AMP PEAK  2(1Q22) WILD-TYPE
  HISPANIC OR LATINO                             8                           3
  NOT HISPANIC OR LATINO                       250                          79
[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   167  78
  AMP PEAK  3(1Q42.3) WILD-TYPE  58  31
  AMP PEAK  3(1Q42.3) MUTATED AMP PEAK  3(1Q42.3) WILD-TYPE 
                          245                            89 
  AMP PEAK  3(1Q42.3) MUTATED AMP PEAK  3(1Q42.3) WILD-TYPE 
                           78                            31 
$`AMP PEAK  3(1Q42.3) MUTATED`
TCGA-2Y-A9GS TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GZ TCGA-2Y-A9H0 
       23.80        63.75        41.79        80.28        27.88       120.82 
TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H5 TCGA-2Y-A9H6 TCGA-2Y-A9H7 
       40.41        56.91        41.33        18.25        11.74        37.25 
TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-5C-A9VH 
       20.81        14.99         8.55        13.02        10.78        10.59 
TCGA-5C-AAPD TCGA-5R-AA1C TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U 
        0.66        11.97        37.32        10.13        27.52        27.52 
TCGA-BC-A10Y TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KG TCGA-BC-A5W4 
       23.34         5.03        44.42        13.84        22.36        17.98 
TCGA-BC-A69H TCGA-BC-A69I TCGA-BD-A2L6 TCGA-BD-A3ER TCGA-BW-A5NO TCGA-CC-5261 
       14.60        12.72        44.81        36.66         0.66         3.19 
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        11.47        12.95        45.11        49.15 
TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39Y 
       33.04        18.35        13.64        21.14        27.19         5.62 
TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A3 TCGA-DD-A3A5 TCGA-DD-A3A7 
       19.76        25.81         7.66        17.59       102.74        13.78 
TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NF TCGA-DD-A4NH 
        0.36        30.61        33.14        32.52        30.97        30.15 
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-A4NV TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G 
        0.30        78.84        22.78         1.45        35.67       114.35 
TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD 
       13.48         0.53        11.41        76.41        55.40        12.53 
TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACL 
       63.48        12.00         6.41        53.19        69.11         3.52 
TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS 
       58.16        42.81        61.68        13.64        14.20        59.31 
TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY 
       51.35        51.52        50.33        46.82         5.59        47.67 
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        42.58        44.22 
TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADD TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI 
       40.08        40.54        40.47         3.78        37.64        35.67 
TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADO TCGA-DD-AADP 
       35.05        34.49        20.91         0.39        14.89        15.06 
TCGA-DD-AADR TCGA-DD-AADU TCGA-DD-AADV TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 
       66.67        18.21        18.87        19.30        18.25        18.25 
TCGA-DD-AAE1 TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAE9 TCGA-DD-AAEA 
       18.15         4.64        21.17        21.83        23.74        18.90 
TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAEK TCGA-DD-AAVP 
       15.72        25.08        23.64        25.78        35.08        79.07 
TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVW TCGA-DD-AAVY TCGA-DD-AAVZ 
       89.69        82.62        59.93        76.18        64.77        62.47 
TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI 
       66.25        65.39        49.48        53.69        13.41        12.69 
TCGA-ED-A5KG TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO 
       15.85        13.35         9.73        12.82         0.20        14.04 
TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-EP-A12J TCGA-EP-A26S 
       13.15        13.41        13.35         1.84        18.74        19.99 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HT 
       20.61        19.59         0.62         9.96        11.93        14.40 
TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I1 TCGA-FV-A3R3 TCGA-FV-A495 
       60.89        23.97        19.10         8.12        12.03         0.03 
TCGA-FV-A496 TCGA-G3-A25S TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z 
        0.33        13.68        30.74        58.49        14.86        21.53 
TCGA-G3-A3CG TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SL TCGA-G3-A5SM 
       22.13        19.53        19.23        25.25        20.42        17.10 
TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M9 TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 
        7.76        12.03         1.84         8.55        11.80         9.70 
TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-HP-A5MZ 
        9.17         0.89         8.75         2.14         3.02         2.99 
TCGA-HP-A5N0 TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-KR-A7K8 
       37.91        16.83         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        13.97         9.57        16.67        18.38        12.85 
TCGA-MI-A75I TCGA-MR-A8JO TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 
       20.71        10.85        17.69        21.01         3.09        21.04 
TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RG-A7D4 TCGA-T1-A6J8 TCGA-UB-A7MA TCGA-UB-A7MC 
       19.04        15.39        24.13         0.76        17.59        16.44 
TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-A7MF TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-A9G7 
        1.71        15.98         7.04        10.75        11.34         0.99 
TCGA-WQ-AB4B TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 
       12.99        35.77        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        40.80        11.21 

$`AMP PEAK  3(1Q42.3) WILD-TYPE`
TCGA-2Y-A9GT TCGA-2Y-A9GV TCGA-2Y-A9GY TCGA-2Y-A9H4 TCGA-2Y-A9HA TCGA-4R-AA8I 
       53.39        83.24        24.89        47.74         1.18         8.61 
TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10S TCGA-BC-A10W 
       11.08         1.51        48.99        27.91        46.78         2.99 
TCGA-BC-A10X TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A3KF TCGA-BC-A8YO TCGA-BD-A3EP 
       25.32         1.12        69.57         0.26        18.48        13.45 
TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-A1HT TCGA-CC-A3MB TCGA-DD-A115 TCGA-DD-A116 
        0.07         2.86         3.32         0.10        83.57        53.33 
TCGA-DD-A11C TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EI TCGA-DD-A39X 
       21.76        66.31        19.79        75.65         6.02        55.69 
TCGA-DD-A3A2 TCGA-DD-A3A4 TCGA-DD-A3A6 TCGA-DD-A4ND TCGA-DD-A4NL TCGA-DD-A4NP 
       70.06        20.12       107.11        90.28        56.25       108.76 
TCGA-DD-A4NS TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-AACA TCGA-DD-AACG 
       80.75        23.93         9.30        23.05        75.65        15.42 
TCGA-DD-AACK TCGA-DD-AAD6 TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADE TCGA-DD-AADN 
        0.30        22.09        40.83        13.97        39.52        29.52 
TCGA-DD-AADQ TCGA-DD-AADS TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAEE 
       14.33        15.58        20.98        18.61        19.99        16.37 
TCGA-DD-AAEI TCGA-DD-AAVU TCGA-DD-AAVX TCGA-ED-A627 TCGA-ED-A7PX TCGA-ED-A97K 
       50.33        72.39        56.48        13.91         0.20         0.20 
TCGA-ES-A2HS TCGA-FV-A3I0 TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25T 
       22.85        27.88         6.38        81.73         0.39        51.06 
TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A5SJ TCGA-G3-A7M7 
       53.79        28.27        25.64         5.92        22.95         5.98 
TCGA-G3-AAUZ TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-AAU7 
       11.24         1.02         2.20        20.75        17.06         3.72 
TCGA-LG-A9QD TCGA-MR-A520 TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-RC-A7SB TCGA-RC-A7SK 
       12.03         0.62        58.88        19.92        19.33        15.52 
TCGA-UB-A7MB TCGA-UB-AA0V TCGA-WX-AA46 TCGA-YA-A8S7 TCGA-ZS-A9CF 
       19.76        10.32        24.85        13.55        79.30 

  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 
                       120.82                        108.76 
  AMP PEAK  3(1Q42.3) MUTATED AMP PEAK  3(1Q42.3) WILD-TYPE 
                        18.74                         20.12 
[1] "0.0 - 120.8 (18.7)" "0.1 - 108.8 (20.1)"
[1] "hr=" "1.1"
D3V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IIIA
  AMP PEAK  3(1Q42.3) MUTATED       118       64         3         38
  AMP PEAK  3(1Q42.3) WILD-TYPE      50       20         0         21
                               vv
clus                            STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK  3(1Q42.3) MUTATED            8          5        3         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                            118                            50
  STAGE II                            64                            20
  STAGE III                            3                             0
  STAGE IIIA                          38                            21
  STAGE IIIB                           8                             0
  STAGE IIIC                           5                             2
  STAGE IV                             3                             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     128  71  51   9
  AMP PEAK  3(1Q42.3) WILD-TYPE    51  20  22   3
D3V4, multiclass
       clus
vv      AMP PEAK  3(1Q42.3) MUTATED AMP PEAK  3(1Q42.3) WILD-TYPE
  T0+T1                         128                            51
  T2                             71                            20
  T3                             51                            22
  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   186   3
  AMP PEAK  3(1Q42.3) WILD-TYPE  63   0
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(1Q42.3) MUTATED    186    3
  AMP PEAK  3(1Q42.3) WILD-TYPE   63    0
   clus
vv  AMP PEAK  3(1Q42.3) MUTATED AMP PEAK  3(1Q42.3) WILD-TYPE
  0                         186                            63
  1                           3                             0
[1] 2 2
[1] FALSE
D3V6, binary
                               cls
clus                              0   1
  AMP PEAK  3(1Q42.3) MUTATED   195   4
  AMP PEAK  3(1Q42.3) WILD-TYPE  65   0
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(1Q42.3) MUTATED    195    4
  AMP PEAK  3(1Q42.3) WILD-TYPE   65    0
   clus
vv  AMP PEAK  3(1Q42.3) MUTATED AMP PEAK  3(1Q42.3) WILD-TYPE
  0                         195                            65
  1                           4                             0
[1] 2 2
[1] FALSE
D3V7, binary
                               cls
clus                              0   1
  AMP PEAK  3(1Q42.3) MUTATED    85 176
  AMP PEAK  3(1Q42.3) WILD-TYPE  28  68
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(1Q42.3) MUTATED     85  176
  AMP PEAK  3(1Q42.3) WILD-TYPE   28   68
        clus
vv       AMP PEAK  3(1Q42.3) MUTATED AMP PEAK  3(1Q42.3) WILD-TYPE
  FEMALE                          85                            28
  MALE                           176                            68
[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                        255
  AMP PEAK  3(1Q42.3) WILD-TYPE                       93
                               vv
clus                            HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK  3(1Q42.3) MUTATED                                  4
  AMP PEAK  3(1Q42.3) WILD-TYPE                                3
D3V8, multiclass
                                  clus
vv                                 AMP PEAK  3(1Q42.3) MUTATED
  FIBROLAMELLAR CARCINOMA                                    2
  HEPATOCELLULAR CARCINOMA                                 255
  HEPATOCHOLANGIOCARCINOMA (MIXED)                           4
                                  clus
vv                                 AMP PEAK  3(1Q42.3) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                      0
  HEPATOCELLULAR CARCINOMA                                    93
  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  3(1Q42.3) MUTATED   231  11   1  13
  AMP PEAK  3(1Q42.3) WILD-TYPE  84   4   0   6
D3V9, multiclass
    clus
vv   AMP PEAK  3(1Q42.3) MUTATED AMP PEAK  3(1Q42.3) WILD-TYPE
  R0                         231                            84
  R1                          11                             4
  R2                           1                             0
  RX                          13                             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
  AMP PEAK  3(1Q42.3) MUTATED                                  1   119
  AMP PEAK  3(1Q42.3) WILD-TYPE                                0    37
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  3(1Q42.3) MUTATED                          13   120
  AMP PEAK  3(1Q42.3) WILD-TYPE                         4    53
D3V10, multiclass
                                  clus
vv                                 AMP PEAK  3(1Q42.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                    119
  BLACK OR AFRICAN AMERICAN                                 13
  WHITE                                                    120
                                  clus
vv                                 AMP PEAK  3(1Q42.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                       37
  BLACK OR AFRICAN AMERICAN                                    4
  WHITE                                                       53
[1] 4 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     7 240
  AMP PEAK  3(1Q42.3) WILD-TYPE   4  89
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(1Q42.3) MUTATED      7  240
  AMP PEAK  3(1Q42.3) WILD-TYPE    4   89
                        clus
vv                       AMP PEAK  3(1Q42.3) MUTATED
  HISPANIC OR LATINO                               7
  NOT HISPANIC OR LATINO                         240
                        clus
vv                       AMP PEAK  3(1Q42.3) WILD-TYPE
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                            89
[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    31  26
  AMP PEAK  4(2P24.1) WILD-TYPE 194  83
  AMP PEAK  4(2P24.1) MUTATED AMP PEAK  4(2P24.1) WILD-TYPE 
                           57                           277 
  AMP PEAK  4(2P24.1) MUTATED AMP PEAK  4(2P24.1) WILD-TYPE 
                           26                            83 
$`AMP PEAK  4(2P24.1) MUTATED`
TCGA-2Y-A9GU TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H2 TCGA-2Y-A9H4 TCGA-2Y-A9H5 
       63.75        24.89        27.88        56.91        47.74        18.25 
TCGA-5R-AA1C TCGA-BC-4072 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A112 
       11.97        48.99        37.32        10.13        27.52         5.03 
TCGA-BC-A5W4 TCGA-BW-A5NO TCGA-CC-5263 TCGA-CC-A3M9 TCGA-DD-A113 TCGA-DD-A115 
       17.98         0.66         4.24         0.10        79.73        83.57 
TCGA-DD-A11A TCGA-DD-A1E9 TCGA-DD-A1EG TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39X 
        2.60        90.71        45.11        33.04        13.64        55.69 
TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NO TCGA-DD-A73B TCGA-DD-A73D TCGA-DD-A73E 
       30.61        33.14        73.81         9.30        22.78         1.45 
TCGA-DD-A73F TCGA-DD-AA3A TCGA-DD-AACB TCGA-DD-AACI TCGA-DD-AAD6 TCGA-DD-AADF 
       35.67        13.48        76.41        53.19        22.09         3.78 
TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADR TCGA-DD-AAE2 TCGA-ED-A7PY TCGA-ED-A82E 
       29.52        14.89        66.67        20.98        12.82        13.41 
TCGA-ED-A8O6 TCGA-EP-A2KA TCGA-ES-A2HS TCGA-G3-A25T TCGA-G3-A25W TCGA-G3-A25Z 
        1.84        20.61        22.85        51.06        30.74        21.53 
TCGA-G3-A7M9 TCGA-G3-AAV0 TCGA-G3-AAV4 TCGA-G3-AAV6 TCGA-LG-A6GG TCGA-UB-A7MA 
        1.84         8.55         0.89         2.14        12.72        17.59 
TCGA-UB-A7MB TCGA-WJ-A86L TCGA-ZS-A9CF 
       19.76        11.34        79.30 

$`AMP PEAK  4(2P24.1) WILD-TYPE`
TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GV TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9H0 
       23.80        53.39        83.24        41.79        80.28       120.82 
TCGA-2Y-A9H1 TCGA-2Y-A9H3 TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-2Y-A9H8 TCGA-2Y-A9H9 
       40.41        41.33        11.74        37.25        20.81        14.99 
TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-A9VH 
        1.18         8.55        13.02         8.61        10.78        10.59 
TCGA-5C-AAPD TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4073 TCGA-BC-A10S TCGA-BC-A10U 
        0.66        11.08         1.51        27.91        46.78        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-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A69I TCGA-BC-A8YO 
       13.84         0.26        22.36        14.60        12.72        18.48 
TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BD-A3ER TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 
       44.81        13.45        36.66         0.07         2.86         3.19 
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        11.47        12.95 
TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EK TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39Y 
       49.15         6.02        18.35        21.14        27.19         5.62 
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-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        90.28 
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-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-A73C TCGA-DD-A73G TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA 
       23.93        23.05       114.35         0.53        11.41        75.65 
TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH 
       55.40        12.53        63.48        12.00        15.42         6.41 
TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO 
       69.11         0.30         3.52        58.16        42.81        61.68 
TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACV 
       13.64        14.20        59.31        51.35        51.52        50.33 
TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 
       46.82         5.59        47.67         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        42.58        44.22        40.08        40.54        40.83 
TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ 
       13.97        40.47        39.52        37.64        35.67        35.05 
TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADS 
       34.49        20.91         0.39        15.06        14.33        15.58 
TCGA-DD-AADU TCGA-DD-AADV TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 
       18.21        18.87        19.30        18.25        18.25        18.15 
TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAE9 
       18.61        19.99         4.64        21.17        21.83        23.74 
TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEH 
       18.90        15.72        25.08        16.37        23.64        25.78 
TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS 
       50.33        35.08        79.07        89.69        82.62        59.93 
TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 
       72.39        76.18        56.48        64.77        62.47        66.25 
TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG 
       65.39        49.48        53.69        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         9.73         0.20         0.20        14.04 
TCGA-ED-A7XP TCGA-ED-A8O5 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KB 
       13.15        13.35         0.20        18.74        19.99        19.59 
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        60.89        23.97 
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        12.03         0.03 
TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25V 
        0.33        81.73         0.39        13.68        53.79        28.27 
TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ 
       58.49        14.86        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        25.25        22.95        20.42        17.10         7.76 
TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-AAUZ TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 
       12.03         5.98        11.24        11.80         9.70         9.17 
TCGA-G3-AAV5 TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 
        8.75         3.02         1.02         2.20         2.99        37.91 
TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K2 
       20.75        17.06        16.83         3.72         2.14        11.84 
TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E 
       13.38        24.36        13.97        12.03         9.57        16.67 
TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 
       18.38        12.85        20.71         0.62        10.85        58.88 
TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SB 
       19.92        17.69        21.01         3.09        21.04        19.33 
TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-T1-A6J8 TCGA-UB-A7MC 
       19.04        15.39        15.52        24.13         0.76        16.44 
TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-A7MF TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WQ-A9G7 
        1.71        15.98         7.04        10.75        10.32         0.99 
TCGA-WQ-AB4B TCGA-WX-AA46 TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ 
       12.99        24.85        13.55        35.77        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        40.80 
TCGA-ZS-A9CG 
       11.21 

  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                        120.82 
  AMP PEAK  4(2P24.1) MUTATED AMP PEAK  4(2P24.1) WILD-TYPE 
                        21.53                         18.90 
[1] "0.1 - 90.7 (21.5)"  "0.0 - 120.8 (18.9)"
[1] "hr=" "1.4"
D4V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IIIA
  AMP PEAK  4(2P24.1) MUTATED        24       14         0         16
  AMP PEAK  4(2P24.1) WILD-TYPE     144       70         3         43
                               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          6          5        2         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                             24                           144
  STAGE II                            14                            70
  STAGE III                            0                             3
  STAGE IIIA                          16                            43
  STAGE IIIB                           2                             6
  STAGE IIIC                           2                             5
  STAGE IV                             1                             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
  AMP PEAK  4(2P24.1) MUTATED      25  17  20   2
  AMP PEAK  4(2P24.1) WILD-TYPE   154  74  53  10
D4V4, multiclass
       clus
vv      AMP PEAK  4(2P24.1) MUTATED AMP PEAK  4(2P24.1) WILD-TYPE
  T0+T1                          25                           154
  T2                             17                            74
  T3                             20                            53
  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    42   2
  AMP PEAK  4(2P24.1) WILD-TYPE 207   1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(2P24.1) MUTATED     42    2
  AMP PEAK  4(2P24.1) WILD-TYPE  207    1
   clus
vv  AMP PEAK  4(2P24.1) MUTATED AMP PEAK  4(2P24.1) WILD-TYPE
  0                          42                           207
  1                           2                             1
[1] 2 2
[1] FALSE
D4V6, binary
                               cls
clus                              0   1
  AMP PEAK  4(2P24.1) MUTATED    42   2
  AMP PEAK  4(2P24.1) WILD-TYPE 218   2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(2P24.1) MUTATED     42    2
  AMP PEAK  4(2P24.1) WILD-TYPE  218    2
   clus
vv  AMP PEAK  4(2P24.1) MUTATED AMP PEAK  4(2P24.1) WILD-TYPE
  0                          42                           218
  1                           2                             2
[1] 2 2
[1] FALSE
D4V7, binary
                               cls
clus                              0   1
  AMP PEAK  4(2P24.1) MUTATED    32  32
  AMP PEAK  4(2P24.1) WILD-TYPE  81 212
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(2P24.1) MUTATED     32   32
  AMP PEAK  4(2P24.1) WILD-TYPE   81  212
        clus
vv       AMP PEAK  4(2P24.1) MUTATED AMP PEAK  4(2P24.1) WILD-TYPE
  FEMALE                          32                            81
  MALE                            32                           212
[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                         62
  AMP PEAK  4(2P24.1) WILD-TYPE                      286
                               vv
clus                            HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK  4(2P24.1) MUTATED                                  2
  AMP PEAK  4(2P24.1) WILD-TYPE                                5
D4V8, multiclass
                                  clus
vv                                 AMP PEAK  4(2P24.1) MUTATED
  FIBROLAMELLAR CARCINOMA                                    0
  HEPATOCELLULAR CARCINOMA                                  62
  HEPATOCHOLANGIOCARCINOMA (MIXED)                           2
                                  clus
vv                                 AMP PEAK  4(2P24.1) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                      2
  HEPATOCELLULAR CARCINOMA                                   286
  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  4(2P24.1) MUTATED    55   5   0   4
  AMP PEAK  4(2P24.1) WILD-TYPE 260  10   1  15
D4V9, multiclass
    clus
vv   AMP PEAK  4(2P24.1) MUTATED AMP PEAK  4(2P24.1) WILD-TYPE
  R0                          55                           260
  R1                           5                            10
  R2                           0                             1
  RX                           4                            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
  AMP PEAK  4(2P24.1) MUTATED                                  0    21
  AMP PEAK  4(2P24.1) WILD-TYPE                                1   135
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  4(2P24.1) MUTATED                           4    39
  AMP PEAK  4(2P24.1) WILD-TYPE                        13   134
D4V10, multiclass
                                  clus
vv                                 AMP PEAK  4(2P24.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                     21
  BLACK OR AFRICAN AMERICAN                                  4
  WHITE                                                     39
                                  clus
vv                                 AMP PEAK  4(2P24.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                      135
  BLACK OR AFRICAN AMERICAN                                   13
  WHITE                                                      134
[1] 4 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  61
  AMP PEAK  4(2P24.1) WILD-TYPE   9 268
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(2P24.1) MUTATED      2   61
  AMP PEAK  4(2P24.1) WILD-TYPE    9  268
                        clus
vv                       AMP PEAK  4(2P24.1) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          61
                        clus
vv                       AMP PEAK  4(2P24.1) WILD-TYPE
  HISPANIC OR LATINO                                 9
  NOT HISPANIC OR LATINO                           268
[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    31  25
  AMP PEAK  5(2Q33.1) WILD-TYPE 194  84
  AMP PEAK  5(2Q33.1) MUTATED AMP PEAK  5(2Q33.1) WILD-TYPE 
                           56                           278 
  AMP PEAK  5(2Q33.1) MUTATED AMP PEAK  5(2Q33.1) WILD-TYPE 
                           25                            84 
$`AMP PEAK  5(2Q33.1) MUTATED`
TCGA-2Y-A9GY TCGA-2Y-A9H0 TCGA-2Y-A9H5 TCGA-5R-AA1C TCGA-BC-4072 TCGA-BC-A10Q 
       24.89       120.82        18.25        11.97        48.99        37.32 
TCGA-BC-A10R TCGA-BC-A10Y TCGA-BC-A217 TCGA-BC-A8YO TCGA-DD-A113 TCGA-DD-A11C 
       10.13        23.34        13.84        18.48        79.73        21.76 
TCGA-DD-A1E9 TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A3A5 
       90.71        33.04        13.64        27.19        55.69       102.74 
TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-AA3A TCGA-DD-AACB 
       13.78        30.61        22.78         1.45        13.48        76.41 
TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACZ TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 
        6.41        53.19         5.62        44.22        22.09        40.08 
TCGA-DD-AADC TCGA-DD-AADF TCGA-DD-AADJ TCGA-DD-AADO TCGA-DD-AADU TCGA-DD-AADW 
       13.97         3.78        35.05        14.89        18.21        19.30 
TCGA-DD-AAE6 TCGA-DD-AAEE TCGA-DD-AAVS TCGA-ED-A7PY TCGA-ED-A82E TCGA-ED-A8O6 
        4.64        16.37        59.93        12.82        13.41         1.84 
TCGA-EP-A2KA TCGA-ES-A2HS TCGA-FV-A495 TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25W 
       20.61        22.85         0.03        13.68        51.06        30.74 
TCGA-G3-A25Z TCGA-G3-A5SM TCGA-G3-AAV6 TCGA-LG-A6GG TCGA-RC-A7SK TCGA-UB-A7MA 
       21.53        17.10         2.14        12.72        15.52        17.59 
TCGA-YA-A8S7 TCGA-ZS-A9CF 
       13.55        79.30 

$`AMP PEAK  5(2Q33.1) WILD-TYPE`
TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GV TCGA-2Y-A9GW TCGA-2Y-A9GX 
       23.80        53.39        63.75        83.24        41.79        80.28 
TCGA-2Y-A9GZ TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H4 TCGA-2Y-A9H6 
       27.88        40.41        56.91        41.33        47.74        11.74 
TCGA-2Y-A9H7 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 
       37.25        20.81        14.99         1.18         8.55        13.02 
TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1D TCGA-5R-AAAM 
        8.61        10.78        10.59         0.66        11.08         1.51 
TCGA-BC-4073 TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X 
       27.91        46.78        27.52        27.52         2.99        25.32 
TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A3KF TCGA-BC-A3KG 
        1.12        69.57         5.03        44.42         0.26        22.36 
TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BD-A3ER 
       17.98        14.60        12.72        44.81        13.45        36.66 
TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 
        0.66         0.07         2.86         3.19         3.39         4.24 
TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A114 
        3.32         0.10         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-A11B 
       83.57        53.33       113.00         7.33         2.60         0.46 
TCGA-DD-A11D TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE 
       51.29        79.40        66.31        19.79        75.65        11.47 
TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EK TCGA-DD-A39V 
       12.95        45.11        49.15         6.02        18.35        21.14 
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-A3A6 TCGA-DD-A3A8 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND 
       20.12       107.11         0.36        33.14        32.52        90.28 
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-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-A73B TCGA-DD-A73C TCGA-DD-A73F TCGA-DD-A73G 
       78.84        23.93         9.30        23.05        35.67       114.35 
TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE 
        0.53        11.41        75.65        55.40        12.53        63.48 
TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM 
       12.00        15.42        69.11         0.30         3.52        58.16 
TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT 
       42.81        61.68        13.64        14.20        59.31        51.35 
TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AAD0 
       51.52        50.33        46.82         5.59        47.67         4.50 
TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADD 
       18.54        21.63        42.58        40.54        40.83        40.47 
TCGA-DD-AADE TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM 
       39.52        37.64        35.67        34.49        20.91         0.39 
TCGA-DD-AADN TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADV 
       29.52        15.06        14.33        66.67        15.58        18.87 
TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 
       18.25        18.25        18.15        20.98        18.61        19.99 
TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAED 
       21.17        21.83        23.74        18.90        15.72        25.08 
TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ 
       23.64        25.78        50.33        35.08        79.07        89.69 
TCGA-DD-AAVR TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ 
       82.62        72.39        76.18        56.48        64.77        62.47 
TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI 
       66.25        65.39        49.48        53.69        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         9.73         0.20         0.20 
TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A8O5 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S 
       14.04        13.15        13.35         0.20        18.74        19.99 
TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B 
       19.59         0.62         9.96        11.93        14.40        60.89 
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        12.03 
TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25X 
        0.33        81.73         0.39        53.79        28.27        58.49 
TCGA-G3-A25Y TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
       14.86        22.13        25.64         5.92        19.53        19.23 
TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 
       25.25        22.95        20.42         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-AAV5 TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ 
        0.89         8.75         3.02         1.02         2.20         2.99 
TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 
       37.91        20.75        17.06        16.83         3.72         2.14 
TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C 
       11.84        13.38        24.36        13.97        12.03         9.57 
TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO 
       16.67        18.38        12.85        20.71         0.62        10.85 
TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 
       58.88        19.92        17.69        21.01         3.09        21.04 
TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RG-A7D4 TCGA-T1-A6J8 TCGA-UB-A7MB 
       19.33        19.04        15.39        24.13         0.76        19.76 
TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-A7MF TCGA-UB-AA0U TCGA-UB-AA0V 
       16.44         1.71        15.98         7.04        10.75        10.32 
TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA46 TCGA-ZP-A9CV TCGA-ZP-A9CY 
       11.34         0.99        12.99        24.85        35.77        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 
       40.80        11.21 

  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 
                       120.82                        114.35 
  AMP PEAK  5(2Q33.1) MUTATED AMP PEAK  5(2Q33.1) WILD-TYPE 
                        18.89                         19.28 
[1] "0.0 - 120.8 (18.9)" "0.1 - 114.3 (19.3)"
[1] "hr=" "1.4"
D5V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IIIA
  AMP PEAK  5(2Q33.1) MUTATED        22       17         2         12
  AMP PEAK  5(2Q33.1) WILD-TYPE     146       67         1         47
                               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          6          5        2         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                             22                           146
  STAGE II                            17                            67
  STAGE III                            2                             1
  STAGE IIIA                          12                            47
  STAGE IIIB                           2                             6
  STAGE IIIC                           2                             5
  STAGE IV                             1                             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
  AMP PEAK  5(2Q33.1) MUTATED      23  19  17   3
  AMP PEAK  5(2Q33.1) WILD-TYPE   156  72  56   9
D5V4, multiclass
       clus
vv      AMP PEAK  5(2Q33.1) MUTATED AMP PEAK  5(2Q33.1) WILD-TYPE
  T0+T1                          23                           156
  T2                             19                            72
  T3                             17                            56
  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    47   1
  AMP PEAK  5(2Q33.1) WILD-TYPE 202   2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(2Q33.1) MUTATED     47    1
  AMP PEAK  5(2Q33.1) WILD-TYPE  202    2
   clus
vv  AMP PEAK  5(2Q33.1) MUTATED AMP PEAK  5(2Q33.1) WILD-TYPE
  0                          47                           202
  1                           1                             2
[1] 2 2
[1] FALSE
D5V6, binary
                               cls
clus                              0   1
  AMP PEAK  5(2Q33.1) MUTATED    49   2
  AMP PEAK  5(2Q33.1) WILD-TYPE 211   2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(2Q33.1) MUTATED     49    2
  AMP PEAK  5(2Q33.1) WILD-TYPE  211    2
   clus
vv  AMP PEAK  5(2Q33.1) MUTATED AMP PEAK  5(2Q33.1) WILD-TYPE
  0                          49                           211
  1                           2                             2
[1] 2 2
[1] FALSE
D5V7, binary
                               cls
clus                              0   1
  AMP PEAK  5(2Q33.1) MUTATED    34  28
  AMP PEAK  5(2Q33.1) WILD-TYPE  79 216
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(2Q33.1) MUTATED     34   28
  AMP PEAK  5(2Q33.1) WILD-TYPE   79  216
        clus
vv       AMP PEAK  5(2Q33.1) MUTATED AMP PEAK  5(2Q33.1) WILD-TYPE
  FEMALE                          34                            79
  MALE                            28                           216
[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                         60
  AMP PEAK  5(2Q33.1) WILD-TYPE                      288
                               vv
clus                            HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK  5(2Q33.1) MUTATED                                  2
  AMP PEAK  5(2Q33.1) WILD-TYPE                                5
D5V8, multiclass
                                  clus
vv                                 AMP PEAK  5(2Q33.1) MUTATED
  FIBROLAMELLAR CARCINOMA                                    0
  HEPATOCELLULAR CARCINOMA                                  60
  HEPATOCHOLANGIOCARCINOMA (MIXED)                           2
                                  clus
vv                                 AMP PEAK  5(2Q33.1) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                      2
  HEPATOCELLULAR CARCINOMA                                   288
  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  5(2Q33.1) MUTATED    56   4   0   2
  AMP PEAK  5(2Q33.1) WILD-TYPE 259  11   1  17
D5V9, multiclass
    clus
vv   AMP PEAK  5(2Q33.1) MUTATED AMP PEAK  5(2Q33.1) WILD-TYPE
  R0                          56                           259
  R1                           4                            11
  R2                           0                             1
  RX                           2                            17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  5(2Q33.1) MUTATED                                  0    26
  AMP PEAK  5(2Q33.1) WILD-TYPE                                1   130
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  5(2Q33.1) MUTATED                           1    34
  AMP PEAK  5(2Q33.1) WILD-TYPE                        16   139
D5V10, multiclass
                                  clus
vv                                 AMP PEAK  5(2Q33.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                     26
  BLACK OR AFRICAN AMERICAN                                  1
  WHITE                                                     34
                                  clus
vv                                 AMP PEAK  5(2Q33.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                      130
  BLACK OR AFRICAN AMERICAN                                   16
  WHITE                                                      139
[1] 4 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     3  57
  AMP PEAK  5(2Q33.1) WILD-TYPE   8 272
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(2Q33.1) MUTATED      3   57
  AMP PEAK  5(2Q33.1) WILD-TYPE    8  272
                        clus
vv                       AMP PEAK  5(2Q33.1) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                          57
                        clus
vv                       AMP PEAK  5(2Q33.1) WILD-TYPE
  HISPANIC OR LATINO                                 8
  NOT HISPANIC OR LATINO                           272
[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    42  27
  AMP PEAK  6(3Q26.31) WILD-TYPE 183  82
  AMP PEAK  6(3Q26.31) MUTATED AMP PEAK  6(3Q26.31) WILD-TYPE 
                            69                            265 
  AMP PEAK  6(3Q26.31) MUTATED AMP PEAK  6(3Q26.31) WILD-TYPE 
                            27                             82 
$`AMP PEAK  6(3Q26.31) MUTATED`
TCGA-2Y-A9GS TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H4 TCGA-2Y-A9H8 TCGA-3K-AAZ8 
       23.80        27.88       120.82        47.74        20.81        13.02 
TCGA-5C-AAPD TCGA-5R-AA1C TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10Y TCGA-BC-A10Z 
        0.66        11.97        10.13        27.52        23.34         1.12 
TCGA-BC-A217 TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BD-A3EP TCGA-BW-A5NO 
       13.84        22.36        17.98        14.60        13.45         0.66 
TCGA-CC-A3MA TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A11C TCGA-DD-A1EF TCGA-DD-A1EJ 
        0.07        37.78        83.57        21.76        12.95        33.04 
TCGA-DD-A1EL TCGA-DD-A39Y TCGA-DD-A3A5 TCGA-DD-A4NI TCGA-DD-A4NV TCGA-DD-A73E 
       13.64         5.62       102.74        26.83        78.84         1.45 
TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AACG TCGA-DD-AACL TCGA-DD-AACS TCGA-DD-AACV 
      114.35        13.48        15.42         3.52        59.31        50.33 
TCGA-DD-AACW TCGA-DD-AACZ TCGA-DD-AAD5 TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADL 
       46.82         5.62        44.22        13.97        40.47        20.91 
TCGA-DD-AADN TCGA-DD-AADR TCGA-DD-AADU TCGA-DD-AAE1 TCGA-DD-AAE6 TCGA-DD-AAE9 
       29.52        66.67        18.21        18.15         4.64        23.74 
TCGA-DD-AAEK TCGA-DD-AAVS TCGA-DD-AAW0 TCGA-ED-A7PX TCGA-ED-A7PZ TCGA-ED-A82E 
       35.08        59.93        66.25         0.20         0.20        13.41 
TCGA-EP-A2KA TCGA-ES-A2HS TCGA-FV-A3R2 TCGA-FV-A495 TCGA-G3-A25X TCGA-G3-A7M9 
       20.61        22.85         6.38         0.03        58.49         1.84 
TCGA-GJ-A6C0 TCGA-KR-A7K8 TCGA-LG-A9QD TCGA-MI-A75G TCGA-PD-A5DF TCGA-UB-A7MC 
        1.02        24.36        12.03        18.38        21.01        16.44 
TCGA-UB-A7MD TCGA-WJ-A86L TCGA-ZS-A9CF 
        1.71        11.34        79.30 

$`AMP PEAK  6(3Q26.31) WILD-TYPE`
TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GV TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GY 
       53.39        63.75        83.24        41.79        80.28        24.89 
TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H5 TCGA-2Y-A9H6 TCGA-2Y-A9H7 
       40.41        56.91        41.33        18.25        11.74        37.25 
TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-A9VH 
       14.99         1.18         8.55         8.61        10.78        10.59 
TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10S 
       11.08         1.51        48.99        27.91        37.32        46.78 
TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 
       27.52         2.99        25.32        69.57         5.03        44.42 
TCGA-BC-A3KF TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3ER TCGA-CC-5258 
        0.26        12.72        18.48        44.81        36.66         0.07 
TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 
        2.86         3.19         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        11.47        45.11        49.15         6.02 
TCGA-DD-A1EK TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Z TCGA-DD-A3A0 
       18.35        21.14        27.19        55.69        19.76        25.81 
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-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NF 
        0.36        30.61        33.14        32.52        90.28        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-A73A TCGA-DD-A73B 
      108.76        12.26         0.30        80.75        23.93         9.30 
TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73F TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA 
       23.05        22.78        35.67         0.53        11.41        75.65 
TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACH 
       76.41        55.40        12.53        63.48        12.00         6.41 
TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO 
       53.19        69.11         0.30        58.16        42.81        61.68 
TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACX TCGA-DD-AACY 
       13.64        14.20        51.35        51.52         5.59        47.67 
TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD6 TCGA-DD-AAD8 
        4.50        18.54        21.63        42.58        22.09        40.08 
TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI 
       40.54        40.83        39.52         3.78        37.64        35.67 
TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADM TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ 
       35.05        34.49         0.39        14.89        15.06        14.33 
TCGA-DD-AADS TCGA-DD-AADV TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE2 
       15.58        18.87        19.30        18.25        18.25        20.98 
TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEB 
       18.61        19.99        21.17        21.83        18.90        15.72 
TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAVP 
       25.08        16.37        23.64        25.78        50.33        79.07 
TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY 
       89.69        82.62        72.39        76.18        56.48        64.77 
TCGA-DD-AAVZ TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI 
       62.47        65.39        49.48        53.69        13.41        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         9.73        12.82        14.04 
TCGA-ED-A7XP TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S 
       13.15        13.35         1.84         0.20        18.74        19.99 
TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B 
       19.59         0.62         9.96        11.93        14.40        60.89 
TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R3 TCGA-FV-A496 
       23.97        19.10        27.88         8.12        12.03         0.33 
TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V 
       81.73         0.39        13.68        51.06        53.79        28.27 
TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI 
       30.74        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        25.25        22.95        20.42        17.10 
TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 
        7.76        12.03         5.98        11.24         8.55        11.80 
TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 
        9.70         9.17         0.89         8.75         2.14         3.02 
TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 
        2.20         2.99        37.91        20.75        17.06        16.83 
TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-LG-A9QC 
        3.72         2.14        11.84        13.38        12.72        13.97 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO 
        9.57        16.67        12.85        20.71         0.62        10.85 
TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SB 
       58.88        19.92        17.69         3.09        21.04        19.33 
TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-T1-A6J8 TCGA-UB-A7MA 
       19.04        15.39        15.52        24.13         0.76        17.59 
TCGA-UB-A7MB TCGA-UB-A7ME TCGA-UB-A7MF TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WQ-A9G7 
       19.76        15.98         7.04        10.75        10.32         0.99 
TCGA-WQ-AB4B TCGA-WX-AA46 TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ 
       12.99        24.85        13.55        35.77        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        40.80 
TCGA-ZS-A9CG 
       11.21 

  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 
                        120.82                         113.00 
  AMP PEAK  6(3Q26.31) MUTATED AMP PEAK  6(3Q26.31) WILD-TYPE 
                         18.38                          19.30 
[1] "0.0 - 120.8 (18.4)" "0.1 - 113.0 (19.3)"
[1] "hr=" "1.2"
D6V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IIIA
  AMP PEAK  6(3Q26.31) MUTATED        31       22         1         12
  AMP PEAK  6(3Q26.31) WILD-TYPE     137       62         2         47
                                vv
clus                             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK  6(3Q26.31) MUTATED            3          1        1         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                              31                            137
  STAGE II                             22                             62
  STAGE III                             1                              2
  STAGE IIIA                           12                             47
  STAGE IIIB                            3                              5
  STAGE IIIC                            1                              6
  STAGE IV                              1                              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      33  22  16   3
  AMP PEAK  6(3Q26.31) WILD-TYPE   146  69  57   9
D6V4, multiclass
       clus
vv      AMP PEAK  6(3Q26.31) MUTATED AMP PEAK  6(3Q26.31) WILD-TYPE
  T0+T1                           33                            146
  T2                              22                             69
  T3                              16                             57
  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    47   1
  AMP PEAK  6(3Q26.31) WILD-TYPE 202   2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  6(3Q26.31) MUTATED     47    1
  AMP PEAK  6(3Q26.31) WILD-TYPE  202    2
   clus
vv  AMP PEAK  6(3Q26.31) MUTATED AMP PEAK  6(3Q26.31) WILD-TYPE
  0                           47                            202
  1                            1                              2
[1] 2 2
[1] FALSE
D6V6, binary
                                cls
clus                               0   1
  AMP PEAK  6(3Q26.31) MUTATED    52   0
  AMP PEAK  6(3Q26.31) WILD-TYPE 208   4
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  6(3Q26.31) MUTATED     52    0
  AMP PEAK  6(3Q26.31) WILD-TYPE  208    4
   clus
vv  AMP PEAK  6(3Q26.31) MUTATED AMP PEAK  6(3Q26.31) WILD-TYPE
  0                           52                            208
  1                            0                              4
[1] 2 2
[1] FALSE
D6V7, binary
                                cls
clus                               0   1
  AMP PEAK  6(3Q26.31) MUTATED    22  52
  AMP PEAK  6(3Q26.31) WILD-TYPE  91 192
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  6(3Q26.31) MUTATED     22   52
  AMP PEAK  6(3Q26.31) WILD-TYPE   91  192
        clus
vv       AMP PEAK  6(3Q26.31) MUTATED AMP PEAK  6(3Q26.31) WILD-TYPE
  FEMALE                           22                             91
  MALE                             52                            192
[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                         72
  AMP PEAK  6(3Q26.31) WILD-TYPE                      276
                                vv
clus                             HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK  6(3Q26.31) MUTATED                                  2
  AMP PEAK  6(3Q26.31) WILD-TYPE                                5
D6V8, multiclass
                                  clus
vv                                 AMP PEAK  6(3Q26.31) MUTATED
  FIBROLAMELLAR CARCINOMA                                     0
  HEPATOCELLULAR CARCINOMA                                   72
  HEPATOCHOLANGIOCARCINOMA (MIXED)                            2
                                  clus
vv                                 AMP PEAK  6(3Q26.31) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                       2
  HEPATOCELLULAR CARCINOMA                                    276
  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  6(3Q26.31) MUTATED    66   2   0   5
  AMP PEAK  6(3Q26.31) WILD-TYPE 249  13   1  14
D6V9, multiclass
    clus
vv   AMP PEAK  6(3Q26.31) MUTATED AMP PEAK  6(3Q26.31) WILD-TYPE
  R0                           66                            249
  R1                            2                             13
  R2                            0                              1
  RX                            5                             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  6(3Q26.31) MUTATED                                  0    30
  AMP PEAK  6(3Q26.31) WILD-TYPE                                1   126
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  6(3Q26.31) MUTATED                           7    36
  AMP PEAK  6(3Q26.31) WILD-TYPE                        10   137
D6V10, multiclass
                                  clus
vv                                 AMP PEAK  6(3Q26.31) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                      30
  BLACK OR AFRICAN AMERICAN                                   7
  WHITE                                                      36
                                  clus
vv                                 AMP PEAK  6(3Q26.31) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                       126
  BLACK OR AFRICAN AMERICAN                                    10
  WHITE                                                       137
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V11, binary
                                cls
clus                               0   1
  AMP PEAK  6(3Q26.31) MUTATED     3  68
  AMP PEAK  6(3Q26.31) WILD-TYPE   8 261
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  6(3Q26.31) MUTATED      3   68
  AMP PEAK  6(3Q26.31) WILD-TYPE    8  261
                        clus
vv                       AMP PEAK  6(3Q26.31) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           68
                        clus
vv                       AMP PEAK  6(3Q26.31) WILD-TYPE
  HISPANIC OR LATINO                                  8
  NOT HISPANIC OR LATINO                            261
[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    37  10
  AMP PEAK  7(4P14) WILD-TYPE 188  99
  AMP PEAK  7(4P14) MUTATED AMP PEAK  7(4P14) WILD-TYPE 
                         47                         287 
  AMP PEAK  7(4P14) MUTATED AMP PEAK  7(4P14) WILD-TYPE 
                         10                          99 
$`AMP PEAK  7(4P14) MUTATED`
TCGA-2Y-A9GU TCGA-2Y-A9GY TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H6 TCGA-2Y-A9H8 
       63.75        24.89        56.91        41.33        11.74        20.81 
TCGA-BC-A10R TCGA-BC-A217 TCGA-BC-A5W4 TCGA-BD-A3EP TCGA-CC-5261 TCGA-CC-A3M9 
       10.13        13.84        17.98        13.45         3.19         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       114.35        15.42        53.19        58.16 
TCGA-DD-AAD3 TCGA-DD-AADB TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADR TCGA-DD-AAED 
       42.58        40.83        14.89        15.06        66.67        25.08 
TCGA-DD-AAVR TCGA-DD-AAVS TCGA-ED-A66X TCGA-ED-A7PZ TCGA-ED-A82E TCGA-ED-A8O5 
       82.62        59.93        13.35         0.20        13.41        13.35 
TCGA-EP-A2KA TCGA-FV-A2QR TCGA-G3-A3CG TCGA-G3-A7M9 TCGA-K7-AAU7 TCGA-LG-A6GG 
       20.61        19.10        22.13         1.84         3.72        12.72 
TCGA-QA-A7B7 TCGA-RC-A7SK TCGA-T1-A6J8 TCGA-WQ-A9G7 TCGA-ZS-A9CF 
        3.09        15.52         0.76         0.99        79.30 

$`AMP PEAK  7(4P14) WILD-TYPE`
TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GV TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GZ 
       23.80        53.39        83.24        41.79        80.28        27.88 
TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H7 TCGA-2Y-A9H9 
      120.82        40.41        47.74        18.25        37.25        14.99 
TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-A9VH 
        1.18         8.55        13.02         8.61        10.78        10.59 
TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-4073 
        0.66        11.97        11.08         1.51        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-A2L6 TCGA-BD-A3ER 
       22.36        14.60        12.72        18.48        44.81        36.66 
TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT 
        0.66         0.07         2.86         3.39         4.24         3.32 
TCGA-CC-A3MA TCGA-CC-A3MC TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A119 
        0.07         0.13        37.78        83.57        53.33         7.33 
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-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EJ TCGA-DD-A1EK 
       75.65        11.47        12.95        45.11        33.04        18.35 
TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z 
       13.64        21.14        27.19        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-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-A4NJ TCGA-DD-A4NK 
       90.28        30.97        30.15        26.83        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-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E 
       78.84        23.93         9.30        23.05        22.78         1.45 
TCGA-DD-A73F TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB 
       35.67        13.48         0.53        11.41        75.65        76.41 
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        69.11 
TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ 
        0.30         3.52        42.81        61.68        13.64        14.20 
TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX 
       59.31        51.35        51.52        50.33        46.82         5.59 
TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD5 
       47.67         5.62         4.50        18.54        21.63        44.22 
TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE 
       22.09        40.08        40.54        13.97        40.47        39.52 
TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL 
        3.78        37.64        35.67        35.05        34.49        20.91 
TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADQ TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADV 
        0.39        29.52        14.33        15.58        18.21        18.87 
TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 
       19.30        18.25        18.25        18.15        20.98        18.61 
TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAE9 TCGA-DD-AAEA 
       19.99         4.64        21.17        21.83        23.74        18.90 
TCGA-DD-AAEB TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAEK 
       15.72        16.37        23.64        25.78        50.33        35.08 
TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY 
       79.07        89.69        72.39        76.18        56.48        64.77 
TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 
       62.47        66.25        65.39        49.48        53.69        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         9.73         0.20        12.82 
TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S 
       14.04        13.15         1.84         0.20        18.74        19.99 
TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT 
       19.59         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 
       60.89        23.97        27.88         8.12         6.38        12.03 
TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T 
        0.03         0.33        81.73         0.39        13.68        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        25.25        22.95 
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-AAV5 
        8.55        11.80         9.70         9.17         0.89         8.75 
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         2.99        37.91 
TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 
       20.75        17.06        16.83         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        13.97        12.03         9.57        16.67        18.38 
TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF 
       12.85        20.71         0.62        10.85        58.88        19.92 
TCGA-O8-A75V TCGA-PD-A5DF TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH 
       17.69        21.01        21.04        19.33        19.04        15.39 
TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME 
       24.13        17.59        19.76        16.44         1.71        15.98 
TCGA-UB-A7MF TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-AB4B TCGA-WX-AA46 
        7.04        10.75        10.32        11.34        12.99        24.85 
TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 
       13.55        35.77        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        40.80        11.21 

  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 
                     114.35                      120.82 
  AMP PEAK  7(4P14) MUTATED AMP PEAK  7(4P14) WILD-TYPE 
                      17.98                       19.33 
[1] "0.1 - 114.3 (18.0)" "0.0 - 120.8 (19.3)"
[1] "hr=" "1.8"
D7V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  7(4P14) MUTATED        20       18         1          9          1
  AMP PEAK  7(4P14) WILD-TYPE     148       66         2         50          7
                             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        3         1         2
D7V3, multiclass
            clus
vv           AMP PEAK  7(4P14) MUTATED AMP PEAK  7(4P14) WILD-TYPE
  STAGE I                           20                         148
  STAGE II                          18                          66
  STAGE III                          1                           2
  STAGE IIIA                         9                          50
  STAGE IIIB                         1                           7
  STAGE IIIC                         0                           7
  STAGE IV                           0                           3
  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      22  17  13   0
  AMP PEAK  7(4P14) WILD-TYPE   157  74  60  12
D7V4, multiclass
       clus
vv      AMP PEAK  7(4P14) MUTATED AMP PEAK  7(4P14) WILD-TYPE
  T0+T1                        22                         157
  T2                           17                          74
  T3                           13                          60
  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    35   0
  AMP PEAK  7(4P14) WILD-TYPE 214   3
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  7(4P14) MUTATED     35    0
  AMP PEAK  7(4P14) WILD-TYPE  214    3
   clus
vv  AMP PEAK  7(4P14) MUTATED AMP PEAK  7(4P14) WILD-TYPE
  0                        35                         214
  1                         0                           3
[1] 2 2
[1] FALSE
D7V6, binary
                             cls
clus                            0   1
  AMP PEAK  7(4P14) MUTATED    40   0
  AMP PEAK  7(4P14) WILD-TYPE 220   4
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  7(4P14) MUTATED     40    0
  AMP PEAK  7(4P14) WILD-TYPE  220    4
   clus
vv  AMP PEAK  7(4P14) MUTATED AMP PEAK  7(4P14) WILD-TYPE
  0                        40                         220
  1                         0                           4
[1] 2 2
[1] FALSE
D7V7, binary
                             cls
clus                            0   1
  AMP PEAK  7(4P14) MUTATED    20  32
  AMP PEAK  7(4P14) WILD-TYPE  93 212
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  7(4P14) MUTATED     20   32
  AMP PEAK  7(4P14) WILD-TYPE   93  212
        clus
vv       AMP PEAK  7(4P14) MUTATED AMP PEAK  7(4P14) WILD-TYPE
  FEMALE                        20                          93
  MALE                          32                         212
[1] 2 2
[1] FALSE
                             vv
clus                          FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  AMP PEAK  7(4P14) MUTATED                         0                       51
  AMP PEAK  7(4P14) WILD-TYPE                       2                      297
                             vv
clus                          HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK  7(4P14) MUTATED                                  1
  AMP PEAK  7(4P14) WILD-TYPE                                6
D7V8, multiclass
                                  clus
vv                                 AMP PEAK  7(4P14) MUTATED
  FIBROLAMELLAR CARCINOMA                                  0
  HEPATOCELLULAR CARCINOMA                                51
  HEPATOCHOLANGIOCARCINOMA (MIXED)                         1
                                  clus
vv                                 AMP PEAK  7(4P14) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                    2
  HEPATOCELLULAR CARCINOMA                                 297
  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    45   2   0   5
  AMP PEAK  7(4P14) WILD-TYPE 270  13   1  14
D7V9, multiclass
    clus
vv   AMP PEAK  7(4P14) MUTATED AMP PEAK  7(4P14) WILD-TYPE
  R0                        45                         270
  R1                         2                          13
  R2                         0                           1
  RX                         5                          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  7(4P14) MUTATED                                  0    25
  AMP PEAK  7(4P14) WILD-TYPE                                1   131
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  7(4P14) MUTATED                           3    24
  AMP PEAK  7(4P14) WILD-TYPE                        14   149
D7V10, multiclass
                                  clus
vv                                 AMP PEAK  7(4P14) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         0
  ASIAN                                                   25
  BLACK OR AFRICAN AMERICAN                                3
  WHITE                                                   24
                                  clus
vv                                 AMP PEAK  7(4P14) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                    131
  BLACK OR AFRICAN AMERICAN                                 14
  WHITE                                                    149
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V11, binary
                             cls
clus                            0   1
  AMP PEAK  7(4P14) MUTATED     1  50
  AMP PEAK  7(4P14) WILD-TYPE  10 279
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  7(4P14) MUTATED      1   50
  AMP PEAK  7(4P14) WILD-TYPE   10  279
                        clus
vv                       AMP PEAK  7(4P14) MUTATED AMP PEAK  7(4P14) WILD-TYPE
  HISPANIC OR LATINO                             1                          10
  NOT HISPANIC OR LATINO                        50                         279
[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    92  54
  AMP PEAK  8(5P15.33) WILD-TYPE 133  55
  AMP PEAK  8(5P15.33) MUTATED AMP PEAK  8(5P15.33) WILD-TYPE 
                           146                            188 
  AMP PEAK  8(5P15.33) MUTATED AMP PEAK  8(5P15.33) WILD-TYPE 
                            54                             55 
$`AMP PEAK  8(5P15.33) MUTATED`
TCGA-2Y-A9GW TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 
       41.79        24.89        27.88       120.82        40.41        56.91 
TCGA-2Y-A9H3 TCGA-2Y-A9H4 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB 
       41.33        47.74        20.81        14.99         1.18         8.55 
TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10W TCGA-BC-A10Z 
       13.02        10.78        37.32        10.13         2.99         1.12 
TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KG TCGA-BC-A8YO TCGA-BD-A3EP 
        5.03        44.42        13.84        22.36        18.48        13.45 
TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MB 
        0.66         0.07         4.24         3.32         0.10         0.10 
TCGA-CC-A3MC TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A11A TCGA-DD-A11D 
        0.13        83.57        53.33       113.00         2.60        51.29 
TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EI TCGA-DD-A1EL 
       90.71        79.40        11.47        12.95         6.02        13.64 
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-A4NJ TCGA-DD-A4NK TCGA-DD-A4NO 
       13.78         0.36        90.28        30.51        39.78        73.81 
TCGA-DD-A4NV TCGA-DD-A73C TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AACA 
       78.84        23.05       114.35        13.48         0.53        75.65 
TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACP TCGA-DD-AACT 
       12.00        15.42        53.19        69.11        13.64        51.35 
TCGA-DD-AACV TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD2 TCGA-DD-AAD5 TCGA-DD-AAD8 
       50.33        47.67         5.62        21.63        44.22        40.08 
TCGA-DD-AADC TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADN TCGA-DD-AADQ TCGA-DD-AADR 
       13.97         3.78        37.64        29.52        14.33        66.67 
TCGA-DD-AADU TCGA-DD-AADV TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE6 TCGA-DD-AAEA 
       18.21        18.87        20.98        18.61         4.64        18.90 
TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEK TCGA-DD-AAVU TCGA-DD-AAVY TCGA-DD-AAW2 
       16.37        23.64        35.08        72.39        64.77        49.48 
TCGA-ED-A459 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E 
       13.41        13.35         9.73        14.04        13.15        13.41 
TCGA-ED-A8O6 TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-ES-A2HT TCGA-FV-A23B 
        1.84        19.59         0.62         9.96        14.40        60.89 
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        81.73         0.39 
TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A3CG TCGA-G3-A3CJ 
       13.68        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 
       25.25        17.10        12.03         1.84        11.24        11.80 
TCGA-G3-AAV2 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A9DB TCGA-HP-A5MZ 
        9.70         8.75         2.14         3.02         2.20         2.99 
TCGA-KR-A7K2 TCGA-LG-A6GG TCGA-LG-A9QC TCGA-MI-A75G TCGA-MI-A75I TCGA-NI-A4U2 
       11.84        12.72        13.97        18.38        20.71        58.88 
TCGA-O8-A75V TCGA-PD-A5DF TCGA-RC-A7SF TCGA-RG-A7D4 TCGA-UB-A7ME TCGA-UB-A7MF 
       17.69        21.01        19.04        24.13        15.98         7.04 
TCGA-UB-AA0U TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-ZP-A9CZ TCGA-ZP-A9D1 TCGA-ZP-A9D2 
       10.75         0.99        12.99        23.21         0.69        24.43 
TCGA-ZP-A9D4 TCGA-ZS-A9CE 
       12.99        40.80 

$`AMP PEAK  8(5P15.33) WILD-TYPE`
TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GV TCGA-2Y-A9GX TCGA-2Y-A9H5 
       23.80        53.39        63.75        83.24        80.28        18.25 
TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C 
       11.74        37.25         8.61        10.59         0.66        11.97 
TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10S TCGA-BC-A10T 
       11.08         1.51        48.99        27.91        46.78        27.52 
TCGA-BC-A10U TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A110 TCGA-BC-A3KF TCGA-BC-A5W4 
       27.52        25.32        23.34        69.57         0.26        17.98 
TCGA-BC-A69H TCGA-BC-A69I TCGA-BD-A2L6 TCGA-BD-A3ER TCGA-CC-5260 TCGA-CC-5261 
       14.60        12.72        44.81        36.66         2.86         3.19 
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-A39W TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A2 
       33.04        18.35        27.19        19.76        25.81        70.06 
TCGA-DD-A3A4 TCGA-DD-A3A6 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NF 
       20.12       107.11        30.61        33.14        32.52        30.97 
TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NP TCGA-DD-A4NQ 
       30.15        26.83        56.25        29.56       108.76        12.26 
TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73D TCGA-DD-A73E 
        0.30        80.75        23.93         9.30        22.78         1.45 
TCGA-DD-A73F TCGA-DD-AAC9 TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE 
       35.67        11.41        76.41        55.40        12.53        63.48 
TCGA-DD-AACH TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO 
        6.41         0.30         3.52        58.16        42.81        61.68 
TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AAD0 
       14.20        59.31        51.52        46.82         5.59         4.50 
TCGA-DD-AAD1 TCGA-DD-AAD3 TCGA-DD-AAD6 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADD 
       18.54        42.58        22.09        40.54        40.83        40.47 
TCGA-DD-AADE TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM 
       39.52        35.67        35.05        34.49        20.91         0.39 
TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADS TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 
       14.89        15.06        15.58        19.30        18.25        18.25 
TCGA-DD-AAE1 TCGA-DD-AAE4 TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAE9 TCGA-DD-AAEB 
       18.15        19.99        21.17        21.83        23.74        15.72 
TCGA-DD-AAED TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR 
       25.08        25.78        50.33        79.07        89.69        82.62 
TCGA-DD-AAVS TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 
       59.93        76.18        56.48        62.47        66.25        65.39 
TCGA-DD-AAW3 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A7PX TCGA-ED-A7PY 
       53.69        12.69        15.85        13.91         0.20        12.82 
TCGA-ED-A7PZ TCGA-ED-A8O5 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
        0.20        13.35         0.20        18.74        19.99        20.61 
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        12.03         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        22.95        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        37.91        20.75        17.06 
TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A9QD 
       16.83         3.72         2.14        13.38        24.36        12.03 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75H TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A8LF 
        9.57        16.67        12.85         0.62        10.85        19.92 
TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SH TCGA-RC-A7SK TCGA-T1-A6J8 
        3.09        21.04        19.33        15.39        15.52         0.76 
TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-AA0V TCGA-WJ-A86L 
       17.59        19.76        16.44         1.71        10.32        11.34 
TCGA-WX-AA46 TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9D0 TCGA-ZS-A9CD 
       24.85        13.55        35.77        25.71        23.57        45.57 
TCGA-ZS-A9CF TCGA-ZS-A9CG 
       79.30        11.21 

  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 
                        120.82                         108.76 
  AMP PEAK  8(5P15.33) MUTATED AMP PEAK  8(5P15.33) WILD-TYPE 
                         17.64                          20.27 
[1] "0.0 - 120.8 (17.6)" "0.1 - 108.8 (20.3)"
[1] "hr=" "1.3"
D8V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IIIA
  AMP PEAK  8(5P15.33) MUTATED        63       41         1         34
  AMP PEAK  8(5P15.33) WILD-TYPE     105       43         2         25
                                vv
clus                             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK  8(5P15.33) MUTATED            5          2        1         1
  AMP PEAK  8(5P15.33) WILD-TYPE          3          5        2         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                              63                            105
  STAGE II                             41                             43
  STAGE III                             1                              2
  STAGE IIIA                           34                             25
  STAGE IIIB                            5                              3
  STAGE IIIC                            2                              5
  STAGE IV                              1                              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
  AMP PEAK  8(5P15.33) MUTATED      68  44  42   4
  AMP PEAK  8(5P15.33) WILD-TYPE   111  47  31   8
D8V4, multiclass
       clus
vv      AMP PEAK  8(5P15.33) MUTATED AMP PEAK  8(5P15.33) WILD-TYPE
  T0+T1                           68                            111
  T2                              44                             47
  T3                              42                             31
  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   109   1
  AMP PEAK  8(5P15.33) WILD-TYPE 140   2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  8(5P15.33) MUTATED    109    1
  AMP PEAK  8(5P15.33) WILD-TYPE  140    2
   clus
vv  AMP PEAK  8(5P15.33) MUTATED AMP PEAK  8(5P15.33) WILD-TYPE
  0                          109                            140
  1                            1                              2
[1] 2 2
[1] FALSE
D8V6, binary
                                cls
clus                               0   1
  AMP PEAK  8(5P15.33) MUTATED   116   1
  AMP PEAK  8(5P15.33) WILD-TYPE 144   3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  8(5P15.33) MUTATED    116    1
  AMP PEAK  8(5P15.33) WILD-TYPE  144    3
   clus
vv  AMP PEAK  8(5P15.33) MUTATED AMP PEAK  8(5P15.33) WILD-TYPE
  0                          116                            144
  1                            1                              3
[1] 2 2
[1] FALSE
D8V7, binary
                                cls
clus                               0   1
  AMP PEAK  8(5P15.33) MUTATED    49 109
  AMP PEAK  8(5P15.33) WILD-TYPE  64 135
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  8(5P15.33) MUTATED     49  109
  AMP PEAK  8(5P15.33) WILD-TYPE   64  135
        clus
vv       AMP PEAK  8(5P15.33) MUTATED AMP PEAK  8(5P15.33) WILD-TYPE
  FEMALE                           49                             64
  MALE                            109                            135
[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                        155
  AMP PEAK  8(5P15.33) WILD-TYPE                      193
                                vv
clus                             HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK  8(5P15.33) MUTATED                                  3
  AMP PEAK  8(5P15.33) WILD-TYPE                                4
D8V8, multiclass
                                  clus
vv                                 AMP PEAK  8(5P15.33) MUTATED
  FIBROLAMELLAR CARCINOMA                                     0
  HEPATOCELLULAR CARCINOMA                                  155
  HEPATOCHOLANGIOCARCINOMA (MIXED)                            3
                                  clus
vv                                 AMP PEAK  8(5P15.33) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                       2
  HEPATOCELLULAR CARCINOMA                                    193
  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  8(5P15.33) MUTATED   140   7   0   8
  AMP PEAK  8(5P15.33) WILD-TYPE 175   8   1  11
D8V9, multiclass
    clus
vv   AMP PEAK  8(5P15.33) MUTATED AMP PEAK  8(5P15.33) WILD-TYPE
  R0                          140                            175
  R1                            7                              8
  R2                            0                              1
  RX                            8                             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  8(5P15.33) MUTATED                                  1    68
  AMP PEAK  8(5P15.33) WILD-TYPE                                0    88
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  8(5P15.33) MUTATED                          10    73
  AMP PEAK  8(5P15.33) WILD-TYPE                         7   100
D8V10, multiclass
                                  clus
vv                                 AMP PEAK  8(5P15.33) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                      68
  BLACK OR AFRICAN AMERICAN                                  10
  WHITE                                                      73
                                  clus
vv                                 AMP PEAK  8(5P15.33) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                        88
  BLACK OR AFRICAN AMERICAN                                     7
  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"
D8V11, binary
                                cls
clus                               0   1
  AMP PEAK  8(5P15.33) MUTATED     6 145
  AMP PEAK  8(5P15.33) WILD-TYPE   5 184
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  8(5P15.33) MUTATED      6  145
  AMP PEAK  8(5P15.33) WILD-TYPE    5  184
                        clus
vv                       AMP PEAK  8(5P15.33) MUTATED
  HISPANIC OR LATINO                                6
  NOT HISPANIC OR LATINO                          145
                        clus
vv                       AMP PEAK  8(5P15.33) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                            184
[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    77  46
  AMP PEAK  9(5Q35.3) WILD-TYPE 148  63
  AMP PEAK  9(5Q35.3) MUTATED AMP PEAK  9(5Q35.3) WILD-TYPE 
                          123                           211 
  AMP PEAK  9(5Q35.3) MUTATED AMP PEAK  9(5Q35.3) WILD-TYPE 
                           46                            63 
$`AMP PEAK  9(5Q35.3) MUTATED`
TCGA-2Y-A9GW TCGA-2Y-A9GZ TCGA-2Y-A9H1 TCGA-2Y-A9H3 TCGA-2Y-A9H4 TCGA-2Y-A9H6 
       41.79        27.88        40.41        41.33        47.74        11.74 
TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-BC-A10Q 
       14.99         1.18         8.55        13.02        10.78        37.32 
TCGA-BC-A10T TCGA-BC-A10W TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 TCGA-CC-A1HT 
       27.52         2.99         5.03        44.42        13.84         3.32 
TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 
        0.10         0.13        83.57        53.33       113.00         7.33 
TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EE TCGA-DD-A39V TCGA-DD-A39W 
       51.29        90.71        79.40        11.47        21.14        27.19 
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-A4NK TCGA-DD-A4NO TCGA-DD-A4NR TCGA-DD-A4NV 
        0.36        90.28        39.78        73.81         0.30        78.84 
TCGA-DD-A73A TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AACC TCGA-DD-AACD 
       23.93       114.35        13.48         0.53        55.40        12.53 
TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACP 
       12.00        15.42         6.41        53.19        69.11        13.64 
TCGA-DD-AACT TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AADC 
       51.35        47.67         5.62        18.54        21.63        13.97 
TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADK TCGA-DD-AADM 
       39.52         3.78        37.64        35.67        34.49         0.39 
TCGA-DD-AADN TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADV 
       29.52        14.33        66.67        15.58        18.21        18.87 
TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE3 TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEK 
       18.25        18.15        18.61        16.37        23.64        35.08 
TCGA-DD-AAVP TCGA-DD-AAVR TCGA-DD-AAVU TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAW0 
       79.07        82.62        72.39        56.48        64.77        66.25 
TCGA-DD-AAW2 TCGA-ED-A66Y TCGA-ED-A7XO TCGA-ED-A7XP TCGA-EP-A2KB TCGA-EP-A2KC 
       49.48         9.73        14.04        13.15        19.59         0.62 
TCGA-EP-A3JL TCGA-ES-A2HT TCGA-FV-A3I0 TCGA-FV-A3R2 TCGA-FV-A495 TCGA-FV-A4ZQ 
        9.96        14.40        27.88         6.38         0.03         0.39 
TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A5SM TCGA-G3-AAV1 
       13.68        51.06        30.74        22.13        17.10        11.80 
TCGA-G3-AAV5 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-LG-A6GG 
        8.75         2.20         2.99         3.72        11.84        12.72 
TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75G TCGA-MI-A75I TCGA-NI-A8LF 
       13.97        12.03         9.57        18.38        20.71        19.92 
TCGA-O8-A75V TCGA-RC-A7SF TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-WQ-A9G7 TCGA-WQ-AB4B 
       17.69        19.04        24.13        17.59         0.99        12.99 
TCGA-ZP-A9CZ TCGA-ZP-A9D1 TCGA-ZS-A9CE 
       23.21         0.69        40.80 

$`AMP PEAK  9(5Q35.3) WILD-TYPE`
TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GV TCGA-2Y-A9GX TCGA-2Y-A9GY 
       23.80        53.39        63.75        83.24        80.28        24.89 
TCGA-2Y-A9H0 TCGA-2Y-A9H2 TCGA-2Y-A9H5 TCGA-2Y-A9H7 TCGA-2Y-A9H8 TCGA-4R-AA8I 
      120.82        56.91        18.25        37.25        20.81         8.61 
TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4072 
       10.59         0.66        11.97        11.08         1.51        48.99 
TCGA-BC-4073 TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10U TCGA-BC-A10X TCGA-BC-A10Y 
       27.91        10.13        46.78        27.52        25.32        23.34 
TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H 
        1.12        69.57         0.26        22.36        17.98        14.60 
TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BD-A3ER TCGA-BW-A5NO 
       12.72        18.48        44.81        13.45        36.66         0.66 
TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A3M9 
        0.07         2.86         3.19         3.39         4.24         0.10 
TCGA-CC-A3MA TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C 
        0.07        79.73        37.78         2.60         0.46        21.76 
TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH 
       66.31        19.79        75.65        12.95        45.11        49.15 
TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39Z TCGA-DD-A3A0 
        6.02        33.04        18.35        13.64        19.76        25.81 
TCGA-DD-A3A2 TCGA-DD-A3A4 TCGA-DD-A3A6 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB 
       70.06        20.12       107.11        30.61        33.14        32.52 
TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NL TCGA-DD-A4NN 
       30.97        30.15        26.83        30.51        56.25        29.56 
TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NS TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D 
      108.76        12.26        80.75         9.30        23.05        22.78 
TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACE 
        1.45        35.67        11.41        75.65        76.41        63.48 
TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACQ 
        0.30         3.52        58.16        42.81        61.68        14.20 
TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AAD0 
       59.31        51.52        50.33        46.82         5.59         4.50 
TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB 
       42.58        44.22        22.09        40.08        40.54        40.83 
TCGA-DD-AADD TCGA-DD-AADJ TCGA-DD-AADL TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADW 
       40.47        35.05        20.91        14.89        15.06        19.30 
TCGA-DD-AADY TCGA-DD-AAE2 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAE8 
       18.25        20.98        19.99         4.64        21.17        21.83 
TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEH TCGA-DD-AAEI 
       23.74        18.90        15.72        25.08        25.78        50.33 
TCGA-DD-AAVQ TCGA-DD-AAVS TCGA-DD-AAVW TCGA-DD-AAVZ TCGA-DD-AAW1 TCGA-DD-AAW3 
       89.69        59.93        76.18        62.47        65.39        53.69 
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-A7PZ TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K 
       12.82         0.20        13.41        13.35         1.84         0.20 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A3RK TCGA-ES-A2HS TCGA-FV-A23B 
       18.74        19.99        20.61        11.93        22.85        60.89 
TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I1 TCGA-FV-A3R3 TCGA-FV-A496 TCGA-FV-A4ZP 
       23.97        19.10         8.12        12.03         0.33        81.73 
TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH 
       53.79        28.27        58.49        14.86        21.53        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        25.25        22.95        20.42 
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-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-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K7 
       37.91        20.75        17.06        16.83         2.14        13.38 
TCGA-KR-A7K8 TCGA-MI-A75E TCGA-MI-A75H TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 
       24.36        16.67        12.85         0.62        10.85        58.88 
TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SH TCGA-RC-A7SK 
       21.01         3.09        21.04        19.33        15.39        15.52 
TCGA-T1-A6J8 TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-A7MF 
        0.76        19.76        16.44         1.71        15.98         7.04 
TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WX-AA46 TCGA-YA-A8S7 TCGA-ZP-A9CV 
       10.75        10.32        11.34        24.85        13.55        35.77 
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        79.30 
TCGA-ZS-A9CG 
       11.21 

  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 
                       114.35                        120.82 
  AMP PEAK  9(5Q35.3) MUTATED AMP PEAK  9(5Q35.3) WILD-TYPE 
                        18.21                         19.99 
[1] "0.0 - 114.3 (18.2)" "0.1 - 120.8 (20.0)"
[1] "hr=" "1.2"
D9V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IIIA
  AMP PEAK  9(5Q35.3) MUTATED        61       33         2         21
  AMP PEAK  9(5Q35.3) WILD-TYPE     107       51         1         38
                               vv
clus                            STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK  9(5Q35.3) MUTATED            3          1        2         0
  AMP PEAK  9(5Q35.3) WILD-TYPE          5          6        1         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                             61                           107
  STAGE II                            33                            51
  STAGE III                            2                             1
  STAGE IIIA                          21                            38
  STAGE IIIB                           3                             5
  STAGE IIIC                           1                             6
  STAGE IV                             2                             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  9(5Q35.3) MUTATED      63  36  29   3
  AMP PEAK  9(5Q35.3) WILD-TYPE   116  55  44   9
D9V4, multiclass
       clus
vv      AMP PEAK  9(5Q35.3) MUTATED AMP PEAK  9(5Q35.3) WILD-TYPE
  T0+T1                          63                           116
  T2                             36                            55
  T3                             29                            44
  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    91   0
  AMP PEAK  9(5Q35.3) WILD-TYPE 158   3
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  9(5Q35.3) MUTATED     91    0
  AMP PEAK  9(5Q35.3) WILD-TYPE  158    3
   clus
vv  AMP PEAK  9(5Q35.3) MUTATED AMP PEAK  9(5Q35.3) WILD-TYPE
  0                          91                           158
  1                           0                             3
[1] 2 2
[1] FALSE
D9V6, binary
                               cls
clus                              0   1
  AMP PEAK  9(5Q35.3) MUTATED    98   2
  AMP PEAK  9(5Q35.3) WILD-TYPE 162   2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  9(5Q35.3) MUTATED     98    2
  AMP PEAK  9(5Q35.3) WILD-TYPE  162    2
   clus
vv  AMP PEAK  9(5Q35.3) MUTATED AMP PEAK  9(5Q35.3) WILD-TYPE
  0                          98                           162
  1                           2                             2
[1] 2 2
[1] FALSE
D9V7, binary
                               cls
clus                              0   1
  AMP PEAK  9(5Q35.3) MUTATED    37  94
  AMP PEAK  9(5Q35.3) WILD-TYPE  76 150
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  9(5Q35.3) MUTATED     37   94
  AMP PEAK  9(5Q35.3) WILD-TYPE   76  150
        clus
vv       AMP PEAK  9(5Q35.3) MUTATED AMP PEAK  9(5Q35.3) WILD-TYPE
  FEMALE                          37                            76
  MALE                            94                           150
[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                        126
  AMP PEAK  9(5Q35.3) WILD-TYPE                      222
                               vv
clus                            HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK  9(5Q35.3) MUTATED                                  5
  AMP PEAK  9(5Q35.3) WILD-TYPE                                2
D9V8, multiclass
                                  clus
vv                                 AMP PEAK  9(5Q35.3) MUTATED
  FIBROLAMELLAR CARCINOMA                                    0
  HEPATOCELLULAR CARCINOMA                                 126
  HEPATOCHOLANGIOCARCINOMA (MIXED)                           5
                                  clus
vv                                 AMP PEAK  9(5Q35.3) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                      2
  HEPATOCELLULAR CARCINOMA                                   222
  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   116   8   1   4
  AMP PEAK  9(5Q35.3) WILD-TYPE 199   7   0  15
D9V9, multiclass
    clus
vv   AMP PEAK  9(5Q35.3) MUTATED AMP PEAK  9(5Q35.3) WILD-TYPE
  R0                         116                           199
  R1                           8                             7
  R2                           1                             0
  RX                           4                            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
  AMP PEAK  9(5Q35.3) MUTATED                                  0    61
  AMP PEAK  9(5Q35.3) WILD-TYPE                                1    95
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  9(5Q35.3) MUTATED                           6    59
  AMP PEAK  9(5Q35.3) WILD-TYPE                        11   114
D9V10, multiclass
                                  clus
vv                                 AMP PEAK  9(5Q35.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                     61
  BLACK OR AFRICAN AMERICAN                                  6
  WHITE                                                     59
                                  clus
vv                                 AMP PEAK  9(5Q35.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                       95
  BLACK OR AFRICAN AMERICAN                                   11
  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"
D9V11, binary
                               cls
clus                              0   1
  AMP PEAK  9(5Q35.3) MUTATED     5 119
  AMP PEAK  9(5Q35.3) WILD-TYPE   6 210
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  9(5Q35.3) MUTATED      5  119
  AMP PEAK  9(5Q35.3) WILD-TYPE    6  210
                        clus
vv                       AMP PEAK  9(5Q35.3) MUTATED
  HISPANIC OR LATINO                               5
  NOT HISPANIC OR LATINO                         119
                        clus
vv                       AMP PEAK  9(5Q35.3) WILD-TYPE
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                           210
[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    87  52
  AMP PEAK 10(6P25.2) WILD-TYPE 138  57
  AMP PEAK 10(6P25.2) MUTATED AMP PEAK 10(6P25.2) WILD-TYPE 
                          139                           195 
  AMP PEAK 10(6P25.2) MUTATED AMP PEAK 10(6P25.2) WILD-TYPE 
                           52                            57 
$`AMP PEAK 10(6P25.2) MUTATED`
TCGA-2Y-A9GS TCGA-2Y-A9GV TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H2 TCGA-2Y-A9H3 
       23.80        83.24        24.89        27.88        56.91        41.33 
TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-2Y-A9HA TCGA-3K-AAZ8 TCGA-5R-AA1C TCGA-BC-4073 
       18.25        20.81         1.18        13.02        11.97        27.91 
TCGA-BC-A10R TCGA-BC-A10U TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KG 
       10.13        27.52         5.03        44.42        13.84        22.36 
TCGA-BC-A69H TCGA-BC-A69I TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5261 
       14.60        12.72        44.81        13.45         0.66         3.19 
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        11.47        12.95        45.11        49.15 
TCGA-DD-A1EJ TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A5 TCGA-DD-A3A7 
       33.04        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        22.78         1.45         0.53        75.65        76.41 
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        69.11 
TCGA-DD-AACN TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACT TCGA-DD-AAD3 TCGA-DD-AADA 
       42.81        13.64        14.20        51.35        42.58        40.54 
TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO 
        3.78        37.64        20.91         0.39        29.52        14.89 
TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADV TCGA-DD-AADW TCGA-DD-AAE0 TCGA-DD-AAE2 
       15.06        14.33        18.87        19.30        18.25        20.98 
TCGA-DD-AAE3 TCGA-DD-AAE9 TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAEK TCGA-DD-AAVR 
       18.61        23.74        23.64        25.78        35.08        82.62 
TCGA-DD-AAVS TCGA-DD-AAVW TCGA-DD-AAVY TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A66X 
       59.93        76.18        64.77        49.48        53.69        13.35 
TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-EP-A2KA 
       12.82         0.20        13.41        13.35         1.84        20.61 
TCGA-EP-A2KB TCGA-EP-A2KC TCGA-ES-A2HS TCGA-FV-A3I0 TCGA-FV-A3R2 TCGA-FV-A3R3 
       19.59         0.62        22.85        27.88         6.38        12.03 
TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A3CG 
        0.39        13.68        53.79        58.49        14.86        22.13 
TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SL TCGA-G3-A6UC TCGA-G3-AAV1 TCGA-G3-AAV3 
       19.23        25.25        20.42         7.76        11.80         9.17 
TCGA-G3-AAV4 TCGA-G3-AAV6 TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-MI-A75G 
        0.89         2.14        11.84        24.36        12.72        18.38 
TCGA-MI-A75H TCGA-MI-A75I TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-RC-A7S9 
       12.85        20.71        19.92        17.69        21.01        21.04 
TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7ME 
       15.52        24.13        17.59        19.76        16.44        15.98 
TCGA-UB-A7MF TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-YA-A8S7 TCGA-ZS-A9CD 
        7.04        10.75        11.34         0.99        13.55        45.57 
TCGA-ZS-A9CF 
       79.30 

$`AMP PEAK 10(6P25.2) WILD-TYPE`
TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9H0 TCGA-2Y-A9H1 
       53.39        63.75        41.79        80.28       120.82        40.41 
TCGA-2Y-A9H4 TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-2Y-A9H9 TCGA-2Y-A9HB TCGA-4R-AA8I 
       47.74        11.74        37.25        14.99         8.55         8.61 
TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4072 
       10.78        10.59         0.66        11.08         1.51        48.99 
TCGA-BC-A10Q TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y 
       37.32        46.78        27.52         2.99        25.32        23.34 
TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A3KF TCGA-BC-A5W4 TCGA-BC-A8YO TCGA-BD-A3ER 
        1.12        69.57         0.26        17.98        18.48        36.66 
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-DD-A113 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A11B TCGA-DD-A11D TCGA-DD-A1E9 
       79.73        83.57        53.33         0.46        51.29        90.71 
TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EI TCGA-DD-A1EK 
       79.40        66.31        19.79        75.65         6.02        18.35 
TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 
       13.64        21.14        27.19        25.81         7.66        70.06 
TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A6 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND 
       17.59        20.12       107.11        33.14        32.52        90.28 
TCGA-DD-A4NF TCGA-DD-A4NI TCGA-DD-A4NL TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ 
       30.97        26.83        56.25        73.81       108.76        12.26 
TCGA-DD-A4NR TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73F 
        0.30        78.84        23.93         9.30        23.05        35.67 
TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC9 TCGA-DD-AACC TCGA-DD-AACG TCGA-DD-AACK 
      114.35        13.48        11.41        55.40        15.42         0.30 
TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACO TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACV 
        3.52        58.16        61.68        59.31        51.52        50.33 
TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 
       46.82         5.59        47.67         5.62         4.50        18.54 
TCGA-DD-AAD2 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADB TCGA-DD-AADC 
       21.63        44.22        22.09        40.08        40.83        13.97 
TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADR 
       40.47        39.52        35.67        35.05        34.49        66.67 
TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADY TCGA-DD-AAE1 TCGA-DD-AAE4 TCGA-DD-AAE6 
       15.58        18.21        18.25        18.15        19.99         4.64 
TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE 
       21.17        21.83        18.90        15.72        25.08        16.37 
TCGA-DD-AAEI TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVU TCGA-DD-AAVX TCGA-DD-AAVZ 
       50.33        79.07        89.69        72.39        56.48        62.47 
TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 
       66.25        65.39        13.41        12.69        15.85        13.91 
TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A97K TCGA-EP-A12J 
        9.73         0.20        14.04        13.15         0.20        18.74 
TCGA-EP-A26S TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ 
       19.99         9.96        11.93        14.40        60.89        23.97 
TCGA-FV-A2QR TCGA-FV-A3I1 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-G3-A25T 
       19.10         8.12         0.03         0.33        81.73        51.06 
TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ 
       28.27        30.74        21.53        25.64         5.92        19.53 
TCGA-G3-A5SJ TCGA-G3-A5SM TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-G3-AAUZ 
       22.95        17.10        12.03         5.98         1.84        11.24 
TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV5 TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB 
        8.55         9.70         8.75         3.02         1.02         2.20 
TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 
        2.99        37.91        20.75        17.06        16.83         3.72 
TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E 
        2.14        13.38        13.97        12.03         9.57        16.67 
TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-QA-A7B7 TCGA-RC-A7SB TCGA-RC-A7SF 
        0.62        10.85        58.88         3.09        19.33        19.04 
TCGA-RC-A7SH TCGA-T1-A6J8 TCGA-UB-A7MD TCGA-UB-AA0V TCGA-WQ-AB4B TCGA-WX-AA46 
       15.39         0.76         1.71        10.32        12.99        24.85 
TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D2 
       35.77        25.71        23.21        23.57         0.69        24.43 
TCGA-ZP-A9D4 TCGA-ZS-A9CE TCGA-ZS-A9CG 
       12.99        40.80        11.21 

  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                        120.82 
  AMP PEAK 10(6P25.2) MUTATED AMP PEAK 10(6P25.2) WILD-TYPE 
                         19.3                          19.1 
[1] "0.1 - 113.0 (19.3)" "0.0 - 120.8 (19.1)"
[1] "hr=" "1.4"
D10V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IIIA
  AMP PEAK 10(6P25.2) MUTATED        63       39         2         27
  AMP PEAK 10(6P25.2) WILD-TYPE     105       45         1         32
                               vv
clus                            STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 10(6P25.2) MUTATED            6          2        3         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                             63                           105
  STAGE II                            39                            45
  STAGE III                            2                             1
  STAGE IIIA                          27                            32
  STAGE IIIB                           6                             2
  STAGE IIIC                           2                             5
  STAGE IV                             3                             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      65  43  37   4
  AMP PEAK 10(6P25.2) WILD-TYPE   114  48  36   8
D10V4, multiclass
       clus
vv      AMP PEAK 10(6P25.2) MUTATED AMP PEAK 10(6P25.2) WILD-TYPE
  T0+T1                          65                           114
  T2                             43                            48
  T3                             37                            36
  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   102   1
  AMP PEAK 10(6P25.2) WILD-TYPE 147   2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(6P25.2) MUTATED    102    1
  AMP PEAK 10(6P25.2) WILD-TYPE  147    2
   clus
vv  AMP PEAK 10(6P25.2) MUTATED AMP PEAK 10(6P25.2) WILD-TYPE
  0                         102                           147
  1                           1                             2
[1] 2 2
[1] FALSE
D10V6, binary
                               cls
clus                              0   1
  AMP PEAK 10(6P25.2) MUTATED   109   3
  AMP PEAK 10(6P25.2) WILD-TYPE 151   1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(6P25.2) MUTATED    109    3
  AMP PEAK 10(6P25.2) WILD-TYPE  151    1
   clus
vv  AMP PEAK 10(6P25.2) MUTATED AMP PEAK 10(6P25.2) WILD-TYPE
  0                         109                           151
  1                           3                             1
[1] 2 2
[1] FALSE
D10V7, binary
                               cls
clus                              0   1
  AMP PEAK 10(6P25.2) MUTATED    52  98
  AMP PEAK 10(6P25.2) WILD-TYPE  61 146
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(6P25.2) MUTATED     52   98
  AMP PEAK 10(6P25.2) WILD-TYPE   61  146
        clus
vv       AMP PEAK 10(6P25.2) MUTATED AMP PEAK 10(6P25.2) WILD-TYPE
  FEMALE                          52                            61
  MALE                            98                           146
[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                        147
  AMP PEAK 10(6P25.2) WILD-TYPE                      201
                               vv
clus                            HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK 10(6P25.2) MUTATED                                  3
  AMP PEAK 10(6P25.2) WILD-TYPE                                4
D10V8, multiclass
                                  clus
vv                                 AMP PEAK 10(6P25.2) MUTATED
  FIBROLAMELLAR CARCINOMA                                    0
  HEPATOCELLULAR CARCINOMA                                 147
  HEPATOCHOLANGIOCARCINOMA (MIXED)                           3
                                  clus
vv                                 AMP PEAK 10(6P25.2) 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 10(6P25.2) MUTATED   134   7   1   7
  AMP PEAK 10(6P25.2) WILD-TYPE 181   8   0  12
D10V9, multiclass
    clus
vv   AMP PEAK 10(6P25.2) MUTATED AMP PEAK 10(6P25.2) WILD-TYPE
  R0                         134                           181
  R1                           7                             8
  R2                           1                             0
  RX                           7                            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 10(6P25.2) MUTATED                                  0    68
  AMP PEAK 10(6P25.2) WILD-TYPE                                1    88
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 10(6P25.2) MUTATED                           8    70
  AMP PEAK 10(6P25.2) WILD-TYPE                         9   103
D10V10, multiclass
                                  clus
vv                                 AMP PEAK 10(6P25.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                     68
  BLACK OR AFRICAN AMERICAN                                  8
  WHITE                                                     70
                                  clus
vv                                 AMP PEAK 10(6P25.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                       88
  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"
D10V11, binary
                               cls
clus                              0   1
  AMP PEAK 10(6P25.2) MUTATED     5 137
  AMP PEAK 10(6P25.2) WILD-TYPE   6 192
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(6P25.2) MUTATED      5  137
  AMP PEAK 10(6P25.2) WILD-TYPE    6  192
                        clus
vv                       AMP PEAK 10(6P25.2) MUTATED
  HISPANIC OR LATINO                               5
  NOT HISPANIC OR LATINO                         137
                        clus
vv                       AMP PEAK 10(6P25.2) WILD-TYPE
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                           192
[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    88  51
  AMP PEAK 11(6P21.1) WILD-TYPE 137  58
  AMP PEAK 11(6P21.1) MUTATED AMP PEAK 11(6P21.1) WILD-TYPE 
                          139                           195 
  AMP PEAK 11(6P21.1) MUTATED AMP PEAK 11(6P21.1) WILD-TYPE 
                           51                            58 
$`AMP PEAK 11(6P21.1) MUTATED`
TCGA-2Y-A9GS TCGA-2Y-A9GV TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H2 TCGA-2Y-A9H3 
       23.80        83.24        24.89        27.88        56.91        41.33 
TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-3K-AAZ8 TCGA-4R-AA8I 
       18.25        20.81        14.99         1.18        13.02         8.61 
TCGA-5C-A9VG TCGA-5R-AA1C TCGA-5R-AAAM TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10Y 
       10.78        11.97         1.51        27.52        27.52        23.34 
TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A69H 
        1.12        44.42        13.84         0.26        22.36        14.60 
TCGA-BC-A69I TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5261 TCGA-CC-5263 
       12.72        44.81        13.45         0.66         3.19         4.24 
TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A118 TCGA-DD-A119 
        0.10         0.13        37.78        83.57       113.00         7.33 
TCGA-DD-A11A TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1EB TCGA-DD-A1EE TCGA-DD-A1EF 
        2.60        21.76        51.29        66.31        11.47        12.95 
TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A5 
       45.11        49.15        55.69         5.62        19.76       102.74 
TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NH TCGA-DD-A4NK TCGA-DD-A4NN TCGA-DD-A4NS 
        0.36        30.61        30.15        39.78        29.56        80.75 
TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 
       22.78         1.45        35.67       114.35        13.48         0.53 
TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACI 
       75.65        76.41        12.53        63.48        12.00        53.19 
TCGA-DD-AACJ TCGA-DD-AACN TCGA-DD-AACP TCGA-DD-AACT TCGA-DD-AACZ TCGA-DD-AAD3 
       69.11        42.81        13.64        51.35         5.62        42.58 
TCGA-DD-AADA TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADL TCGA-DD-AADN TCGA-DD-AADO 
       40.54         3.78        37.64        20.91        29.52        14.89 
TCGA-DD-AADQ TCGA-DD-AADV TCGA-DD-AAE0 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE7 
       14.33        18.87        18.25        18.61        19.99        21.17 
TCGA-DD-AAE9 TCGA-DD-AAEH TCGA-DD-AAEK TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVW 
       23.74        25.78        35.08        82.62        59.93        76.18 
TCGA-DD-AAVY TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A66X TCGA-ED-A7PZ TCGA-ED-A7XO 
       64.77        49.48        53.69        13.35         0.20        14.04 
TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC 
       13.41        13.35         1.84        20.61        19.59         0.62 
TCGA-ES-A2HS TCGA-FV-A23B TCGA-FV-A3I0 TCGA-FV-A3R2 TCGA-FV-A4ZQ TCGA-G3-A25S 
       22.85        60.89        27.88         6.38         0.39        13.68 
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        37.91        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        19.92        17.69 
TCGA-RC-A7S9 TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC 
       21.04        15.52        24.13        17.59        19.76        16.44 
TCGA-UB-A7ME TCGA-UB-A7MF TCGA-UB-AA0U TCGA-WQ-A9G7 TCGA-YA-A8S7 TCGA-ZS-A9CD 
       15.98         7.04        10.75         0.99        13.55        45.57 
TCGA-ZS-A9CF 
       79.30 

$`AMP PEAK 11(6P21.1) WILD-TYPE`
TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9H0 TCGA-2Y-A9H1 
       53.39        63.75        41.79        80.28       120.82        40.41 
TCGA-2Y-A9H4 TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-2Y-A9HB TCGA-5C-A9VH TCGA-5C-AAPD 
       47.74        11.74        37.25         8.55        10.59         0.66 
TCGA-5R-AA1D TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S 
       11.08        48.99        27.91        37.32        10.13        46.78 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A5W4 TCGA-BC-A8YO 
        2.99        25.32        69.57         5.03        17.98        18.48 
TCGA-BD-A3ER TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5262 TCGA-CC-A1HT TCGA-CC-A3M9 
       36.66         0.07         2.86         3.39         3.32         0.10 
TCGA-CC-A3MA TCGA-DD-A113 TCGA-DD-A116 TCGA-DD-A11B TCGA-DD-A1E9 TCGA-DD-A1EA 
        0.07        79.73        53.33         0.46        90.71        79.40 
TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL 
       19.79        75.65         6.02        33.04        18.35        13.64 
TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 
       21.14        27.19        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        90.28 
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        23.93         9.30        23.05 
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         3.52 
TCGA-DD-AACM TCGA-DD-AACO TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACV 
       58.16        61.68        14.20        59.31        51.52        50.33 
TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 
       46.82         5.59        47.67         4.50        18.54        21.63 
TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD 
       44.22        22.09        40.08        40.83        13.97        40.47 
TCGA-DD-AADE TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADM TCGA-DD-AADP 
       39.52        35.67        35.05        34.49         0.39        15.06 
TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE1 
       66.67        15.58        18.21        19.30        18.25        18.15 
TCGA-DD-AAE2 TCGA-DD-AAE6 TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAED 
       20.98         4.64        21.83        18.90        15.72        25.08 
TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEI TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVU 
       16.37        23.64        50.33        79.07        89.69        72.39 
TCGA-DD-AAVX TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-ED-A459 TCGA-ED-A4XI 
       56.48        62.47        66.25        65.39        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         9.73         0.20        12.82        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        12.03         0.03         0.33 
TCGA-FV-A4ZP TCGA-G3-A25T TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z 
       81.73        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        25.25        22.95        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-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ 
        8.75         2.14         3.02         1.02         2.20         2.99 
TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K7 
       20.75        17.06        16.83         3.72         2.14        13.38 
TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MR-A520 TCGA-MR-A8JO 
       13.97        12.03         9.57        16.67         0.62        10.85 
TCGA-NI-A4U2 TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH 
       58.88        21.01         3.09        19.33        19.04        15.39 
TCGA-T1-A6J8 TCGA-UB-A7MD TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-AB4B TCGA-WX-AA46 
        0.76         1.71        10.32        11.34        12.99        24.85 
TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D2 
       35.77        25.71        23.21        23.57         0.69        24.43 
TCGA-ZP-A9D4 TCGA-ZS-A9CE TCGA-ZS-A9CG 
       12.99        40.80        11.21 

  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 
                       114.35                        120.82 
  AMP PEAK 11(6P21.1) MUTATED AMP PEAK 11(6P21.1) WILD-TYPE 
                        19.92                         18.74 
[1] "0.1 - 114.3 (19.9)" "0.0 - 120.8 (18.7)"
[1] "hr=" "1.2"
D11V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IIIA
  AMP PEAK 11(6P21.1) MUTATED        67       38         2         27
  AMP PEAK 11(6P21.1) WILD-TYPE     101       46         1         32
                               vv
clus                            STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 11(6P21.1) MUTATED            4          1        3         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                             67                           101
  STAGE II                            38                            46
  STAGE III                            2                             1
  STAGE IIIA                          27                            32
  STAGE IIIB                           4                             4
  STAGE IIIC                           1                             6
  STAGE IV                             3                             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      68  42  34   5
  AMP PEAK 11(6P21.1) WILD-TYPE   111  49  39   7
D11V4, multiclass
       clus
vv      AMP PEAK 11(6P21.1) MUTATED AMP PEAK 11(6P21.1) WILD-TYPE
  T0+T1                          68                           111
  T2                             42                            49
  T3                             34                            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"
D11V5, binary
                               cls
clus                              0   1
  AMP PEAK 11(6P21.1) MUTATED   104   0
  AMP PEAK 11(6P21.1) WILD-TYPE 145   3
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 11(6P21.1) MUTATED    104    0
  AMP PEAK 11(6P21.1) WILD-TYPE  145    3
   clus
vv  AMP PEAK 11(6P21.1) MUTATED AMP PEAK 11(6P21.1) WILD-TYPE
  0                         104                           145
  1                           0                             3
[1] 2 2
[1] FALSE
D11V6, binary
                               cls
clus                              0   1
  AMP PEAK 11(6P21.1) MUTATED   109   3
  AMP PEAK 11(6P21.1) WILD-TYPE 151   1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 11(6P21.1) MUTATED    109    3
  AMP PEAK 11(6P21.1) WILD-TYPE  151    1
   clus
vv  AMP PEAK 11(6P21.1) MUTATED AMP PEAK 11(6P21.1) WILD-TYPE
  0                         109                           151
  1                           3                             1
[1] 2 2
[1] FALSE
D11V7, binary
                               cls
clus                              0   1
  AMP PEAK 11(6P21.1) MUTATED    55  96
  AMP PEAK 11(6P21.1) WILD-TYPE  58 148
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 11(6P21.1) MUTATED     55   96
  AMP PEAK 11(6P21.1) WILD-TYPE   58  148
        clus
vv       AMP PEAK 11(6P21.1) MUTATED AMP PEAK 11(6P21.1) WILD-TYPE
  FEMALE                          55                            58
  MALE                            96                           148
[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                        147
  AMP PEAK 11(6P21.1) WILD-TYPE                      201
                               vv
clus                            HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK 11(6P21.1) MUTATED                                  4
  AMP PEAK 11(6P21.1) WILD-TYPE                                3
D11V8, multiclass
                                  clus
vv                                 AMP PEAK 11(6P21.1) MUTATED
  FIBROLAMELLAR CARCINOMA                                    0
  HEPATOCELLULAR CARCINOMA                                 147
  HEPATOCHOLANGIOCARCINOMA (MIXED)                           4
                                  clus
vv                                 AMP PEAK 11(6P21.1) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                      2
  HEPATOCELLULAR CARCINOMA                                   201
  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 11(6P21.1) MUTATED   136   7   1   7
  AMP PEAK 11(6P21.1) WILD-TYPE 179   8   0  12
D11V9, multiclass
    clus
vv   AMP PEAK 11(6P21.1) MUTATED AMP PEAK 11(6P21.1) WILD-TYPE
  R0                         136                           179
  R1                           7                             8
  R2                           1                             0
  RX                           7                            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 11(6P21.1) MUTATED                                  0    63
  AMP PEAK 11(6P21.1) WILD-TYPE                                1    93
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 11(6P21.1) MUTATED                           8    75
  AMP PEAK 11(6P21.1) WILD-TYPE                         9    98
D11V10, multiclass
                                  clus
vv                                 AMP PEAK 11(6P21.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                     63
  BLACK OR AFRICAN AMERICAN                                  8
  WHITE                                                     75
                                  clus
vv                                 AMP PEAK 11(6P21.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                       93
  BLACK OR AFRICAN AMERICAN                                    9
  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"
D11V11, binary
                               cls
clus                              0   1
  AMP PEAK 11(6P21.1) MUTATED     5 135
  AMP PEAK 11(6P21.1) WILD-TYPE   6 194
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 11(6P21.1) MUTATED      5  135
  AMP PEAK 11(6P21.1) WILD-TYPE    6  194
                        clus
vv                       AMP PEAK 11(6P21.1) MUTATED
  HISPANIC OR LATINO                               5
  NOT HISPANIC OR LATINO                         135
                        clus
vv                       AMP PEAK 11(6P21.1) WILD-TYPE
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                           194
[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    59  34
  AMP PEAK 12(6Q12) WILD-TYPE 166  75
  AMP PEAK 12(6Q12) MUTATED AMP PEAK 12(6Q12) WILD-TYPE 
                         93                         241 
  AMP PEAK 12(6Q12) MUTATED AMP PEAK 12(6Q12) WILD-TYPE 
                         34                          75 
$`AMP PEAK 12(6Q12) MUTATED`
TCGA-2Y-A9GS TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H3 TCGA-2Y-A9H5 TCGA-2Y-A9H8 
       23.80        24.89        27.88        41.33        18.25        20.81 
TCGA-2Y-A9HA TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-BC-A10Q TCGA-BC-A10T TCGA-BC-A217 
        1.18        13.02        10.78        37.32        27.52        13.84 
TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP 
        0.26        22.36        14.60        18.48        44.81        13.45 
TCGA-BW-A5NO TCGA-CC-5263 TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A114 TCGA-DD-A115 
        0.66         4.24         0.10         0.13        37.78        83.57 
TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11C TCGA-DD-A1EE TCGA-DD-A1EF 
      113.00         7.33         2.60        21.76        11.47        12.95 
TCGA-DD-A1EH TCGA-DD-A1EJ TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A5 TCGA-DD-A3A7 
       49.15        33.04         5.62        19.76       102.74        13.78 
TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NH TCGA-DD-A4NK TCGA-DD-A4NN 
        0.36        30.61        33.14        30.15        39.78        29.56 
TCGA-DD-A4NS TCGA-DD-A73E TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AACB TCGA-DD-AACD 
       80.75         1.45       114.35        13.48        76.41        12.53 
TCGA-DD-AACJ TCGA-DD-AACN TCGA-DD-AACT TCGA-DD-AAD3 TCGA-DD-AADF TCGA-DD-AADL 
       69.11        42.81        51.35        42.58         3.78        20.91 
TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADQ TCGA-DD-AADV TCGA-DD-AAE0 TCGA-DD-AAE3 
       29.52        14.89        14.33        18.87        18.25        18.61 
TCGA-DD-AAEG TCGA-DD-AAEK TCGA-DD-AAVS TCGA-DD-AAVW TCGA-DD-AAW2 TCGA-DD-AAW3 
       23.64        35.08        59.93        76.18        49.48        53.69 
TCGA-ED-A66X TCGA-ED-A7PZ TCGA-ED-A8O5 TCGA-EP-A2KB TCGA-EP-A2KC TCGA-ES-A2HS 
       13.35         0.20        13.35        19.59         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-T1-A6J8 
       11.84        12.72        17.69        15.52        24.13         0.76 
TCGA-UB-A7MA TCGA-UB-A7MC TCGA-UB-A7ME TCGA-UB-A7MF TCGA-UB-AA0U TCGA-WQ-A9G7 
       17.59        16.44        15.98         7.04        10.75         0.99 
TCGA-YA-A8S7 TCGA-ZS-A9CD TCGA-ZS-A9CF 
       13.55        45.57        79.30 

$`AMP PEAK 12(6Q12) WILD-TYPE`
TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GV TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9H0 
       53.39        63.75        83.24        41.79        80.28       120.82 
TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H4 TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-2Y-A9H9 
       40.41        56.91        47.74        11.74        37.25        14.99 
TCGA-2Y-A9HB TCGA-4R-AA8I TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D 
        8.55         8.61        10.59         0.66        11.97        11.08 
TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10U 
        1.51        48.99        27.91        10.13        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-A5W4 TCGA-BC-A69I TCGA-BD-A3ER TCGA-CC-5258 TCGA-CC-5260 
       44.42        17.98        12.72        36.66         0.07         2.86 
TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-DD-A113 
        3.19         3.39         3.32         0.10         0.07        79.73 
TCGA-DD-A116 TCGA-DD-A11B TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB 
       53.33         0.46        51.29        90.71        79.40        66.31 
TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EG TCGA-DD-A1EI TCGA-DD-A1EK TCGA-DD-A1EL 
       19.79        75.65        45.11         6.02        18.35        13.64 
TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 
       21.14        27.19        55.69        25.81         7.66        70.06 
TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A6 TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NF 
       17.59        20.12       107.11        32.52        90.28        30.97 
TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NL TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ 
       26.83        30.51        56.25        73.81       108.76        12.26 
TCGA-DD-A4NR TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D 
        0.30        78.84        23.93         9.30        23.05        22.78 
TCGA-DD-A73F TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACC TCGA-DD-AACE 
       35.67         0.53        11.41        75.65        55.40        63.48 
TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACK TCGA-DD-AACL 
       12.00        15.42         6.41        53.19         0.30         3.52 
TCGA-DD-AACM TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACU 
       58.16        61.68        13.64        14.20        59.31        51.52 
TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD0 
       50.33        46.82         5.59        47.67         5.62         4.50 
TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA 
       18.54        21.63        44.22        22.09        40.08        40.54 
TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADG TCGA-DD-AADI 
       40.83        13.97        40.47        39.52        37.64        35.67 
TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADM TCGA-DD-AADP TCGA-DD-AADR TCGA-DD-AADS 
       35.05        34.49         0.39        15.06        66.67        15.58 
TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE4 
       18.21        19.30        18.25        18.15        20.98        19.99 
TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB 
        4.64        21.17        21.83        23.74        18.90        15.72 
TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAVP TCGA-DD-AAVQ 
       25.08        16.37        25.78        50.33        79.07        89.69 
TCGA-DD-AAVR TCGA-DD-AAVU TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 
       82.62        72.39        56.48        64.77        62.47        66.25 
TCGA-DD-AAW1 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66Y 
       65.39        13.41        12.69        15.85        13.91         9.73 
TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O6 
        0.20        12.82        14.04        13.15        13.41         1.84 
TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A3JL TCGA-EP-A3RK 
        0.20        18.74        19.99        20.61         9.96        11.93 
TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I1 TCGA-FV-A3R2 
       14.40        60.89        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 
       12.03         0.03         0.33        81.73         0.39        13.68 
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        25.25        22.95        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-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 
        9.70         9.17         0.89         8.75         2.14         3.02 
TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG 
        1.02         2.20         2.99        37.91        20.75        17.06 
TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A9QC 
       16.83         3.72         2.14        13.38        24.36        13.97 
TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I 
       12.03         9.57        16.67        18.38        12.85        20.71 
TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-PD-A5DF TCGA-QA-A7B7 
        0.62        10.85        58.88        19.92        21.01         3.09 
TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH TCGA-UB-A7MB TCGA-UB-A7MD 
       21.04        19.33        19.04        15.39        19.76         1.71 
TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-AB4B TCGA-WX-AA46 TCGA-ZP-A9CV TCGA-ZP-A9CY 
       10.32        11.34        12.99        24.85        35.77        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        40.80 
TCGA-ZS-A9CG 
       11.21 

  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 
                     114.35                      120.82 
  AMP PEAK 12(6Q12) MUTATED AMP PEAK 12(6Q12) WILD-TYPE 
                      18.87                       19.33 
[1] "0.1 - 114.3 (18.9)" "0.0 - 120.8 (19.3)"
[1] "hr=" "1.2"
D12V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 12(6Q12) MUTATED        39       26         2         18          5
  AMP PEAK 12(6Q12) WILD-TYPE     129       58         1         41          3
                             vv
clus                          STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 12(6Q12) MUTATED            4        2         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                           39                         129
  STAGE II                          26                          58
  STAGE III                          2                           1
  STAGE IIIA                        18                          41
  STAGE IIIB                         5                           3
  STAGE IIIC                         4                           3
  STAGE IV                           2                           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      42  29  26   5
  AMP PEAK 12(6Q12) WILD-TYPE   137  62  47   7
D12V4, multiclass
       clus
vv      AMP PEAK 12(6Q12) MUTATED AMP PEAK 12(6Q12) WILD-TYPE
  T0+T1                        42                         137
  T2                           29                          62
  T3                           26                          47
  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    67   2
  AMP PEAK 12(6Q12) WILD-TYPE 182   1
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 12(6Q12) MUTATED     67    2
  AMP PEAK 12(6Q12) WILD-TYPE  182    1
   clus
vv  AMP PEAK 12(6Q12) MUTATED AMP PEAK 12(6Q12) WILD-TYPE
  0                        67                         182
  1                         2                           1
[1] 2 2
[1] FALSE
D12V6, binary
                             cls
clus                            0   1
  AMP PEAK 12(6Q12) MUTATED    74   2
  AMP PEAK 12(6Q12) WILD-TYPE 186   2
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 12(6Q12) MUTATED     74    2
  AMP PEAK 12(6Q12) WILD-TYPE  186    2
   clus
vv  AMP PEAK 12(6Q12) MUTATED AMP PEAK 12(6Q12) WILD-TYPE
  0                        74                         186
  1                         2                           2
[1] 2 2
[1] FALSE
D12V7, binary
                             cls
clus                            0   1
  AMP PEAK 12(6Q12) MUTATED    37  65
  AMP PEAK 12(6Q12) WILD-TYPE  76 179
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 12(6Q12) MUTATED     37   65
  AMP PEAK 12(6Q12) WILD-TYPE   76  179
        clus
vv       AMP PEAK 12(6Q12) MUTATED AMP PEAK 12(6Q12) WILD-TYPE
  FEMALE                        37                          76
  MALE                          65                         179
[1] 2 2
[1] FALSE
                             vv
clus                          FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  AMP PEAK 12(6Q12) MUTATED                         0                       98
  AMP PEAK 12(6Q12) WILD-TYPE                       2                      250
                             vv
clus                          HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK 12(6Q12) MUTATED                                  4
  AMP PEAK 12(6Q12) WILD-TYPE                                3
D12V8, multiclass
                                  clus
vv                                 AMP PEAK 12(6Q12) MUTATED
  FIBROLAMELLAR CARCINOMA                                  0
  HEPATOCELLULAR CARCINOMA                                98
  HEPATOCHOLANGIOCARCINOMA (MIXED)                         4
                                  clus
vv                                 AMP PEAK 12(6Q12) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                    2
  HEPATOCELLULAR CARCINOMA                                 250
  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 12(6Q12) MUTATED    89   6   1   6
  AMP PEAK 12(6Q12) WILD-TYPE 226   9   0  13
D12V9, multiclass
    clus
vv   AMP PEAK 12(6Q12) MUTATED AMP PEAK 12(6Q12) WILD-TYPE
  R0                        89                         226
  R1                         6                           9
  R2                         1                           0
  RX                         6                          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 12(6Q12) MUTATED                                  0    41
  AMP PEAK 12(6Q12) WILD-TYPE                                1   115
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 12(6Q12) MUTATED                           7    51
  AMP PEAK 12(6Q12) WILD-TYPE                        10   122
D12V10, multiclass
                                  clus
vv                                 AMP PEAK 12(6Q12) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         0
  ASIAN                                                   41
  BLACK OR AFRICAN AMERICAN                                7
  WHITE                                                   51
                                  clus
vv                                 AMP PEAK 12(6Q12) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                    115
  BLACK OR AFRICAN AMERICAN                                 10
  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"
D12V11, binary
                             cls
clus                            0   1
  AMP PEAK 12(6Q12) MUTATED     4  91
  AMP PEAK 12(6Q12) WILD-TYPE   7 238
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 12(6Q12) MUTATED      4   91
  AMP PEAK 12(6Q12) WILD-TYPE    7  238
                        clus
vv                       AMP PEAK 12(6Q12) MUTATED AMP PEAK 12(6Q12) WILD-TYPE
  HISPANIC OR LATINO                             4                           7
  NOT HISPANIC OR LATINO                        91                         238
[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    46  23
  AMP PEAK 13(6Q12) WILD-TYPE 179  86
  AMP PEAK 13(6Q12) MUTATED AMP PEAK 13(6Q12) WILD-TYPE 
                         69                         265 
  AMP PEAK 13(6Q12) MUTATED AMP PEAK 13(6Q12) WILD-TYPE 
                         23                          86 
$`AMP PEAK 13(6Q12) MUTATED`
TCGA-2Y-A9GS TCGA-2Y-A9GY TCGA-2Y-A9H3 TCGA-2Y-A9H5 TCGA-2Y-A9H7 TCGA-2Y-A9H8 
       23.80        24.89        41.33        18.25        37.25        20.81 
TCGA-2Y-A9HA TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG 
        1.18        13.02        10.78        13.84         0.26        22.36 
TCGA-BC-A69H TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-CC-5260 TCGA-CC-5263 TCGA-CC-A3MB 
       14.60        44.81        13.45         2.86         4.24         0.10 
TCGA-CC-A3MC TCGA-DD-A115 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11D 
        0.13        83.57       113.00         7.33         2.60        51.29 
TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A39Y TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A73G 
       12.95        49.15         5.62         0.36        30.61       114.35 
TCGA-DD-AACJ TCGA-DD-AACN TCGA-DD-AACT TCGA-DD-AADF TCGA-DD-AADN TCGA-DD-AADO 
       69.11        42.81        51.35         3.78        29.52        14.89 
TCGA-DD-AADP TCGA-DD-AAE0 TCGA-DD-AAE3 TCGA-DD-AAE9 TCGA-DD-AAEG TCGA-DD-AAEK 
       15.06        18.25        18.61        23.74        23.64        35.08 
TCGA-DD-AAVW TCGA-DD-AAW2 TCGA-ED-A66X TCGA-ED-A7PZ TCGA-ED-A8O5 TCGA-EP-A12J 
       76.18        49.48        13.35         0.20        13.35        18.74 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-ES-A2HS TCGA-FV-A3I0 TCGA-G3-A25U 
       20.61        19.59         0.62        22.85        27.88        53.79 
TCGA-G3-A3CK TCGA-G3-AAV1 TCGA-KR-A7K2 TCGA-LG-A6GG TCGA-O8-A75V TCGA-RC-A7SK 
       19.23        11.80        11.84        12.72        17.69        15.52 
TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MC TCGA-UB-A7ME TCGA-UB-A7MF TCGA-UB-AA0U 
       24.13        17.59        16.44        15.98         7.04        10.75 
TCGA-WQ-A9G7 TCGA-YA-A8S7 TCGA-ZS-A9CD 
        0.99        13.55        45.57 

$`AMP PEAK 13(6Q12) WILD-TYPE`
TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GV TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GZ 
       53.39        63.75        83.24        41.79        80.28        27.88 
TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H4 TCGA-2Y-A9H6 TCGA-2Y-A9H9 
      120.82        40.41        56.91        47.74        11.74        14.99 
TCGA-2Y-A9HB TCGA-4R-AA8I TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D 
        8.55         8.61        10.59         0.66        11.97        11.08 
TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S 
        1.51        48.99        27.91        37.32        10.13        46.78 
TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z 
       27.52        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-BC-A8YO 
       69.57         5.03        44.42        17.98        12.72        18.48 
TCGA-BD-A3ER TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-A1HT 
       36.66         0.66         0.07         3.19         3.39         3.32 
TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A116 TCGA-DD-A11B 
        0.10         0.07        79.73        37.78        53.33         0.46 
TCGA-DD-A11C TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED 
       21.76        90.71        79.40        66.31        19.79        75.65 
TCGA-DD-A1EE TCGA-DD-A1EG TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL 
       11.47        45.11         6.02        33.04        18.35        13.64 
TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 
       21.14        27.19        55.69        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-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI 
       33.14        32.52        90.28        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        23.93         9.30 
TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-AA3A TCGA-DD-AAC8 
       23.05        22.78         1.45        35.67        13.48         0.53 
TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE 
       11.41        75.65        76.41        55.40        12.53        63.48 
TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACK TCGA-DD-AACL 
       12.00        15.42         6.41        53.19         0.30         3.52 
TCGA-DD-AACM TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACU 
       58.16        61.68        13.64        14.20        59.31        51.52 
TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD0 
       50.33        46.82         5.59        47.67         5.62         4.50 
TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 
       18.54        21.63        42.58        44.22        22.09        40.08 
TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADG 
       40.54        40.83        13.97        40.47        39.52        37.64 
TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADQ 
       35.67        35.05        34.49        20.91         0.39        14.33 
TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADV TCGA-DD-AADW TCGA-DD-AADY 
       66.67        15.58        18.21        18.87        19.30        18.25 
TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAE8 
       18.15        20.98        19.99         4.64        21.17        21.83 
TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAEI 
       18.90        15.72        25.08        16.37        25.78        50.33 
TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVX 
       79.07        89.69        82.62        59.93        72.39        56.48 
TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW3 TCGA-ED-A459 
       64.77        62.47        66.25        65.39        53.69        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         9.73         0.20        12.82 
TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A26S 
       14.04        13.15        13.41         1.84         0.20        19.99 
TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR 
        9.96        11.93        14.40        60.89        23.97        19.10 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP 
        8.12         6.38        12.03         0.03         0.33        81.73 
TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X 
        0.39        13.68        51.06        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-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M6 
       25.25        22.95        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-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB 
        0.89         8.75         2.14         3.02         1.02         2.20 
TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 
        2.99        37.91        20.75        17.06        16.83         3.72 
TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C 
        2.14        13.38        24.36        13.97        12.03         9.57 
TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO 
       16.67        18.38        12.85        20.71         0.62        10.85 
TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SB 
       58.88        19.92        21.01         3.09        21.04        19.33 
TCGA-RC-A7SF TCGA-RC-A7SH TCGA-T1-A6J8 TCGA-UB-A7MB TCGA-UB-A7MD TCGA-UB-AA0V 
       19.04        15.39         0.76        19.76         1.71        10.32 
TCGA-WJ-A86L TCGA-WQ-AB4B TCGA-WX-AA46 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ 
       11.34        12.99        24.85        35.77        25.71        23.21 
TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CE TCGA-ZS-A9CF 
       23.57         0.69        24.43        12.99        40.80        79.30 
TCGA-ZS-A9CG 
       11.21 

  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 
                     114.35                      120.82 
  AMP PEAK 13(6Q12) MUTATED AMP PEAK 13(6Q12) WILD-TYPE 
                      17.69                       19.79 
[1] "0.1 - 114.3 (17.7)" "0.0 - 120.8 (19.8)"
[1] "hr=" "1.1"
D13V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 13(6Q12) MUTATED        31       21         1         16          2
  AMP PEAK 13(6Q12) WILD-TYPE     137       63         2         43          6
                             vv
clus                          STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 13(6Q12) MUTATED            2        2         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                           31                         137
  STAGE II                          21                          63
  STAGE III                          1                           2
  STAGE IIIA                        16                          43
  STAGE IIIB                         2                           6
  STAGE IIIC                         2                           5
  STAGE IV                           2                           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      32  22  20   4
  AMP PEAK 13(6Q12) WILD-TYPE   147  69  53   8
D13V4, multiclass
       clus
vv      AMP PEAK 13(6Q12) MUTATED AMP PEAK 13(6Q12) WILD-TYPE
  T0+T1                        32                         147
  T2                           22                          69
  T3                           20                          53
  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    51   0
  AMP PEAK 13(6Q12) WILD-TYPE 198   3
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 13(6Q12) MUTATED     51    0
  AMP PEAK 13(6Q12) WILD-TYPE  198    3
   clus
vv  AMP PEAK 13(6Q12) MUTATED AMP PEAK 13(6Q12) WILD-TYPE
  0                        51                         198
  1                         0                           3
[1] 2 2
[1] FALSE
D13V6, binary
                             cls
clus                            0   1
  AMP PEAK 13(6Q12) MUTATED    53   2
  AMP PEAK 13(6Q12) WILD-TYPE 207   2
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 13(6Q12) MUTATED     53    2
  AMP PEAK 13(6Q12) WILD-TYPE  207    2
   clus
vv  AMP PEAK 13(6Q12) MUTATED AMP PEAK 13(6Q12) WILD-TYPE
  0                        53                         207
  1                         2                           2
[1] 2 2
[1] FALSE
D13V7, binary
                             cls
clus                            0   1
  AMP PEAK 13(6Q12) MUTATED    29  49
  AMP PEAK 13(6Q12) WILD-TYPE  84 195
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 13(6Q12) MUTATED     29   49
  AMP PEAK 13(6Q12) WILD-TYPE   84  195
        clus
vv       AMP PEAK 13(6Q12) MUTATED AMP PEAK 13(6Q12) WILD-TYPE
  FEMALE                        29                          84
  MALE                          49                         195
[1] 2 2
[1] FALSE
                             vv
clus                          FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  AMP PEAK 13(6Q12) MUTATED                         0                       75
  AMP PEAK 13(6Q12) WILD-TYPE                       2                      273
                             vv
clus                          HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK 13(6Q12) MUTATED                                  3
  AMP PEAK 13(6Q12) WILD-TYPE                                4
D13V8, multiclass
                                  clus
vv                                 AMP PEAK 13(6Q12) MUTATED
  FIBROLAMELLAR CARCINOMA                                  0
  HEPATOCELLULAR CARCINOMA                                75
  HEPATOCHOLANGIOCARCINOMA (MIXED)                         3
                                  clus
vv                                 AMP PEAK 13(6Q12) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                    2
  HEPATOCELLULAR CARCINOMA                                 273
  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 13(6Q12) MUTATED    70   3   1   4
  AMP PEAK 13(6Q12) WILD-TYPE 245  12   0  15
D13V9, multiclass
    clus
vv   AMP PEAK 13(6Q12) MUTATED AMP PEAK 13(6Q12) WILD-TYPE
  R0                        70                         245
  R1                         3                          12
  R2                         1                           0
  RX                         4                          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
  AMP PEAK 13(6Q12) MUTATED                                  0    36
  AMP PEAK 13(6Q12) WILD-TYPE                                1   120
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 13(6Q12) MUTATED                           6    35
  AMP PEAK 13(6Q12) WILD-TYPE                        11   138
D13V10, multiclass
                                  clus
vv                                 AMP PEAK 13(6Q12) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         0
  ASIAN                                                   36
  BLACK OR AFRICAN AMERICAN                                6
  WHITE                                                   35
                                  clus
vv                                 AMP PEAK 13(6Q12) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                    120
  BLACK OR AFRICAN AMERICAN                                 11
  WHITE                                                    138
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V11, binary
                             cls
clus                            0   1
  AMP PEAK 13(6Q12) MUTATED     4  69
  AMP PEAK 13(6Q12) WILD-TYPE   7 260
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 13(6Q12) MUTATED      4   69
  AMP PEAK 13(6Q12) WILD-TYPE    7  260
                        clus
vv                       AMP PEAK 13(6Q12) MUTATED AMP PEAK 13(6Q12) WILD-TYPE
  HISPANIC OR LATINO                             4                           7
  NOT HISPANIC OR LATINO                        69                         260
[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    70  35
  AMP PEAK 14(7Q31.2) WILD-TYPE 155  74
  AMP PEAK 14(7Q31.2) MUTATED AMP PEAK 14(7Q31.2) WILD-TYPE 
                          105                           229 
  AMP PEAK 14(7Q31.2) MUTATED AMP PEAK 14(7Q31.2) WILD-TYPE 
                           35                            74 
$`AMP PEAK 14(7Q31.2) MUTATED`
TCGA-2Y-A9GS TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H2 
       23.80        63.75        41.79        24.89        27.88        56.91 
TCGA-2Y-A9H3 TCGA-2Y-A9H9 TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-5C-A9VH TCGA-BC-A10Q 
       41.33        14.99        13.02        10.78        10.59        37.32 
TCGA-BC-A10R TCGA-BC-A10U TCGA-BC-A3KF TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BD-A3EP 
       10.13        27.52         0.26        17.98        14.60        13.45 
TCGA-BD-A3ER TCGA-BW-A5NO TCGA-CC-5260 TCGA-CC-A3M9 TCGA-CC-A3MB TCGA-DD-A118 
       36.66         0.66         2.86         0.10         0.10       113.00 
TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EC TCGA-DD-A1EE TCGA-DD-A1EJ TCGA-DD-A39V 
       51.29        90.71        19.79        11.47        33.04        21.14 
TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A2 TCGA-DD-A4NA TCGA-DD-A4NI TCGA-DD-A4NK 
        5.62        19.76        70.06        33.14        26.83        39.78 
TCGA-DD-A4NQ TCGA-DD-A4NV TCGA-DD-A73C TCGA-DD-A73E TCGA-DD-A73G TCGA-DD-AAC9 
       12.26        78.84        23.05         1.45       114.35        11.41 
TCGA-DD-AACA TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACI TCGA-DD-AACP 
       75.65        12.53        63.48        12.00        53.19        13.64 
TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AADD TCGA-DD-AADG TCGA-DD-AADL TCGA-DD-AADM 
       59.31        51.35        40.47        37.64        20.91         0.39 
TCGA-DD-AADS TCGA-DD-AADV TCGA-DD-AADW TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE6 
       15.58        18.87        19.30        20.98        18.61         4.64 
TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAEI TCGA-DD-AAVX TCGA-DD-AAW2 
       23.74        18.90        15.72        50.33        56.48        49.48 
TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A66Y TCGA-ED-A7PY TCGA-EP-A26S TCGA-EP-A2KA 
       53.69        13.41         9.73        12.82        19.99        20.61 
TCGA-EP-A2KC TCGA-EP-A3JL TCGA-ES-A2HS TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A4ZP 
        0.62         9.96        22.85         8.12         6.38        81.73 
TCGA-G3-A25T TCGA-G3-A25V TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A3CG TCGA-G3-A3CJ 
       51.06        28.27        58.49        14.86        22.13        19.53 
TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-AAV1 TCGA-G3-AAV5 TCGA-G3-AAV6 
       20.42        17.10         7.76        11.80         8.75         2.14 
TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-MI-A75E TCGA-MI-A75G TCGA-NI-A4U2 
       11.84        24.36        12.72        16.67        18.38        58.88 
TCGA-NI-A8LF TCGA-RC-A7S9 TCGA-UB-A7MD TCGA-UB-AA0U TCGA-WQ-A9G7 TCGA-WQ-AB4B 
       19.92        21.04         1.71        10.75         0.99        12.99 
TCGA-WX-AA46 TCGA-YA-A8S7 TCGA-ZP-A9D1 
       24.85        13.55         0.69 

$`AMP PEAK 14(7Q31.2) WILD-TYPE`
TCGA-2Y-A9GT TCGA-2Y-A9GV TCGA-2Y-A9GX TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H4 
       53.39        83.24        80.28       120.82        40.41        47.74 
TCGA-2Y-A9H5 TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-2Y-A9H8 TCGA-2Y-A9HA TCGA-2Y-A9HB 
       18.25        11.74        37.25        20.81         1.18         8.55 
TCGA-4R-AA8I TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4072 
        8.61         0.66        11.97        11.08         1.51        48.99 
TCGA-BC-4073 TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y 
       27.91        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-A3KG 
        1.12        69.57         5.03        44.42        13.84        22.36 
TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-CC-5258 TCGA-CC-5261 TCGA-CC-5262 
       12.72        18.48        44.81         0.07         3.19         3.39 
TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3MA TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 
        4.24         3.32         0.07         0.13        79.73        37.78 
TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C 
       83.57        53.33         7.33         2.60         0.46        21.76 
TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1ED TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH 
       79.40        66.31        75.65        12.95        45.11        49.15 
TCGA-DD-A1EI TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A3A0 
        6.02        18.35        13.64        27.19        55.69        25.81 
TCGA-DD-A3A1 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 
        7.66        17.59        20.12       102.74       107.11        13.78 
TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH 
        0.36        30.61        32.52        90.28        30.97        30.15 
TCGA-DD-A4NJ TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NR 
       30.51        56.25        29.56        73.81       108.76         0.30 
TCGA-DD-A4NS TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73D TCGA-DD-A73F TCGA-DD-AA3A 
       80.75        23.93         9.30        22.78        35.67        13.48 
TCGA-DD-AAC8 TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACJ 
        0.53        76.41        55.40        15.42         6.41        69.11 
TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACQ 
        0.30         3.52        58.16        42.81        61.68        14.20 
TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AACZ 
       51.52        50.33        46.82         5.59        47.67         5.62 
TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 
        4.50        18.54        21.63        42.58        44.22        22.09 
TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADE TCGA-DD-AADF 
       40.08        40.54        40.83        13.97        39.52         3.78 
TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP 
       35.67        35.05        34.49        29.52        14.89        15.06 
TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADU TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 
       14.33        66.67        18.21        18.25        18.25        18.15 
TCGA-DD-AAE4 TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEG 
       19.99        21.17        21.83        25.08        16.37        23.64 
TCGA-DD-AAEH TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS 
       25.78        35.08        79.07        89.69        82.62        59.93 
TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 
       72.39        76.18        64.77        62.47        66.25        65.39 
TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A7PX TCGA-ED-A7PZ 
       12.69        15.85        13.91        13.35         0.20         0.20 
TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K 
       14.04        13.15        13.41        13.35         1.84         0.20 
TCGA-EP-A12J TCGA-EP-A2KB TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ 
       18.74        19.59        11.93        14.40        60.89        23.97 
TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ 
       19.10        27.88        12.03         0.03         0.33         0.39 
TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25W TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI 
       13.68        53.79        30.74        21.53        25.64         5.92 
TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M9 
       19.23        25.25        22.95        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         2.99        37.91        20.75        17.06 
TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A9QC TCGA-LG-A9QD 
       16.83         3.72         2.14        13.38        13.97        12.03 
TCGA-MI-A75C TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-O8-A75V 
        9.57        12.85        20.71         0.62        10.85        17.69 
TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK 
       21.01         3.09        19.33        19.04        15.39        15.52 
TCGA-RG-A7D4 TCGA-T1-A6J8 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7ME 
       24.13         0.76        17.59        19.76        16.44        15.98 
TCGA-UB-A7MF TCGA-UB-AA0V TCGA-WJ-A86L TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ 
        7.04        10.32        11.34        35.77        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        40.80        79.30 
TCGA-ZS-A9CG 
       11.21 

  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 
                       114.35                        120.82 
  AMP PEAK 14(7Q31.2) MUTATED AMP PEAK 14(7Q31.2) WILD-TYPE 
                        19.53                         19.10 
[1] "0.1 - 114.3 (19.5)" "0.0 - 120.8 (19.1)"
[1] "hr=" "1"  
D14V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IIIA
  AMP PEAK 14(7Q31.2) MUTATED        51       28         0         21
  AMP PEAK 14(7Q31.2) WILD-TYPE     117       56         3         38
                               vv
clus                            STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 14(7Q31.2) MUTATED            3          5        2         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                             51                           117
  STAGE II                            28                            56
  STAGE III                            0                             3
  STAGE IIIA                          21                            38
  STAGE IIIB                           3                             5
  STAGE IIIC                           5                             2
  STAGE IV                             2                             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      53  33  25   4
  AMP PEAK 14(7Q31.2) WILD-TYPE   126  58  48   8
D14V4, multiclass
       clus
vv      AMP PEAK 14(7Q31.2) MUTATED AMP PEAK 14(7Q31.2) WILD-TYPE
  T0+T1                          53                           126
  T2                             33                            58
  T3                             25                            48
  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    76   2
  AMP PEAK 14(7Q31.2) WILD-TYPE 173   1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 14(7Q31.2) MUTATED     76    2
  AMP PEAK 14(7Q31.2) WILD-TYPE  173    1
   clus
vv  AMP PEAK 14(7Q31.2) MUTATED AMP PEAK 14(7Q31.2) WILD-TYPE
  0                          76                           173
  1                           2                             1
[1] 2 2
[1] FALSE
D14V6, binary
                               cls
clus                              0   1
  AMP PEAK 14(7Q31.2) MUTATED    84   1
  AMP PEAK 14(7Q31.2) WILD-TYPE 176   3
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 14(7Q31.2) MUTATED     84    1
  AMP PEAK 14(7Q31.2) WILD-TYPE  176    3
   clus
vv  AMP PEAK 14(7Q31.2) MUTATED AMP PEAK 14(7Q31.2) WILD-TYPE
  0                          84                           176
  1                           1                             3
[1] 2 2
[1] FALSE
D14V7, binary
                               cls
clus                              0   1
  AMP PEAK 14(7Q31.2) MUTATED    35  80
  AMP PEAK 14(7Q31.2) WILD-TYPE  78 164
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 14(7Q31.2) MUTATED     35   80
  AMP PEAK 14(7Q31.2) WILD-TYPE   78  164
        clus
vv       AMP PEAK 14(7Q31.2) MUTATED AMP PEAK 14(7Q31.2) WILD-TYPE
  FEMALE                          35                            78
  MALE                            80                           164
[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                        114
  AMP PEAK 14(7Q31.2) WILD-TYPE                      234
                               vv
clus                            HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK 14(7Q31.2) MUTATED                                  1
  AMP PEAK 14(7Q31.2) WILD-TYPE                                6
D14V8, multiclass
                                  clus
vv                                 AMP PEAK 14(7Q31.2) MUTATED
  FIBROLAMELLAR CARCINOMA                                    0
  HEPATOCELLULAR CARCINOMA                                 114
  HEPATOCHOLANGIOCARCINOMA (MIXED)                           1
                                  clus
vv                                 AMP PEAK 14(7Q31.2) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                      2
  HEPATOCELLULAR CARCINOMA                                   234
  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 14(7Q31.2) MUTATED   101   6   0   6
  AMP PEAK 14(7Q31.2) WILD-TYPE 214   9   1  13
D14V9, multiclass
    clus
vv   AMP PEAK 14(7Q31.2) MUTATED AMP PEAK 14(7Q31.2) WILD-TYPE
  R0                         101                           214
  R1                           6                             9
  R2                           0                             1
  RX                           6                            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 14(7Q31.2) MUTATED                                  1    45
  AMP PEAK 14(7Q31.2) WILD-TYPE                                0   111
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 14(7Q31.2) MUTATED                           5    62
  AMP PEAK 14(7Q31.2) WILD-TYPE                        12   111
D14V10, multiclass
                                  clus
vv                                 AMP PEAK 14(7Q31.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                     45
  BLACK OR AFRICAN AMERICAN                                  5
  WHITE                                                     62
                                  clus
vv                                 AMP PEAK 14(7Q31.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                      111
  BLACK OR AFRICAN AMERICAN                                   12
  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"
D14V11, binary
                               cls
clus                              0   1
  AMP PEAK 14(7Q31.2) MUTATED     5 106
  AMP PEAK 14(7Q31.2) WILD-TYPE   6 223
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 14(7Q31.2) MUTATED      5  106
  AMP PEAK 14(7Q31.2) WILD-TYPE    6  223
                        clus
vv                       AMP PEAK 14(7Q31.2) MUTATED
  HISPANIC OR LATINO                               5
  NOT HISPANIC OR LATINO                         106
                        clus
vv                       AMP PEAK 14(7Q31.2) WILD-TYPE
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                           223
[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   127  57
  AMP PEAK 15(8Q13.3) WILD-TYPE  98  52
  AMP PEAK 15(8Q13.3) MUTATED AMP PEAK 15(8Q13.3) WILD-TYPE 
                          184                           150 
  AMP PEAK 15(8Q13.3) MUTATED AMP PEAK 15(8Q13.3) WILD-TYPE 
                           57                            52 
$`AMP PEAK 15(8Q13.3) MUTATED`
TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GY TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H5 
       41.79        80.28        24.89        40.41        56.91        18.25 
TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5R-AA1C 
       14.99         1.18        13.02        10.78        10.59        11.97 
TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-A10S TCGA-BC-A10U TCGA-BC-A10W 
       11.08         1.51        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        36.66         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 
       11.47        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        90.28 
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        22.78       114.35         0.53 
TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACD TCGA-DD-AACF TCGA-DD-AACG 
       11.41        75.65        76.41        12.53        12.00        15.42 
TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO 
        6.41        53.19        69.11        58.16        42.81        61.68 
TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACT TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD1 
       13.64        14.20        51.35        47.67         5.62        18.54 
TCGA-DD-AAD2 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC 
       21.63        44.22        22.09        40.54        40.83        13.97 
TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADI TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM 
       40.47        39.52        35.67        34.49        20.91         0.39 
TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADU 
       29.52        14.89        15.06        14.33        66.67        18.21 
TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE3 TCGA-DD-AAE6 TCGA-DD-AAE8 TCGA-DD-AAE9 
       18.25        18.15        18.61         4.64        21.83        23.74 
TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEG TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVQ 
       15.72        25.08        23.64        50.33        35.08        89.69 
TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ 
       59.93        72.39        76.18        56.48        64.77        62.47 
TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A66X 
       66.25        65.39        49.48        53.69        13.41        13.35 
TCGA-ED-A66Y TCGA-ED-A7PZ TCGA-ED-A8O6 TCGA-EP-A12J TCGA-EP-A2KA TCGA-EP-A2KB 
        9.73         0.20         1.84        18.74        20.61        19.59 
TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A2QQ 
        0.62         9.96        11.93        22.85        14.40        23.97 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25V 
        8.12         6.38        81.73         0.39        51.06        28.27 
TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CJ 
       30.74        58.49        21.53        22.13        25.64        19.53 
TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M9 
       25.25        22.95        20.42        12.03         5.98         1.84 
TCGA-G3-AAUZ TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV5 TCGA-G3-AAV6 
       11.24        11.80         9.70         9.17         8.75         2.14 
TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-KR-A7K8 
        2.99        16.83         3.72        11.84        13.38        24.36 
TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A8JO 
       12.03         9.57        16.67        12.85        20.71        10.85 
TCGA-NI-A8LF TCGA-O8-A75V TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RG-A7D4 TCGA-UB-A7MA 
       19.92        17.69        19.04        15.39        24.13        17.59 
TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-YA-A8S7 
        1.71        15.98        10.75         0.99        12.99        13.55 
TCGA-ZP-A9CV TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CG 
       35.77        12.99        45.57        11.21 

$`AMP PEAK 15(8Q13.3) WILD-TYPE`
TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GV TCGA-2Y-A9GZ TCGA-2Y-A9H0 
       23.80        53.39        63.75        83.24        27.88       120.82 
TCGA-2Y-A9H3 TCGA-2Y-A9H4 TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-2Y-A9H8 TCGA-2Y-A9HB 
       41.33        47.74        11.74        37.25        20.81         8.55 
TCGA-4R-AA8I TCGA-5C-AAPD TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T 
        8.61         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-A2L6 TCGA-BD-A3EP 
       22.36        17.98        12.72        18.48        44.81        13.45 
TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A3MA TCGA-DD-A114 
        2.86         3.19         3.39         4.24         0.07        37.78 
TCGA-DD-A115 TCGA-DD-A11B TCGA-DD-A11D TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1ED 
       83.57         0.46        51.29        79.40        66.31        75.65 
TCGA-DD-A1EH TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A3A0 
       49.15        33.04        18.35        27.19        55.69        25.81 
TCGA-DD-A3A2 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A9 
       70.06        20.12       102.74       107.11        13.78        30.61 
TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NH TCGA-DD-A4NL TCGA-DD-A4NP TCGA-DD-A4NV 
       33.14        32.52        30.15        56.25       108.76        78.84 
TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-AA3A 
       23.93         9.30        23.05         1.45        35.67        13.48 
TCGA-DD-AACC TCGA-DD-AACE TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACS TCGA-DD-AACU 
       55.40        63.48         0.30         3.52        59.31        51.52 
TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AAD0 TCGA-DD-AAD3 TCGA-DD-AAD8 
       50.33        46.82         5.59         4.50        42.58        40.08 
TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADJ TCGA-DD-AADS TCGA-DD-AADV TCGA-DD-AADW 
        3.78        37.64        35.05        15.58        18.87        19.30 
TCGA-DD-AADY TCGA-DD-AAE2 TCGA-DD-AAE4 TCGA-DD-AAE7 TCGA-DD-AAEA TCGA-DD-AAEE 
       18.25        20.98        19.99        21.17        18.90        16.37 
TCGA-DD-AAEH TCGA-DD-AAVP TCGA-DD-AAVR TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 
       25.78        79.07        82.62        12.69        15.85        13.91 
TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 
        0.20        12.82        14.04        13.15        13.41        13.35 
TCGA-ED-A97K TCGA-EP-A26S TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R3 
        0.20        19.99        60.89        19.10        27.88        12.03 
TCGA-FV-A495 TCGA-FV-A496 TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25Y TCGA-G3-A3CI 
        0.03         0.33        13.68        53.79        14.86         5.92 
TCGA-G3-A3CK TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-AAV0 TCGA-G3-AAV4 TCGA-G3-AAV7 
       19.23        17.10         7.76         8.55         0.89         3.02 
TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-KR-A7K0 
        1.02         2.20        37.91        20.75        17.06         2.14 
TCGA-LG-A6GG TCGA-LG-A9QC TCGA-MI-A75G TCGA-MR-A520 TCGA-NI-A4U2 TCGA-PD-A5DF 
       12.72        13.97        18.38         0.62        58.88        21.01 
TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SK TCGA-T1-A6J8 TCGA-UB-A7MB 
        3.09        21.04        19.33        15.52         0.76        19.76 
TCGA-UB-A7MC TCGA-UB-A7MF TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WX-AA46 TCGA-ZP-A9CY 
       16.44         7.04        10.32        11.34        24.85        25.71 
TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZS-A9CE TCGA-ZS-A9CF 
       23.21        23.57         0.69        24.43        40.80        79.30 

  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 
                       114.35                        120.82 
  AMP PEAK 15(8Q13.3) MUTATED AMP PEAK 15(8Q13.3) WILD-TYPE 
                       18.575                        19.875 
[1] "0.1 - 114.3 (18.6)" "0.0 - 120.8 (19.9)"
[1] "hr=" "1.1"
D15V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IIIA
  AMP PEAK 15(8Q13.3) MUTATED        94       52         0         37
  AMP PEAK 15(8Q13.3) WILD-TYPE      74       32         3         22
                               vv
clus                            STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 15(8Q13.3) MUTATED            4          2        2         1
  AMP PEAK 15(8Q13.3) WILD-TYPE          4          5        1         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                             94                            74
  STAGE II                            52                            32
  STAGE III                            0                             3
  STAGE IIIA                          37                            22
  STAGE IIIB                           4                             4
  STAGE IIIC                           2                             5
  STAGE IV                             2                             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 15(8Q13.3) MUTATED      97 55 43  4
  AMP PEAK 15(8Q13.3) WILD-TYPE    82 36 30  8
D15V4, multiclass
       clus
vv      AMP PEAK 15(8Q13.3) MUTATED AMP PEAK 15(8Q13.3) WILD-TYPE
  T0+T1                          97                            82
  T2                             55                            36
  T3                             43                            30
  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   148   1
  AMP PEAK 15(8Q13.3) WILD-TYPE 101   2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 15(8Q13.3) MUTATED    148    1
  AMP PEAK 15(8Q13.3) WILD-TYPE  101    2
   clus
vv  AMP PEAK 15(8Q13.3) MUTATED AMP PEAK 15(8Q13.3) WILD-TYPE
  0                         148                           101
  1                           1                             2
[1] 2 2
[1] FALSE
D15V6, binary
                               cls
clus                              0   1
  AMP PEAK 15(8Q13.3) MUTATED   152   2
  AMP PEAK 15(8Q13.3) WILD-TYPE 108   2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 15(8Q13.3) MUTATED    152    2
  AMP PEAK 15(8Q13.3) WILD-TYPE  108    2
   clus
vv  AMP PEAK 15(8Q13.3) MUTATED AMP PEAK 15(8Q13.3) WILD-TYPE
  0                         152                           108
  1                           2                             2
[1] 2 2
[1] FALSE
D15V7, binary
                               cls
clus                              0   1
  AMP PEAK 15(8Q13.3) MUTATED    48 152
  AMP PEAK 15(8Q13.3) WILD-TYPE  65  92
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 15(8Q13.3) MUTATED     48  152
  AMP PEAK 15(8Q13.3) WILD-TYPE   65   92
        clus
vv       AMP PEAK 15(8Q13.3) MUTATED AMP PEAK 15(8Q13.3) WILD-TYPE
  FEMALE                          48                            65
  MALE                           152                            92
[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                        196
  AMP PEAK 15(8Q13.3) WILD-TYPE                      152
                               vv
clus                            HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK 15(8Q13.3) MUTATED                                  3
  AMP PEAK 15(8Q13.3) WILD-TYPE                                4
D15V8, multiclass
                                  clus
vv                                 AMP PEAK 15(8Q13.3) MUTATED
  FIBROLAMELLAR CARCINOMA                                    1
  HEPATOCELLULAR CARCINOMA                                 196
  HEPATOCHOLANGIOCARCINOMA (MIXED)                           3
                                  clus
vv                                 AMP PEAK 15(8Q13.3) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                      1
  HEPATOCELLULAR CARCINOMA                                   152
  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   176  10   1  10
  AMP PEAK 15(8Q13.3) WILD-TYPE 139   5   0   9
D15V9, multiclass
    clus
vv   AMP PEAK 15(8Q13.3) MUTATED AMP PEAK 15(8Q13.3) WILD-TYPE
  R0                         176                           139
  R1                          10                             5
  R2                           1                             0
  RX                          10                             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 15(8Q13.3) MUTATED                                  1    97
  AMP PEAK 15(8Q13.3) WILD-TYPE                                0    59
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 15(8Q13.3) MUTATED                          10    86
  AMP PEAK 15(8Q13.3) WILD-TYPE                         7    87
D15V10, multiclass
                                  clus
vv                                 AMP PEAK 15(8Q13.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                     97
  BLACK OR AFRICAN AMERICAN                                 10
  WHITE                                                     86
                                  clus
vv                                 AMP PEAK 15(8Q13.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                       59
  BLACK OR AFRICAN AMERICAN                                    7
  WHITE                                                       87
[1] 4 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     6 185
  AMP PEAK 15(8Q13.3) WILD-TYPE   5 144
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 15(8Q13.3) MUTATED      6  185
  AMP PEAK 15(8Q13.3) WILD-TYPE    5  144
                        clus
vv                       AMP PEAK 15(8Q13.3) MUTATED
  HISPANIC OR LATINO                               6
  NOT HISPANIC OR LATINO                         185
                        clus
vv                       AMP PEAK 15(8Q13.3) WILD-TYPE
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                           144
[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   145  60
  AMP PEAK 16(8Q24.21) WILD-TYPE  80  49
  AMP PEAK 16(8Q24.21) MUTATED AMP PEAK 16(8Q24.21) WILD-TYPE 
                           205                            129 
  AMP PEAK 16(8Q24.21) MUTATED AMP PEAK 16(8Q24.21) WILD-TYPE 
                            60                             49 
$`AMP PEAK 16(8Q24.21) MUTATED`
TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GY TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H4 
       41.79        80.28        24.89        40.41        56.91        47.74 
TCGA-2Y-A9H5 TCGA-2Y-A9HA TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5R-AA1C 
       18.25         1.18        13.02        10.78        10.59        11.97 
TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
       11.08         1.51        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        36.66         0.07 
TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB 
        3.19         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        11.47        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        90.28        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        23.93        22.78       114.35         0.53 
TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACD TCGA-DD-AACF TCGA-DD-AACG 
       11.41        75.65        76.41        12.53        12.00        15.42 
TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO 
        6.41        53.19        69.11        58.16        42.81        61.68 
TCGA-DD-AACP TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACW TCGA-DD-AACY TCGA-DD-AACZ 
       13.64        59.31        51.35        46.82        47.67         5.62 
TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AADA 
        4.50        18.54        21.63        44.22        22.09        40.54 
TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADI TCGA-DD-AADK 
       40.83        13.97        40.47        39.52        35.67        34.49 
TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ 
       20.91         0.39        29.52        14.89        15.06        14.33 
TCGA-DD-AADR TCGA-DD-AADU TCGA-DD-AADV TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE3 
       66.67        18.21        18.87        18.25        18.15        18.61 
TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAED 
        4.64        21.17        21.83        23.74        15.72        25.08 
TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVQ 
       16.37        23.64        25.78        50.33        35.08        89.69 
TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY 
       82.62        59.93        72.39        76.18        56.48        64.77 
TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 
       62.47        66.25        65.39        49.48        53.69        13.41 
TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-ED-A82E 
       13.35         9.73        12.82         0.20        13.15        13.41 
TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC 
        1.84         0.20        18.74        20.61        19.59         0.62 
TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A2QQ TCGA-FV-A3I0 
        9.96        11.93        22.85        14.40        23.97        27.88 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25U 
        8.12         6.38        81.73         0.39        51.06        53.79 
TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH 
       28.27        30.74        58.49        21.53        22.13        25.64 
TCGA-G3-A3CJ TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A7M6 TCGA-G3-A7M7 
       19.53        25.25        22.95        20.42        12.03         5.98 
TCGA-G3-AAUZ TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV5 TCGA-G3-AAV6 
       11.24        11.80         9.70         9.17         8.75         2.14 
TCGA-G3-AAV7 TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-KR-A7K7 
        3.02         2.99        16.83         3.72        11.84        13.38 
TCGA-KR-A7K8 TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75H TCGA-MI-A75I 
       24.36        12.03         9.57        16.67        12.85        20.71 
TCGA-MR-A8JO TCGA-NI-A8LF TCGA-O8-A75V TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK 
       10.85        19.92        17.69        19.04        15.39        15.52 
TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0U 
       24.13        17.59        16.44         1.71        15.98        10.75 
TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9D4 TCGA-ZS-A9CD 
        0.99        12.99        13.55        35.77        12.99        45.57 
TCGA-ZS-A9CG 
       11.21 

$`AMP PEAK 16(8Q24.21) WILD-TYPE`
TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GV TCGA-2Y-A9GZ TCGA-2Y-A9H0 
       23.80        53.39        63.75        83.24        27.88       120.82 
TCGA-2Y-A9H3 TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HB 
       41.33        11.74        37.25        20.81        14.99         8.55 
TCGA-4R-AA8I TCGA-5C-AAPD TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10X 
        8.61         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-BD-A2L6 TCGA-BW-A5NO 
       22.36        17.98        12.72        18.48        44.81         0.66 
TCGA-CC-5260 TCGA-CC-5263 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A11B TCGA-DD-A11D 
        2.86         4.24        37.78        83.57         0.46        51.29 
TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1ED TCGA-DD-A1EH TCGA-DD-A1EJ TCGA-DD-A1EK 
       79.40        66.31        75.65        49.15        33.04        18.35 
TCGA-DD-A39W TCGA-DD-A3A0 TCGA-DD-A3A2 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 
       27.19        25.81        70.06        20.12       102.74       107.11 
TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NH TCGA-DD-A4NL TCGA-DD-A4NP 
       30.61        33.14        32.52        30.15        56.25       108.76 
TCGA-DD-A4NV TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-AA3A 
       78.84         9.30        23.05         1.45        35.67        13.48 
TCGA-DD-AACC TCGA-DD-AACE TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACQ TCGA-DD-AACU 
       55.40        63.48         0.30         3.52        14.20        51.52 
TCGA-DD-AACV TCGA-DD-AACX TCGA-DD-AAD3 TCGA-DD-AAD8 TCGA-DD-AADF TCGA-DD-AADG 
       50.33         5.59        42.58        40.08         3.78        37.64 
TCGA-DD-AADJ TCGA-DD-AADS TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE2 TCGA-DD-AAE4 
       35.05        15.58        19.30        18.25        20.98        19.99 
TCGA-DD-AAEA TCGA-DD-AAVP TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A7PX 
       18.90        79.07        12.69        15.85        13.91         0.20 
TCGA-ED-A7XO TCGA-ED-A8O5 TCGA-EP-A26S TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3R3 
       14.04        13.35        19.99        60.89        19.10        12.03 
TCGA-FV-A495 TCGA-FV-A496 TCGA-G3-A25S TCGA-G3-A25Y TCGA-G3-A3CI TCGA-G3-A3CK 
        0.03         0.33        13.68        14.86         5.92        19.23 
TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M9 TCGA-G3-AAV0 TCGA-G3-AAV4 TCGA-GJ-A6C0 
       17.10         7.76         1.84         8.55         0.89         1.02 
TCGA-GJ-A9DB TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-KR-A7K0 TCGA-LG-A6GG 
        2.20        37.91        20.75        17.06         2.14        12.72 
TCGA-LG-A9QC TCGA-MI-A75G TCGA-MR-A520 TCGA-NI-A4U2 TCGA-PD-A5DF TCGA-QA-A7B7 
       13.97        18.38         0.62        58.88        21.01         3.09 
TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-T1-A6J8 TCGA-UB-A7MB TCGA-UB-A7MF TCGA-UB-AA0V 
       21.04        19.33         0.76        19.76         7.04        10.32 
TCGA-WJ-A86L TCGA-WX-AA46 TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 
       11.34        24.85        25.71        23.21        23.57         0.69 
TCGA-ZP-A9D2 TCGA-ZS-A9CE TCGA-ZS-A9CF 
       24.43        40.80        79.30 

  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 
                        114.35                         120.82 
  AMP PEAK 16(8Q24.21) MUTATED AMP PEAK 16(8Q24.21) WILD-TYPE 
                         18.61                          19.99 
[1] "0.1 - 114.3 (18.6)" "0.0 - 120.8 (20.0)"
[1] "hr=" "1.2"
D16V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IIIA
  AMP PEAK 16(8Q24.21) MUTATED       107       57         0         41
  AMP PEAK 16(8Q24.21) WILD-TYPE      61       27         3         18
                                vv
clus                             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 16(8Q24.21) MUTATED            4          3        2         1
  AMP PEAK 16(8Q24.21) WILD-TYPE          4          4        1         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                             107                             61
  STAGE II                             57                             27
  STAGE III                             0                              3
  STAGE IIIA                           41                             18
  STAGE IIIB                            4                              4
  STAGE IIIC                            3                              4
  STAGE IV                              2                              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 16(8Q24.21) MUTATED     110  60  47   6
  AMP PEAK 16(8Q24.21) WILD-TYPE    69  31  26   6
D16V4, multiclass
       clus
vv      AMP PEAK 16(8Q24.21) MUTATED AMP PEAK 16(8Q24.21) WILD-TYPE
  T0+T1                          110                             69
  T2                              60                             31
  T3                              47                             26
  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   171   1
  AMP PEAK 16(8Q24.21) WILD-TYPE  78   2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(8Q24.21) MUTATED    171    1
  AMP PEAK 16(8Q24.21) WILD-TYPE   78    2
   clus
vv  AMP PEAK 16(8Q24.21) MUTATED AMP PEAK 16(8Q24.21) WILD-TYPE
  0                          171                             78
  1                            1                              2
[1] 2 2
[1] FALSE
D16V6, binary
                                cls
clus                               0   1
  AMP PEAK 16(8Q24.21) MUTATED   176   2
  AMP PEAK 16(8Q24.21) WILD-TYPE  84   2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(8Q24.21) MUTATED    176    2
  AMP PEAK 16(8Q24.21) WILD-TYPE   84    2
   clus
vv  AMP PEAK 16(8Q24.21) MUTATED AMP PEAK 16(8Q24.21) WILD-TYPE
  0                          176                             84
  1                            2                              2
[1] 2 2
[1] FALSE
D16V7, binary
                                cls
clus                               0   1
  AMP PEAK 16(8Q24.21) MUTATED    55 169
  AMP PEAK 16(8Q24.21) WILD-TYPE  58  75
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(8Q24.21) MUTATED     55  169
  AMP PEAK 16(8Q24.21) WILD-TYPE   58   75
        clus
vv       AMP PEAK 16(8Q24.21) MUTATED AMP PEAK 16(8Q24.21) WILD-TYPE
  FEMALE                           55                             58
  MALE                            169                             75
[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                        218
  AMP PEAK 16(8Q24.21) WILD-TYPE                      130
                                vv
clus                             HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK 16(8Q24.21) MUTATED                                  5
  AMP PEAK 16(8Q24.21) WILD-TYPE                                2
D16V8, multiclass
                                  clus
vv                                 AMP PEAK 16(8Q24.21) MUTATED
  FIBROLAMELLAR CARCINOMA                                     1
  HEPATOCELLULAR CARCINOMA                                  218
  HEPATOCHOLANGIOCARCINOMA (MIXED)                            5
                                  clus
vv                                 AMP PEAK 16(8Q24.21) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                       1
  HEPATOCELLULAR CARCINOMA                                    130
  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   198  11   1  10
  AMP PEAK 16(8Q24.21) WILD-TYPE 117   4   0   9
D16V9, multiclass
    clus
vv   AMP PEAK 16(8Q24.21) MUTATED AMP PEAK 16(8Q24.21) WILD-TYPE
  R0                          198                            117
  R1                           11                              4
  R2                            1                              0
  RX                           10                              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 16(8Q24.21) MUTATED                                  1   117
  AMP PEAK 16(8Q24.21) WILD-TYPE                                0    39
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 16(8Q24.21) MUTATED                          11    88
  AMP PEAK 16(8Q24.21) WILD-TYPE                         6    85
D16V10, multiclass
                                  clus
vv                                 AMP PEAK 16(8Q24.21) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                     117
  BLACK OR AFRICAN AMERICAN                                  11
  WHITE                                                      88
                                  clus
vv                                 AMP PEAK 16(8Q24.21) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                        39
  BLACK OR AFRICAN AMERICAN                                     6
  WHITE                                                        85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V11, binary
                                cls
clus                               0   1
  AMP PEAK 16(8Q24.21) MUTATED     6 209
  AMP PEAK 16(8Q24.21) WILD-TYPE   5 120
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(8Q24.21) MUTATED      6  209
  AMP PEAK 16(8Q24.21) WILD-TYPE    5  120
                        clus
vv                       AMP PEAK 16(8Q24.21) MUTATED
  HISPANIC OR LATINO                                6
  NOT HISPANIC OR LATINO                          209
                        clus
vv                       AMP PEAK 16(8Q24.21) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                            120
[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    23  15
  AMP PEAK 17(9Q34.2) WILD-TYPE 202  94
  AMP PEAK 17(9Q34.2) MUTATED AMP PEAK 17(9Q34.2) WILD-TYPE 
                           38                           296 
  AMP PEAK 17(9Q34.2) MUTATED AMP PEAK 17(9Q34.2) WILD-TYPE 
                           15                            94 
$`AMP PEAK 17(9Q34.2) MUTATED`
TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H9 TCGA-5R-AA1C TCGA-BC-A10T 
       24.89        27.88       120.82        14.99        11.97        27.52 
TCGA-BC-A10Y TCGA-BC-A8YO TCGA-BW-A5NO TCGA-CC-5261 TCGA-CC-5263 TCGA-DD-A1EG 
       23.34        18.48         0.66         3.19         4.24        45.11 
TCGA-DD-A3A0 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A4NV TCGA-DD-A73G TCGA-DD-AACY 
       25.81       102.74       107.11        78.84       114.35        47.67 
TCGA-DD-AAD6 TCGA-DD-AADJ TCGA-DD-AADO TCGA-DD-AAE0 TCGA-DD-AAE2 TCGA-DD-AAVZ 
       22.09        35.05        14.89        18.25        20.98        62.47 
TCGA-ED-A66Y TCGA-ED-A82E TCGA-EP-A2KB TCGA-ES-A2HS TCGA-FV-A2QQ TCGA-FV-A495 
        9.73        13.41        19.59        22.85        23.97         0.03 
TCGA-FV-A4ZP TCGA-G3-A25U TCGA-G3-A3CG TCGA-G3-A7M9 TCGA-KR-A7K2 TCGA-KR-A7K8 
       81.73        53.79        22.13         1.84        11.84        24.36 
TCGA-WQ-A9G7 TCGA-ZS-A9CF 
        0.99        79.30 

$`AMP PEAK 17(9Q34.2) WILD-TYPE`
TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GV TCGA-2Y-A9GW TCGA-2Y-A9GX 
       23.80        53.39        63.75        83.24        41.79        80.28 
TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H6 
       40.41        56.91        41.33        47.74        18.25        11.74 
TCGA-2Y-A9H7 TCGA-2Y-A9H8 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-4R-AA8I 
       37.25        20.81         1.18         8.55        13.02         8.61 
TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4072 
       10.78        10.59         0.66        11.08         1.51        48.99 
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10U TCGA-BC-A10W 
       27.91        37.32        10.13        46.78        27.52         2.99 
TCGA-BC-A10X TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 
       25.32         1.12        69.57         5.03        44.42        13.84 
TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I TCGA-BD-A2L6 
        0.26        22.36        17.98        14.60        12.72        44.81 
TCGA-BD-A3EP TCGA-BD-A3ER TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5262 TCGA-CC-A1HT 
       13.45        36.66         0.07         2.86         3.39         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-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B 
       83.57        53.33       113.00         7.33         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-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ 
       75.65        11.47        12.95        49.15         6.02        33.04 
TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Y 
       18.35        13.64        21.14        27.19        55.69         5.62 
TCGA-DD-A39Z TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A7 
       19.76         7.66        70.06        17.59        20.12        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        90.28        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-A73A 
       73.81       108.76        12.26         0.30        80.75        23.93 
TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-AA3A 
        9.30        23.05        22.78         1.45        35.67        13.48 
TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD 
        0.53        11.41        75.65        76.41        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        69.11 
TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP 
        0.30         3.52        58.16        42.81        61.68        13.64 
TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW 
       14.20        59.31        51.35        51.52        50.33        46.82 
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        42.58 
TCGA-DD-AAD5 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD 
       44.22        40.08        40.54        40.83        13.97        40.47 
TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADK TCGA-DD-AADL 
       39.52         3.78        37.64        35.67        34.49        20.91 
TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS 
        0.39        29.52        15.06        14.33        66.67        15.58 
TCGA-DD-AADU TCGA-DD-AADV TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE1 TCGA-DD-AAE3 
       18.21        18.87        19.30        18.25        18.15        18.61 
TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAE9 TCGA-DD-AAEA 
       19.99         4.64        21.17        21.83        23.74        18.90 
TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAEI 
       15.72        25.08        16.37        23.64        25.78        50.33 
TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU 
       35.08        79.07        89.69        82.62        59.93        72.39 
TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 
       76.18        56.48        64.77        66.25        65.39        49.48 
TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X 
       53.69        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        12.82         0.20        14.04        13.15        13.35 
TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC 
        1.84         0.20        18.74        19.99        20.61         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        60.89        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        12.03         0.33         0.39        13.68 
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        25.25        22.95 
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-AAV5 
        8.55        11.80         9.70         9.17         0.89         8.75 
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         2.99        37.91 
TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K7 
       20.75        17.06        16.83         3.72         2.14        13.38 
TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G 
       12.72        13.97        12.03         9.57        16.67        18.38 
TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF 
       12.85        20.71         0.62        10.85        58.88        19.92 
TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF 
       17.69        21.01         3.09        21.04        19.33        19.04 
TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-T1-A6J8 TCGA-UB-A7MA TCGA-UB-A7MB 
       15.39        15.52        24.13         0.76        17.59        19.76 
TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-A7MF TCGA-UB-AA0U TCGA-UB-AA0V 
       16.44         1.71        15.98         7.04        10.75        10.32 
TCGA-WJ-A86L TCGA-WQ-AB4B TCGA-WX-AA46 TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY 
       11.34        12.99        24.85        13.55        35.77        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 
       40.80        11.21 

  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 
                       120.82                        113.00 
  AMP PEAK 17(9Q34.2) MUTATED AMP PEAK 17(9Q34.2) WILD-TYPE 
                       23.095                        18.805 
[1] "0.0 - 120.8 (23.1)" "0.1 - 113.0 (18.8)"
[1] "hr=" "1.2"
D17V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IIIA
  AMP PEAK 17(9Q34.2) MUTATED        15        8         1         13
  AMP PEAK 17(9Q34.2) WILD-TYPE     153       76         2         46
                               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          7          6        2         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                             15                           153
  STAGE II                             8                            76
  STAGE III                            1                             2
  STAGE IIIA                          13                            46
  STAGE IIIB                           1                             7
  STAGE IIIC                           1                             6
  STAGE IV                             1                             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
  AMP PEAK 17(9Q34.2) MUTATED      16   9  16   3
  AMP PEAK 17(9Q34.2) WILD-TYPE   163  82  57   9
D17V4, multiclass
       clus
vv      AMP PEAK 17(9Q34.2) MUTATED AMP PEAK 17(9Q34.2) WILD-TYPE
  T0+T1                          16                           163
  T2                              9                            82
  T3                             16                            57
  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    30   1
  AMP PEAK 17(9Q34.2) WILD-TYPE 219   2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 17(9Q34.2) MUTATED     30    1
  AMP PEAK 17(9Q34.2) WILD-TYPE  219    2
   clus
vv  AMP PEAK 17(9Q34.2) MUTATED AMP PEAK 17(9Q34.2) WILD-TYPE
  0                          30                           219
  1                           1                             2
[1] 2 2
[1] FALSE
D17V6, binary
                               cls
clus                              0   1
  AMP PEAK 17(9Q34.2) MUTATED    32   1
  AMP PEAK 17(9Q34.2) WILD-TYPE 228   3
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 17(9Q34.2) MUTATED     32    1
  AMP PEAK 17(9Q34.2) WILD-TYPE  228    3
   clus
vv  AMP PEAK 17(9Q34.2) MUTATED AMP PEAK 17(9Q34.2) WILD-TYPE
  0                          32                           228
  1                           1                             3
[1] 2 2
[1] FALSE
D17V7, binary
                               cls
clus                              0   1
  AMP PEAK 17(9Q34.2) MUTATED    16  28
  AMP PEAK 17(9Q34.2) WILD-TYPE  97 216
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 17(9Q34.2) MUTATED     16   28
  AMP PEAK 17(9Q34.2) WILD-TYPE   97  216
        clus
vv       AMP PEAK 17(9Q34.2) MUTATED AMP PEAK 17(9Q34.2) WILD-TYPE
  FEMALE                          16                            97
  MALE                            28                           216
[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                         43
  AMP PEAK 17(9Q34.2) WILD-TYPE                      305
                               vv
clus                            HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK 17(9Q34.2) MUTATED                                  1
  AMP PEAK 17(9Q34.2) WILD-TYPE                                6
D17V8, multiclass
                                  clus
vv                                 AMP PEAK 17(9Q34.2) MUTATED
  FIBROLAMELLAR CARCINOMA                                    0
  HEPATOCELLULAR CARCINOMA                                  43
  HEPATOCHOLANGIOCARCINOMA (MIXED)                           1
                                  clus
vv                                 AMP PEAK 17(9Q34.2) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                      2
  HEPATOCELLULAR CARCINOMA                                   305
  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 17(9Q34.2) MUTATED    36   3   0   5
  AMP PEAK 17(9Q34.2) WILD-TYPE 279  12   1  14
D17V9, multiclass
    clus
vv   AMP PEAK 17(9Q34.2) MUTATED AMP PEAK 17(9Q34.2) WILD-TYPE
  R0                          36                           279
  R1                           3                            12
  R2                           0                             1
  RX                           5                            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 17(9Q34.2) MUTATED                                  0    17
  AMP PEAK 17(9Q34.2) WILD-TYPE                                1   139
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 17(9Q34.2) MUTATED                           1    25
  AMP PEAK 17(9Q34.2) WILD-TYPE                        16   148
D17V10, multiclass
                                  clus
vv                                 AMP PEAK 17(9Q34.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                     17
  BLACK OR AFRICAN AMERICAN                                  1
  WHITE                                                     25
                                  clus
vv                                 AMP PEAK 17(9Q34.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                      139
  BLACK OR AFRICAN AMERICAN                                   16
  WHITE                                                      148
[1] 4 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     2  40
  AMP PEAK 17(9Q34.2) WILD-TYPE   9 289
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 17(9Q34.2) MUTATED      2   40
  AMP PEAK 17(9Q34.2) WILD-TYPE    9  289
                        clus
vv                       AMP PEAK 17(9Q34.2) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          40
                        clus
vv                       AMP PEAK 17(9Q34.2) WILD-TYPE
  HISPANIC OR LATINO                                 9
  NOT HISPANIC OR LATINO                           289
[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    38  13
  AMP PEAK 18(11Q13.3) WILD-TYPE 187  96
  AMP PEAK 18(11Q13.3) MUTATED AMP PEAK 18(11Q13.3) WILD-TYPE 
                            51                            283 
  AMP PEAK 18(11Q13.3) MUTATED AMP PEAK 18(11Q13.3) WILD-TYPE 
                            13                             96 
$`AMP PEAK 18(11Q13.3) MUTATED`
TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GZ TCGA-2Y-A9H9 TCGA-BC-4073 TCGA-BC-A10T 
       23.80        53.39        27.88        14.99        27.91        27.52 
TCGA-BC-A3KG TCGA-BC-A69I TCGA-BD-A3EP TCGA-BD-A3ER TCGA-CC-A3M9 TCGA-CC-A3MB 
       22.36        12.72        13.45        36.66         0.10         0.10 
TCGA-DD-A115 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A1EB TCGA-DD-A39Y TCGA-DD-A3A0 
       83.57         7.33         2.60        66.31         5.62        25.81 
TCGA-DD-A4ND TCGA-DD-A4NN TCGA-DD-A4NV TCGA-DD-A73E TCGA-DD-A73G TCGA-DD-AACB 
       90.28        29.56        78.84         1.45       114.35        76.41 
TCGA-DD-AAD1 TCGA-DD-AAD8 TCGA-DD-AADL TCGA-DD-AADP TCGA-DD-AADV TCGA-DD-AADY 
       18.54        40.08        20.91        15.06        18.87        18.25 
TCGA-DD-AAE0 TCGA-DD-AAE6 TCGA-DD-AAED TCGA-ED-A66Y TCGA-ED-A82E TCGA-EP-A2KA 
       18.25         4.64        25.08         9.73        13.41        20.61 
TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A5SJ 
        0.33         0.39        13.68        30.74        22.13        22.95 
TCGA-G3-AAV0 TCGA-GJ-A9DB TCGA-K7-A5RG TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-RC-A7SB 
        8.55         2.20        17.06        24.36        12.72        19.33 
TCGA-RC-A7SF TCGA-UB-A7ME TCGA-WQ-A9G7 
       19.04        15.98         0.99 

$`AMP PEAK 18(11Q13.3) WILD-TYPE`
TCGA-2Y-A9GU TCGA-2Y-A9GV TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GY TCGA-2Y-A9H0 
       63.75        83.24        41.79        80.28        24.89       120.82 
TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H6 
       40.41        56.91        41.33        47.74        18.25        11.74 
TCGA-2Y-A9H7 TCGA-2Y-A9H8 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-4R-AA8I 
       37.25        20.81         1.18         8.55        13.02         8.61 
TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM 
       10.78        10.59         0.66        11.97        11.08         1.51 
TCGA-BC-4072 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10U TCGA-BC-A10W 
       48.99        37.32        10.13        46.78        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-A217 TCGA-BC-A3KF TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A8YO TCGA-BD-A2L6 
       13.84         0.26        17.98        14.60        18.48        44.81 
TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 
        0.66         0.07         2.86         3.19         3.39         4.24 
TCGA-CC-A1HT TCGA-CC-A3MA TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A116 
        3.32         0.07         0.13        79.73        37.78        53.33 
TCGA-DD-A118 TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA 
      113.00         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        11.47        12.95        45.11        49.15 
TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W 
        6.02        33.04        18.35        13.64        21.14        27.19 
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-A4NA 
      102.74       107.11        13.78         0.36        30.61        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-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-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73F TCGA-DD-AA3A 
       23.93         9.30        23.05        22.78        35.67        13.48 
TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE 
        0.53        11.41        75.65        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        69.11         0.30 
TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ 
        3.52        58.16        42.81        61.68        13.64        14.20 
TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX 
       59.31        51.35        51.52        50.33        46.82         5.59 
TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 
       47.67         5.62         4.50        21.63        42.58        44.22 
TCGA-DD-AAD6 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE 
       22.09        40.54        40.83        13.97        40.47        39.52 
TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADM 
        3.78        37.64        35.67        35.05        34.49         0.39 
TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU 
       29.52        14.89        14.33        66.67        15.58        18.21 
TCGA-DD-AADW TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE7 
       19.30        18.15        20.98        18.61        19.99        21.17 
TCGA-DD-AAE8 TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAEE TCGA-DD-AAEG 
       21.83        23.74        18.90        15.72        16.37        23.64 
TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR 
       25.78        50.33        35.08        79.07        89.69        82.62 
TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ 
       59.93        72.39        76.18        56.48        64.77        62.47 
TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI 
       66.25        65.39        49.48        53.69        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        12.82         0.20 
TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J 
       14.04        13.15        13.35         1.84         0.20        18.74 
TCGA-EP-A26S TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS 
       19.99        19.59         0.62         9.96        11.93        22.85 
TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 
       14.40        60.89        23.97        19.10        27.88         8.12 
TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A4ZP TCGA-G3-A25T TCGA-G3-A25U 
        6.38        12.03         0.03        81.73        51.06        53.79 
TCGA-G3-A25V TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI 
       28.27        58.49        14.86        21.53        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        25.25        20.42        17.10         7.76 
TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV1 TCGA-G3-AAV2 
       12.03         5.98         1.84        11.24        11.80         9.70 
TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A6C0 
        9.17         0.89         8.75         2.14         3.02         1.02 
TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 
        2.99        37.91        20.75        16.83         3.72         2.14 
TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E 
       11.84        13.38        13.97        12.03         9.57        16.67 
TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 
       18.38        12.85        20.71         0.62        10.85        58.88 
TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SH 
       19.92        17.69        21.01         3.09        21.04        15.39 
TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-T1-A6J8 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC 
       15.52        24.13         0.76        17.59        19.76        16.44 
TCGA-UB-A7MD TCGA-UB-A7MF TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-AB4B 
        1.71         7.04        10.75        10.32        11.34        12.99 
TCGA-WX-AA46 TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 
       24.85        13.55        35.77        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        40.80        79.30 
TCGA-ZS-A9CG 
       11.21 

  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 
                        114.35                         120.82 
  AMP PEAK 18(11Q13.3) MUTATED AMP PEAK 18(11Q13.3) WILD-TYPE 
                         18.87                          19.53 
[1] "0.1 - 114.3 (18.9)" "0.0 - 120.8 (19.5)"
[1] "hr=" "1.3"
D18V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IIIA
  AMP PEAK 18(11Q13.3) MUTATED        33        6         0         12
  AMP PEAK 18(11Q13.3) WILD-TYPE     135       78         3         47
                                vv
clus                             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 18(11Q13.3) MUTATED            1          0        2         0
  AMP PEAK 18(11Q13.3) WILD-TYPE          7          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                              33                            135
  STAGE II                              6                             78
  STAGE III                             0                              3
  STAGE IIIA                           12                             47
  STAGE IIIB                            1                              7
  STAGE IIIC                            0                              7
  STAGE IV                              2                              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      33   7  15   1
  AMP PEAK 18(11Q13.3) WILD-TYPE   146  84  58  11
D18V4, multiclass
       clus
vv      AMP PEAK 18(11Q13.3) MUTATED AMP PEAK 18(11Q13.3) WILD-TYPE
  T0+T1                           33                            146
  T2                               7                             84
  T3                              15                             58
  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    40   0
  AMP PEAK 18(11Q13.3) WILD-TYPE 209   3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 18(11Q13.3) MUTATED     40    0
  AMP PEAK 18(11Q13.3) WILD-TYPE  209    3
   clus
vv  AMP PEAK 18(11Q13.3) MUTATED AMP PEAK 18(11Q13.3) WILD-TYPE
  0                           40                            209
  1                            0                              3
[1] 2 2
[1] FALSE
D18V6, binary
                                cls
clus                               0   1
  AMP PEAK 18(11Q13.3) MUTATED    43   1
  AMP PEAK 18(11Q13.3) WILD-TYPE 217   3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 18(11Q13.3) MUTATED     43    1
  AMP PEAK 18(11Q13.3) WILD-TYPE  217    3
   clus
vv  AMP PEAK 18(11Q13.3) MUTATED AMP PEAK 18(11Q13.3) WILD-TYPE
  0                           43                            217
  1                            1                              3
[1] 2 2
[1] FALSE
D18V7, binary
                                cls
clus                               0   1
  AMP PEAK 18(11Q13.3) MUTATED    20  36
  AMP PEAK 18(11Q13.3) WILD-TYPE  93 208
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 18(11Q13.3) MUTATED     20   36
  AMP PEAK 18(11Q13.3) WILD-TYPE   93  208
        clus
vv       AMP PEAK 18(11Q13.3) MUTATED AMP PEAK 18(11Q13.3) WILD-TYPE
  FEMALE                           20                             93
  MALE                             36                            208
[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                         56
  AMP PEAK 18(11Q13.3) WILD-TYPE                      292
                                vv
clus                             HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK 18(11Q13.3) MUTATED                                  0
  AMP PEAK 18(11Q13.3) WILD-TYPE                                7
D18V8, multiclass
                                  clus
vv                                 AMP PEAK 18(11Q13.3) MUTATED
  FIBROLAMELLAR CARCINOMA                                     0
  HEPATOCELLULAR CARCINOMA                                   56
  HEPATOCHOLANGIOCARCINOMA (MIXED)                            0
                                  clus
vv                                 AMP PEAK 18(11Q13.3) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                       2
  HEPATOCELLULAR CARCINOMA                                    292
  HEPATOCHOLANGIOCARCINOMA (MIXED)                              7
[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    48   5   1   2
  AMP PEAK 18(11Q13.3) WILD-TYPE 267  10   0  17
D18V9, multiclass
    clus
vv   AMP PEAK 18(11Q13.3) MUTATED AMP PEAK 18(11Q13.3) WILD-TYPE
  R0                           48                            267
  R1                            5                             10
  R2                            1                              0
  RX                            2                             17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 18(11Q13.3) MUTATED                                  0    24
  AMP PEAK 18(11Q13.3) WILD-TYPE                                1   132
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 18(11Q13.3) MUTATED                           3    27
  AMP PEAK 18(11Q13.3) WILD-TYPE                        14   146
D18V10, multiclass
                                  clus
vv                                 AMP PEAK 18(11Q13.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                      24
  BLACK OR AFRICAN AMERICAN                                   3
  WHITE                                                      27
                                  clus
vv                                 AMP PEAK 18(11Q13.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                       132
  BLACK OR AFRICAN AMERICAN                                    14
  WHITE                                                       146
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V11, binary
                                cls
clus                               0   1
  AMP PEAK 18(11Q13.3) MUTATED     1  51
  AMP PEAK 18(11Q13.3) WILD-TYPE  10 278
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 18(11Q13.3) MUTATED      1   51
  AMP PEAK 18(11Q13.3) WILD-TYPE   10  278
                        clus
vv                       AMP PEAK 18(11Q13.3) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           51
                        clus
vv                       AMP PEAK 18(11Q13.3) WILD-TYPE
  HISPANIC OR LATINO                                 10
  NOT HISPANIC OR LATINO                            278
[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    37  20
  AMP PEAK 19(13Q32.3) WILD-TYPE 188  89
  AMP PEAK 19(13Q32.3) MUTATED AMP PEAK 19(13Q32.3) WILD-TYPE 
                            57                            277 
  AMP PEAK 19(13Q32.3) MUTATED AMP PEAK 19(13Q32.3) WILD-TYPE 
                            20                             89 
$`AMP PEAK 19(13Q32.3) MUTATED`
TCGA-2Y-A9GW TCGA-2Y-A9GZ TCGA-2Y-A9H8 TCGA-BC-A10W TCGA-BC-A10Z TCGA-BC-A216 
       41.79        27.88        20.81         2.99         1.12        44.42 
TCGA-BC-A3KF TCGA-BC-A8YO TCGA-BD-A3EP TCGA-CC-5258 TCGA-CC-5261 TCGA-CC-5263 
        0.26        18.48        13.45         0.07         3.19         4.24 
TCGA-CC-A3MA TCGA-DD-A113 TCGA-DD-A11A TCGA-DD-A11C TCGA-DD-A1EG TCGA-DD-A1EJ 
        0.07        79.73         2.60        21.76        45.11        33.04 
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        75.65        76.41 
TCGA-DD-AACE TCGA-DD-AACO TCGA-DD-AAD5 TCGA-DD-AADD TCGA-DD-AADF TCGA-DD-AADV 
       63.48        61.68        44.22        40.47         3.78        18.87 
TCGA-DD-AADW TCGA-DD-AAE0 TCGA-DD-AAE3 TCGA-DD-AAE6 TCGA-DD-AAE8 TCGA-DD-AAEK 
       19.30        18.25        18.61         4.64        21.83        35.08 
TCGA-DD-AAVW TCGA-ED-A7PY TCGA-EP-A2KA TCGA-EP-A3JL TCGA-FV-A23B TCGA-FV-A3I0 
       76.18        12.82        20.61         9.96        60.89        27.88 
TCGA-FV-A496 TCGA-G3-A7M6 TCGA-G3-AAV1 TCGA-G3-AAV6 TCGA-KR-A7K2 TCGA-KR-A7K8 
        0.33        12.03        11.80         2.14        11.84        24.36 
TCGA-NI-A8LF TCGA-PD-A5DF TCGA-RC-A7S9 TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MC 
       19.92        21.01        21.04        24.13        17.59        16.44 
TCGA-UB-A7MF TCGA-UB-AA0U TCGA-ZP-A9CZ 
        7.04        10.75        23.21 

$`AMP PEAK 19(13Q32.3) WILD-TYPE`
TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GV TCGA-2Y-A9GX TCGA-2Y-A9GY 
       23.80        53.39        63.75        83.24        80.28        24.89 
TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H4 TCGA-2Y-A9H5 
      120.82        40.41        56.91        41.33        47.74        18.25 
TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 
       11.74        37.25        14.99         1.18         8.55        13.02 
TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D 
        8.61        10.78        10.59         0.66        11.97        11.08 
TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S 
        1.51        48.99        27.91        37.32        10.13        46.78 
TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A110 TCGA-BC-A112 
       27.52        27.52        25.32        23.34        69.57         5.03 
TCGA-BC-A217 TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I TCGA-BD-A2L6 
       13.84        22.36        17.98        14.60        12.72        44.81 
TCGA-BD-A3ER TCGA-BW-A5NO TCGA-CC-5260 TCGA-CC-5262 TCGA-CC-A1HT TCGA-CC-A3M9 
       36.66         0.66         2.86         3.39         3.32         0.10 
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-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-A1EF TCGA-DD-A1EH TCGA-DD-A1EI 
       19.79        75.65        11.47        12.95        49.15         6.02 
TCGA-DD-A1EK TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 
       18.35        21.14        27.19        19.76        25.81         7.66 
TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A8 
       70.06        17.59        20.12       102.74       107.11         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        90.28        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        23.93 
TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G 
        9.30        23.05        22.78         1.45        35.67       114.35 
TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACF 
       13.48         0.53        11.41        55.40        12.53        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        69.11         0.30         3.52 
TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT 
       58.16        42.81        13.64        14.20        59.31        51.35 
TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AACZ 
       51.52        50.33        46.82         5.59        47.67         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        42.58        22.09        40.08 
TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADE TCGA-DD-AADG TCGA-DD-AADI 
       40.54        40.83        13.97        39.52        37.64        35.67 
TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO 
       35.05        34.49        20.91         0.39        29.52        14.89 
TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADY 
       15.06        14.33        66.67        15.58        18.21        18.25 
TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE4 TCGA-DD-AAE7 TCGA-DD-AAE9 TCGA-DD-AAEA 
       18.15        20.98        19.99        21.17        23.74        18.90 
TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAEI 
       15.72        25.08        16.37        23.64        25.78        50.33 
TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVX 
       79.07        89.69        82.62        59.93        72.39        56.48 
TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 
       64.77        62.47        66.25        65.39        49.48        53.69 
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         9.73 
TCGA-ED-A7PX TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 
        0.20         0.20        14.04        13.15        13.41        13.35 
TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KB TCGA-EP-A2KC 
        1.84         0.20        18.74        19.99        19.59         0.62 
TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I1 
       11.93        22.85        14.40        23.97        19.10         8.12 
TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S 
        6.38        12.03         0.03        81.73         0.39        13.68 
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-A7M7 
       25.25        22.95        20.42        17.10         7.76         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-AAV5 TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 
        8.75         3.02         1.02         2.20         2.99        37.91 
TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K7 
       20.75        17.06        16.83         3.72         2.14        13.38 
TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G 
       12.72        13.97        12.03         9.57        16.67        18.38 
TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-O8-A75V 
       12.85        20.71         0.62        10.85        58.88        17.69 
TCGA-QA-A7B7 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-T1-A6J8 
        3.09        19.33        19.04        15.39        15.52         0.76 
TCGA-UB-A7MB TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-A9G7 
       19.76         1.71        15.98        10.32        11.34         0.99 
TCGA-WQ-AB4B TCGA-WX-AA46 TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9D0 
       12.99        24.85        13.55        35.77        25.71        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        40.80        79.30 
TCGA-ZS-A9CG 
       11.21 

  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                         120.82 
  AMP PEAK 19(13Q32.3) MUTATED AMP PEAK 19(13Q32.3) WILD-TYPE 
                         18.87                          19.33 
[1] "0.1 - 79.7 (18.9)"  "0.0 - 120.8 (19.3)"
[1] "hr=" "1.3"
D19V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IIIA
  AMP PEAK 19(13Q32.3) MUTATED        29       14         0         12
  AMP PEAK 19(13Q32.3) WILD-TYPE     139       70         3         47
                                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          6          4        2         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                              29                            139
  STAGE II                             14                             70
  STAGE III                             0                              3
  STAGE IIIA                           12                             47
  STAGE IIIB                            2                              6
  STAGE IIIC                            3                              4
  STAGE IV                              1                              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 19(13Q32.3) MUTATED      32  14  13   4
  AMP PEAK 19(13Q32.3) WILD-TYPE   147  77  60   8
D19V4, multiclass
       clus
vv      AMP PEAK 19(13Q32.3) MUTATED AMP PEAK 19(13Q32.3) WILD-TYPE
  T0+T1                           32                            147
  T2                              14                             77
  T3                              13                             60
  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    45   1
  AMP PEAK 19(13Q32.3) WILD-TYPE 204   2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 19(13Q32.3) MUTATED     45    1
  AMP PEAK 19(13Q32.3) WILD-TYPE  204    2
   clus
vv  AMP PEAK 19(13Q32.3) MUTATED AMP PEAK 19(13Q32.3) WILD-TYPE
  0                           45                            204
  1                            1                              2
[1] 2 2
[1] FALSE
D19V6, binary
                                cls
clus                               0   1
  AMP PEAK 19(13Q32.3) MUTATED    49   1
  AMP PEAK 19(13Q32.3) WILD-TYPE 211   3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 19(13Q32.3) MUTATED     49    1
  AMP PEAK 19(13Q32.3) WILD-TYPE  211    3
   clus
vv  AMP PEAK 19(13Q32.3) MUTATED AMP PEAK 19(13Q32.3) WILD-TYPE
  0                           49                            211
  1                            1                              3
[1] 2 2
[1] FALSE
D19V7, binary
                                cls
clus                               0   1
  AMP PEAK 19(13Q32.3) MUTATED    27  36
  AMP PEAK 19(13Q32.3) WILD-TYPE  86 208
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 19(13Q32.3) MUTATED     27   36
  AMP PEAK 19(13Q32.3) WILD-TYPE   86  208
        clus
vv       AMP PEAK 19(13Q32.3) MUTATED AMP PEAK 19(13Q32.3) WILD-TYPE
  FEMALE                           27                             86
  MALE                             36                            208
[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                         60
  AMP PEAK 19(13Q32.3) WILD-TYPE                      288
                                vv
clus                             HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK 19(13Q32.3) MUTATED                                  3
  AMP PEAK 19(13Q32.3) WILD-TYPE                                4
D19V8, multiclass
                                  clus
vv                                 AMP PEAK 19(13Q32.3) MUTATED
  FIBROLAMELLAR CARCINOMA                                     0
  HEPATOCELLULAR CARCINOMA                                   60
  HEPATOCHOLANGIOCARCINOMA (MIXED)                            3
                                  clus
vv                                 AMP PEAK 19(13Q32.3) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                       2
  HEPATOCELLULAR CARCINOMA                                    288
  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 19(13Q32.3) MUTATED    53   3   0   5
  AMP PEAK 19(13Q32.3) WILD-TYPE 262  12   1  14
D19V9, multiclass
    clus
vv   AMP PEAK 19(13Q32.3) MUTATED AMP PEAK 19(13Q32.3) WILD-TYPE
  R0                           53                            262
  R1                            3                             12
  R2                            0                              1
  RX                            5                             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 19(13Q32.3) MUTATED                                  0    30
  AMP PEAK 19(13Q32.3) WILD-TYPE                                1   126
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 19(13Q32.3) MUTATED                           4    27
  AMP PEAK 19(13Q32.3) WILD-TYPE                        13   146
D19V10, multiclass
                                  clus
vv                                 AMP PEAK 19(13Q32.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                      30
  BLACK OR AFRICAN AMERICAN                                   4
  WHITE                                                      27
                                  clus
vv                                 AMP PEAK 19(13Q32.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                       126
  BLACK OR AFRICAN AMERICAN                                    13
  WHITE                                                       146
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V11, binary
                                cls
clus                               0   1
  AMP PEAK 19(13Q32.3) MUTATED     1  57
  AMP PEAK 19(13Q32.3) WILD-TYPE  10 272
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 19(13Q32.3) MUTATED      1   57
  AMP PEAK 19(13Q32.3) WILD-TYPE   10  272
                        clus
vv                       AMP PEAK 19(13Q32.3) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           57
                        clus
vv                       AMP PEAK 19(13Q32.3) WILD-TYPE
  HISPANIC OR LATINO                                 10
  NOT HISPANIC OR LATINO                            272
[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    39  19
  AMP PEAK 20(13Q33.3) WILD-TYPE 186  90
  AMP PEAK 20(13Q33.3) MUTATED AMP PEAK 20(13Q33.3) WILD-TYPE 
                            58                            276 
  AMP PEAK 20(13Q33.3) MUTATED AMP PEAK 20(13Q33.3) WILD-TYPE 
                            19                             90 
$`AMP PEAK 20(13Q33.3) MUTATED`
TCGA-2Y-A9GW TCGA-2Y-A9GZ TCGA-2Y-A9H8 TCGA-BC-A10W TCGA-BC-A217 TCGA-BC-A3KF 
       41.79        27.88        20.81         2.99        13.84         0.26 
TCGA-BD-A3EP TCGA-CC-5258 TCGA-CC-5261 TCGA-CC-5263 TCGA-CC-A3MA TCGA-DD-A113 
       13.45         0.07         3.19         4.24         0.07        79.73 
TCGA-DD-A11A TCGA-DD-A1EG TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39X TCGA-DD-A39Y 
        2.60        45.11        33.04        13.64        55.69         5.62 
TCGA-DD-A3A7 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACE TCGA-DD-AACO TCGA-DD-AAD5 
       13.78        75.65        76.41        63.48        61.68        44.22 
TCGA-DD-AADD TCGA-DD-AADF TCGA-DD-AADQ TCGA-DD-AADW TCGA-DD-AAE0 TCGA-DD-AAE1 
       40.47         3.78        14.33        19.30        18.25        18.15 
TCGA-DD-AAE3 TCGA-DD-AAE6 TCGA-DD-AAE8 TCGA-DD-AAEK TCGA-DD-AAVW TCGA-ED-A66Y 
       18.61         4.64        21.83        35.08        76.18         9.73 
TCGA-ED-A7PY TCGA-EP-A26S TCGA-EP-A2KC TCGA-EP-A3JL TCGA-FV-A23B TCGA-FV-A3I0 
       12.82        19.99         0.62         9.96        60.89        27.88 
TCGA-FV-A496 TCGA-G3-A7M6 TCGA-G3-AAV1 TCGA-G3-AAV6 TCGA-KR-A7K2 TCGA-KR-A7K8 
        0.33        12.03        11.80         2.14        11.84        24.36 
TCGA-NI-A8LF TCGA-RC-A7S9 TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MC 
       19.92        21.04        15.52        24.13        17.59        16.44 
TCGA-UB-A7MF TCGA-UB-AA0U TCGA-WJ-A86L TCGA-ZP-A9CZ 
        7.04        10.75        11.34        23.21 

$`AMP PEAK 20(13Q33.3) WILD-TYPE`
TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GV TCGA-2Y-A9GX TCGA-2Y-A9GY 
       23.80        53.39        63.75        83.24        80.28        24.89 
TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H4 TCGA-2Y-A9H5 
      120.82        40.41        56.91        41.33        47.74        18.25 
TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 
       11.74        37.25        14.99         1.18         8.55        13.02 
TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D 
        8.61        10.78        10.59         0.66        11.97        11.08 
TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S 
        1.51        48.99        27.91        37.32        10.13        46.78 
TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 
       27.52        27.52        25.32        23.34         1.12        69.57 
TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I 
        5.03        44.42        22.36        17.98        14.60        12.72 
TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3ER TCGA-BW-A5NO TCGA-CC-5260 TCGA-CC-5262 
       18.48        44.81        36.66         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-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        11.47 
TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EK TCGA-DD-A39V TCGA-DD-A39W 
       12.95        49.15         6.02        18.35        21.14        27.19 
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-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB 
      102.74       107.11         0.36        30.61        33.14        32.52 
TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK 
       90.28        30.97        30.15        26.83        30.51        39.78 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR 
       56.25        29.56        73.81       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        23.93         9.30        23.05        22.78 
TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 
        1.45        35.67       114.35        13.48         0.53        11.41 
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-AACN TCGA-DD-AACP 
       69.11         0.30         3.52        58.16        42.81        13.64 
TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW 
       14.20        59.31        51.35        51.52        50.33        46.82 
TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 
        5.59        47.67         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 
       42.58        22.09        40.08        40.54        40.83        13.97 
TCGA-DD-AADE TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL 
       39.52        37.64        35.67        35.05        34.49        20.91 
TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADR TCGA-DD-AADS 
        0.39        29.52        14.89        15.06        66.67        15.58 
TCGA-DD-AADU TCGA-DD-AADV TCGA-DD-AADY TCGA-DD-AAE2 TCGA-DD-AAE4 TCGA-DD-AAE7 
       18.21        18.87        18.25        20.98        19.99        21.17 
TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEG 
       23.74        18.90        15.72        25.08        16.37        23.64 
TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS 
       25.78        50.33        79.07        89.69        82.62        59.93 
TCGA-DD-AAVU TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 
       72.39        56.48        64.77        62.47        66.25        65.39 
TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 
       49.48        53.69        13.41        12.69        15.85        13.91 
TCGA-ED-A66X TCGA-ED-A7PX TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E 
       13.35         0.20         0.20        14.04        13.15        13.41 
TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A2KA TCGA-EP-A2KB 
       13.35         1.84         0.20        18.74        20.61        19.59 
TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I1 
       11.93        22.85        14.40        23.97        19.10         8.12 
TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S 
        6.38        12.03         0.03        81.73         0.39        13.68 
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-A7M7 
       25.25        22.95        20.42        17.10         7.76         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-AAV5 TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 
        8.75         3.02         1.02         2.20         2.99        37.91 
TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K7 
       20.75        17.06        16.83         3.72         2.14        13.38 
TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G 
       12.72        13.97        12.03         9.57        16.67        18.38 
TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-O8-A75V 
       12.85        20.71         0.62        10.85        58.88        17.69 
TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH TCGA-T1-A6J8 
       21.01         3.09        19.33        19.04        15.39         0.76 
TCGA-UB-A7MB TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0V TCGA-WQ-A9G7 TCGA-WQ-AB4B 
       19.76         1.71        15.98        10.32         0.99        12.99 
TCGA-WX-AA46 TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9D0 TCGA-ZP-A9D1 
       24.85        13.55        35.77        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        40.80        79.30        11.21 

  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                         120.82 
  AMP PEAK 20(13Q33.3) MUTATED AMP PEAK 20(13Q33.3) WILD-TYPE 
                        17.015                         19.760 
[1] "0.1 - 79.7 (17.0)"  "0.0 - 120.8 (19.8)"
[1] "hr=" "1.2"
D20V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IIIA
  AMP PEAK 20(13Q33.3) MUTATED        31       16         0         11
  AMP PEAK 20(13Q33.3) WILD-TYPE     137       68         3         48
                                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          7          5        2         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                              31                            137
  STAGE II                             16                             68
  STAGE III                             0                              3
  STAGE IIIA                           11                             48
  STAGE IIIB                            1                              7
  STAGE IIIC                            2                              5
  STAGE IV                              1                              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 20(13Q33.3) MUTATED      34  16  12   2
  AMP PEAK 20(13Q33.3) WILD-TYPE   145  75  61  10
D20V4, multiclass
       clus
vv      AMP PEAK 20(13Q33.3) MUTATED AMP PEAK 20(13Q33.3) WILD-TYPE
  T0+T1                           34                            145
  T2                              16                             75
  T3                              12                             61
  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    45   1
  AMP PEAK 20(13Q33.3) WILD-TYPE 204   2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(13Q33.3) MUTATED     45    1
  AMP PEAK 20(13Q33.3) WILD-TYPE  204    2
   clus
vv  AMP PEAK 20(13Q33.3) MUTATED AMP PEAK 20(13Q33.3) WILD-TYPE
  0                           45                            204
  1                            1                              2
[1] 2 2
[1] FALSE
D20V6, binary
                                cls
clus                               0   1
  AMP PEAK 20(13Q33.3) MUTATED    49   1
  AMP PEAK 20(13Q33.3) WILD-TYPE 211   3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(13Q33.3) MUTATED     49    1
  AMP PEAK 20(13Q33.3) WILD-TYPE  211    3
   clus
vv  AMP PEAK 20(13Q33.3) MUTATED AMP PEAK 20(13Q33.3) WILD-TYPE
  0                           49                            211
  1                            1                              3
[1] 2 2
[1] FALSE
D20V7, binary
                                cls
clus                               0   1
  AMP PEAK 20(13Q33.3) MUTATED    25  39
  AMP PEAK 20(13Q33.3) WILD-TYPE  88 205
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(13Q33.3) MUTATED     25   39
  AMP PEAK 20(13Q33.3) WILD-TYPE   88  205
        clus
vv       AMP PEAK 20(13Q33.3) MUTATED AMP PEAK 20(13Q33.3) WILD-TYPE
  FEMALE                           25                             88
  MALE                             39                            205
[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                         61
  AMP PEAK 20(13Q33.3) WILD-TYPE                      287
                                vv
clus                             HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK 20(13Q33.3) MUTATED                                  3
  AMP PEAK 20(13Q33.3) WILD-TYPE                                4
D20V8, multiclass
                                  clus
vv                                 AMP PEAK 20(13Q33.3) MUTATED
  FIBROLAMELLAR CARCINOMA                                     0
  HEPATOCELLULAR CARCINOMA                                   61
  HEPATOCHOLANGIOCARCINOMA (MIXED)                            3
                                  clus
vv                                 AMP PEAK 20(13Q33.3) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                       2
  HEPATOCELLULAR CARCINOMA                                    287
  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 20(13Q33.3) MUTATED    55   3   0   4
  AMP PEAK 20(13Q33.3) WILD-TYPE 260  12   1  15
D20V9, multiclass
    clus
vv   AMP PEAK 20(13Q33.3) MUTATED AMP PEAK 20(13Q33.3) WILD-TYPE
  R0                           55                            260
  R1                            3                             12
  R2                            0                              1
  RX                            4                             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
  AMP PEAK 20(13Q33.3) MUTATED                                  0    33
  AMP PEAK 20(13Q33.3) WILD-TYPE                                1   123
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 20(13Q33.3) MUTATED                           5    24
  AMP PEAK 20(13Q33.3) WILD-TYPE                        12   149
D20V10, multiclass
                                  clus
vv                                 AMP PEAK 20(13Q33.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                      33
  BLACK OR AFRICAN AMERICAN                                   5
  WHITE                                                      24
                                  clus
vv                                 AMP PEAK 20(13Q33.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                       123
  BLACK OR AFRICAN AMERICAN                                    12
  WHITE                                                       149
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V11, binary
                                cls
clus                               0   1
  AMP PEAK 20(13Q33.3) MUTATED     1  58
  AMP PEAK 20(13Q33.3) WILD-TYPE  10 271
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(13Q33.3) MUTATED      1   58
  AMP PEAK 20(13Q33.3) WILD-TYPE   10  271
                        clus
vv                       AMP PEAK 20(13Q33.3) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           58
                        clus
vv                       AMP PEAK 20(13Q33.3) WILD-TYPE
  HISPANIC OR LATINO                                 10
  NOT HISPANIC OR LATINO                            271
[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    37  12
  AMP PEAK 21(15Q26.3) WILD-TYPE 188  97
  AMP PEAK 21(15Q26.3) MUTATED AMP PEAK 21(15Q26.3) WILD-TYPE 
                            49                            285 
  AMP PEAK 21(15Q26.3) MUTATED AMP PEAK 21(15Q26.3) WILD-TYPE 
                            12                             97 
$`AMP PEAK 21(15Q26.3) MUTATED`
TCGA-2Y-A9GS TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9HB TCGA-5C-A9VG TCGA-BC-A10Q 
       23.80        56.91        41.33         8.55        10.78        37.32 
TCGA-BC-A10Y TCGA-BC-A217 TCGA-BC-A3KF TCGA-BW-A5NO TCGA-CC-5262 TCGA-CC-5263 
       23.34        13.84         0.26         0.66         3.39         4.24 
TCGA-CC-A3M9 TCGA-DD-A11A TCGA-DD-A39Z TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NV 
        0.10         2.60        19.76        26.83        30.51        78.84 
TCGA-DD-A73G TCGA-DD-AACB TCGA-DD-AACP TCGA-DD-AACV TCGA-DD-AACZ TCGA-DD-AADO 
      114.35        76.41        13.64        50.33         5.62        14.89 
TCGA-DD-AADU TCGA-DD-AADV TCGA-DD-AAE0 TCGA-DD-AAE3 TCGA-DD-AAE6 TCGA-DD-AAE8 
       18.21        18.87        18.25        18.61         4.64        21.83 
TCGA-DD-AAEA TCGA-ED-A5KG TCGA-ED-A66X TCGA-ED-A7PZ TCGA-ED-A8O6 TCGA-EP-A2KA 
       18.90        15.85        13.35         0.20         1.84        20.61 
TCGA-ES-A2HS TCGA-FV-A23B TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25Y TCGA-G3-A3CH 
       22.85        60.89         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        17.69        15.52        17.59 
TCGA-WQ-AB4B 
       12.99 

$`AMP PEAK 21(15Q26.3) WILD-TYPE`
TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GV TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GY 
       53.39        63.75        83.24        41.79        80.28        24.89 
TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H6 
       27.88       120.82        40.41        47.74        18.25        11.74 
TCGA-2Y-A9H7 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-3K-AAZ8 TCGA-4R-AA8I 
       37.25        20.81        14.99         1.18        13.02         8.61 
TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4072 
       10.59         0.66        11.97        11.08         1.51        48.99 
TCGA-BC-4073 TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W 
       27.91        10.13        46.78        27.52        27.52         2.99 
TCGA-BC-A10X TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A3KG 
       25.32         1.12        69.57         5.03        44.42        22.36 
TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP 
       17.98        14.60        12.72        18.48        44.81        13.45 
TCGA-BD-A3ER TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-A1HT TCGA-CC-A3MA 
       36.66         0.07         2.86         3.19         3.32         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-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 
      113.00         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        11.47        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        33.04        18.35        13.64 
TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A3A0 TCGA-DD-A3A1 
       21.14        27.19        55.69         5.62        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        90.28        30.97 
TCGA-DD-A4NH TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP 
       30.15        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        23.93         9.30        23.05 
TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 
       22.78         1.45        35.67        13.48         0.53        11.41 
TCGA-DD-AACA TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG 
       75.65        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        69.11         0.30         3.52        58.16 
TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACU 
       42.81        61.68        14.20        59.31        51.35        51.52 
TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 
       46.82         5.59        47.67         4.50        18.54        21.63 
TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB 
       42.58        44.22        22.09        40.08        40.54        40.83 
TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI 
       13.97        40.47        39.52         3.78        37.64        35.67 
TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADP 
       35.05        34.49        20.91         0.39        29.52        15.06 
TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE1 
       14.33        66.67        15.58        19.30        18.25        18.15 
TCGA-DD-AAE2 TCGA-DD-AAE4 TCGA-DD-AAE7 TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAED 
       20.98        19.99        21.17        23.74        15.72        25.08 
TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP 
       16.37        23.64        25.78        50.33        35.08        79.07 
TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVX 
       89.69        82.62        59.93        72.39        76.18        56.48 
TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 
       64.77        62.47        66.25        65.39        49.48        53.69 
TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A627 TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY 
       13.41        12.69        13.91         9.73         0.20        12.82 
TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A97K TCGA-EP-A12J 
       14.04        13.15        13.41        13.35         0.20        18.74 
TCGA-EP-A26S TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HT 
       19.99        19.59         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        12.03 
TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25V 
        0.03         0.33        81.73        13.68        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        25.25        22.95        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-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A6C0 
        9.17         0.89         8.75         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         2.99        37.91        20.75        17.06        16.83 
TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG 
        3.72         2.14        11.84        13.38        24.36        12.72 
TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75H TCGA-MI-A75I 
       13.97        12.03         9.57        16.67        12.85        20.71 
TCGA-MR-A520 TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 
        0.62        58.88        19.92        21.01         3.09        21.04 
TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RG-A7D4 TCGA-T1-A6J8 TCGA-UB-A7MB 
       19.33        19.04        15.39        24.13         0.76        19.76 
TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-A7MF TCGA-UB-AA0U TCGA-UB-AA0V 
       16.44         1.71        15.98         7.04        10.75        10.32 
TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WX-AA46 TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY 
       11.34         0.99        24.85        13.55        35.77        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 
       40.80        79.30        11.21 

  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 
                        114.35                         120.82 
  AMP PEAK 21(15Q26.3) MUTATED AMP PEAK 21(15Q26.3) WILD-TYPE 
                         17.69                          19.92 
[1] "0.1 - 114.3 (17.7)" "0.0 - 120.8 (19.9)"
[1] "hr=" "1.1"
D21V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IIIA
  AMP PEAK 21(15Q26.3) MUTATED        21       13         0         12
  AMP PEAK 21(15Q26.3) WILD-TYPE     147       71         3         47
                                vv
clus                             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 21(15Q26.3) MUTATED            2          1        2         0
  AMP PEAK 21(15Q26.3) WILD-TYPE          6          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                              21                            147
  STAGE II                             13                             71
  STAGE III                             0                              3
  STAGE IIIA                           12                             47
  STAGE IIIB                            2                              6
  STAGE IIIC                            1                              6
  STAGE IV                              2                              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      21  16  13   3
  AMP PEAK 21(15Q26.3) WILD-TYPE   158  75  60   9
D21V4, multiclass
       clus
vv      AMP PEAK 21(15Q26.3) MUTATED AMP PEAK 21(15Q26.3) WILD-TYPE
  T0+T1                           21                            158
  T2                              16                             75
  T3                              13                             60
  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    37   0
  AMP PEAK 21(15Q26.3) WILD-TYPE 212   3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 21(15Q26.3) MUTATED     37    0
  AMP PEAK 21(15Q26.3) WILD-TYPE  212    3
   clus
vv  AMP PEAK 21(15Q26.3) MUTATED AMP PEAK 21(15Q26.3) WILD-TYPE
  0                           37                            212
  1                            0                              3
[1] 2 2
[1] FALSE
D21V6, binary
                                cls
clus                               0   1
  AMP PEAK 21(15Q26.3) MUTATED    41   1
  AMP PEAK 21(15Q26.3) WILD-TYPE 219   3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 21(15Q26.3) MUTATED     41    1
  AMP PEAK 21(15Q26.3) WILD-TYPE  219    3
   clus
vv  AMP PEAK 21(15Q26.3) MUTATED AMP PEAK 21(15Q26.3) WILD-TYPE
  0                           41                            219
  1                            1                              3
[1] 2 2
[1] FALSE
D21V7, binary
                                cls
clus                               0   1
  AMP PEAK 21(15Q26.3) MUTATED    19  34
  AMP PEAK 21(15Q26.3) WILD-TYPE  94 210
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 21(15Q26.3) MUTATED     19   34
  AMP PEAK 21(15Q26.3) WILD-TYPE   94  210
        clus
vv       AMP PEAK 21(15Q26.3) MUTATED AMP PEAK 21(15Q26.3) WILD-TYPE
  FEMALE                           19                             94
  MALE                             34                            210
[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                         51
  AMP PEAK 21(15Q26.3) WILD-TYPE                      297
                                vv
clus                             HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK 21(15Q26.3) MUTATED                                  1
  AMP PEAK 21(15Q26.3) WILD-TYPE                                6
D21V8, multiclass
                                  clus
vv                                 AMP PEAK 21(15Q26.3) MUTATED
  FIBROLAMELLAR CARCINOMA                                     1
  HEPATOCELLULAR CARCINOMA                                   51
  HEPATOCHOLANGIOCARCINOMA (MIXED)                            1
                                  clus
vv                                 AMP PEAK 21(15Q26.3) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                       1
  HEPATOCELLULAR CARCINOMA                                    297
  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 21(15Q26.3) MUTATED    45   3   0   4
  AMP PEAK 21(15Q26.3) WILD-TYPE 270  12   1  15
D21V9, multiclass
    clus
vv   AMP PEAK 21(15Q26.3) MUTATED AMP PEAK 21(15Q26.3) WILD-TYPE
  R0                           45                            270
  R1                            3                             12
  R2                            0                              1
  RX                            4                             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
  AMP PEAK 21(15Q26.3) MUTATED                                  0    25
  AMP PEAK 21(15Q26.3) WILD-TYPE                                1   131
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 21(15Q26.3) MUTATED                           2    23
  AMP PEAK 21(15Q26.3) WILD-TYPE                        15   150
D21V10, multiclass
                                  clus
vv                                 AMP PEAK 21(15Q26.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                      25
  BLACK OR AFRICAN AMERICAN                                   2
  WHITE                                                      23
                                  clus
vv                                 AMP PEAK 21(15Q26.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                       131
  BLACK OR AFRICAN AMERICAN                                    15
  WHITE                                                       150
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V11, binary
                                cls
clus                               0   1
  AMP PEAK 21(15Q26.3) MUTATED     5  44
  AMP PEAK 21(15Q26.3) WILD-TYPE   6 285
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 21(15Q26.3) MUTATED      5   44
  AMP PEAK 21(15Q26.3) WILD-TYPE    6  285
                        clus
vv                       AMP PEAK 21(15Q26.3) MUTATED
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                           44
                        clus
vv                       AMP PEAK 21(15Q26.3) WILD-TYPE
  HISPANIC OR LATINO                                  6
  NOT HISPANIC OR LATINO                            285
[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    26  15
  AMP PEAK 22(17P11.2) WILD-TYPE 199  94
  AMP PEAK 22(17P11.2) MUTATED AMP PEAK 22(17P11.2) WILD-TYPE 
                            41                            293 
  AMP PEAK 22(17P11.2) MUTATED AMP PEAK 22(17P11.2) WILD-TYPE 
                            15                             94 
$`AMP PEAK 22(17P11.2) MUTATED`
TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-3K-AAZ8 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A217 
       27.88       120.82        13.02        27.91        37.32        13.84 
TCGA-BC-A3KF TCGA-CC-5260 TCGA-CC-A3M9 TCGA-DD-A115 TCGA-DD-A119 TCGA-DD-A11A 
        0.26         2.86         0.10        83.57         7.33         2.60 
TCGA-DD-A3A3 TCGA-DD-A3A5 TCGA-DD-A3A7 TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A73E 
       17.59       102.74        13.78        73.81       108.76         1.45 
TCGA-DD-AACB TCGA-DD-AACI TCGA-DD-AAD0 TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADO 
       76.41        53.19         4.50        40.47        39.52        14.89 
TCGA-DD-AADR TCGA-DD-AAVR TCGA-DD-AAW1 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PZ 
       66.67        82.62        65.39        13.35         9.73         0.20 
TCGA-ED-A8O6 TCGA-EP-A2KA TCGA-EP-A2KB TCGA-ES-A2HS TCGA-FV-A4ZP TCGA-G3-AAUZ 
        1.84        20.61        19.59        22.85        81.73        11.24 
TCGA-G3-AAV6 TCGA-MI-A75G TCGA-O8-A75V TCGA-UB-A7MA TCGA-UB-A7MB 
        2.14        18.38        17.69        17.59        19.76 

$`AMP PEAK 22(17P11.2) WILD-TYPE`
TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GV TCGA-2Y-A9GW TCGA-2Y-A9GX 
       23.80        53.39        63.75        83.24        41.79        80.28 
TCGA-2Y-A9GY TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H4 TCGA-2Y-A9H5 
       24.89        40.41        56.91        41.33        47.74        18.25 
TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB 
       11.74        37.25        20.81        14.99         1.18         8.55 
TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D 
        8.61        10.78        10.59         0.66        11.97        11.08 
TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
        1.51        48.99        10.13        46.78        27.52        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-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I TCGA-BC-A8YO 
       44.42        22.36        17.98        14.60        12.72        18.48 
TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BD-A3ER TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5261 
       44.81        13.45        36.66         0.66         0.07         3.19 
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-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-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-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ 
       11.47        12.95        45.11        49.15         6.02        33.04 
TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Y 
       18.35        13.64        21.14        27.19        55.69         5.62 
TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A4 TCGA-DD-A3A6 
       19.76        25.81         7.66        70.06        20.12       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        90.28        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-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B 
       12.26         0.30        80.75        78.84        23.93         9.30 
TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 
       23.05        22.78        35.67       114.35        13.48         0.53 
TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF 
       11.41        75.65        55.40        12.53        63.48        12.00 
TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM 
       15.42         6.41        69.11         0.30         3.52        58.16 
TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT 
       42.81        61.68        13.64        14.20        59.31        51.35 
TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AACZ 
       51.52        50.33        46.82         5.59        47.67         5.62 
TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 
       18.54        21.63        42.58        44.22        22.09        40.08 
TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI 
       40.54        40.83        13.97         3.78        37.64        35.67 
TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADP 
       35.05        34.49        20.91         0.39        29.52        15.06 
TCGA-DD-AADQ TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADV TCGA-DD-AADW TCGA-DD-AADY 
       14.33        15.58        18.21        18.87        19.30        18.25 
TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 
       18.25        18.15        20.98        18.61        19.99         4.64 
TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAED 
       21.17        21.83        23.74        18.90        15.72        25.08 
TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP 
       16.37        23.64        25.78        50.33        35.08        79.07 
TCGA-DD-AAVQ TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY 
       89.69        59.93        72.39        76.18        56.48        64.77 
TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI 
       62.47        66.25        49.48        53.69        13.41        12.69 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7XO TCGA-ED-A7XP 
       15.85        13.91         0.20        12.82        14.04        13.15 
TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KC 
       13.41        13.35         0.20        18.74        19.99         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        60.89        23.97        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        12.03         0.03         0.33 
TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W 
        0.39        13.68        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        25.25        22.95        20.42        17.10 
TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-G3-AAV0 TCGA-G3-AAV1 
        7.76        12.03         5.98         1.84         8.55        11.80 
TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV7 TCGA-GJ-A6C0 
        9.70         9.17         0.89         8.75         3.02         1.02 
TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 
        2.20         2.99        37.91        20.75        17.06        16.83 
TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG 
        3.72         2.14        11.84        13.38        24.36        12.72 
TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75H TCGA-MI-A75I 
       13.97        12.03         9.57        16.67        12.85        20.71 
TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-PD-A5DF TCGA-QA-A7B7 
        0.62        10.85        58.88        19.92        21.01         3.09 
TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 
       21.04        19.33        19.04        15.39        15.52        24.13 
TCGA-T1-A6J8 TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-A7MF TCGA-UB-AA0U 
        0.76        16.44         1.71        15.98         7.04        10.75 
TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA46 TCGA-YA-A8S7 
       10.32        11.34         0.99        12.99        24.85        13.55 
TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D2 
       35.77        25.71        23.21        23.57         0.69        24.43 
TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       12.99        45.57        40.80        79.30        11.21 

  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 
                        120.82                         114.35 
  AMP PEAK 22(17P11.2) MUTATED AMP PEAK 22(17P11.2) WILD-TYPE 
                         18.38                          19.30 
[1] "0.1 - 120.8 (18.4)" "0.0 - 114.3 (19.3)"
[1] "hr=" "1.1"
D22V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IIIA
  AMP PEAK 22(17P11.2) MUTATED        17        7         1         15
  AMP PEAK 22(17P11.2) WILD-TYPE     151       77         2         44
                                vv
clus                             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 22(17P11.2) MUTATED            3          1        1         0
  AMP PEAK 22(17P11.2) WILD-TYPE          5          6        2         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                              17                            151
  STAGE II                              7                             77
  STAGE III                             1                              2
  STAGE IIIA                           15                             44
  STAGE IIIB                            3                              5
  STAGE IIIC                            1                              6
  STAGE IV                              1                              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 22(17P11.2) MUTATED      17   8  19   2
  AMP PEAK 22(17P11.2) WILD-TYPE   162  83  54  10
D22V4, multiclass
       clus
vv      AMP PEAK 22(17P11.2) MUTATED AMP PEAK 22(17P11.2) WILD-TYPE
  T0+T1                           17                            162
  T2                               8                             83
  T3                              19                             54
  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    34   0
  AMP PEAK 22(17P11.2) WILD-TYPE 215   3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 22(17P11.2) MUTATED     34    0
  AMP PEAK 22(17P11.2) WILD-TYPE  215    3
   clus
vv  AMP PEAK 22(17P11.2) MUTATED AMP PEAK 22(17P11.2) WILD-TYPE
  0                           34                            215
  1                            0                              3
[1] 2 2
[1] FALSE
D22V6, binary
                                cls
clus                               0   1
  AMP PEAK 22(17P11.2) MUTATED    36   1
  AMP PEAK 22(17P11.2) WILD-TYPE 224   3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 22(17P11.2) MUTATED     36    1
  AMP PEAK 22(17P11.2) WILD-TYPE  224    3
   clus
vv  AMP PEAK 22(17P11.2) MUTATED AMP PEAK 22(17P11.2) WILD-TYPE
  0                           36                            224
  1                            1                              3
[1] 2 2
[1] FALSE
D22V7, binary
                                cls
clus                               0   1
  AMP PEAK 22(17P11.2) MUTATED    14  32
  AMP PEAK 22(17P11.2) WILD-TYPE  99 212
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 22(17P11.2) MUTATED     14   32
  AMP PEAK 22(17P11.2) WILD-TYPE   99  212
        clus
vv       AMP PEAK 22(17P11.2) MUTATED AMP PEAK 22(17P11.2) WILD-TYPE
  FEMALE                           14                             99
  MALE                             32                            212
[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                         45
  AMP PEAK 22(17P11.2) WILD-TYPE                      303
                                vv
clus                             HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK 22(17P11.2) MUTATED                                  1
  AMP PEAK 22(17P11.2) WILD-TYPE                                6
D22V8, multiclass
                                  clus
vv                                 AMP PEAK 22(17P11.2) MUTATED
  FIBROLAMELLAR CARCINOMA                                     0
  HEPATOCELLULAR CARCINOMA                                   45
  HEPATOCHOLANGIOCARCINOMA (MIXED)                            1
                                  clus
vv                                 AMP PEAK 22(17P11.2) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                       2
  HEPATOCELLULAR CARCINOMA                                    303
  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 22(17P11.2) MUTATED    37   5   1   3
  AMP PEAK 22(17P11.2) WILD-TYPE 278  10   0  16
D22V9, multiclass
    clus
vv   AMP PEAK 22(17P11.2) MUTATED AMP PEAK 22(17P11.2) WILD-TYPE
  R0                           37                            278
  R1                            5                             10
  R2                            1                              0
  RX                            3                             16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 22(17P11.2) MUTATED                                  0    22
  AMP PEAK 22(17P11.2) WILD-TYPE                                1   134
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 22(17P11.2) MUTATED                           2    19
  AMP PEAK 22(17P11.2) WILD-TYPE                        15   154
D22V10, multiclass
                                  clus
vv                                 AMP PEAK 22(17P11.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                      22
  BLACK OR AFRICAN AMERICAN                                   2
  WHITE                                                      19
                                  clus
vv                                 AMP PEAK 22(17P11.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                       134
  BLACK OR AFRICAN AMERICAN                                    15
  WHITE                                                       154
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V11, binary
                                cls
clus                               0   1
  AMP PEAK 22(17P11.2) MUTATED     3  39
  AMP PEAK 22(17P11.2) WILD-TYPE   8 290
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 22(17P11.2) MUTATED      3   39
  AMP PEAK 22(17P11.2) WILD-TYPE    8  290
                        clus
vv                       AMP PEAK 22(17P11.2) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           39
                        clus
vv                       AMP PEAK 22(17P11.2) WILD-TYPE
  HISPANIC OR LATINO                                  8
  NOT HISPANIC OR LATINO                            290
[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    84  43
  AMP PEAK 23(17Q25.3) WILD-TYPE 141  66
  AMP PEAK 23(17Q25.3) MUTATED AMP PEAK 23(17Q25.3) WILD-TYPE 
                           127                            207 
  AMP PEAK 23(17Q25.3) MUTATED AMP PEAK 23(17Q25.3) WILD-TYPE 
                            43                             66 
$`AMP PEAK 23(17Q25.3) MUTATED`
TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H9 
       24.89        27.88       120.82        40.41        56.91        14.99 
TCGA-3K-AAZ8 TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-A10Q TCGA-BC-A10T TCGA-BC-A10U 
       13.02         1.51        48.99        37.32        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 
        2.99        23.34         1.12         5.03        44.42        13.84 
TCGA-BC-A3KG TCGA-BC-A69H TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5260 TCGA-CC-5261 
       22.36        14.60        13.45         0.66         2.86         3.19 
TCGA-CC-5263 TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 
        4.24         0.10         0.13        37.78        83.57        53.33 
TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11C TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EI 
        7.33         2.60        21.76        79.40        66.31         6.02 
TCGA-DD-A1EJ TCGA-DD-A39Y TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A3 TCGA-DD-A3A4 
       33.04         5.62        25.81         7.66        17.59        20.12 
TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NO 
       13.78        30.61        30.15        26.83        30.51        73.81 
TCGA-DD-A4NP TCGA-DD-A73A TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-AAC8 
      108.76        23.93        22.78         1.45        35.67         0.53 
TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACE TCGA-DD-AACI TCGA-DD-AACJ 
       11.41        75.65        76.41        63.48        53.19        69.11 
TCGA-DD-AACS TCGA-DD-AACX TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AADC TCGA-DD-AADD 
       59.31         5.59        44.22        22.09        13.97        40.47 
TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADR 
       39.52         3.78        37.64        29.52        14.89        66.67 
TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AAE0 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAEA 
       18.21        19.30        18.25        20.98        18.61        18.90 
TCGA-DD-AAEE TCGA-DD-AAEK TCGA-DD-AAVR TCGA-DD-AAW1 TCGA-ED-A66X TCGA-ED-A66Y 
       16.37        35.08        82.62        65.39        13.35         9.73 
TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-ED-A8O6 TCGA-EP-A2KB TCGA-EP-A2KC TCGA-ES-A2HS 
        0.20        13.15         1.84        19.59         0.62        22.85 
TCGA-FV-A2QR TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-G3-A25S TCGA-G3-A25U 
       19.10         0.03         0.33        81.73        13.68        53.79 
TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Z TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI 
       30.74        58.49        21.53        19.53        19.23        25.25 
TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A7M6 TCGA-G3-AAUZ TCGA-G3-AAV1 TCGA-G3-AAV5 
       22.95        20.42        12.03        11.24        11.80         8.75 
TCGA-G3-AAV6 TCGA-K7-AAU7 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC TCGA-MI-A75G 
        2.14         3.72        24.36        12.72        13.97        18.38 
TCGA-MI-A75I TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-RG-A7D4 
       20.71        58.88        19.92        17.69        21.01        24.13 
TCGA-UB-A7MA TCGA-UB-A7MC TCGA-UB-AA0U TCGA-ZP-A9CZ TCGA-ZP-A9D2 TCGA-ZP-A9D4 
       17.59        16.44        10.75        23.21        24.43        12.99 
TCGA-ZS-A9CF 
       79.30 

$`AMP PEAK 23(17Q25.3) WILD-TYPE`
TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GV TCGA-2Y-A9GW TCGA-2Y-A9GX 
       23.80        53.39        63.75        83.24        41.79        80.28 
TCGA-2Y-A9H3 TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-2Y-A9H8 
       41.33        47.74        18.25        11.74        37.25        20.81 
TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD 
        1.18         8.55         8.61        10.78        10.59         0.66 
TCGA-5R-AA1C TCGA-5R-AA1D TCGA-BC-4073 TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10X 
       11.97        11.08        27.91        10.13        46.78        25.32 
TCGA-BC-A110 TCGA-BC-A3KF TCGA-BC-A5W4 TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A2L6 
       69.57         0.26        17.98        12.72        18.48        44.81 
TCGA-BD-A3ER TCGA-CC-5258 TCGA-CC-5262 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA 
       36.66         0.07         3.39         3.32         0.10         0.07 
TCGA-DD-A113 TCGA-DD-A118 TCGA-DD-A11B TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EC 
       79.73       113.00         0.46        51.29        90.71        19.79 
TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EK 
       75.65        11.47        12.95        45.11        49.15        18.35 
TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Z TCGA-DD-A3A2 
       13.64        21.14        27.19        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        90.28 
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        23.05       114.35        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-AACN TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ 
        3.52        58.16        42.81        61.68        13.64        14.20 
TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACY TCGA-DD-AACZ 
       51.35        51.52        50.33        46.82        47.67         5.62 
TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD8 TCGA-DD-AADA 
        4.50        18.54        21.63        42.58        40.08        40.54 
TCGA-DD-AADB TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM 
       40.83        35.67        35.05        34.49        20.91         0.39 
TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADS TCGA-DD-AADV TCGA-DD-AADY TCGA-DD-AAE1 
       15.06        14.33        15.58        18.87        18.25        18.15 
TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAE9 TCGA-DD-AAEB 
       19.99         4.64        21.17        21.83        23.74        15.72 
TCGA-DD-AAED TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAVP TCGA-DD-AAVQ 
       25.08        23.64        25.78        50.33        79.07        89.69 
TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ 
       59.93        72.39        76.18        56.48        64.77        62.47 
TCGA-DD-AAW0 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG 
       66.25        49.48        53.69        13.41        12.69        15.85 
TCGA-ED-A627 TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7XO TCGA-ED-A82E TCGA-ED-A8O5 
       13.91         0.20        12.82        14.04        13.41        13.35 
TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A3JL TCGA-EP-A3RK 
        0.20        18.74        19.99        20.61         9.96        11.93 
TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 
       14.40        60.89        23.97        27.88         8.12         6.38 
TCGA-FV-A3R3 TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25V TCGA-G3-A25Y TCGA-G3-A3CG 
       12.03         0.39        51.06        28.27        14.86        22.13 
TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-A7M9 
       25.64         5.92        17.10         7.76         5.98         1.84 
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         2.99        37.91        20.75        17.06        16.83 
TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E 
        2.14        11.84        13.38        12.03         9.57        16.67 
TCGA-MI-A75H TCGA-MR-A520 TCGA-MR-A8JO TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SB 
       12.85         0.62        10.85         3.09        21.04        19.33 
TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-T1-A6J8 TCGA-UB-A7MB TCGA-UB-A7MD 
       19.04        15.39        15.52         0.76        19.76         1.71 
TCGA-UB-A7ME TCGA-UB-A7MF TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B 
       15.98         7.04        10.32        11.34         0.99        12.99 
TCGA-WX-AA46 TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9D0 TCGA-ZP-A9D1 
       24.85        13.55        35.77        25.71        23.57         0.69 
TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CG 
       45.57        40.80        11.21 

  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 
                        120.82                         114.35 
  AMP PEAK 23(17Q25.3) MUTATED AMP PEAK 23(17Q25.3) WILD-TYPE 
                         20.12                          18.48 
[1] "0.0 - 120.8 (20.1)" "0.1 - 114.3 (18.5)"
[1] "hr=" "1.1"
D23V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IIIA
  AMP PEAK 23(17Q25.3) MUTATED        54       34         0         32
  AMP PEAK 23(17Q25.3) WILD-TYPE     114       50         3         27
                                vv
clus                             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 23(17Q25.3) MUTATED            6          3        1         0
  AMP PEAK 23(17Q25.3) WILD-TYPE          2          4        2         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                              54                            114
  STAGE II                             34                             50
  STAGE III                             0                              3
  STAGE IIIA                           32                             27
  STAGE IIIB                            6                              2
  STAGE IIIC                            3                              4
  STAGE IV                              1                              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
  AMP PEAK 23(17Q25.3) MUTATED      57  38  38   8
  AMP PEAK 23(17Q25.3) WILD-TYPE   122  53  35   4
D23V4, multiclass
       clus
vv      AMP PEAK 23(17Q25.3) MUTATED AMP PEAK 23(17Q25.3) WILD-TYPE
  T0+T1                           57                            122
  T2                              38                             53
  T3                              38                             35
  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    97   1
  AMP PEAK 23(17Q25.3) WILD-TYPE 152   2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 23(17Q25.3) MUTATED     97    1
  AMP PEAK 23(17Q25.3) WILD-TYPE  152    2
   clus
vv  AMP PEAK 23(17Q25.3) MUTATED AMP PEAK 23(17Q25.3) WILD-TYPE
  0                           97                            152
  1                            1                              2
[1] 2 2
[1] FALSE
D23V6, binary
                                cls
clus                               0   1
  AMP PEAK 23(17Q25.3) MUTATED   107   2
  AMP PEAK 23(17Q25.3) WILD-TYPE 153   2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 23(17Q25.3) MUTATED    107    2
  AMP PEAK 23(17Q25.3) WILD-TYPE  153    2
   clus
vv  AMP PEAK 23(17Q25.3) MUTATED AMP PEAK 23(17Q25.3) WILD-TYPE
  0                          107                            153
  1                            2                              2
[1] 2 2
[1] FALSE
D23V7, binary
                                cls
clus                               0   1
  AMP PEAK 23(17Q25.3) MUTATED    38 103
  AMP PEAK 23(17Q25.3) WILD-TYPE  75 141
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 23(17Q25.3) MUTATED     38  103
  AMP PEAK 23(17Q25.3) WILD-TYPE   75  141
        clus
vv       AMP PEAK 23(17Q25.3) MUTATED AMP PEAK 23(17Q25.3) WILD-TYPE
  FEMALE                           38                             75
  MALE                            103                            141
[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                        139
  AMP PEAK 23(17Q25.3) WILD-TYPE                      209
                                vv
clus                             HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK 23(17Q25.3) MUTATED                                  2
  AMP PEAK 23(17Q25.3) WILD-TYPE                                5
D23V8, multiclass
                                  clus
vv                                 AMP PEAK 23(17Q25.3) MUTATED
  FIBROLAMELLAR CARCINOMA                                     0
  HEPATOCELLULAR CARCINOMA                                  139
  HEPATOCHOLANGIOCARCINOMA (MIXED)                            2
                                  clus
vv                                 AMP PEAK 23(17Q25.3) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                       2
  HEPATOCELLULAR CARCINOMA                                    209
  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   119  10   1  10
  AMP PEAK 23(17Q25.3) WILD-TYPE 196   5   0   9
D23V9, multiclass
    clus
vv   AMP PEAK 23(17Q25.3) MUTATED AMP PEAK 23(17Q25.3) WILD-TYPE
  R0                          119                            196
  R1                           10                              5
  R2                            1                              0
  RX                           10                              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 23(17Q25.3) MUTATED                                  1    66
  AMP PEAK 23(17Q25.3) WILD-TYPE                                0    90
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 23(17Q25.3) MUTATED                           8    60
  AMP PEAK 23(17Q25.3) WILD-TYPE                         9   113
D23V10, multiclass
                                  clus
vv                                 AMP PEAK 23(17Q25.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                      66
  BLACK OR AFRICAN AMERICAN                                   8
  WHITE                                                      60
                                  clus
vv                                 AMP PEAK 23(17Q25.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                        90
  BLACK OR AFRICAN AMERICAN                                     9
  WHITE                                                       113
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V11, binary
                                cls
clus                               0   1
  AMP PEAK 23(17Q25.3) MUTATED     3 131
  AMP PEAK 23(17Q25.3) WILD-TYPE   8 198
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 23(17Q25.3) MUTATED      3  131
  AMP PEAK 23(17Q25.3) WILD-TYPE    8  198
                        clus
vv                       AMP PEAK 23(17Q25.3) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                          131
                        clus
vv                       AMP PEAK 23(17Q25.3) WILD-TYPE
  HISPANIC OR LATINO                                  8
  NOT HISPANIC OR LATINO                            198
[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    40  23
  AMP PEAK 24(19P13.12) WILD-TYPE 185  86
  AMP PEAK 24(19P13.12) MUTATED AMP PEAK 24(19P13.12) WILD-TYPE 
                             63                             271 
  AMP PEAK 24(19P13.12) MUTATED AMP PEAK 24(19P13.12) WILD-TYPE 
                             23                              86 
$`AMP PEAK 24(19P13.12) MUTATED`
TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9H3 TCGA-2Y-A9H6 TCGA-3K-AAZ8 TCGA-BC-A10Q 
       63.75        41.79        41.33        11.74        13.02        37.32 
TCGA-BC-A10R TCGA-BC-A112 TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5261 TCGA-DD-A113 
       10.13         5.03        13.45         0.66         3.19        79.73 
TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A1E9 TCGA-DD-A1EC TCGA-DD-A1EF TCGA-DD-A39V 
      113.00         7.33        90.71        19.79        12.95        21.14 
TCGA-DD-A39X TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4ND TCGA-DD-A4NN TCGA-DD-A4NO 
       55.69        13.78        30.61        90.28        29.56        73.81 
TCGA-DD-A4NV TCGA-DD-A73G TCGA-DD-AACL TCGA-DD-AACT TCGA-DD-AACY TCGA-DD-AAD5 
       78.84       114.35         3.52        51.35        47.67        44.22 
TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADF TCGA-DD-AAE0 TCGA-DD-AAE3 TCGA-DD-AAE6 
       40.54        40.83         3.78        18.25        18.61         4.64 
TCGA-DD-AAE9 TCGA-DD-AAEG TCGA-DD-AAEK TCGA-DD-AAVR TCGA-ED-A66X TCGA-ED-A66Y 
       23.74        23.64        35.08        82.62        13.35         9.73 
TCGA-ED-A82E TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-ES-A2HS TCGA-FV-A2QQ 
       13.41        20.61        19.59         0.62        22.85        23.97 
TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A4ZP TCGA-G3-A25T TCGA-G3-A25X TCGA-G3-A5SM 
       27.88         8.12        81.73        51.06        58.49        17.10 
TCGA-G3-A7M7 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV7 TCGA-KR-A7K2 TCGA-RC-A7S9 
        5.98        11.24         8.55         3.02        11.84        21.04 
TCGA-UB-A7MA TCGA-YA-A8S7 TCGA-ZP-A9D1 
       17.59        13.55         0.69 

$`AMP PEAK 24(19P13.12) WILD-TYPE`
TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GV TCGA-2Y-A9GX TCGA-2Y-A9GY TCGA-2Y-A9GZ 
       23.80        53.39        83.24        80.28        24.89        27.88 
TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H7 
      120.82        40.41        56.91        47.74        18.25        37.25 
TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-4R-AA8I TCGA-5C-A9VG 
       20.81        14.99         1.18         8.55         8.61        10.78 
TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4072 
       10.59         0.66        11.97        11.08         1.51        48.99 
TCGA-BC-4073 TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X 
       27.91        46.78        27.52        27.52         2.99        25.32 
TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF 
       23.34         1.12        69.57        44.42        13.84         0.26 
TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A2L6 
       22.36        17.98        14.60        12.72        18.48        44.81 
TCGA-BD-A3ER TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT 
       36.66         0.07         2.86         3.39         4.24         3.32 
TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A114 TCGA-DD-A115 
        0.10         0.07         0.10         0.13        37.78        83.57 
TCGA-DD-A116 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1EA 
       53.33         2.60         0.46        21.76        51.29        79.40 
TCGA-DD-A1EB TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI 
       66.31        75.65        11.47        45.11        49.15         6.02 
TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39W TCGA-DD-A39Y TCGA-DD-A39Z 
       33.04        18.35        13.64        27.19         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-A4NQ 
       26.83        30.51        39.78        56.25       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        23.93         9.30        23.05        22.78 
TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA 
        1.45        35.67        13.48         0.53        11.41        75.65 
TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG 
       76.41        55.40        12.53        63.48        12.00        15.42 
TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACM TCGA-DD-AACN 
        6.41        53.19        69.11         0.30        58.16        42.81 
TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACV 
       61.68        13.64        14.20        59.31        51.52        50.33 
TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 
       46.82         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-AADE 
       42.58        22.09        40.08        13.97        40.47        39.52 
TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM 
       37.64        35.67        35.05        34.49        20.91         0.39 
TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS 
       29.52        14.89        15.06        14.33        66.67        15.58 
TCGA-DD-AADU TCGA-DD-AADV TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE1 TCGA-DD-AAE2 
       18.21        18.87        19.30        18.25        18.15        20.98 
TCGA-DD-AAE4 TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAED 
       19.99        21.17        21.83        18.90        15.72        25.08 
TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVS 
       16.37        25.78        50.33        79.07        89.69        59.93 
TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 
       72.39        76.18        56.48        64.77        62.47        66.25 
TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG 
       65.39        49.48        53.69        13.41        12.69        15.85 
TCGA-ED-A627 TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP 
       13.91         0.20        12.82         0.20        14.04        13.15 
TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A3JL 
       13.35         1.84         0.20        18.74        19.99         9.96 
TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3R2 TCGA-FV-A3R3 
       11.93        14.40        60.89        19.10         6.38        12.03 
TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25V 
        0.03         0.33         0.39        13.68        53.79        28.27 
TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI 
       30.74        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-A6UC 
       19.53        19.23        25.25        22.95        20.42         7.76 
TCGA-G3-A7M6 TCGA-G3-A7M9 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 
       12.03         1.84        11.80         9.70         9.17         0.89 
TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 
        8.75         2.14         1.02         2.20         2.99        37.91 
TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K7 
       20.75        17.06        16.83         3.72         2.14        13.38 
TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E 
       24.36        12.72        13.97        12.03         9.57        16.67 
TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 
       18.38        12.85        20.71         0.62        10.85        58.88 
TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7SB TCGA-RC-A7SF 
       19.92        17.69        21.01         3.09        19.33        19.04 
TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-T1-A6J8 TCGA-UB-A7MB TCGA-UB-A7MC 
       15.39        15.52        24.13         0.76        19.76        16.44 
TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-A7MF TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WJ-A86L 
        1.71        15.98         7.04        10.75        10.32        11.34 
TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA46 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ 
        0.99        12.99        24.85        35.77        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        40.80        79.30 
TCGA-ZS-A9CG 
       11.21 

  AMP PEAK 24(19P13.12) MUTATED AMP PEAK 24(19P13.12) WILD-TYPE 
                           0.62                            0.03 
  AMP PEAK 24(19P13.12) MUTATED AMP PEAK 24(19P13.12) WILD-TYPE 
                         114.35                          120.82 
  AMP PEAK 24(19P13.12) MUTATED AMP PEAK 24(19P13.12) WILD-TYPE 
                          20.61                           19.04 
[1] "0.6 - 114.3 (20.6)" "0.0 - 120.8 (19.0)"
[1] "hr=" "1.1"
D24V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE III STAGE IIIA
  AMP PEAK 24(19P13.12) MUTATED        32       13         0         11
  AMP PEAK 24(19P13.12) WILD-TYPE     136       71         3         48
                                 vv
clus                              STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 24(19P13.12) MUTATED            2          0        2         1
  AMP PEAK 24(19P13.12) WILD-TYPE          6          7        1         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                               32                             136
  STAGE II                              13                              71
  STAGE III                              0                               3
  STAGE IIIA                            11                              48
  STAGE IIIB                             2                               6
  STAGE IIIC                             0                               7
  STAGE IV                               2                               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 24(19P13.12) MUTATED      34  15  16   1
  AMP PEAK 24(19P13.12) WILD-TYPE   145  76  57  11
D24V4, multiclass
       clus
vv      AMP PEAK 24(19P13.12) MUTATED AMP PEAK 24(19P13.12) WILD-TYPE
  T0+T1                            34                             145
  T2                               15                              76
  T3                               16                              57
  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    46   1
  AMP PEAK 24(19P13.12) WILD-TYPE 203   2
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 24(19P13.12) MUTATED     46    1
  AMP PEAK 24(19P13.12) WILD-TYPE  203    2
   clus
vv  AMP PEAK 24(19P13.12) MUTATED AMP PEAK 24(19P13.12) WILD-TYPE
  0                            46                             203
  1                             1                               2
[1] 2 2
[1] FALSE
D24V6, binary
                                 cls
clus                                0   1
  AMP PEAK 24(19P13.12) MUTATED    45   3
  AMP PEAK 24(19P13.12) WILD-TYPE 215   1
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 24(19P13.12) MUTATED     45    3
  AMP PEAK 24(19P13.12) WILD-TYPE  215    1
   clus
vv  AMP PEAK 24(19P13.12) MUTATED AMP PEAK 24(19P13.12) WILD-TYPE
  0                            45                             215
  1                             3                               1
[1] 2 2
[1] FALSE
D24V7, binary
                                 cls
clus                                0   1
  AMP PEAK 24(19P13.12) MUTATED    32  34
  AMP PEAK 24(19P13.12) WILD-TYPE  81 210
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 24(19P13.12) MUTATED     32   34
  AMP PEAK 24(19P13.12) WILD-TYPE   81  210
        clus
vv       AMP PEAK 24(19P13.12) MUTATED AMP PEAK 24(19P13.12) WILD-TYPE
  FEMALE                            32                              81
  MALE                              34                             210
[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                         63
  AMP PEAK 24(19P13.12) WILD-TYPE                      285
                                 vv
clus                              HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK 24(19P13.12) MUTATED                                  3
  AMP PEAK 24(19P13.12) WILD-TYPE                                4
D24V8, multiclass
                                  clus
vv                                 AMP PEAK 24(19P13.12) MUTATED
  FIBROLAMELLAR CARCINOMA                                      0
  HEPATOCELLULAR CARCINOMA                                    63
  HEPATOCHOLANGIOCARCINOMA (MIXED)                             3
                                  clus
vv                                 AMP PEAK 24(19P13.12) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                        2
  HEPATOCELLULAR CARCINOMA                                     285
  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 24(19P13.12) MUTATED    58   3   1   4
  AMP PEAK 24(19P13.12) WILD-TYPE 257  12   0  15
D24V9, multiclass
    clus
vv   AMP PEAK 24(19P13.12) MUTATED AMP PEAK 24(19P13.12) WILD-TYPE
  R0                            58                             257
  R1                             3                              12
  R2                             1                               0
  RX                             4                              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
  AMP PEAK 24(19P13.12) MUTATED                                  0    25
  AMP PEAK 24(19P13.12) WILD-TYPE                                1   131
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 24(19P13.12) MUTATED                           4    35
  AMP PEAK 24(19P13.12) WILD-TYPE                        13   138
D24V10, multiclass
                                  clus
vv                                 AMP PEAK 24(19P13.12) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                       25
  BLACK OR AFRICAN AMERICAN                                    4
  WHITE                                                       35
                                  clus
vv                                 AMP PEAK 24(19P13.12) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               1
  ASIAN                                                        131
  BLACK OR AFRICAN AMERICAN                                     13
  WHITE                                                        138
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V11, binary
                                 cls
clus                                0   1
  AMP PEAK 24(19P13.12) MUTATED     4  60
  AMP PEAK 24(19P13.12) WILD-TYPE   7 269
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 24(19P13.12) MUTATED      4   60
  AMP PEAK 24(19P13.12) WILD-TYPE    7  269
                        clus
vv                       AMP PEAK 24(19P13.12) MUTATED
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                            60
                        clus
vv                       AMP PEAK 24(19P13.12) WILD-TYPE
  HISPANIC OR LATINO                                   7
  NOT HISPANIC OR LATINO                             269
[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    48  25
  AMP PEAK 25(19Q12) WILD-TYPE 177  84
  AMP PEAK 25(19Q12) MUTATED AMP PEAK 25(19Q12) WILD-TYPE 
                          73                          261 
  AMP PEAK 25(19Q12) MUTATED AMP PEAK 25(19Q12) WILD-TYPE 
                          25                           84 
$`AMP PEAK 25(19Q12) MUTATED`
TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GY TCGA-2Y-A9H0 TCGA-2Y-A9H3 TCGA-3K-AAZ8 
       63.75        41.79        24.89       120.82        41.33        13.02 
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         3.19        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        90.28        29.56        73.81        12.26        78.84 
TCGA-DD-A73G TCGA-DD-AACG TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACT TCGA-DD-AACV 
      114.35        15.42        61.68        13.64        51.35        50.33 
TCGA-DD-AADB TCGA-DD-AADF TCGA-DD-AADM TCGA-DD-AADV TCGA-DD-AAE0 TCGA-DD-AAE4 
       40.83         3.78         0.39        18.87        18.25        19.99 
TCGA-DD-AAE7 TCGA-DD-AAEK TCGA-DD-AAVW TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PZ 
       21.17        35.08        76.18        13.35         9.73         0.20 
TCGA-ED-A7XO TCGA-ED-A82E TCGA-EP-A2KB TCGA-EP-A2KC TCGA-ES-A2HS TCGA-FV-A2QQ 
       14.04        13.41        19.59         0.62        22.85        23.97 
TCGA-FV-A3I0 TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25X TCGA-G3-A5SM TCGA-G3-A7M6 
       27.88         0.39        51.06        58.49        17.10        12.03 
TCGA-G3-A7M7 TCGA-G3-AAV0 TCGA-KR-A7K2 TCGA-MI-A75G TCGA-NI-A8LF TCGA-RC-A7S9 
        5.98         8.55        11.84        18.38        19.92        21.04 
TCGA-RC-A7SH TCGA-UB-A7MA TCGA-UB-A7ME TCGA-WJ-A86L TCGA-WQ-AB4B TCGA-YA-A8S7 
       15.39        17.59        15.98        11.34        12.99        13.55 
TCGA-ZP-A9D1 
        0.69 

$`AMP PEAK 25(19Q12) WILD-TYPE`
TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GV TCGA-2Y-A9GX TCGA-2Y-A9GZ TCGA-2Y-A9H1 
       23.80        53.39        83.24        80.28        27.88        40.41 
TCGA-2Y-A9H2 TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-2Y-A9H8 
       56.91        47.74        18.25        11.74        37.25        20.81 
TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-A9VH 
       14.99         1.18         8.55         8.61        10.78        10.59 
TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-4073 
        0.66        11.97        11.08         1.51        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        17.98 
TCGA-BC-A69H TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3ER TCGA-CC-5258 
       14.60        12.72        18.48        44.81        36.66         0.07 
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-CC-A3MC TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A11A TCGA-DD-A11B 
        0.13        37.78        83.57        53.33         2.60         0.46 
TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1ED TCGA-DD-A1EE 
       21.76        51.29        79.40        66.31        75.65        11.47 
TCGA-DD-A1EH TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39W TCGA-DD-A39X 
       49.15        33.04        18.35        13.64        27.19        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        23.93         9.30        23.05 
TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 
       22.78         1.45        35.67        13.48         0.53        11.41 
TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF 
       75.65        76.41        55.40        12.53        63.48        12.00 
TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM 
        6.41        53.19        69.11         0.30         3.52        58.16 
TCGA-DD-AACN TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACW TCGA-DD-AACX 
       42.81        14.20        59.31        51.52        46.82         5.59 
TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 
       47.67         5.62         4.50        18.54        21.63        42.58 
TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADC TCGA-DD-AADD 
       44.22        22.09        40.08        40.54        13.97        40.47 
TCGA-DD-AADE TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL 
       39.52        37.64        35.67        35.05        34.49        20.91 
TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS 
       29.52        14.89        15.06        14.33        66.67        15.58 
TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 
       18.21        19.30        18.25        18.15        20.98        18.61 
TCGA-DD-AAE6 TCGA-DD-AAE8 TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAED 
        4.64        21.83        23.74        18.90        15.72        25.08 
TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAVP TCGA-DD-AAVQ 
       16.37        23.64        25.78        50.33        79.07        89.69 
TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ 
       82.62        59.93        72.39        56.48        64.77        62.47 
TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI 
       66.25        65.39        49.48        53.69        13.41        12.69 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7XP TCGA-ED-A8O5 
       15.85        13.91         0.20        12.82        13.15        13.35 
TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A3JL 
        1.84         0.20        18.74        19.99        20.61         9.96 
TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I1 TCGA-FV-A3R2 
       11.93        14.40        60.89        19.10         8.12         6.38 
TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-G3-A25S TCGA-G3-A25U 
       12.03         0.03         0.33        81.73        13.68        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        25.25        22.95        20.42 
TCGA-G3-A6UC TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 
        7.76         1.84        11.24        11.80         9.70         9.17 
TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB 
        0.89         8.75         2.14         3.02         1.02         2.20 
TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 
        2.99        37.91        20.75        17.06        16.83         3.72 
TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD 
        2.14        13.38        24.36        12.72        13.97        12.03 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO 
        9.57        16.67        12.85        20.71         0.62        10.85 
TCGA-NI-A4U2 TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7SB TCGA-RC-A7SF 
       58.88        17.69        21.01         3.09        19.33        19.04 
TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-T1-A6J8 TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD 
       15.52        24.13         0.76        19.76        16.44         1.71 
TCGA-UB-A7MF TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WQ-A9G7 TCGA-WX-AA46 TCGA-ZP-A9CV 
        7.04        10.75        10.32         0.99        24.85        35.77 
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-A9CF TCGA-ZS-A9CG 
       40.80        79.30        11.21 

  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 
                      120.82                       108.76 
  AMP PEAK 25(19Q12) MUTATED AMP PEAK 25(19Q12) WILD-TYPE 
                       18.38                        19.33 
[1] "0.2 - 120.8 (18.4)" "0.0 - 108.8 (19.3)"
[1] "hr=" "1.1"
D25V2, continuous
                              vv
clus                           STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 25(19Q12) MUTATED        34       18         0         11          2
  AMP PEAK 25(19Q12) WILD-TYPE     134       66         3         48          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        1         0         1
D25V3, multiclass
            clus
vv           AMP PEAK 25(19Q12) MUTATED AMP PEAK 25(19Q12) WILD-TYPE
  STAGE I                            34                          134
  STAGE II                           18                           66
  STAGE III                           0                            3
  STAGE IIIA                         11                           48
  STAGE IIIB                          2                            6
  STAGE IIIC                          1                            6
  STAGE IV                            2                            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 25(19Q12) MUTATED      36  20  16   3
  AMP PEAK 25(19Q12) WILD-TYPE   143  71  57   9
D25V4, multiclass
       clus
vv      AMP PEAK 25(19Q12) MUTATED AMP PEAK 25(19Q12) WILD-TYPE
  T0+T1                         36                          143
  T2                            20                           71
  T3                            16                           57
  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    50   1
  AMP PEAK 25(19Q12) WILD-TYPE 199   2
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 25(19Q12) MUTATED     50    1
  AMP PEAK 25(19Q12) WILD-TYPE  199    2
   clus
vv  AMP PEAK 25(19Q12) MUTATED AMP PEAK 25(19Q12) WILD-TYPE
  0                         50                          199
  1                          1                            2
[1] 2 2
[1] FALSE
D25V6, binary
                              cls
clus                             0   1
  AMP PEAK 25(19Q12) MUTATED    51   3
  AMP PEAK 25(19Q12) WILD-TYPE 209   1
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 25(19Q12) MUTATED     51    3
  AMP PEAK 25(19Q12) WILD-TYPE  209    1
   clus
vv  AMP PEAK 25(19Q12) MUTATED AMP PEAK 25(19Q12) WILD-TYPE
  0                         51                          209
  1                          3                            1
[1] 2 2
[1] FALSE
D25V7, binary
                              cls
clus                             0   1
  AMP PEAK 25(19Q12) MUTATED    29  46
  AMP PEAK 25(19Q12) WILD-TYPE  84 198
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 25(19Q12) MUTATED     29   46
  AMP PEAK 25(19Q12) WILD-TYPE   84  198
        clus
vv       AMP PEAK 25(19Q12) MUTATED AMP PEAK 25(19Q12) WILD-TYPE
  FEMALE                         29                           84
  MALE                           46                          198
[1] 2 2
[1] FALSE
                              vv
clus                           FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  AMP PEAK 25(19Q12) MUTATED                         0                       72
  AMP PEAK 25(19Q12) WILD-TYPE                       2                      276
                              vv
clus                           HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK 25(19Q12) MUTATED                                  3
  AMP PEAK 25(19Q12) WILD-TYPE                                4
D25V8, multiclass
                                  clus
vv                                 AMP PEAK 25(19Q12) MUTATED
  FIBROLAMELLAR CARCINOMA                                   0
  HEPATOCELLULAR CARCINOMA                                 72
  HEPATOCHOLANGIOCARCINOMA (MIXED)                          3
                                  clus
vv                                 AMP PEAK 25(19Q12) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                     2
  HEPATOCELLULAR CARCINOMA                                  276
  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 25(19Q12) MUTATED    66   3   1   5
  AMP PEAK 25(19Q12) WILD-TYPE 249  12   0  14
D25V9, multiclass
    clus
vv   AMP PEAK 25(19Q12) MUTATED AMP PEAK 25(19Q12) WILD-TYPE
  R0                         66                          249
  R1                          3                           12
  R2                          1                            0
  RX                          5                           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 25(19Q12) MUTATED                                  0    29
  AMP PEAK 25(19Q12) WILD-TYPE                                1   127
                              vv
clus                           BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 25(19Q12) MUTATED                           4    41
  AMP PEAK 25(19Q12) WILD-TYPE                        13   132
D25V10, multiclass
                                  clus
vv                                 AMP PEAK 25(19Q12) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          0
  ASIAN                                                    29
  BLACK OR AFRICAN AMERICAN                                 4
  WHITE                                                    41
                                  clus
vv                                 AMP PEAK 25(19Q12) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                     127
  BLACK OR AFRICAN AMERICAN                                  13
  WHITE                                                     132
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V11, binary
                              cls
clus                             0   1
  AMP PEAK 25(19Q12) MUTATED     5  68
  AMP PEAK 25(19Q12) WILD-TYPE   6 261
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 25(19Q12) MUTATED      5   68
  AMP PEAK 25(19Q12) WILD-TYPE    6  261
                        clus
vv                       AMP PEAK 25(19Q12) MUTATED
  HISPANIC OR LATINO                              5
  NOT HISPANIC OR LATINO                         68
                        clus
vv                       AMP PEAK 25(19Q12) WILD-TYPE
  HISPANIC OR LATINO                                6
  NOT HISPANIC OR LATINO                          261
[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    51  31
  AMP PEAK 26(19Q13.11) WILD-TYPE 174  78
  AMP PEAK 26(19Q13.11) MUTATED AMP PEAK 26(19Q13.11) WILD-TYPE 
                             82                             252 
  AMP PEAK 26(19Q13.11) MUTATED AMP PEAK 26(19Q13.11) WILD-TYPE 
                             31                              78 
$`AMP PEAK 26(19Q13.11) MUTATED`
TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GY TCGA-2Y-A9H3 TCGA-3K-AAZ8 TCGA-BC-A10Q 
       63.75        41.79        24.89        41.33        13.02        37.32 
TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10Y TCGA-BC-A112 TCGA-BC-A217 TCGA-BC-A3KG 
       10.13        27.52        23.34         5.03        13.84        22.36 
TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5261 TCGA-CC-A3M9 TCGA-DD-A113 TCGA-DD-A118 
       13.45         0.66         3.19         0.10        79.73       113.00 
TCGA-DD-A119 TCGA-DD-A1E9 TCGA-DD-A1EC TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EI 
        7.33        90.71        19.79        12.95        45.11         6.02 
TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4ND TCGA-DD-A4NN 
       13.64        21.14        13.78        30.61        90.28        29.56 
TCGA-DD-A4NO TCGA-DD-A4NQ TCGA-DD-A4NV TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AACG 
       73.81        12.26        78.84        35.67       114.35        15.42 
TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACT TCGA-DD-AACW TCGA-DD-AADB TCGA-DD-AADC 
       61.68        13.64        51.35        46.82        40.83        13.97 
TCGA-DD-AADD TCGA-DD-AADF TCGA-DD-AADM TCGA-DD-AAE0 TCGA-DD-AAE7 TCGA-DD-AAEA 
       40.47         3.78         0.39        18.25        21.17        18.90 
TCGA-DD-AAEK TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A82E 
       35.08        13.35         9.73         0.20        14.04        13.41 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-ES-A2HS TCGA-FV-A2QQ TCGA-FV-A3I0 
       20.61        19.59         0.62        22.85        23.97        27.88 
TCGA-FV-A495 TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25X TCGA-G3-A5SM TCGA-G3-A7M6 
        0.03         0.39        51.06        58.49        17.10        12.03 
TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-G3-AAV0 TCGA-GJ-A6C0 TCGA-K7-AAU7 TCGA-KR-A7K2 
        5.98         1.84         8.55         1.02         3.72        11.84 
TCGA-MI-A75G TCGA-NI-A8LF TCGA-PD-A5DF TCGA-RC-A7S9 TCGA-RC-A7SH TCGA-UB-A7ME 
       18.38        19.92        21.01        21.04        15.39        15.98 
TCGA-WQ-AB4B TCGA-YA-A8S7 TCGA-ZP-A9D1 TCGA-ZS-A9CF 
       12.99        13.55         0.69        79.30 

$`AMP PEAK 26(19Q13.11) WILD-TYPE`
TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GV TCGA-2Y-A9GX TCGA-2Y-A9GZ TCGA-2Y-A9H0 
       23.80        53.39        83.24        80.28        27.88       120.82 
TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H6 TCGA-2Y-A9H7 
       40.41        56.91        47.74        18.25        11.74        37.25 
TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-4R-AA8I TCGA-5C-A9VG 
       20.81        14.99         1.18         8.55         8.61        10.78 
TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4072 
       10.59         0.66        11.97        11.08         1.51        48.99 
TCGA-BC-4073 TCGA-BC-A10S TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Z 
       27.91        46.78        27.52         2.99        25.32         1.12 
TCGA-BC-A110 TCGA-BC-A216 TCGA-BC-A3KF TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I 
       69.57        44.42         0.26        17.98        14.60        12.72 
TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3ER TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5262 
       18.48        44.81        36.66         0.07         2.86         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-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D 
       83.57        53.33         2.60         0.46        21.76        51.29 
TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EH TCGA-DD-A1EJ 
       79.40        66.31        75.65        11.47        49.15        33.04 
TCGA-DD-A1EK TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 
       18.35        27.19        55.69         5.62        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-A4NA TCGA-DD-A4NB TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI 
        0.36        33.14        32.52        30.97        30.15        26.83 
TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NP TCGA-DD-A4NR TCGA-DD-A4NS 
       30.51        39.78        56.25       108.76         0.30        80.75 
TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-AA3A 
       23.93         9.30        23.05        22.78         1.45        13.48 
TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD 
        0.53        11.41        75.65        76.41        55.40        12.53 
TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK 
       63.48        12.00         6.41        53.19        69.11         0.30 
TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACU 
        3.52        58.16        42.81        14.20        59.31        51.52 
TCGA-DD-AACV TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 
       50.33         5.59        47.67         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        42.58        44.22        22.09        40.08        40.54 
TCGA-DD-AADE TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL 
       39.52        37.64        35.67        35.05        34.49        20.91 
TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS 
       29.52        14.89        15.06        14.33        66.67        15.58 
TCGA-DD-AADU TCGA-DD-AADV TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE1 TCGA-DD-AAE2 
       18.21        18.87        19.30        18.25        18.15        20.98 
TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE8 TCGA-DD-AAE9 TCGA-DD-AAEB 
       18.61        19.99         4.64        21.83        23.74        15.72 
TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAVP 
       25.08        16.37        23.64        25.78        50.33        79.07 
TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVX 
       89.69        82.62        59.93        72.39        76.18        56.48 
TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 
       64.77        62.47        66.25        65.39        49.48        53.69 
TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A7PX TCGA-ED-A7PY 
       13.41        12.69        15.85        13.91         0.20        12.82 
TCGA-ED-A7XP TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S 
       13.15        13.35         1.84         0.20        18.74        19.99 
TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I1 
        9.96        11.93        14.40        60.89        19.10         8.12 
TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-G3-A25S TCGA-G3-A25U 
        6.38        12.03         0.33        81.73        13.68        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        25.25        22.95        20.42 
TCGA-G3-A6UC TCGA-G3-AAUZ TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 
        7.76        11.24        11.80         9.70         9.17         0.89 
TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 
        8.75         2.14         3.02         2.20         2.99        37.91 
TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-KR-A7K8 
       20.75        17.06        16.83         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        13.97        12.03         9.57        16.67        12.85 
TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-O8-A75V TCGA-QA-A7B7 
       20.71         0.62        10.85        58.88        17.69         3.09 
TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-T1-A6J8 TCGA-UB-A7MA 
       19.33        19.04        15.52        24.13         0.76        17.59 
TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7MF TCGA-UB-AA0U TCGA-UB-AA0V 
       19.76        16.44         1.71         7.04        10.75        10.32 
TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WX-AA46 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ 
       11.34         0.99        24.85        35.77        25.71        23.21 
TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CG 
       23.57        24.43        12.99        45.57        40.80        11.21 

  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 
                         114.35                          120.82 
  AMP PEAK 26(19Q13.11) MUTATED AMP PEAK 26(19Q13.11) WILD-TYPE 
                         18.315                          19.430 
[1] "0.0 - 114.3 (18.3)" "0.1 - 120.8 (19.4)"
[1] "hr=" "1.2"
D26V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE III STAGE IIIA
  AMP PEAK 26(19Q13.11) MUTATED        35       24         0         14
  AMP PEAK 26(19Q13.11) WILD-TYPE     133       60         3         45
                                 vv
clus                              STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 26(19Q13.11) MUTATED            4          0        2         1
  AMP PEAK 26(19Q13.11) WILD-TYPE          4          7        1         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                               35                             133
  STAGE II                              24                              60
  STAGE III                              0                               3
  STAGE IIIA                            14                              45
  STAGE IIIB                             4                               4
  STAGE IIIC                             0                               7
  STAGE IV                               2                               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 26(19Q13.11) MUTATED      37  26  20   4
  AMP PEAK 26(19Q13.11) WILD-TYPE   142  65  53   8
D26V4, multiclass
       clus
vv      AMP PEAK 26(19Q13.11) MUTATED AMP PEAK 26(19Q13.11) WILD-TYPE
  T0+T1                            37                             142
  T2                               26                              65
  T3                               20                              53
  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    54   1
  AMP PEAK 26(19Q13.11) WILD-TYPE 195   2
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 26(19Q13.11) MUTATED     54    1
  AMP PEAK 26(19Q13.11) WILD-TYPE  195    2
   clus
vv  AMP PEAK 26(19Q13.11) MUTATED AMP PEAK 26(19Q13.11) WILD-TYPE
  0                            54                             195
  1                             1                               2
[1] 2 2
[1] FALSE
D26V6, binary
                                 cls
clus                                0   1
  AMP PEAK 26(19Q13.11) MUTATED    57   3
  AMP PEAK 26(19Q13.11) WILD-TYPE 203   1
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 26(19Q13.11) MUTATED     57    3
  AMP PEAK 26(19Q13.11) WILD-TYPE  203    1
   clus
vv  AMP PEAK 26(19Q13.11) MUTATED AMP PEAK 26(19Q13.11) WILD-TYPE
  0                            57                             203
  1                             3                               1
[1] 2 2
[1] FALSE
D26V7, binary
                                 cls
clus                                0   1
  AMP PEAK 26(19Q13.11) MUTATED    34  53
  AMP PEAK 26(19Q13.11) WILD-TYPE  79 191
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 26(19Q13.11) MUTATED     34   53
  AMP PEAK 26(19Q13.11) WILD-TYPE   79  191
        clus
vv       AMP PEAK 26(19Q13.11) MUTATED AMP PEAK 26(19Q13.11) WILD-TYPE
  FEMALE                            34                              79
  MALE                              53                             191
[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                         84
  AMP PEAK 26(19Q13.11) WILD-TYPE                      264
                                 vv
clus                              HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK 26(19Q13.11) MUTATED                                  3
  AMP PEAK 26(19Q13.11) WILD-TYPE                                4
D26V8, multiclass
                                  clus
vv                                 AMP PEAK 26(19Q13.11) MUTATED
  FIBROLAMELLAR CARCINOMA                                      0
  HEPATOCELLULAR CARCINOMA                                    84
  HEPATOCHOLANGIOCARCINOMA (MIXED)                             3
                                  clus
vv                                 AMP PEAK 26(19Q13.11) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                        2
  HEPATOCELLULAR CARCINOMA                                     264
  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    76   2   1   7
  AMP PEAK 26(19Q13.11) WILD-TYPE 239  13   0  12
D26V9, multiclass
    clus
vv   AMP PEAK 26(19Q13.11) MUTATED AMP PEAK 26(19Q13.11) WILD-TYPE
  R0                            76                             239
  R1                             2                              13
  R2                             1                               0
  RX                             7                              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 26(19Q13.11) MUTATED                                  0    31
  AMP PEAK 26(19Q13.11) WILD-TYPE                                1   125
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 26(19Q13.11) MUTATED                           5    50
  AMP PEAK 26(19Q13.11) WILD-TYPE                        12   123
D26V10, multiclass
                                  clus
vv                                 AMP PEAK 26(19Q13.11) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                       31
  BLACK OR AFRICAN AMERICAN                                    5
  WHITE                                                       50
                                  clus
vv                                 AMP PEAK 26(19Q13.11) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               1
  ASIAN                                                        125
  BLACK OR AFRICAN AMERICAN                                     12
  WHITE                                                        123
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V11, binary
                                 cls
clus                                0   1
  AMP PEAK 26(19Q13.11) MUTATED     4  80
  AMP PEAK 26(19Q13.11) WILD-TYPE   7 249
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 26(19Q13.11) MUTATED      4   80
  AMP PEAK 26(19Q13.11) WILD-TYPE    7  249
                        clus
vv                       AMP PEAK 26(19Q13.11) MUTATED
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                            80
                        clus
vv                       AMP PEAK 26(19Q13.11) WILD-TYPE
  HISPANIC OR LATINO                                   7
  NOT HISPANIC OR LATINO                             249
[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    67  42
  AMP PEAK 27(20Q13.13) WILD-TYPE 158  67
  AMP PEAK 27(20Q13.13) MUTATED AMP PEAK 27(20Q13.13) WILD-TYPE 
                            109                             225 
  AMP PEAK 27(20Q13.13) MUTATED AMP PEAK 27(20Q13.13) WILD-TYPE 
                             42                              67 
$`AMP PEAK 27(20Q13.13) MUTATED`
TCGA-2Y-A9GS TCGA-2Y-A9GX TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H8 
       23.80        80.28        24.89        27.88       120.82        20.81 
TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-5C-A9VH TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-A10Q 
       14.99         1.18        10.59         1.51        48.99        37.32 
TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10Y TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A69H 
       10.13        27.52        23.34        13.84         0.26        14.60 
TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5261 TCGA-CC-A1HT TCGA-CC-A3M9 
       44.81        13.45         0.66         3.19         3.32         0.10 
TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B 
        0.10         0.13       113.00         7.33         2.60         0.46 
TCGA-DD-A11C TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EJ TCGA-DD-A39V 
       21.76        12.95        45.11        49.15        33.04        21.14 
TCGA-DD-A3A5 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4ND TCGA-DD-A4NN TCGA-DD-A4NO 
      102.74        13.78        30.61        90.28        29.56        73.81 
TCGA-DD-A4NR TCGA-DD-A4NV TCGA-DD-A73G TCGA-DD-AAC8 TCGA-DD-AACB TCGA-DD-AACC 
        0.30        78.84       114.35         0.53        76.41        55.40 
TCGA-DD-AACI TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACV 
       53.19        61.68        13.64        59.31        51.35        50.33 
TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD6 TCGA-DD-AADA TCGA-DD-AADD TCGA-DD-AADF 
        5.62         4.50        22.09        40.54        40.47         3.78 
TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AAE0 
       29.52        14.89        15.58        18.21        19.30        18.25 
TCGA-DD-AAE3 TCGA-DD-AAE6 TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-DD-AAEH 
       18.61         4.64        23.74        18.90        23.64        25.78 
TCGA-DD-AAEK TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7XO TCGA-ED-A82E TCGA-ED-A8O6 
       35.08        13.35         9.73        14.04        13.41         1.84 
TCGA-EP-A2KB TCGA-EP-A3JL TCGA-ES-A2HS TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A3R2 
       19.59         9.96        22.85        60.89        23.97         6.38 
TCGA-FV-A495 TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25W TCGA-G3-A5SM TCGA-G3-A7M6 
        0.03         0.39        13.68        30.74        17.10        12.03 
TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-G3-AAV1 TCGA-G3-AAV6 TCGA-HP-A5MZ TCGA-KR-A7K2 
        5.98         1.84        11.80         2.14         2.99        11.84 
TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75G TCGA-PD-A5DF TCGA-RG-A7D4 TCGA-UB-A7MA 
       13.38        12.72        18.38        21.01        24.13        17.59 
TCGA-UB-A7MB TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-YA-A8S7 
       19.76        15.98        10.75         0.99        12.99        13.55 
TCGA-ZS-A9CD 
       45.57 

$`AMP PEAK 27(20Q13.13) WILD-TYPE`
TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GV TCGA-2Y-A9GW TCGA-2Y-A9H1 TCGA-2Y-A9H2 
       53.39        63.75        83.24        41.79        40.41        56.91 
TCGA-2Y-A9H3 TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-2Y-A9HB 
       41.33        47.74        18.25        11.74        37.25         8.55 
TCGA-3K-AAZ8 TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D 
       13.02         8.61        10.78         0.66        11.97        11.08 
TCGA-BC-4073 TCGA-BC-A10S TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Z 
       27.91        46.78        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-A69I 
       69.57         5.03        44.42        22.36        17.98        12.72 
TCGA-BC-A8YO TCGA-BD-A3ER TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5262 TCGA-CC-5263 
       18.48        36.66         0.07         2.86         3.39         4.24 
TCGA-CC-A3MA TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A11D 
        0.07        79.73        37.78        83.57        53.33        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        11.47 
TCGA-DD-A1EI TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Y 
        6.02        18.35        13.64        27.19        55.69         5.62 
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-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-A4NQ 
       26.83        30.51        39.78        56.25       108.76        12.26 
TCGA-DD-A4NS TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E 
       80.75        23.93         9.30        23.05        22.78         1.45 
TCGA-DD-A73F TCGA-DD-AA3A TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACD TCGA-DD-AACE 
       35.67        13.48        11.41        75.65        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        69.11         0.30         3.52 
TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACQ TCGA-DD-AACU TCGA-DD-AACW TCGA-DD-AACX 
       58.16        42.81        14.20        51.52        46.82         5.59 
TCGA-DD-AACY TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD8 
       47.67        18.54        21.63        42.58        44.22        40.08 
TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADE TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ 
       40.83        13.97        39.52        37.64        35.67        35.05 
TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR 
       34.49        20.91         0.39        15.06        14.33        66.67 
TCGA-DD-AADV TCGA-DD-AADY TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE4 TCGA-DD-AAE7 
       18.87        18.25        18.15        20.98        19.99        21.17 
TCGA-DD-AAE8 TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEI TCGA-DD-AAVP 
       21.83        15.72        25.08        16.37        50.33        79.07 
TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVX 
       89.69        82.62        59.93        72.39        76.18        56.48 
TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 
       64.77        62.47        66.25        65.39        49.48        53.69 
TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A7PX TCGA-ED-A7PY 
       13.41        12.69        15.85        13.91         0.20        12.82 
TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-ED-A8O5 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S 
        0.20        13.15        13.35         0.20        18.74        19.99 
TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A2QR TCGA-FV-A3I0 
       20.61         0.62        11.93        14.40        19.10        27.88 
TCGA-FV-A3I1 TCGA-FV-A3R3 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-G3-A25T TCGA-G3-A25U 
        8.12        12.03         0.33        81.73        51.06        53.79 
TCGA-G3-A25V TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH 
       28.27        58.49        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        25.25        22.95        20.42 
TCGA-G3-A6UC TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 
        7.76        11.24         8.55         9.70         9.17         0.89 
TCGA-G3-AAV5 TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5N0 TCGA-K7-A5RF 
        8.75         3.02         1.02         2.20        37.91        20.75 
TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K8 TCGA-LG-A9QC 
       17.06        16.83         3.72         2.14        24.36        13.97 
TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A520 
       12.03         9.57        16.67        12.85        20.71         0.62 
TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-QA-A7B7 TCGA-RC-A7S9 
       10.85        58.88        19.92        17.69         3.09        21.04 
TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-T1-A6J8 TCGA-UB-A7MC 
       19.33        19.04        15.39        15.52         0.76        16.44 
TCGA-UB-A7MD TCGA-UB-A7MF TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WX-AA46 TCGA-ZP-A9CV 
        1.71         7.04        10.32        11.34        24.85        35.77 
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-A9CF TCGA-ZS-A9CG 
       40.80        79.30        11.21 

  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 
                         120.82                          108.76 
  AMP PEAK 27(20Q13.13) MUTATED AMP PEAK 27(20Q13.13) WILD-TYPE 
                          17.59                           19.99 
[1] "0.0 - 120.8 (17.6)" "0.1 - 108.8 (20.0)"
[1] "hr=" "1.4"
D27V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE III STAGE IIIA
  AMP PEAK 27(20Q13.13) MUTATED        49       25         2         25
  AMP PEAK 27(20Q13.13) WILD-TYPE     119       59         1         34
                                 vv
clus                              STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 27(20Q13.13) MUTATED            5          2        2         1
  AMP PEAK 27(20Q13.13) WILD-TYPE          3          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                               49                             119
  STAGE II                              25                              59
  STAGE III                              2                               1
  STAGE IIIA                            25                              34
  STAGE IIIB                             5                               3
  STAGE IIIC                             2                               5
  STAGE IV                               2                               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      52  27  33   6
  AMP PEAK 27(20Q13.13) WILD-TYPE   127  64  40   6
D27V4, multiclass
       clus
vv      AMP PEAK 27(20Q13.13) MUTATED AMP PEAK 27(20Q13.13) WILD-TYPE
  T0+T1                            52                             127
  T2                               27                              64
  T3                               33                              40
  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    81   2
  AMP PEAK 27(20Q13.13) WILD-TYPE 168   1
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 27(20Q13.13) MUTATED     81    2
  AMP PEAK 27(20Q13.13) WILD-TYPE  168    1
   clus
vv  AMP PEAK 27(20Q13.13) MUTATED AMP PEAK 27(20Q13.13) WILD-TYPE
  0                            81                             168
  1                             2                               1
[1] 2 2
[1] FALSE
D27V6, binary
                                 cls
clus                                0   1
  AMP PEAK 27(20Q13.13) MUTATED    89   2
  AMP PEAK 27(20Q13.13) WILD-TYPE 171   2
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 27(20Q13.13) MUTATED     89    2
  AMP PEAK 27(20Q13.13) WILD-TYPE  171    2
   clus
vv  AMP PEAK 27(20Q13.13) MUTATED AMP PEAK 27(20Q13.13) WILD-TYPE
  0                            89                             171
  1                             2                               2
[1] 2 2
[1] FALSE
D27V7, binary
                                 cls
clus                                0   1
  AMP PEAK 27(20Q13.13) MUTATED    44  74
  AMP PEAK 27(20Q13.13) WILD-TYPE  69 170
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 27(20Q13.13) MUTATED     44   74
  AMP PEAK 27(20Q13.13) WILD-TYPE   69  170
        clus
vv       AMP PEAK 27(20Q13.13) MUTATED AMP PEAK 27(20Q13.13) WILD-TYPE
  FEMALE                            44                              69
  MALE                              74                             170
[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                        116
  AMP PEAK 27(20Q13.13) WILD-TYPE                      232
                                 vv
clus                              HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK 27(20Q13.13) MUTATED                                  2
  AMP PEAK 27(20Q13.13) WILD-TYPE                                5
D27V8, multiclass
                                  clus
vv                                 AMP PEAK 27(20Q13.13) MUTATED
  FIBROLAMELLAR CARCINOMA                                      0
  HEPATOCELLULAR CARCINOMA                                   116
  HEPATOCHOLANGIOCARCINOMA (MIXED)                             2
                                  clus
vv                                 AMP PEAK 27(20Q13.13) 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
  AMP PEAK 27(20Q13.13) MUTATED   102   7   1   5
  AMP PEAK 27(20Q13.13) WILD-TYPE 213   8   0  14
D27V9, multiclass
    clus
vv   AMP PEAK 27(20Q13.13) MUTATED AMP PEAK 27(20Q13.13) WILD-TYPE
  R0                           102                             213
  R1                             7                               8
  R2                             1                               0
  RX                             5                              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 27(20Q13.13) MUTATED                                  0    50
  AMP PEAK 27(20Q13.13) WILD-TYPE                                1   106
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 27(20Q13.13) MUTATED                           4    62
  AMP PEAK 27(20Q13.13) WILD-TYPE                        13   111
D27V10, multiclass
                                  clus
vv                                 AMP PEAK 27(20Q13.13) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                       50
  BLACK OR AFRICAN AMERICAN                                    4
  WHITE                                                       62
                                  clus
vv                                 AMP PEAK 27(20Q13.13) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               1
  ASIAN                                                        106
  BLACK OR AFRICAN AMERICAN                                     13
  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"
D27V11, binary
                                 cls
clus                                0   1
  AMP PEAK 27(20Q13.13) MUTATED     3 108
  AMP PEAK 27(20Q13.13) WILD-TYPE   8 221
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 27(20Q13.13) MUTATED      3  108
  AMP PEAK 27(20Q13.13) WILD-TYPE    8  221
                        clus
vv                       AMP PEAK 27(20Q13.13) MUTATED
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           108
                        clus
vv                       AMP PEAK 27(20Q13.13) WILD-TYPE
  HISPANIC OR LATINO                                   8
  NOT HISPANIC OR LATINO                             221
[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    71  41
  AMP PEAK 28(20Q13.33) WILD-TYPE 154  68
  AMP PEAK 28(20Q13.33) MUTATED AMP PEAK 28(20Q13.33) WILD-TYPE 
                            112                             222 
  AMP PEAK 28(20Q13.33) MUTATED AMP PEAK 28(20Q13.33) WILD-TYPE 
                             41                              68 
$`AMP PEAK 28(20Q13.33) MUTATED`
TCGA-2Y-A9GS TCGA-2Y-A9GX TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H9 TCGA-2Y-A9HA 
       23.80        80.28        24.89        27.88        14.99         1.18 
TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-A10Q TCGA-BC-A10R 
       10.78        10.59         1.51        48.99        37.32        10.13 
TCGA-BC-A10Y TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A69H TCGA-BD-A2L6 TCGA-BD-A3EP 
       23.34        13.84         0.26        14.60        44.81        13.45 
TCGA-BW-A5NO TCGA-CC-5261 TCGA-CC-A3M9 TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 
        0.66         3.19         0.10         0.10         0.13        79.73 
TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A1EF 
      113.00         7.33         2.60         0.46        21.76        12.95 
TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EJ TCGA-DD-A39V TCGA-DD-A3A5 TCGA-DD-A3A7 
       45.11        49.15        33.04        21.14       102.74        13.78 
TCGA-DD-A3A9 TCGA-DD-A4ND TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NR TCGA-DD-A4NV 
       30.61        90.28        29.56        73.81         0.30        78.84 
TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AAC8 TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACI 
       35.67       114.35         0.53        76.41        55.40        53.19 
TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACV 
       61.68        13.64        14.20        59.31        51.35        50.33 
TCGA-DD-AACX TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD6 TCGA-DD-AADA TCGA-DD-AADD 
        5.59         5.62         4.50        22.09        40.54        40.47 
TCGA-DD-AADF TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW 
        3.78        29.52        14.89        15.58        18.21        19.30 
TCGA-DD-AAE0 TCGA-DD-AAE3 TCGA-DD-AAE6 TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEG 
       18.25        18.61         4.64        23.74        18.90        23.64 
TCGA-DD-AAEH TCGA-DD-AAEK TCGA-DD-AAVR TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7XO 
       25.78        35.08        82.62        13.35         9.73        14.04 
TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A3JL 
       13.41        13.35         1.84        20.61        19.59         9.96 
TCGA-ES-A2HS TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A3R2 TCGA-FV-A4ZQ TCGA-G3-A25S 
       22.85        60.89        23.97         6.38         0.39        13.68 
TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A5SM TCGA-G3-A7M6 TCGA-G3-A7M9 TCGA-G3-AAV1 
       30.74        58.49        17.10        12.03         1.84        11.80 
TCGA-G3-AAV6 TCGA-HP-A5MZ TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75G 
        2.14         2.99        11.84        13.38        12.72        18.38 
TCGA-PD-A5DF TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7ME TCGA-UB-AA0U 
       21.01        24.13        17.59        19.76        15.98        10.75 
TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-YA-A8S7 TCGA-ZS-A9CD 
        0.99        12.99        13.55        45.57 

$`AMP PEAK 28(20Q13.33) WILD-TYPE`
TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GV TCGA-2Y-A9GW TCGA-2Y-A9H0 TCGA-2Y-A9H1 
       53.39        63.75        83.24        41.79       120.82        40.41 
TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H6 TCGA-2Y-A9H7 
       56.91        41.33        47.74        18.25        11.74        37.25 
TCGA-2Y-A9H8 TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-4R-AA8I TCGA-5C-AAPD TCGA-5R-AA1C 
       20.81         8.55        13.02         8.61         0.66        11.97 
TCGA-5R-AA1D TCGA-BC-4073 TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W 
       11.08        27.91        46.78        27.52        27.52         2.99 
TCGA-BC-A10X TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A3KG 
       25.32         1.12        69.57         5.03        44.42        22.36 
TCGA-BC-A5W4 TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A3ER TCGA-CC-5258 TCGA-CC-5260 
       17.98        12.72        18.48        36.66         0.07         2.86 
TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3MA TCGA-DD-A114 TCGA-DD-A115 
        3.39         4.24         3.32         0.07        37.78        83.57 
TCGA-DD-A116 TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC 
       53.33        51.29        90.71        79.40        66.31        19.79 
TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EI TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39W 
       75.65        11.47         6.02        18.35        13.64        27.19 
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        23.93         9.30        23.05 
TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-AA3A TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACD 
       22.78         1.45        13.48        11.41        75.65        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        69.11         0.30 
TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACU TCGA-DD-AACW TCGA-DD-AACY 
        3.52        58.16        42.81        51.52        46.82        47.67 
TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD8 TCGA-DD-AADB 
       18.54        21.63        42.58        44.22        40.08        40.83 
TCGA-DD-AADC TCGA-DD-AADE TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK 
       13.97        39.52        37.64        35.67        35.05        34.49 
TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADV 
       20.91         0.39        15.06        14.33        66.67        18.87 
TCGA-DD-AADY TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE4 TCGA-DD-AAE7 TCGA-DD-AAE8 
       18.25        18.15        20.98        19.99        21.17        21.83 
TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEI TCGA-DD-AAVP TCGA-DD-AAVQ 
       15.72        25.08        16.37        50.33        79.07        89.69 
TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ 
       59.93        72.39        76.18        56.48        64.77        62.47 
TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI 
       66.25        65.39        49.48        53.69        13.41        12.69 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XP 
       15.85        13.91         0.20        12.82         0.20        13.15 
TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HT 
        0.20        18.74        19.99         0.62        11.93        14.40 
TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 
       19.10        27.88         8.12        12.03         0.03         0.33 
TCGA-FV-A4ZP TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25Y TCGA-G3-A25Z 
       81.73        51.06        53.79        28.27        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        25.25 
TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-AAUZ TCGA-G3-AAV0 
       22.95        20.42         7.76         5.98        11.24         8.55 
TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV7 TCGA-GJ-A6C0 
        9.70         9.17         0.89         8.75         3.02         1.02 
TCGA-GJ-A9DB TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 
        2.20        37.91        20.75        17.06        16.83         3.72 
TCGA-KR-A7K0 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E 
        2.14        24.36        13.97        12.03         9.57        16.67 
TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF 
       12.85        20.71         0.62        10.85        58.88        19.92 
TCGA-O8-A75V TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH 
       17.69         3.09        21.04        19.33        19.04        15.39 
TCGA-RC-A7SK TCGA-T1-A6J8 TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7MF TCGA-UB-AA0V 
       15.52         0.76        16.44         1.71         7.04        10.32 
TCGA-WJ-A86L TCGA-WX-AA46 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 
       11.34        24.85        35.77        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        40.80        79.30        11.21 

  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 
                         114.35                          120.82 
  AMP PEAK 28(20Q13.33) MUTATED AMP PEAK 28(20Q13.33) WILD-TYPE 
                         17.900                          19.955 
[1] "0.1 - 114.3 (17.9)" "0.0 - 120.8 (20.0)"
[1] "hr=" "1.3"
D28V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE III STAGE IIIA
  AMP PEAK 28(20Q13.33) MUTATED        50       29         2         25
  AMP PEAK 28(20Q13.33) WILD-TYPE     118       55         1         34
                                 vv
clus                              STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 28(20Q13.33) MUTATED            5          2        3         1
  AMP PEAK 28(20Q13.33) WILD-TYPE          3          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                               50                             118
  STAGE II                              29                              55
  STAGE III                              2                               1
  STAGE IIIA                            25                              34
  STAGE IIIB                             5                               3
  STAGE IIIC                             2                               5
  STAGE IV                               3                               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      52  33  33   5
  AMP PEAK 28(20Q13.33) WILD-TYPE   127  58  40   7
D28V4, multiclass
       clus
vv      AMP PEAK 28(20Q13.33) MUTATED AMP PEAK 28(20Q13.33) WILD-TYPE
  T0+T1                            52                             127
  T2                               33                              58
  T3                               33                              40
  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    89   2
  AMP PEAK 28(20Q13.33) WILD-TYPE 160   1
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 28(20Q13.33) MUTATED     89    2
  AMP PEAK 28(20Q13.33) WILD-TYPE  160    1
   clus
vv  AMP PEAK 28(20Q13.33) MUTATED AMP PEAK 28(20Q13.33) WILD-TYPE
  0                            89                             160
  1                             2                               1
[1] 2 2
[1] FALSE
D28V6, binary
                                 cls
clus                                0   1
  AMP PEAK 28(20Q13.33) MUTATED    95   3
  AMP PEAK 28(20Q13.33) WILD-TYPE 165   1
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 28(20Q13.33) MUTATED     95    3
  AMP PEAK 28(20Q13.33) WILD-TYPE  165    1
   clus
vv  AMP PEAK 28(20Q13.33) MUTATED AMP PEAK 28(20Q13.33) WILD-TYPE
  0                            95                             165
  1                             3                               1
[1] 2 2
[1] FALSE
D28V7, binary
                                 cls
clus                                0   1
  AMP PEAK 28(20Q13.33) MUTATED    48  75
  AMP PEAK 28(20Q13.33) WILD-TYPE  65 169
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 28(20Q13.33) MUTATED     48   75
  AMP PEAK 28(20Q13.33) WILD-TYPE   65  169
        clus
vv       AMP PEAK 28(20Q13.33) MUTATED AMP PEAK 28(20Q13.33) WILD-TYPE
  FEMALE                            48                              65
  MALE                              75                             169
[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                        121
  AMP PEAK 28(20Q13.33) WILD-TYPE                      227
                                 vv
clus                              HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK 28(20Q13.33) MUTATED                                  2
  AMP PEAK 28(20Q13.33) WILD-TYPE                                5
D28V8, multiclass
                                  clus
vv                                 AMP PEAK 28(20Q13.33) MUTATED
  FIBROLAMELLAR CARCINOMA                                      0
  HEPATOCELLULAR CARCINOMA                                   121
  HEPATOCHOLANGIOCARCINOMA (MIXED)                             2
                                  clus
vv                                 AMP PEAK 28(20Q13.33) 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 28(20Q13.33) MUTATED   108   6   1   6
  AMP PEAK 28(20Q13.33) WILD-TYPE 207   9   0  13
D28V9, multiclass
    clus
vv   AMP PEAK 28(20Q13.33) MUTATED AMP PEAK 28(20Q13.33) WILD-TYPE
  R0                           108                             207
  R1                             6                               9
  R2                             1                               0
  RX                             6                              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 28(20Q13.33) MUTATED                                  0    55
  AMP PEAK 28(20Q13.33) WILD-TYPE                                1   101
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 28(20Q13.33) MUTATED                           4    62
  AMP PEAK 28(20Q13.33) WILD-TYPE                        13   111
D28V10, multiclass
                                  clus
vv                                 AMP PEAK 28(20Q13.33) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                       55
  BLACK OR AFRICAN AMERICAN                                    4
  WHITE                                                       62
                                  clus
vv                                 AMP PEAK 28(20Q13.33) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               1
  ASIAN                                                        101
  BLACK OR AFRICAN AMERICAN                                     13
  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"
D28V11, binary
                                 cls
clus                                0   1
  AMP PEAK 28(20Q13.33) MUTATED     3 113
  AMP PEAK 28(20Q13.33) WILD-TYPE   8 216
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 28(20Q13.33) MUTATED      3  113
  AMP PEAK 28(20Q13.33) WILD-TYPE    8  216
                        clus
vv                       AMP PEAK 28(20Q13.33) MUTATED
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           113
                        clus
vv                       AMP PEAK 28(20Q13.33) WILD-TYPE
  HISPANIC OR LATINO                                   8
  NOT HISPANIC OR LATINO                             216
[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    55  21
  AMP PEAK 29(XQ28) WILD-TYPE 170  88
  AMP PEAK 29(XQ28) MUTATED AMP PEAK 29(XQ28) WILD-TYPE 
                         76                         258 
  AMP PEAK 29(XQ28) MUTATED AMP PEAK 29(XQ28) WILD-TYPE 
                         21                          88 
$`AMP PEAK 29(XQ28) MUTATED`
TCGA-2Y-A9GT TCGA-2Y-A9GW TCGA-2Y-A9GZ TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H4 
       53.39        41.79        27.88        40.41        56.91        47.74 
TCGA-5R-AA1C TCGA-BC-A10U TCGA-BC-A69I TCGA-BW-A5NO TCGA-CC-A3MA TCGA-DD-A114 
       11.97        27.52        12.72         0.66         0.07        37.78 
TCGA-DD-A11A TCGA-DD-A39V TCGA-DD-A39Y TCGA-DD-A3A3 TCGA-DD-A3A7 TCGA-DD-A4NF 
        2.60        21.14         5.62        17.59        13.78        30.97 
TCGA-DD-A4NK TCGA-DD-A4NV TCGA-DD-A73D TCGA-DD-A73G TCGA-DD-AACI TCGA-DD-AACJ 
       39.78        78.84        22.78       114.35        53.19        69.11 
TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACY TCGA-DD-AAD2 TCGA-DD-AADN TCGA-DD-AADO 
       59.31        51.35        47.67        21.63        29.52        14.89 
TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE9 TCGA-DD-AAEH 
       18.21        19.30        18.61        19.99        23.74        25.78 
TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVY TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-ED-A66Y 
       79.07        89.69        64.77        65.39        49.48         9.73 
TCGA-ED-A7PZ TCGA-EP-A12J TCGA-EP-A2KA TCGA-EP-A3JL TCGA-ES-A2HS TCGA-FV-A2QR 
        0.20        18.74        20.61         9.96        22.85        19.10 
TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25U TCGA-G3-A3CG TCGA-G3-A3CJ TCGA-G3-A5SI 
        0.33         0.39        53.79        22.13        19.53        25.25 
TCGA-G3-A5SL TCGA-G3-A6UC TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV5 
       20.42         7.76         8.55         9.70         9.17         8.75 
TCGA-G3-AAV7 TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A6G5 TCGA-KR-A7K8 TCGA-LG-A6GG 
        3.02         2.99        37.91        16.83        24.36        12.72 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-NI-A4U2 TCGA-O8-A75V TCGA-UB-A7ME 
        9.57        16.67        18.38        58.88        17.69        15.98 
TCGA-WQ-A9G7 TCGA-ZP-A9CV TCGA-ZS-A9CD TCGA-ZS-A9CG 
        0.99        35.77        45.57        11.21 

$`AMP PEAK 29(XQ28) WILD-TYPE`
TCGA-2Y-A9GS TCGA-2Y-A9GU TCGA-2Y-A9GV TCGA-2Y-A9GX TCGA-2Y-A9GY TCGA-2Y-A9H0 
       23.80        63.75        83.24        80.28        24.89       120.82 
TCGA-2Y-A9H3 TCGA-2Y-A9H5 TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-2Y-A9H8 TCGA-2Y-A9H9 
       41.33        18.25        11.74        37.25        20.81        14.99 
TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-A9VH 
        1.18         8.55        13.02         8.61        10.78        10.59 
TCGA-5C-AAPD TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q 
        0.66        11.08         1.51        48.99        27.91        37.32 
TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T 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-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP 
       22.36        17.98        14.60        18.48        44.81        13.45 
TCGA-BD-A3ER TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 
       36.66         0.07         2.86         3.19         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        11.47 
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        33.04        18.35 
TCGA-DD-A1EL TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 
       13.64        27.19        55.69        19.76        25.81         7.66 
TCGA-DD-A3A2 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A8 TCGA-DD-A3A9 
       70.06        20.12       102.74       107.11         0.36        30.61 
TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ 
       33.14        32.52        90.28        30.15        26.83        30.51 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR 
       56.25        29.56        73.81       108.76        12.26         0.30 
TCGA-DD-A4NS TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73E TCGA-DD-A73F 
       80.75        23.93         9.30        23.05         1.45        35.67 
TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC 
       13.48         0.53        11.41        75.65        76.41        55.40 
TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACK 
       12.53        63.48        12.00        15.42         6.41         0.30 
TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ 
        3.52        58.16        42.81        61.68        13.64        14.20 
TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACZ TCGA-DD-AAD0 
       51.52        50.33        46.82         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        42.58        44.22        22.09        40.08        40.54 
TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG 
       40.83        13.97        40.47        39.52         3.78        37.64 
TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADP 
       35.67        35.05        34.49        20.91         0.39        15.06 
TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADV TCGA-DD-AADY TCGA-DD-AAE0 
       14.33        66.67        15.58        18.87        18.25        18.25 
TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEA 
       18.15        20.98         4.64        21.17        21.83        18.90 
TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEI TCGA-DD-AAEK 
       15.72        25.08        16.37        23.64        50.33        35.08 
TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVZ 
       82.62        59.93        72.39        76.18        56.48        62.47 
TCGA-DD-AAW0 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 
       66.25        53.69        13.41        12.69        15.85        13.91 
TCGA-ED-A66X TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E 
       13.35         0.20        12.82        14.04        13.15        13.41 
TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A26S TCGA-EP-A2KB TCGA-EP-A2KC 
       13.35         1.84         0.20        19.99        19.59         0.62 
TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A3I0 TCGA-FV-A3I1 
       11.93        14.40        60.89        23.97        27.88         8.12 
TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A4ZP TCGA-G3-A25S TCGA-G3-A25T 
        6.38        12.03         0.03        81.73        13.68        51.06 
TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH 
       28.27        30.74        58.49        14.86        21.53        25.64 
TCGA-G3-A3CI TCGA-G3-A3CK TCGA-G3-A5SJ TCGA-G3-A5SM TCGA-G3-A7M6 TCGA-G3-A7M7 
        5.92        19.23        22.95        17.10        12.03         5.98 
TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV1 TCGA-G3-AAV4 TCGA-G3-AAV6 TCGA-GJ-A6C0 
        1.84        11.24        11.80         0.89         2.14         1.02 
TCGA-GJ-A9DB TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K2 
        2.20        20.75        17.06         3.72         2.14        11.84 
TCGA-KR-A7K7 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A520 
       13.38        13.97        12.03        12.85        20.71         0.62 
TCGA-MR-A8JO TCGA-NI-A8LF TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SB 
       10.85        19.92        21.01         3.09        21.04        19.33 
TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-T1-A6J8 TCGA-UB-A7MA 
       19.04        15.39        15.52        24.13         0.76        17.59 
TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7MF TCGA-UB-AA0U TCGA-UB-AA0V 
       19.76        16.44         1.71         7.04        10.75        10.32 
TCGA-WJ-A86L TCGA-WQ-AB4B TCGA-WX-AA46 TCGA-YA-A8S7 TCGA-ZP-A9CY TCGA-ZP-A9CZ 
       11.34        12.99        24.85        13.55        25.71        23.21 
TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CE TCGA-ZS-A9CF 
       23.57         0.69        24.43        12.99        40.80        79.30 

  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 
                     114.35                      120.82 
  AMP PEAK 29(XQ28) MUTATED AMP PEAK 29(XQ28) WILD-TYPE 
                     20.515                      18.705 
[1] "0.1 - 114.3 (20.5)" "0.0 - 120.8 (18.7)"
[1] "hr=" "1.3"
D29V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 29(XQ28) MUTATED        42       21         0         12          3
  AMP PEAK 29(XQ28) WILD-TYPE     126       63         3         47          5
                             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        3         1         2
D29V3, multiclass
            clus
vv           AMP PEAK 29(XQ28) MUTATED AMP PEAK 29(XQ28) WILD-TYPE
  STAGE I                           42                         126
  STAGE II                          21                          63
  STAGE III                          0                           3
  STAGE IIIA                        12                          47
  STAGE IIIB                         3                           5
  STAGE IIIC                         1                           6
  STAGE IV                           0                           3
  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      43  22  15   2
  AMP PEAK 29(XQ28) WILD-TYPE   136  69  58  10
D29V4, multiclass
       clus
vv      AMP PEAK 29(XQ28) MUTATED AMP PEAK 29(XQ28) WILD-TYPE
  T0+T1                        43                         136
  T2                           22                          69
  T3                           15                          58
  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    54   0
  AMP PEAK 29(XQ28) WILD-TYPE 195   3
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 29(XQ28) MUTATED     54    0
  AMP PEAK 29(XQ28) WILD-TYPE  195    3
   clus
vv  AMP PEAK 29(XQ28) MUTATED AMP PEAK 29(XQ28) WILD-TYPE
  0                        54                         195
  1                         0                           3
[1] 2 2
[1] FALSE
D29V6, binary
                             cls
clus                            0   1
  AMP PEAK 29(XQ28) MUTATED    61   0
  AMP PEAK 29(XQ28) WILD-TYPE 199   4
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 29(XQ28) MUTATED     61    0
  AMP PEAK 29(XQ28) WILD-TYPE  199    4
   clus
vv  AMP PEAK 29(XQ28) MUTATED AMP PEAK 29(XQ28) WILD-TYPE
  0                        61                         199
  1                         0                           4
[1] 2 2
[1] FALSE
D29V7, binary
                             cls
clus                            0   1
  AMP PEAK 29(XQ28) MUTATED    15  68
  AMP PEAK 29(XQ28) WILD-TYPE  98 176
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 29(XQ28) MUTATED     15   68
  AMP PEAK 29(XQ28) WILD-TYPE   98  176
        clus
vv       AMP PEAK 29(XQ28) MUTATED AMP PEAK 29(XQ28) WILD-TYPE
  FEMALE                        15                          98
  MALE                          68                         176
[1] 2 2
[1] FALSE
                             vv
clus                          FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  AMP PEAK 29(XQ28) MUTATED                         0                       83
  AMP PEAK 29(XQ28) WILD-TYPE                       2                      265
                             vv
clus                          HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK 29(XQ28) MUTATED                                  0
  AMP PEAK 29(XQ28) WILD-TYPE                                7
D29V8, multiclass
                                  clus
vv                                 AMP PEAK 29(XQ28) MUTATED
  FIBROLAMELLAR CARCINOMA                                  0
  HEPATOCELLULAR CARCINOMA                                83
  HEPATOCHOLANGIOCARCINOMA (MIXED)                         0
                                  clus
vv                                 AMP PEAK 29(XQ28) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                    2
  HEPATOCELLULAR CARCINOMA                                 265
  HEPATOCHOLANGIOCARCINOMA (MIXED)                           7
[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    75   3   0   4
  AMP PEAK 29(XQ28) WILD-TYPE 240  12   1  15
D29V9, multiclass
    clus
vv   AMP PEAK 29(XQ28) MUTATED AMP PEAK 29(XQ28) WILD-TYPE
  R0                        75                         240
  R1                         3                          12
  R2                         0                           1
  RX                         4                          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
  AMP PEAK 29(XQ28) MUTATED                                  1    36
  AMP PEAK 29(XQ28) WILD-TYPE                                0   120
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 29(XQ28) MUTATED                           5    36
  AMP PEAK 29(XQ28) WILD-TYPE                        12   137
D29V10, multiclass
                                  clus
vv                                 AMP PEAK 29(XQ28) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         1
  ASIAN                                                   36
  BLACK OR AFRICAN AMERICAN                                5
  WHITE                                                   36
                                  clus
vv                                 AMP PEAK 29(XQ28) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                    120
  BLACK OR AFRICAN AMERICAN                                 12
  WHITE                                                    137
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V11, binary
                             cls
clus                            0   1
  AMP PEAK 29(XQ28) MUTATED     1  77
  AMP PEAK 29(XQ28) WILD-TYPE  10 252
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 29(XQ28) MUTATED      1   77
  AMP PEAK 29(XQ28) WILD-TYPE   10  252
                        clus
vv                       AMP PEAK 29(XQ28) MUTATED AMP PEAK 29(XQ28) WILD-TYPE
  HISPANIC OR LATINO                             1                          10
  NOT HISPANIC OR LATINO                        77                         252
[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    98  49
  DEL PEAK  1(1P36.31) WILD-TYPE 127  60
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                           147                            187 
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                            49                             60 
$`DEL PEAK  1(1P36.31) MUTATED`
TCGA-2Y-A9GX TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H5 TCGA-2Y-A9H6 TCGA-2Y-A9H7 
       80.28        56.91        41.33        18.25        11.74        37.25 
TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-5C-A9VH TCGA-BC-A10Q TCGA-BC-A10S TCGA-BC-A10T 
       13.02        10.78        10.59        37.32        46.78        27.52 
TCGA-BC-A10W TCGA-BC-A10Y TCGA-BC-A217 TCGA-BC-A69H TCGA-BD-A3ER TCGA-CC-5260 
        2.99        23.34        13.84        14.60        36.66         2.86 
TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-DD-A113 
        3.19         3.39         4.24         0.07         0.10        79.73 
TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C 
       53.33       113.00         7.33         2.60         0.46        21.76 
TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EB TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH 
       51.29        90.71        66.31        12.95        45.11        49.15 
TCGA-DD-A1EJ TCGA-DD-A39X TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A9 
       33.04        55.69        19.76        25.81         7.66        30.61 
TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NR 
       30.15        26.83        30.51        29.56        73.81         0.30 
TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 
       23.93         9.30        35.67       114.35        13.48         0.53 
TCGA-DD-AACA TCGA-DD-AACC TCGA-DD-AACH TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACN 
       75.65        55.40         6.41        69.11         0.30        42.81 
TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACW TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD5 
       61.68        13.64        46.82         4.50        18.54        44.22 
TCGA-DD-AAD6 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADF 
       22.09        40.54        40.83        13.97        40.47         3.78 
TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO 
       35.67        35.05        34.49         0.39        29.52        14.89 
TCGA-DD-AADP TCGA-DD-AADR TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 
       15.06        66.67        19.30        18.25        18.25        18.15 
TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAEH TCGA-DD-AAEK TCGA-DD-AAVQ TCGA-DD-AAVS 
       20.98        18.61        25.78        35.08        89.69        59.93 
TCGA-DD-AAVW TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-ED-A4XI TCGA-ED-A66X TCGA-ED-A66Y 
       76.18        62.47        66.25        12.69        13.35         9.73 
TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K 
        0.20        12.82        13.41        13.35         1.84         0.20 
TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HS TCGA-FV-A23B TCGA-FV-A2QQ 
       19.59         0.62        11.93        22.85        60.89        23.97 
TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP 
       19.10        27.88        12.03         0.03         0.33        81.73 
TCGA-G3-A25S TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A5SI 
       13.68        28.27        30.74        58.49        14.86        25.25 
TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A7M9 TCGA-G3-AAV1 TCGA-G3-AAV6 TCGA-KR-A7K2 
       20.42        17.10         1.84        11.80         2.14        11.84 
TCGA-KR-A7K7 TCGA-LG-A9QC TCGA-MI-A75G TCGA-MI-A75H TCGA-O8-A75V TCGA-RC-A7S9 
       13.38        13.97        18.38        12.85        17.69        21.04 
TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-T1-A6J8 TCGA-UB-A7MA TCGA-UB-A7MC 
       15.39        15.52        24.13         0.76        17.59        16.44 
TCGA-UB-A7ME TCGA-UB-A7MF TCGA-UB-AA0U TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-ZP-A9CY 
       15.98         7.04        10.75         0.99        12.99        25.71 
TCGA-ZP-A9CZ TCGA-ZP-A9D1 TCGA-ZS-A9CE 
       23.21         0.69        40.80 

$`DEL PEAK  1(1P36.31) WILD-TYPE`
TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GV TCGA-2Y-A9GW TCGA-2Y-A9GY 
       23.80        53.39        63.75        83.24        41.79        24.89 
TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H4 TCGA-2Y-A9H8 TCGA-2Y-A9H9 
       27.88       120.82        40.41        47.74        20.81        14.99 
TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-4R-AA8I TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D 
        1.18         8.55         8.61         0.66        11.97        11.08 
TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10R TCGA-BC-A10U TCGA-BC-A10X 
        1.51        48.99        27.91        10.13        27.52        25.32 
TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A3KF TCGA-BC-A3KG 
        1.12        69.57         5.03        44.42         0.26        22.36 
TCGA-BC-A5W4 TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BW-A5NO 
       17.98        12.72        18.48        44.81        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        11.47         6.02        18.35 
TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39Y TCGA-DD-A3A2 TCGA-DD-A3A3 
       13.64        21.14        27.19         5.62        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-A4ND TCGA-DD-A4NF TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NP 
       32.52        90.28        30.97        39.78        56.25       108.76 
TCGA-DD-A4NQ TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E 
       12.26        80.75        78.84        23.05        22.78         1.45 
TCGA-DD-AAC9 TCGA-DD-AACB TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG 
       11.41        76.41        12.53        63.48        12.00        15.42 
TCGA-DD-AACI TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT 
       53.19         3.52        58.16        14.20        59.31        51.35 
TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD2 
       51.52        50.33         5.59        47.67         5.62        21.63 
TCGA-DD-AAD3 TCGA-DD-AAD8 TCGA-DD-AADE TCGA-DD-AADG TCGA-DD-AADL TCGA-DD-AADQ 
       42.58        40.08        39.52        37.64        20.91        14.33 
TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADV TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE7 
       15.58        18.21        18.87        19.99         4.64        21.17 
TCGA-DD-AAE8 TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE 
       21.83        23.74        18.90        15.72        25.08        16.37 
TCGA-DD-AAEG TCGA-DD-AAEI TCGA-DD-AAVP TCGA-DD-AAVR TCGA-DD-AAVU TCGA-DD-AAVX 
       23.64        50.33        79.07        82.62        72.39        56.48 
TCGA-DD-AAVY TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A5KG 
       64.77        65.39        49.48        53.69        13.41        15.85 
TCGA-ED-A627 TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-EP-A12J TCGA-EP-A26S 
       13.91         0.20        14.04        13.15        18.74        19.99 
TCGA-EP-A2KA TCGA-EP-A3JL TCGA-ES-A2HT TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A4ZQ 
       20.61         9.96        14.40         8.12         6.38         0.39 
TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI 
       51.06        53.79        21.53        22.13        25.64         5.92 
TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SJ TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 
       19.53        19.23        22.95         7.76        12.03         5.98 
TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 
       11.24         8.55         9.70         9.17         0.89         8.75 
TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF 
        3.02         1.02         2.20         2.99        37.91        20.75 
TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K8 TCGA-LG-A6GG 
       17.06        16.83         3.72         2.14        24.36        12.72 
TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO 
       12.03         9.57        16.67        20.71         0.62        10.85 
TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7SB TCGA-RC-A7SF 
       58.88        19.92        21.01         3.09        19.33        19.04 
TCGA-UB-A7MB TCGA-UB-A7MD TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WX-AA46 TCGA-YA-A8S7 
       19.76         1.71        10.32        11.34        24.85        13.55 
TCGA-ZP-A9CV TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CF 
       35.77        23.57        24.43        12.99        45.57        79.30 
TCGA-ZS-A9CG 
       11.21 

  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 
                        114.35                         120.82 
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                         18.61                          19.53 
[1] "0.0 - 114.3 (18.6)" "0.1 - 120.8 (19.5)"
[1] "hr=" "1.1"
D30V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IIIA
  DEL PEAK  1(1P36.31) MUTATED        73       37         1         25
  DEL PEAK  1(1P36.31) WILD-TYPE      95       47         2         34
                                vv
clus                             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK  1(1P36.31) MUTATED            4          4        2         1
  DEL PEAK  1(1P36.31) WILD-TYPE          4          3        1         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                              73                             95
  STAGE II                             37                             47
  STAGE III                             1                              2
  STAGE IIIA                           25                             34
  STAGE IIIB                            4                              4
  STAGE IIIC                            4                              3
  STAGE IV                              2                              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  1(1P36.31) MUTATED      79  39  33   7
  DEL PEAK  1(1P36.31) WILD-TYPE   100  52  40   5
D30V4, multiclass
       clus
vv      DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE
  T0+T1                           79                            100
  T2                              39                             52
  T3                              33                             40
  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   112   2
  DEL PEAK  1(1P36.31) WILD-TYPE 137   1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.31) MUTATED    112    2
  DEL PEAK  1(1P36.31) WILD-TYPE  137    1
   clus
vv  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE
  0                          112                            137
  1                            2                              1
[1] 2 2
[1] FALSE
D30V6, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.31) MUTATED   123   3
  DEL PEAK  1(1P36.31) WILD-TYPE 137   1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.31) MUTATED    123    3
  DEL PEAK  1(1P36.31) WILD-TYPE  137    1
   clus
vv  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE
  0                          123                            137
  1                            3                              1
[1] 2 2
[1] FALSE
D30V7, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.31) MUTATED    57 102
  DEL PEAK  1(1P36.31) WILD-TYPE  56 142
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.31) MUTATED     57  102
  DEL PEAK  1(1P36.31) WILD-TYPE   56  142
        clus
vv       DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE
  FEMALE                           57                             56
  MALE                            102                            142
[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                        154
  DEL PEAK  1(1P36.31) WILD-TYPE                      194
                                vv
clus                             HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK  1(1P36.31) MUTATED                                  5
  DEL PEAK  1(1P36.31) WILD-TYPE                                2
D30V8, multiclass
                                  clus
vv                                 DEL PEAK  1(1P36.31) MUTATED
  FIBROLAMELLAR CARCINOMA                                     0
  HEPATOCELLULAR CARCINOMA                                  154
  HEPATOCHOLANGIOCARCINOMA (MIXED)                            5
                                  clus
vv                                 DEL PEAK  1(1P36.31) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                       2
  HEPATOCELLULAR CARCINOMA                                    194
  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  1(1P36.31) MUTATED   137  10   1   9
  DEL PEAK  1(1P36.31) WILD-TYPE 178   5   0  10
D30V9, multiclass
    clus
vv   DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE
  R0                          137                            178
  R1                           10                              5
  R2                            1                              0
  RX                            9                             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  1(1P36.31) MUTATED                                  0    78
  DEL PEAK  1(1P36.31) WILD-TYPE                                1    78
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  1(1P36.31) MUTATED                           4    73
  DEL PEAK  1(1P36.31) WILD-TYPE                        13   100
D30V10, multiclass
                                  clus
vv                                 DEL PEAK  1(1P36.31) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                      78
  BLACK OR AFRICAN AMERICAN                                   4
  WHITE                                                      73
                                  clus
vv                                 DEL PEAK  1(1P36.31) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        78
  BLACK OR AFRICAN AMERICAN                                    13
  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"
D30V11, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.31) MUTATED     4 149
  DEL PEAK  1(1P36.31) WILD-TYPE   7 180
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.31) MUTATED      4  149
  DEL PEAK  1(1P36.31) WILD-TYPE    7  180
                        clus
vv                       DEL PEAK  1(1P36.31) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                          149
                        clus
vv                       DEL PEAK  1(1P36.31) WILD-TYPE
  HISPANIC OR LATINO                                  7
  NOT HISPANIC OR LATINO                            180
[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    87  39
  DEL PEAK  2(1P36.11) WILD-TYPE 138  70
  DEL PEAK  2(1P36.11) MUTATED DEL PEAK  2(1P36.11) WILD-TYPE 
                           126                            208 
  DEL PEAK  2(1P36.11) MUTATED DEL PEAK  2(1P36.11) WILD-TYPE 
                            39                             70 
$`DEL PEAK  2(1P36.11) MUTATED`
TCGA-2Y-A9GX TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H5 TCGA-2Y-A9H6 TCGA-2Y-A9H7 
       80.28        56.91        41.33        18.25        11.74        37.25 
TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-5C-A9VH TCGA-BC-A10Q TCGA-BC-A10S TCGA-BC-A10T 
       13.02        10.78        10.59        37.32        46.78        27.52 
TCGA-BC-A10W TCGA-BC-A112 TCGA-BC-A69H TCGA-BD-A3ER TCGA-CC-5258 TCGA-CC-5260 
        2.99         5.03        14.60        36.66         0.07         2.86 
TCGA-CC-5261 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-DD-A113 TCGA-DD-A116 TCGA-DD-A118 
        3.19         0.07         0.10        79.73        53.33       113.00 
TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A1E9 TCGA-DD-A1EG 
        7.33         2.60         0.46        21.76        90.71        45.11 
TCGA-DD-A1EH TCGA-DD-A1EJ TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A3A1 TCGA-DD-A3A9 
       49.15        33.04        21.14        55.69         7.66        30.61 
TCGA-DD-A4NA TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NN TCGA-DD-A4NO 
       33.14        30.15        26.83        30.51        29.56        73.81 
TCGA-DD-A73B TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AAC8 TCGA-DD-AACA TCGA-DD-AACC 
        9.30        35.67       114.35         0.53        75.65        55.40 
TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACW 
       69.11         0.30        42.81        61.68        13.64        46.82 
TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AADA TCGA-DD-AADB 
        4.50        18.54        44.22        22.09        40.54        40.83 
TCGA-DD-AADC TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADM TCGA-DD-AADO 
       13.97        35.67        35.05        34.49         0.39        14.89 
TCGA-DD-AADP TCGA-DD-AADR TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 
       15.06        66.67        19.30        18.25        18.25        18.15 
TCGA-DD-AAE3 TCGA-DD-AAEE TCGA-DD-AAEK TCGA-DD-AAVQ TCGA-DD-AAVS TCGA-DD-AAVU 
       18.61        16.37        35.08        89.69        59.93        72.39 
TCGA-DD-AAVW TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-ED-A459 TCGA-ED-A66X TCGA-ED-A66Y 
       76.18        62.47        66.25        13.41        13.35         9.73 
TCGA-ED-A7PY TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A2KB 
       12.82        13.41        13.35         1.84         0.20        19.59 
TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HS TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A3I0 
        0.62        11.93        22.85        60.89        23.97        27.88 
TCGA-FV-A3R3 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-G3-A25S TCGA-G3-A25W TCGA-G3-A25X 
       12.03         0.33        81.73        13.68        30.74        58.49 
TCGA-G3-A25Y TCGA-G3-A5SI TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A7M9 TCGA-G3-AAV1 
       14.86        25.25        20.42        17.10         1.84        11.80 
TCGA-G3-AAV6 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-LG-A9QC TCGA-MI-A75G 
        2.14        11.84        13.38        12.72        13.97        18.38 
TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-T1-A6J8 TCGA-UB-A7MA TCGA-UB-A7MC 
       15.39        15.52        24.13         0.76        17.59        16.44 
TCGA-UB-A7MF TCGA-UB-AA0U TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-ZP-A9CZ TCGA-ZP-A9D1 
        7.04        10.75         0.99        12.99        23.21         0.69 

$`DEL PEAK  2(1P36.11) WILD-TYPE`
TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GV TCGA-2Y-A9GW TCGA-2Y-A9GY 
       23.80        53.39        63.75        83.24        41.79        24.89 
TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H4 TCGA-2Y-A9H8 TCGA-2Y-A9H9 
       27.88       120.82        40.41        47.74        20.81        14.99 
TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-4R-AA8I TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D 
        1.18         8.55         8.61         0.66        11.97        11.08 
TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10R TCGA-BC-A10U TCGA-BC-A10X 
        1.51        48.99        27.91        10.13        27.52        25.32 
TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF 
       23.34         1.12        69.57        44.42        13.84         0.26 
TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP 
       22.36        17.98        12.72        18.48        44.81        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        11.47        12.95         6.02        18.35        13.64 
TCGA-DD-A39W TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A2 TCGA-DD-A3A3 
       27.19         5.62        19.76        25.81        70.06        17.59 
TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A4NB 
       20.12       102.74       107.11        13.78         0.36        32.52 
TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NP TCGA-DD-A4NQ 
       90.28        30.97        39.78        56.25       108.76        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        23.93        23.05        22.78 
TCGA-DD-A73E TCGA-DD-AA3A TCGA-DD-AAC9 TCGA-DD-AACB TCGA-DD-AACD TCGA-DD-AACE 
        1.45        13.48        11.41        76.41        12.53        63.48 
TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACL TCGA-DD-AACM 
       12.00        15.42         6.41        53.19         3.52        58.16 
TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACX 
       14.20        59.31        51.35        51.52        50.33         5.59 
TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD8 TCGA-DD-AADD 
       47.67         5.62        21.63        42.58        40.08        40.47 
TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADL TCGA-DD-AADN TCGA-DD-AADQ 
       39.52         3.78        37.64        20.91        29.52        14.33 
TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADV TCGA-DD-AAE2 TCGA-DD-AAE4 TCGA-DD-AAE6 
       15.58        18.21        18.87        20.98        19.99         4.64 
TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAED 
       21.17        21.83        23.74        18.90        15.72        25.08 
TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAVP TCGA-DD-AAVR TCGA-DD-AAVX 
       23.64        25.78        50.33        79.07        82.62        56.48 
TCGA-DD-AAVY TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A4XI TCGA-ED-A5KG 
       64.77        65.39        49.48        53.69        12.69        15.85 
TCGA-ED-A627 TCGA-ED-A7PX TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-EP-A12J 
       13.91         0.20         0.20        14.04        13.15        18.74 
TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A3JL TCGA-ES-A2HT TCGA-FV-A2QR TCGA-FV-A3I1 
       19.99        20.61         9.96        14.40        19.10         8.12 
TCGA-FV-A3R2 TCGA-FV-A495 TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V 
        6.38         0.03         0.39        51.06        53.79        28.27 
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-A5SJ TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-AAUZ TCGA-G3-AAV0 
       22.95         7.76        12.03         5.98        11.24         8.55 
TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV7 TCGA-GJ-A6C0 
        9.70         9.17         0.89         8.75         3.02         1.02 
TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 
        2.20         2.99        37.91        20.75        17.06        16.83 
TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K8 TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E 
        3.72         2.14        24.36        12.03         9.57        16.67 
TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF 
       12.85        20.71         0.62        10.85        58.88        19.92 
TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF 
       17.69        21.01         3.09        21.04        19.33        19.04 
TCGA-UB-A7MB TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WX-AA46 
       19.76         1.71        15.98        10.32        11.34        24.85 
TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 
       13.55        35.77        25.71        23.57        24.43        12.99 
TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       45.57        40.80        79.30        11.21 

  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 
                        114.35                         120.82 
  DEL PEAK  2(1P36.11) MUTATED DEL PEAK  2(1P36.11) WILD-TYPE 
                        18.460                         19.645 
[1] "0.1 - 114.3 (18.5)" "0.0 - 120.8 (19.6)"
[1] "hr=" "1.1"
D31V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IIIA
  DEL PEAK  2(1P36.11) MUTATED        57       36         1         24
  DEL PEAK  2(1P36.11) WILD-TYPE     111       48         2         35
                                vv
clus                             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK  2(1P36.11) MUTATED            4          4        2         1
  DEL PEAK  2(1P36.11) WILD-TYPE          4          3        1         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                              57                            111
  STAGE II                             36                             48
  STAGE III                             1                              2
  STAGE IIIA                           24                             35
  STAGE IIIB                            4                              4
  STAGE IIIC                            4                              3
  STAGE IV                              2                              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  2(1P36.11) MUTATED      62  39  33   5
  DEL PEAK  2(1P36.11) WILD-TYPE   117  52  40   7
D31V4, multiclass
       clus
vv      DEL PEAK  2(1P36.11) MUTATED DEL PEAK  2(1P36.11) WILD-TYPE
  T0+T1                           62                            117
  T2                              39                             52
  T3                              33                             40
  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   100   3
  DEL PEAK  2(1P36.11) WILD-TYPE 149   0
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  2(1P36.11) MUTATED    100    3
  DEL PEAK  2(1P36.11) WILD-TYPE  149    0
   clus
vv  DEL PEAK  2(1P36.11) MUTATED DEL PEAK  2(1P36.11) WILD-TYPE
  0                          100                            149
  1                            3                              0
[1] 2 2
[1] FALSE
D31V6, binary
                                cls
clus                               0   1
  DEL PEAK  2(1P36.11) MUTATED   110   3
  DEL PEAK  2(1P36.11) WILD-TYPE 150   1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  2(1P36.11) MUTATED    110    3
  DEL PEAK  2(1P36.11) WILD-TYPE  150    1
   clus
vv  DEL PEAK  2(1P36.11) MUTATED DEL PEAK  2(1P36.11) WILD-TYPE
  0                          110                            150
  1                            3                              1
[1] 2 2
[1] FALSE
D31V7, binary
                                cls
clus                               0   1
  DEL PEAK  2(1P36.11) MUTATED    47  92
  DEL PEAK  2(1P36.11) WILD-TYPE  66 152
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  2(1P36.11) MUTATED     47   92
  DEL PEAK  2(1P36.11) WILD-TYPE   66  152
        clus
vv       DEL PEAK  2(1P36.11) MUTATED DEL PEAK  2(1P36.11) WILD-TYPE
  FEMALE                           47                             66
  MALE                             92                            152
[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                        135
  DEL PEAK  2(1P36.11) WILD-TYPE                      213
                                vv
clus                             HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK  2(1P36.11) MUTATED                                  4
  DEL PEAK  2(1P36.11) WILD-TYPE                                3
D31V8, multiclass
                                  clus
vv                                 DEL PEAK  2(1P36.11) MUTATED
  FIBROLAMELLAR CARCINOMA                                     0
  HEPATOCELLULAR CARCINOMA                                  135
  HEPATOCHOLANGIOCARCINOMA (MIXED)                            4
                                  clus
vv                                 DEL PEAK  2(1P36.11) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                       2
  HEPATOCELLULAR CARCINOMA                                    213
  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  2(1P36.11) MUTATED   120   9   1   8
  DEL PEAK  2(1P36.11) WILD-TYPE 195   6   0  11
D31V9, multiclass
    clus
vv   DEL PEAK  2(1P36.11) MUTATED DEL PEAK  2(1P36.11) WILD-TYPE
  R0                          120                            195
  R1                            9                              6
  R2                            1                              0
  RX                            8                             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  2(1P36.11) MUTATED                                  0    71
  DEL PEAK  2(1P36.11) WILD-TYPE                                1    85
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  2(1P36.11) MUTATED                           4    63
  DEL PEAK  2(1P36.11) WILD-TYPE                        13   110
D31V10, multiclass
                                  clus
vv                                 DEL PEAK  2(1P36.11) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                      71
  BLACK OR AFRICAN AMERICAN                                   4
  WHITE                                                      63
                                  clus
vv                                 DEL PEAK  2(1P36.11) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        85
  BLACK OR AFRICAN AMERICAN                                    13
  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"
D31V11, binary
                                cls
clus                               0   1
  DEL PEAK  2(1P36.11) MUTATED     3 133
  DEL PEAK  2(1P36.11) WILD-TYPE   8 196
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  2(1P36.11) MUTATED      3  133
  DEL PEAK  2(1P36.11) WILD-TYPE    8  196
                        clus
vv                       DEL PEAK  2(1P36.11) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                          133
                        clus
vv                       DEL PEAK  2(1P36.11) WILD-TYPE
  HISPANIC OR LATINO                                  8
  NOT HISPANIC OR LATINO                            196
[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    29  16
  DEL PEAK  3(2Q22.1) WILD-TYPE 196  93
  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                           45                           289 
  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                           16                            93 
$`DEL PEAK  3(2Q22.1) MUTATED`
TCGA-2Y-A9GU TCGA-2Y-A9H0 TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H6 TCGA-2Y-A9H8 
       63.75       120.82        47.74        18.25        11.74        20.81 
TCGA-3K-AAZ8 TCGA-4R-AA8I TCGA-5C-A9VG TCGA-BC-A10R TCGA-BC-A10Y TCGA-BC-A3KF 
       13.02         8.61        10.78        10.13        23.34         0.26 
TCGA-BD-A3EP TCGA-DD-A115 TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39Y TCGA-DD-A3A1 
       13.45        83.57        13.64        21.14         5.62         7.66 
TCGA-DD-A4NJ TCGA-DD-A73B TCGA-DD-AACE TCGA-DD-AACU TCGA-DD-AACZ TCGA-DD-AADI 
       30.51         9.30        63.48        51.52         5.62        35.67 
TCGA-DD-AADL TCGA-DD-AADN TCGA-DD-AADV TCGA-DD-AADW TCGA-DD-AAE2 TCGA-DD-AAE4 
       20.91        29.52        18.87        19.30        20.98        19.99 
TCGA-DD-AAE6 TCGA-DD-AAED TCGA-ED-A459 TCGA-ED-A66Y TCGA-ED-A7PZ TCGA-ED-A7XO 
        4.64        25.08        13.41         9.73         0.20        14.04 
TCGA-FV-A3I1 TCGA-G3-AAV7 TCGA-GJ-A9DB TCGA-KR-A7K2 TCGA-RC-A7SH TCGA-T1-A6J8 
        8.12         3.02         2.20        11.84        15.39         0.76 
TCGA-UB-A7MF TCGA-WQ-AB4B TCGA-ZP-A9D2 
        7.04        12.99        24.43 

$`DEL PEAK  3(2Q22.1) WILD-TYPE`
TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GV TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GY 
       23.80        53.39        83.24        41.79        80.28        24.89 
TCGA-2Y-A9GZ TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H7 TCGA-2Y-A9H9 
       27.88        40.41        56.91        41.33        37.25        14.99 
TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D 
        1.18         8.55        10.59         0.66        11.97        11.08 
TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10S TCGA-BC-A10T 
        1.51        48.99        27.91        37.32        46.78        27.52 
TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 
       27.52         2.99        25.32         1.12        69.57         5.03 
TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I 
       44.42        13.84        22.36        17.98        14.60        12.72 
TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3ER TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5260 
       18.48        44.81        36.66         0.66         0.07         2.86 
TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA 
        3.19         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        11.47        12.95 
TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A39W 
       45.11        49.15         6.02        33.04        18.35        27.19 
TCGA-DD-A39X TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 
       55.69        19.76        25.81        70.06        17.59        20.12 
TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA 
      102.74       107.11        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-A4NK 
       32.52        90.28        30.97        30.15        26.83        39.78 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR 
       56.25        29.56        73.81       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        23.93        23.05        22.78         1.45 
TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA 
       35.67       114.35        13.48         0.53        11.41        75.65 
TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH 
       76.41        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-AACN 
       53.19        69.11         0.30         3.52        58.16        42.81 
TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACV 
       61.68        13.64        14.20        59.31        51.35        50.33 
TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 
       46.82         5.59        47.67         4.50        18.54        21.63 
TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB 
       42.58        44.22        22.09        40.08        40.54        40.83 
TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADJ 
       13.97        40.47        39.52         3.78        37.64        35.05 
TCGA-DD-AADK TCGA-DD-AADM TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR 
       34.49         0.39        14.89        15.06        14.33        66.67 
TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE3 
       15.58        18.21        18.25        18.25        18.15        18.61 
TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAEE 
       21.17        21.83        23.74        18.90        15.72        16.37 
TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ 
       23.64        25.78        50.33        35.08        79.07        89.69 
TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY 
       82.62        59.93        72.39        76.18        56.48        64.77 
TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A4XI 
       62.47        66.25        65.39        49.48        53.69        12.69 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7XP 
       15.85        13.91        13.35         0.20        12.82        13.15 
TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S 
       13.41        13.35         1.84         0.20        18.74        19.99 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS 
       20.61        19.59         0.62         9.96        11.93        22.85 
TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R2 
       14.40        60.89        23.97        19.10        27.88         6.38 
TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S 
       12.03         0.03         0.33        81.73         0.39        13.68 
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 
       25.25        22.95        20.42        17.10         7.76        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-AAV5 TCGA-G3-AAV6 TCGA-GJ-A6C0 TCGA-HP-A5MZ 
        9.17         0.89         8.75         2.14         1.02         2.99 
TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 
       37.91        20.75        17.06        16.83         3.72         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        13.97        12.03         9.57 
TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO 
       16.67        18.38        12.85        20.71         0.62        10.85 
TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 
       58.88        19.92        17.69        21.01         3.09        21.04 
TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB 
       19.33        19.04        15.52        24.13        17.59        19.76 
TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WJ-A86L 
       16.44         1.71        15.98        10.75        10.32        11.34 
TCGA-WQ-A9G7 TCGA-WX-AA46 TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ 
        0.99        24.85        13.55        35.77        25.71        23.21 
TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CF 
       23.57         0.69        12.99        45.57        40.80        79.30 
TCGA-ZS-A9CG 
       11.21 

  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 
                       120.82                        114.35 
  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                        13.64                         19.76 
[1] "0.2 - 120.8 (13.6)" "0.0 - 114.3 (19.8)"
[1] "hr=" "1.4"
D32V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IIIA
  DEL PEAK  3(2Q22.1) MUTATED        23       14         0          9
  DEL PEAK  3(2Q22.1) WILD-TYPE     145       70         3         50
                               vv
clus                            STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK  3(2Q22.1) MUTATED            1          0        0         0
  DEL PEAK  3(2Q22.1) WILD-TYPE          7          7        3         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                             23                           145
  STAGE II                            14                            70
  STAGE III                            0                             3
  STAGE IIIA                           9                            50
  STAGE IIIB                           1                             7
  STAGE IIIC                           0                             7
  STAGE IV                             0                             3
  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      25  14  11   1
  DEL PEAK  3(2Q22.1) WILD-TYPE   154  77  62  11
D32V4, multiclass
       clus
vv      DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  T0+T1                          25                           154
  T2                             14                            77
  T3                             11                            62
  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    34   0
  DEL PEAK  3(2Q22.1) WILD-TYPE 215   3
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2Q22.1) MUTATED     34    0
  DEL PEAK  3(2Q22.1) WILD-TYPE  215    3
   clus
vv  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  0                          34                           215
  1                           0                             3
[1] 2 2
[1] FALSE
D32V6, binary
                               cls
clus                              0   1
  DEL PEAK  3(2Q22.1) MUTATED    36   0
  DEL PEAK  3(2Q22.1) WILD-TYPE 224   4
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2Q22.1) MUTATED     36    0
  DEL PEAK  3(2Q22.1) WILD-TYPE  224    4
   clus
vv  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  0                          36                           224
  1                           0                             4
[1] 2 2
[1] FALSE
D32V7, binary
                               cls
clus                              0   1
  DEL PEAK  3(2Q22.1) MUTATED    15  36
  DEL PEAK  3(2Q22.1) WILD-TYPE  98 208
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2Q22.1) MUTATED     15   36
  DEL PEAK  3(2Q22.1) WILD-TYPE   98  208
        clus
vv       DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  FEMALE                          15                            98
  MALE                            36                           208
[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                         50
  DEL PEAK  3(2Q22.1) WILD-TYPE                      298
                               vv
clus                            HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK  3(2Q22.1) MUTATED                                  1
  DEL PEAK  3(2Q22.1) WILD-TYPE                                6
D32V8, multiclass
                                  clus
vv                                 DEL PEAK  3(2Q22.1) MUTATED
  FIBROLAMELLAR CARCINOMA                                    0
  HEPATOCELLULAR CARCINOMA                                  50
  HEPATOCHOLANGIOCARCINOMA (MIXED)                           1
                                  clus
vv                                 DEL PEAK  3(2Q22.1) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                      2
  HEPATOCELLULAR CARCINOMA                                   298
  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  3(2Q22.1) MUTATED    47   0   0   4
  DEL PEAK  3(2Q22.1) WILD-TYPE 268  15   1  15
D32V9, multiclass
    clus
vv   DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  R0                          47                           268
  R1                           0                            15
  R2                           0                             1
  RX                           4                            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  3(2Q22.1) MUTATED                                  0    24
  DEL PEAK  3(2Q22.1) WILD-TYPE                                1   132
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  3(2Q22.1) MUTATED                           4    22
  DEL PEAK  3(2Q22.1) WILD-TYPE                        13   151
D32V10, multiclass
                                  clus
vv                                 DEL PEAK  3(2Q22.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                     24
  BLACK OR AFRICAN AMERICAN                                  4
  WHITE                                                     22
                                  clus
vv                                 DEL PEAK  3(2Q22.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                      132
  BLACK OR AFRICAN AMERICAN                                   13
  WHITE                                                      151
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V11, binary
                               cls
clus                              0   1
  DEL PEAK  3(2Q22.1) MUTATED     2  45
  DEL PEAK  3(2Q22.1) WILD-TYPE   9 284
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2Q22.1) MUTATED      2   45
  DEL PEAK  3(2Q22.1) WILD-TYPE    9  284
                        clus
vv                       DEL PEAK  3(2Q22.1) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          45
                        clus
vv                       DEL PEAK  3(2Q22.1) WILD-TYPE
  HISPANIC OR LATINO                                 9
  NOT HISPANIC OR LATINO                           284
[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    39  17
  DEL PEAK  4(2Q37.3) WILD-TYPE 186  92
  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                           56                           278 
  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                           17                            92 
$`DEL PEAK  4(2Q37.3) MUTATED`
TCGA-2Y-A9GU TCGA-2Y-A9GZ TCGA-2Y-A9H3 TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-BC-A10Y 
       63.75        27.88        41.33        13.02        10.78        23.34 
TCGA-BC-A216 TCGA-BC-A3KF TCGA-BC-A5W4 TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-A3M9 
       44.42         0.26        17.98        13.45         0.66         0.10 
TCGA-DD-A113 TCGA-DD-A115 TCGA-DD-A11A TCGA-DD-A11C TCGA-DD-A1EB TCGA-DD-A1EL 
       79.73        83.57         2.60        21.76        66.31        13.64 
TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A4NA TCGA-DD-A4NJ TCGA-DD-A4NQ TCGA-DD-A73B 
        5.62        19.76        33.14        30.51        12.26         9.30 
TCGA-DD-AACE TCGA-DD-AACO TCGA-DD-AACU TCGA-DD-AAD5 TCGA-DD-AADC TCGA-DD-AADF 
       63.48        61.68        51.52        44.22        13.97         3.78 
TCGA-DD-AADI TCGA-DD-AADL TCGA-DD-AADN TCGA-DD-AADP TCGA-DD-AAED TCGA-DD-AAEG 
       35.67        20.91        29.52        15.06        25.08        23.64 
TCGA-ED-A459 TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-FV-A3I0 
       13.41         9.73         0.20         0.20        14.04        27.88 
TCGA-FV-A3I1 TCGA-FV-A496 TCGA-G3-A5SI TCGA-G3-A7M9 TCGA-G3-AAV7 TCGA-GJ-A9DB 
        8.12         0.33        25.25         1.84         3.02         2.20 
TCGA-KR-A7K2 TCGA-RC-A7SH TCGA-RC-A7SK TCGA-T1-A6J8 TCGA-UB-A7MA TCGA-UB-A7MB 
       11.84        15.39        15.52         0.76        17.59        19.76 
TCGA-UB-A7MF TCGA-WQ-AB4B 
        7.04        12.99 

$`DEL PEAK  4(2Q37.3) WILD-TYPE`
TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GV TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GY 
       23.80        53.39        83.24        41.79        80.28        24.89 
TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H6 
      120.82        40.41        56.91        47.74        18.25        11.74 
TCGA-2Y-A9H7 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-4R-AA8I 
       37.25        20.81        14.99         1.18         8.55         8.61 
TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4072 
       10.59         0.66        11.97        11.08         1.51        48.99 
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
       27.91        37.32        10.13        46.78        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A217 
        2.99        25.32         1.12        69.57         5.03        13.84 
TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3ER 
       22.36        14.60        12.72        18.48        44.81        36.66 
TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT 
        0.07         2.86         3.19         3.39         4.24         3.32 
TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A114 TCGA-DD-A116 TCGA-DD-A118 
        0.07         0.10         0.13        37.78        53.33       113.00 
TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EC 
        7.33         0.46        51.29        90.71        79.40        19.79 
TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI 
       75.65        11.47        12.95        45.11        49.15         6.02 
TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A3A0 
       33.04        18.35        21.14        27.19        55.69        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-A3A9 TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NF 
       13.78         0.36        30.61        32.52        90.28        30.97 
TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO 
       30.15        26.83        39.78        56.25        29.56        73.81 
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        23.93        23.05 
TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 
       22.78         1.45        35.67       114.35        13.48         0.53 
TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACF 
       11.41        75.65        76.41        55.40        12.53        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        69.11         0.30         3.52 
TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT 
       58.16        42.81        13.64        14.20        59.31        51.35 
TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD0 
       50.33        46.82         5.59        47.67         5.62         4.50 
TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA 
       18.54        21.63        42.58        22.09        40.08        40.54 
TCGA-DD-AADB TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADG TCGA-DD-AADJ TCGA-DD-AADK 
       40.83        40.47        39.52        37.64        35.05        34.49 
TCGA-DD-AADM TCGA-DD-AADO TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU 
        0.39        14.89        14.33        66.67        15.58        18.21 
TCGA-DD-AADV TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 
       18.87        19.30        18.25        18.25        18.15        20.98 
TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAE9 
       18.61        19.99         4.64        21.17        21.83        23.74 
TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAEK 
       18.90        15.72        16.37        25.78        50.33        35.08 
TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW 
       79.07        89.69        82.62        59.93        72.39        76.18 
TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 
       56.48        64.77        62.47        66.25        65.39        49.48 
TCGA-DD-AAW3 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A7PY 
       53.69        12.69        15.85        13.91        13.35        12.82 
TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J 
       13.15        13.41        13.35         1.84         0.20        18.74 
TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK 
       19.99        20.61        19.59         0.62         9.96        11.93 
TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3R2 
       22.85        14.40        60.89        23.97        19.10         6.38 
TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T 
       12.03         0.03        81.73         0.39        13.68        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-A5SJ 
       22.13        25.64         5.92        19.53        19.23        22.95 
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-AAV5 
        8.55        11.80         9.70         9.17         0.89         8.75 
TCGA-G3-AAV6 TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG 
        2.14         1.02         2.99        37.91        20.75        17.06 
TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG 
       16.83         3.72         2.14        13.38        24.36        12.72 
TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H 
       13.97        12.03         9.57        16.67        18.38        12.85 
TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V 
       20.71         0.62        10.85        58.88        19.92        17.69 
TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RG-A7D4 
       21.01         3.09        21.04        19.33        19.04        24.13 
TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WJ-A86L 
       16.44         1.71        15.98        10.75        10.32        11.34 
TCGA-WQ-A9G7 TCGA-WX-AA46 TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ 
        0.99        24.85        13.55        35.77        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        40.80 
TCGA-ZS-A9CF TCGA-ZS-A9CG 
       79.30        11.21 

  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                        120.82 
  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                       15.225                        19.690 
[1] "0.1 - 83.6 (15.2)"  "0.0 - 120.8 (19.7)"
[1] "hr=" "1.2"
D33V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IIIA
  DEL PEAK  4(2Q37.3) MUTATED        25       19         0         11
  DEL PEAK  4(2Q37.3) WILD-TYPE     143       65         3         48
                               vv
clus                            STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK  4(2Q37.3) MUTATED            2          1        0         0
  DEL PEAK  4(2Q37.3) WILD-TYPE          6          6        3         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                             25                           143
  STAGE II                            19                            65
  STAGE III                            0                             3
  STAGE IIIA                          11                            48
  STAGE IIIB                           2                             6
  STAGE IIIC                           1                             6
  STAGE IV                             0                             3
  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      26  20  13   1
  DEL PEAK  4(2Q37.3) WILD-TYPE   153  71  60  11
D33V4, multiclass
       clus
vv      DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE
  T0+T1                          26                           153
  T2                             20                            71
  T3                             13                            60
  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    37   1
  DEL PEAK  4(2Q37.3) WILD-TYPE 212   2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q37.3) MUTATED     37    1
  DEL PEAK  4(2Q37.3) WILD-TYPE  212    2
   clus
vv  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE
  0                          37                           212
  1                           1                             2
[1] 2 2
[1] FALSE
D33V6, binary
                               cls
clus                              0   1
  DEL PEAK  4(2Q37.3) MUTATED    47   0
  DEL PEAK  4(2Q37.3) WILD-TYPE 213   4
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q37.3) MUTATED     47    0
  DEL PEAK  4(2Q37.3) WILD-TYPE  213    4
   clus
vv  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE
  0                          47                           213
  1                           0                             4
[1] 2 2
[1] FALSE
D33V7, binary
                               cls
clus                              0   1
  DEL PEAK  4(2Q37.3) MUTATED    20  40
  DEL PEAK  4(2Q37.3) WILD-TYPE  93 204
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q37.3) MUTATED     20   40
  DEL PEAK  4(2Q37.3) WILD-TYPE   93  204
        clus
vv       DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE
  FEMALE                          20                            93
  MALE                            40                           204
[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                         57
  DEL PEAK  4(2Q37.3) WILD-TYPE                      291
                               vv
clus                            HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK  4(2Q37.3) MUTATED                                  3
  DEL PEAK  4(2Q37.3) WILD-TYPE                                4
D33V8, multiclass
                                  clus
vv                                 DEL PEAK  4(2Q37.3) MUTATED
  FIBROLAMELLAR CARCINOMA                                    0
  HEPATOCELLULAR CARCINOMA                                  57
  HEPATOCHOLANGIOCARCINOMA (MIXED)                           3
                                  clus
vv                                 DEL PEAK  4(2Q37.3) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                      2
  HEPATOCELLULAR CARCINOMA                                   291
  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  4(2Q37.3) MUTATED    52   2   0   6
  DEL PEAK  4(2Q37.3) WILD-TYPE 263  13   1  13
D33V9, multiclass
    clus
vv   DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE
  R0                          52                           263
  R1                           2                            13
  R2                           0                             1
  RX                           6                            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  4(2Q37.3) MUTATED                                  0    26
  DEL PEAK  4(2Q37.3) WILD-TYPE                                1   130
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  4(2Q37.3) MUTATED                           5    27
  DEL PEAK  4(2Q37.3) WILD-TYPE                        12   146
D33V10, multiclass
                                  clus
vv                                 DEL PEAK  4(2Q37.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                     26
  BLACK OR AFRICAN AMERICAN                                  5
  WHITE                                                     27
                                  clus
vv                                 DEL PEAK  4(2Q37.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                      130
  BLACK OR AFRICAN AMERICAN                                   12
  WHITE                                                      146
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V11, binary
                               cls
clus                              0   1
  DEL PEAK  4(2Q37.3) MUTATED     3  51
  DEL PEAK  4(2Q37.3) WILD-TYPE   8 278
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q37.3) MUTATED      3   51
  DEL PEAK  4(2Q37.3) WILD-TYPE    8  278
                        clus
vv                       DEL PEAK  4(2Q37.3) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                          51
                        clus
vv                       DEL PEAK  4(2Q37.3) WILD-TYPE
  HISPANIC OR LATINO                                 8
  NOT HISPANIC OR LATINO                           278
[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    41  18
  DEL PEAK  5(3P13) WILD-TYPE 184  91
  DEL PEAK  5(3P13) MUTATED DEL PEAK  5(3P13) WILD-TYPE 
                         59                         275 
  DEL PEAK  5(3P13) MUTATED DEL PEAK  5(3P13) WILD-TYPE 
                         18                          91 
$`DEL PEAK  5(3P13) MUTATED`
TCGA-2Y-A9GY TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H5 TCGA-3K-AAZ8 TCGA-5C-A9VG 
       24.89        56.91        41.33        18.25        13.02        10.78 
TCGA-5C-AAPD TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A112 TCGA-BC-A217 TCGA-CC-5260 
        0.66        37.32        10.13         5.03        13.84         2.86 
TCGA-CC-5263 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-DD-A113 TCGA-DD-A11A TCGA-DD-A1E9 
        4.24         0.07         0.10        79.73         2.60        90.71 
TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NO TCGA-DD-A73G 
       30.61        33.14        30.15        26.83        73.81       114.35 
TCGA-DD-AA3A TCGA-DD-AACO TCGA-DD-AAD2 TCGA-DD-AADC TCGA-DD-AADJ TCGA-DD-AADO 
       13.48        61.68        21.63        13.97        35.05        14.89 
TCGA-DD-AADY TCGA-DD-AAE3 TCGA-DD-AAVQ TCGA-DD-AAVU TCGA-ED-A66Y TCGA-ED-A7PX 
       18.25        18.61        89.69        72.39         9.73         0.20 
TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A82E TCGA-ED-A97K TCGA-EP-A2KA TCGA-FV-A3I0 
        0.20        14.04        13.41         0.20        20.61        27.88 
TCGA-FV-A3R3 TCGA-G3-A25T TCGA-G3-A25X TCGA-G3-AAV1 TCGA-G3-AAV6 TCGA-KR-A7K2 
       12.03        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        13.97        15.39        16.44         1.71         7.04 
TCGA-WQ-AB4B TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZS-A9CE TCGA-ZS-A9CF 
       12.99        23.57         0.69        40.80        79.30 

$`DEL PEAK  5(3P13) WILD-TYPE`
TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GV TCGA-2Y-A9GW TCGA-2Y-A9GX 
       23.80        53.39        63.75        83.24        41.79        80.28 
TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H4 TCGA-2Y-A9H6 TCGA-2Y-A9H7 
       27.88       120.82        40.41        47.74        11.74        37.25 
TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-4R-AA8I TCGA-5C-A9VH 
       20.81        14.99         1.18         8.55         8.61        10.59 
TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10S 
       11.97        11.08         1.51        48.99        27.91        46.78 
TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z 
       27.52        27.52         2.99        25.32        23.34         1.12 
TCGA-BC-A110 TCGA-BC-A216 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H 
       69.57        44.42         0.26        22.36        17.98        14.60 
TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BD-A3ER TCGA-BW-A5NO 
       12.72        18.48        44.81        13.45        36.66         0.66 
TCGA-CC-5258 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MC 
        0.07         3.19         3.39         3.32         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-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-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ 
       11.47        12.95        45.11        49.15         6.02        33.04 
TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Y 
       18.35        13.64        21.14        27.19        55.69         5.62 
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-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        90.28 
TCGA-DD-A4NF TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NP 
       30.97        30.51        39.78        56.25        29.56       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        23.93         9.30 
TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-AAC8 TCGA-DD-AAC9 
       23.05        22.78         1.45        35.67         0.53        11.41 
TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF 
       75.65        76.41        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        69.11         0.30         3.52 
TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT 
       58.16        42.81        13.64        14.20        59.31        51.35 
TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AACZ 
       51.52        50.33        46.82         5.59        47.67         5.62 
TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 
        4.50        18.54        42.58        44.22        22.09        40.08 
TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG 
       40.54        40.83        40.47        39.52         3.78        37.64 
TCGA-DD-AADI TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADP 
       35.67        34.49        20.91         0.39        29.52        15.06 
TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADV TCGA-DD-AADW 
       14.33        66.67        15.58        18.21        18.87        19.30 
TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE7 
       18.25        18.15        20.98        19.99         4.64        21.17 
TCGA-DD-AAE8 TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE 
       21.83        23.74        18.90        15.72        25.08        16.37 
TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVR 
       23.64        25.78        50.33        35.08        79.07        82.62 
TCGA-DD-AAVS TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 
       59.93        76.18        56.48        64.77        62.47        66.25 
TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG 
       65.39        49.48        53.69        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        12.82        13.15        13.35         1.84 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK 
       18.74        19.99        19.59         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        60.89        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        81.73         0.39        13.68 
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        25.25        22.95 
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-AAV5 
       11.24         8.55         9.70         9.17         0.89         8.75 
TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF 
        3.02         1.02         2.20         2.99        37.91        20.75 
TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K8 TCGA-LG-A6GG 
       17.06        16.83         3.72         2.14        24.36        12.72 
TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I 
       12.03         9.57        16.67        18.38        12.85        20.71 
TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF 
        0.62        10.85        58.88        19.92        17.69        21.01 
TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SK TCGA-RG-A7D4 
        3.09        21.04        19.33        19.04        15.52        24.13 
TCGA-T1-A6J8 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7ME TCGA-UB-AA0U TCGA-UB-AA0V 
        0.76        17.59        19.76        15.98        10.75        10.32 
TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WX-AA46 TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY 
       11.34         0.99        24.85        13.55        35.77        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        11.21 

  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 
                     114.35                      120.82 
  DEL PEAK  5(3P13) MUTATED DEL PEAK  5(3P13) WILD-TYPE 
                      14.89                       19.76 
[1] "0.1 - 114.3 (14.9)" "0.0 - 120.8 (19.8)"
[1] "hr=" "1"  
D34V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  5(3P13) MUTATED        20       20         0         16          3
  DEL PEAK  5(3P13) WILD-TYPE     148       64         3         43          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        2         1         1
D34V3, multiclass
            clus
vv           DEL PEAK  5(3P13) MUTATED DEL PEAK  5(3P13) WILD-TYPE
  STAGE I                           20                         148
  STAGE II                          20                          64
  STAGE III                          0                           3
  STAGE IIIA                        16                          43
  STAGE IIIB                         3                           5
  STAGE IIIC                         3                           4
  STAGE IV                           1                           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  5(3P13) MUTATED      22  23  20   4
  DEL PEAK  5(3P13) WILD-TYPE   157  68  53   8
D34V4, multiclass
       clus
vv      DEL PEAK  5(3P13) MUTATED DEL PEAK  5(3P13) WILD-TYPE
  T0+T1                        22                         157
  T2                           23                          68
  T3                           20                          53
  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    47   1
  DEL PEAK  5(3P13) WILD-TYPE 202   2
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  5(3P13) MUTATED     47    1
  DEL PEAK  5(3P13) WILD-TYPE  202    2
   clus
vv  DEL PEAK  5(3P13) MUTATED DEL PEAK  5(3P13) WILD-TYPE
  0                        47                         202
  1                         1                           2
[1] 2 2
[1] FALSE
D34V6, binary
                             cls
clus                            0   1
  DEL PEAK  5(3P13) MUTATED    48   2
  DEL PEAK  5(3P13) WILD-TYPE 212   2
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  5(3P13) MUTATED     48    2
  DEL PEAK  5(3P13) WILD-TYPE  212    2
   clus
vv  DEL PEAK  5(3P13) MUTATED DEL PEAK  5(3P13) WILD-TYPE
  0                        48                         212
  1                         2                           2
[1] 2 2
[1] FALSE
D34V7, binary
                             cls
clus                            0   1
  DEL PEAK  5(3P13) MUTATED    30  39
  DEL PEAK  5(3P13) WILD-TYPE  83 205
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  5(3P13) MUTATED     30   39
  DEL PEAK  5(3P13) WILD-TYPE   83  205
        clus
vv       DEL PEAK  5(3P13) MUTATED DEL PEAK  5(3P13) WILD-TYPE
  FEMALE                        30                          83
  MALE                          39                         205
[1] 2 2
[1] FALSE
                             vv
clus                          FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  DEL PEAK  5(3P13) MUTATED                         0                       64
  DEL PEAK  5(3P13) WILD-TYPE                       2                      284
                             vv
clus                          HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK  5(3P13) MUTATED                                  5
  DEL PEAK  5(3P13) WILD-TYPE                                2
D34V8, multiclass
                                  clus
vv                                 DEL PEAK  5(3P13) MUTATED
  FIBROLAMELLAR CARCINOMA                                  0
  HEPATOCELLULAR CARCINOMA                                64
  HEPATOCHOLANGIOCARCINOMA (MIXED)                         5
                                  clus
vv                                 DEL PEAK  5(3P13) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                    2
  HEPATOCELLULAR CARCINOMA                                 284
  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  5(3P13) MUTATED    64   1   0   4
  DEL PEAK  5(3P13) WILD-TYPE 251  14   1  15
D34V9, multiclass
    clus
vv   DEL PEAK  5(3P13) MUTATED DEL PEAK  5(3P13) WILD-TYPE
  R0                        64                         251
  R1                         1                          14
  R2                         0                           1
  RX                         4                          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  5(3P13) MUTATED                                  0    32
  DEL PEAK  5(3P13) WILD-TYPE                                1   124
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  5(3P13) MUTATED                           4    33
  DEL PEAK  5(3P13) WILD-TYPE                        13   140
D34V10, multiclass
                                  clus
vv                                 DEL PEAK  5(3P13) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         0
  ASIAN                                                   32
  BLACK OR AFRICAN AMERICAN                                4
  WHITE                                                   33
                                  clus
vv                                 DEL PEAK  5(3P13) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                    124
  BLACK OR AFRICAN AMERICAN                                 13
  WHITE                                                    140
[1] 4 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     2  64
  DEL PEAK  5(3P13) WILD-TYPE   9 265
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  5(3P13) MUTATED      2   64
  DEL PEAK  5(3P13) WILD-TYPE    9  265
                        clus
vv                       DEL PEAK  5(3P13) MUTATED DEL PEAK  5(3P13) WILD-TYPE
  HISPANIC OR LATINO                             2                           9
  NOT HISPANIC OR LATINO                        64                         265
[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    43  25
  DEL PEAK  6(4P16.3) WILD-TYPE 182  84
  DEL PEAK  6(4P16.3) MUTATED DEL PEAK  6(4P16.3) WILD-TYPE 
                           68                           266 
  DEL PEAK  6(4P16.3) MUTATED DEL PEAK  6(4P16.3) WILD-TYPE 
                           25                            84 
$`DEL PEAK  6(4P16.3) MUTATED`
TCGA-2Y-A9GS TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-5C-AAPD TCGA-BC-A10Y TCGA-BC-A112 
       23.80        13.02        10.78         0.66        23.34         5.03 
TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BW-A5NO TCGA-CC-A3MC TCGA-DD-A114 TCGA-DD-A119 
       17.98        14.60         0.66         0.13        37.78         7.33 
TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A4NI TCGA-DD-A4NJ 
        6.02        33.04        55.69         5.62        26.83        30.51 
TCGA-DD-A4NN TCGA-DD-A73A TCGA-DD-AAC8 TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG 
       29.56        23.93         0.53        63.48        12.00        15.42 
TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACP TCGA-DD-AACU TCGA-DD-AACY TCGA-DD-AAD5 
       58.16        42.81        13.64        51.52        47.67        44.22 
TCGA-DD-AAD8 TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADV TCGA-DD-AAE8 TCGA-DD-AAED 
       40.08        13.97        40.47        18.87        21.83        25.08 
TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVQ TCGA-DD-AAVU TCGA-ED-A459 TCGA-ED-A7XO 
       50.33        35.08        89.69        72.39        13.41        14.04 
TCGA-ED-A8O6 TCGA-EP-A2KB TCGA-EP-A2KC TCGA-FV-A2QQ TCGA-FV-A4ZP TCGA-G3-A25S 
        1.84        19.59         0.62        23.97        81.73        13.68 
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 
       37.91        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        16.44        15.98         7.04        12.99        13.55 
TCGA-ZP-A9D2 TCGA-ZS-A9CE 
       24.43        40.80 

$`DEL PEAK  6(4P16.3) WILD-TYPE`
TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GV TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GY 
       53.39        63.75        83.24        41.79        80.28        24.89 
TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H4 
       27.88       120.82        40.41        56.91        41.33        47.74 
TCGA-2Y-A9H5 TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA 
       18.25        11.74        37.25        20.81        14.99         1.18 
TCGA-2Y-A9HB TCGA-4R-AA8I TCGA-5C-A9VH TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM 
        8.55         8.61        10.59        11.97        11.08         1.51 
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T 
       48.99        27.91        37.32        10.13        46.78        27.52 
TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A216 
       27.52         2.99        25.32         1.12        69.57        44.42 
TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A2L6 
       13.84         0.26        22.36        12.72        18.48        44.81 
TCGA-BD-A3EP TCGA-BD-A3ER TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
       13.45        36.66         0.07         2.86         3.19         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-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C 
       83.57        53.33       113.00         2.60         0.46        21.76 
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-A1EH TCGA-DD-A1EK TCGA-DD-A1EL 
       11.47        12.95        45.11        49.15        18.35        13.64 
TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 
       21.14        27.19        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        90.28        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        23.05        22.78         1.45 
TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB 
       35.67       114.35        13.48        11.41        75.65        76.41 
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        69.11         0.30 
TCGA-DD-AACL TCGA-DD-AACO TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACV 
        3.52        61.68        14.20        59.31        51.35        50.33 
TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 
       46.82         5.59         5.62         4.50        18.54        21.63 
TCGA-DD-AAD3 TCGA-DD-AAD6 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADE TCGA-DD-AADF 
       42.58        22.09        40.54        40.83        39.52         3.78 
TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM 
       37.64        35.67        35.05        34.49        20.91         0.39 
TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS 
       29.52        14.89        15.06        14.33        66.67        15.58 
TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 
       18.21        19.30        18.25        18.25        18.15        20.98 
TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAE9 TCGA-DD-AAEA 
       18.61        19.99         4.64        21.17        23.74        18.90 
TCGA-DD-AAEB TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAVP TCGA-DD-AAVR 
       15.72        16.37        23.64        25.78        79.07        82.62 
TCGA-DD-AAVS TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 
       59.93        76.18        56.48        64.77        62.47        66.25 
TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 
       65.39        49.48        53.69        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         9.73         0.20        12.82         0.20        13.15 
TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
       13.41        13.35         0.20        18.74        19.99        20.61 
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        60.89        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        12.03         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        25.25        22.95 
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-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 
        8.55         9.70         9.17         8.75         2.14         3.02 
TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-K7-A5RF TCGA-K7-A6G5 TCGA-K7-AAU7 
        1.02         2.20         2.99        20.75        16.83         3.72 
TCGA-KR-A7K0 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C 
        2.14        24.36        12.72        13.97        12.03         9.57 
TCGA-MI-A75E TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 
       16.67        12.85        20.71         0.62        10.85        58.88 
TCGA-NI-A8LF TCGA-O8-A75V TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF 
       19.92        17.69         3.09        21.04        19.33        19.04 
TCGA-RC-A7SH TCGA-RC-A7SK TCGA-T1-A6J8 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MD 
       15.39        15.52         0.76        17.59        19.76         1.71 
TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WX-AA46 TCGA-ZP-A9CV 
       10.75        10.32        11.34         0.99        24.85        35.77 
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 
       79.30        11.21 

  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 
                        89.69                        120.82 
  DEL PEAK  6(4P16.3) MUTATED DEL PEAK  6(4P16.3) WILD-TYPE 
                       19.230                        19.265 
[1] "0.1 - 89.7 (19.2)"  "0.0 - 120.8 (19.3)"
[1] "hr=" "1.3"
D35V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IIIA
  DEL PEAK  6(4P16.3) MUTATED        32       18         0         18
  DEL PEAK  6(4P16.3) WILD-TYPE     136       66         3         41
                               vv
clus                            STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK  6(4P16.3) MUTATED            2          2        3         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                             32                           136
  STAGE II                            18                            66
  STAGE III                            0                             3
  STAGE IIIA                          18                            41
  STAGE IIIB                           2                             6
  STAGE IIIC                           2                             5
  STAGE IV                             3                             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      34  21  21   3
  DEL PEAK  6(4P16.3) WILD-TYPE   145  70  52   9
D35V4, multiclass
       clus
vv      DEL PEAK  6(4P16.3) MUTATED DEL PEAK  6(4P16.3) WILD-TYPE
  T0+T1                          34                           145
  T2                             21                            70
  T3                             21                            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"
D35V5, binary
                               cls
clus                              0   1
  DEL PEAK  6(4P16.3) MUTATED    55   2
  DEL PEAK  6(4P16.3) WILD-TYPE 194   1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(4P16.3) MUTATED     55    2
  DEL PEAK  6(4P16.3) WILD-TYPE  194    1
   clus
vv  DEL PEAK  6(4P16.3) MUTATED DEL PEAK  6(4P16.3) WILD-TYPE
  0                          55                           194
  1                           2                             1
[1] 2 2
[1] FALSE
D35V6, binary
                               cls
clus                              0   1
  DEL PEAK  6(4P16.3) MUTATED    61   2
  DEL PEAK  6(4P16.3) WILD-TYPE 199   2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(4P16.3) MUTATED     61    2
  DEL PEAK  6(4P16.3) WILD-TYPE  199    2
   clus
vv  DEL PEAK  6(4P16.3) MUTATED DEL PEAK  6(4P16.3) WILD-TYPE
  0                          61                           199
  1                           2                             2
[1] 2 2
[1] FALSE
D35V7, binary
                               cls
clus                              0   1
  DEL PEAK  6(4P16.3) MUTATED    16  64
  DEL PEAK  6(4P16.3) WILD-TYPE  97 180
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(4P16.3) MUTATED     16   64
  DEL PEAK  6(4P16.3) WILD-TYPE   97  180
        clus
vv       DEL PEAK  6(4P16.3) MUTATED DEL PEAK  6(4P16.3) WILD-TYPE
  FEMALE                          16                            97
  MALE                            64                           180
[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                         78
  DEL PEAK  6(4P16.3) WILD-TYPE                      270
                               vv
clus                            HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK  6(4P16.3) MUTATED                                  2
  DEL PEAK  6(4P16.3) WILD-TYPE                                5
D35V8, multiclass
                                  clus
vv                                 DEL PEAK  6(4P16.3) MUTATED
  FIBROLAMELLAR CARCINOMA                                    0
  HEPATOCELLULAR CARCINOMA                                  78
  HEPATOCHOLANGIOCARCINOMA (MIXED)                           2
                                  clus
vv                                 DEL PEAK  6(4P16.3) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                      2
  HEPATOCELLULAR CARCINOMA                                   270
  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  6(4P16.3) MUTATED    70   3   1   5
  DEL PEAK  6(4P16.3) WILD-TYPE 245  12   0  14
D35V9, multiclass
    clus
vv   DEL PEAK  6(4P16.3) MUTATED DEL PEAK  6(4P16.3) WILD-TYPE
  R0                          70                           245
  R1                           3                            12
  R2                           1                             0
  RX                           5                            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  6(4P16.3) MUTATED                                  0    43
  DEL PEAK  6(4P16.3) WILD-TYPE                                1   113
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  6(4P16.3) MUTATED                           6    29
  DEL PEAK  6(4P16.3) WILD-TYPE                        11   144
D35V10, multiclass
                                  clus
vv                                 DEL PEAK  6(4P16.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                     43
  BLACK OR AFRICAN AMERICAN                                  6
  WHITE                                                     29
                                  clus
vv                                 DEL PEAK  6(4P16.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                      113
  BLACK OR AFRICAN AMERICAN                                   11
  WHITE                                                      144
[1] 4 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     4  73
  DEL PEAK  6(4P16.3) WILD-TYPE   7 256
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(4P16.3) MUTATED      4   73
  DEL PEAK  6(4P16.3) WILD-TYPE    7  256
                        clus
vv                       DEL PEAK  6(4P16.3) MUTATED
  HISPANIC OR LATINO                               4
  NOT HISPANIC OR LATINO                          73
                        clus
vv                       DEL PEAK  6(4P16.3) WILD-TYPE
  HISPANIC OR LATINO                                 7
  NOT HISPANIC OR LATINO                           256
[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    99  48
  DEL PEAK  7(4Q21.3) WILD-TYPE 126  61
  DEL PEAK  7(4Q21.3) MUTATED DEL PEAK  7(4Q21.3) WILD-TYPE 
                          147                           187 
  DEL PEAK  7(4Q21.3) MUTATED DEL PEAK  7(4Q21.3) WILD-TYPE 
                           48                            61 
$`DEL PEAK  7(4Q21.3) MUTATED`
TCGA-2Y-A9GS TCGA-2Y-A9GV TCGA-2Y-A9GY TCGA-2Y-A9H0 TCGA-2Y-A9H2 TCGA-2Y-A9H3 
       23.80        83.24        24.89       120.82        56.91        41.33 
TCGA-2Y-A9H8 TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-BC-A10T 
       20.81        13.02        10.78        10.59         0.66        27.52 
TCGA-BC-A10U TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A112 TCGA-BC-A217 TCGA-BC-A3KF 
       27.52        23.34         1.12         5.03        13.84         0.26 
TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5258 
       17.98        14.60        44.81        13.45         0.66         0.07 
TCGA-CC-5261 TCGA-CC-5263 TCGA-CC-A3M9 TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 
        3.19         4.24         0.10         0.10         0.13        79.73 
TCGA-DD-A114 TCGA-DD-A116 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A1EB TCGA-DD-A1EF 
       37.78        53.33         7.33         2.60        66.31        12.95 
TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39X 
       45.11        49.15         6.02        33.04        13.64        55.69 
TCGA-DD-A39Y TCGA-DD-A3A5 TCGA-DD-A3A9 TCGA-DD-A4ND TCGA-DD-A4NH TCGA-DD-A4NI 
        5.62       102.74        30.61        90.28        30.15        26.83 
TCGA-DD-A4NJ TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NQ TCGA-DD-A73B TCGA-DD-A73G 
       30.51        29.56        73.81        12.26         9.30       114.35 
TCGA-DD-AAC8 TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG 
        0.53        76.41        55.40        63.48        12.00        15.42 
TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACP TCGA-DD-AACS TCGA-DD-AACU 
        3.52        58.16        42.81        13.64        59.31        51.52 
TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACZ TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD8 
       50.33        46.82         5.62        42.58        44.22        40.08 
TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADI TCGA-DD-AADL TCGA-DD-AADO 
       40.83        13.97        40.47        35.67        20.91        14.89 
TCGA-DD-AADP TCGA-DD-AADR TCGA-DD-AADV TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 
       15.06        66.67        18.87        18.25        18.25        18.15 
TCGA-DD-AAE6 TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAED TCGA-DD-AAEK TCGA-DD-AAVQ 
        4.64        21.83        18.90        25.08        35.08        89.69 
TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-ED-A459 
       59.93        72.39        76.18        62.47        66.25        13.41 
TCGA-ED-A66X TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP 
       13.35         0.20        12.82         0.20        14.04        13.15 
TCGA-ED-A8O5 TCGA-ED-A97K TCGA-EP-A2KB TCGA-EP-A2KC TCGA-FV-A2QQ TCGA-FV-A3I1 
       13.35         0.20        19.59         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        81.73        13.68        58.49        14.86        21.53 
TCGA-G3-A5SI TCGA-G3-A5SM TCGA-G3-A7M9 TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 
       25.25        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        37.91        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        13.97        18.38 
TCGA-O8-A75V TCGA-RC-A7SB TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-T1-A6J8 
       17.69        19.33        15.39        15.52        24.13         0.76 
TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7ME TCGA-UB-A7MF TCGA-WQ-A9G7 TCGA-WQ-AB4B 
       19.76        16.44        15.98         7.04         0.99        12.99 
TCGA-YA-A8S7 TCGA-ZP-A9D2 TCGA-ZS-A9CE 
       13.55        24.43        40.80 

$`DEL PEAK  7(4Q21.3) WILD-TYPE`
TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GZ TCGA-2Y-A9H1 
       53.39        63.75        41.79        80.28        27.88        40.41 
TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-2Y-A9H9 TCGA-2Y-A9HA 
       47.74        18.25        11.74        37.25        14.99         1.18 
TCGA-2Y-A9HB TCGA-4R-AA8I TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4072 
        8.55         8.61        11.97        11.08         1.51        48.99 
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10W TCGA-BC-A10X 
       27.91        37.32        10.13        46.78         2.99        25.32 
TCGA-BC-A110 TCGA-BC-A216 TCGA-BC-A3KG TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A3ER 
       69.57        44.42        22.36        12.72        18.48        36.66 
TCGA-CC-5260 TCGA-CC-5262 TCGA-CC-A1HT TCGA-CC-A3MA TCGA-DD-A115 TCGA-DD-A118 
        2.86         3.39         3.32         0.07        83.57       113.00 
TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EC 
        0.46        21.76        51.29        90.71        79.40        19.79 
TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EK TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39Z 
       75.65        11.47        18.35        21.14        27.19        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-A4NA TCGA-DD-A4NB TCGA-DD-A4NF TCGA-DD-A4NK 
       13.78         0.36        33.14        32.52        30.97        39.78 
TCGA-DD-A4NL TCGA-DD-A4NP TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A 
       56.25       108.76         0.30        80.75        78.84        23.93 
TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-AA3A TCGA-DD-AAC9 
       23.05        22.78         1.45        35.67        13.48        11.41 
TCGA-DD-AACA TCGA-DD-AACD TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK 
       75.65        12.53         6.41        53.19        69.11         0.30 
TCGA-DD-AACO TCGA-DD-AACQ TCGA-DD-AACT TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AAD0 
       61.68        14.20        51.35         5.59        47.67         4.50 
TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD6 TCGA-DD-AADA TCGA-DD-AADE TCGA-DD-AADF 
       18.54        21.63        22.09        40.54        39.52         3.78 
TCGA-DD-AADG TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADQ 
       37.64        35.05        34.49         0.39        29.52        14.33 
TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 
       15.58        18.21        19.30        20.98        18.61        19.99 
TCGA-DD-AAE7 TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEH 
       21.17        23.74        15.72        16.37        23.64        25.78 
TCGA-DD-AAEI TCGA-DD-AAVP TCGA-DD-AAVR TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAW1 
       50.33        79.07        82.62        56.48        64.77        65.39 
TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66Y 
       49.48        53.69        12.69        15.85        13.91         9.73 
TCGA-ED-A82E TCGA-ED-A8O6 TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A3JL 
       13.41         1.84        18.74        19.99        20.61         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        60.89        19.10        27.88 
TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25U 
        6.38        12.03         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        22.95        20.42         7.76        12.03         5.98 
TCGA-G3-AAUZ TCGA-G3-AAV3 TCGA-G3-AAV5 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-K7-A5RF 
       11.24         9.17         8.75         2.20         2.99        20.75 
TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E 
       16.83         3.72         2.14        12.03         9.57        16.67 
TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF 
       12.85        20.71         0.62        10.85        58.88        19.92 
TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SF TCGA-UB-A7MA TCGA-UB-A7MD 
       21.01         3.09        21.04        19.04        17.59         1.71 
TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WX-AA46 TCGA-ZP-A9CV TCGA-ZP-A9CY 
       10.75        10.32        11.34        24.85        35.77        25.71 
TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CF 
       23.21        23.57         0.69        12.99        45.57        79.30 
TCGA-ZS-A9CG 
       11.21 

  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 
                       120.82                        113.00 
  DEL PEAK  7(4Q21.3) MUTATED DEL PEAK  7(4Q21.3) WILD-TYPE 
                        17.98                         19.99 
[1] "0.1 - 120.8 (18.0)" "0.0 - 113.0 (20.0)"
[1] "hr=" "1"  
D36V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IIIA
  DEL PEAK  7(4Q21.3) MUTATED        72       43         2         28
  DEL PEAK  7(4Q21.3) WILD-TYPE      96       41         1         31
                               vv
clus                            STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK  7(4Q21.3) MUTATED            4          2        3         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                             72                            96
  STAGE II                            43                            41
  STAGE III                            2                             1
  STAGE IIIA                          28                            31
  STAGE IIIB                           4                             4
  STAGE IIIC                           2                             5
  STAGE IV                             3                             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      76  47  36   5
  DEL PEAK  7(4Q21.3) WILD-TYPE   103  44  37   7
D36V4, multiclass
       clus
vv      DEL PEAK  7(4Q21.3) MUTATED DEL PEAK  7(4Q21.3) WILD-TYPE
  T0+T1                          76                           103
  T2                             47                            44
  T3                             36                            37
  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   118   2
  DEL PEAK  7(4Q21.3) WILD-TYPE 131   1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(4Q21.3) MUTATED    118    2
  DEL PEAK  7(4Q21.3) WILD-TYPE  131    1
   clus
vv  DEL PEAK  7(4Q21.3) MUTATED DEL PEAK  7(4Q21.3) WILD-TYPE
  0                         118                           131
  1                           2                             1
[1] 2 2
[1] FALSE
D36V6, binary
                               cls
clus                              0   1
  DEL PEAK  7(4Q21.3) MUTATED   131   3
  DEL PEAK  7(4Q21.3) WILD-TYPE 129   1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(4Q21.3) MUTATED    131    3
  DEL PEAK  7(4Q21.3) WILD-TYPE  129    1
   clus
vv  DEL PEAK  7(4Q21.3) MUTATED DEL PEAK  7(4Q21.3) WILD-TYPE
  0                         131                           129
  1                           3                             1
[1] 2 2
[1] FALSE
D36V7, binary
                               cls
clus                              0   1
  DEL PEAK  7(4Q21.3) MUTATED    49 116
  DEL PEAK  7(4Q21.3) WILD-TYPE  64 128
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(4Q21.3) MUTATED     49  116
  DEL PEAK  7(4Q21.3) WILD-TYPE   64  128
        clus
vv       DEL PEAK  7(4Q21.3) MUTATED DEL PEAK  7(4Q21.3) WILD-TYPE
  FEMALE                          49                            64
  MALE                           116                           128
[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                        162
  DEL PEAK  7(4Q21.3) WILD-TYPE                      186
                               vv
clus                            HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK  7(4Q21.3) MUTATED                                  3
  DEL PEAK  7(4Q21.3) WILD-TYPE                                4
D36V8, multiclass
                                  clus
vv                                 DEL PEAK  7(4Q21.3) MUTATED
  FIBROLAMELLAR CARCINOMA                                    0
  HEPATOCELLULAR CARCINOMA                                 162
  HEPATOCHOLANGIOCARCINOMA (MIXED)                           3
                                  clus
vv                                 DEL PEAK  7(4Q21.3) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                      2
  HEPATOCELLULAR CARCINOMA                                   186
  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  7(4Q21.3) MUTATED   148   6   1  10
  DEL PEAK  7(4Q21.3) WILD-TYPE 167   9   0   9
D36V9, multiclass
    clus
vv   DEL PEAK  7(4Q21.3) MUTATED DEL PEAK  7(4Q21.3) WILD-TYPE
  R0                         148                           167
  R1                           6                             9
  R2                           1                             0
  RX                          10                             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  7(4Q21.3) MUTATED                                  0    88
  DEL PEAK  7(4Q21.3) WILD-TYPE                                1    68
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  7(4Q21.3) MUTATED                           9    64
  DEL PEAK  7(4Q21.3) WILD-TYPE                         8   109
D36V10, multiclass
                                  clus
vv                                 DEL PEAK  7(4Q21.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                     88
  BLACK OR AFRICAN AMERICAN                                  9
  WHITE                                                     64
                                  clus
vv                                 DEL PEAK  7(4Q21.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                       68
  BLACK OR AFRICAN AMERICAN                                    8
  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"
D36V11, binary
                               cls
clus                              0   1
  DEL PEAK  7(4Q21.3) MUTATED     8 149
  DEL PEAK  7(4Q21.3) WILD-TYPE   3 180
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(4Q21.3) MUTATED      8  149
  DEL PEAK  7(4Q21.3) WILD-TYPE    3  180
                        clus
vv                       DEL PEAK  7(4Q21.3) MUTATED
  HISPANIC OR LATINO                               8
  NOT HISPANIC OR LATINO                         149
                        clus
vv                       DEL PEAK  7(4Q21.3) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           180
[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    99  49
  DEL PEAK  8(4Q22.3) WILD-TYPE 126  60
  DEL PEAK  8(4Q22.3) MUTATED DEL PEAK  8(4Q22.3) WILD-TYPE 
                          148                           186 
  DEL PEAK  8(4Q22.3) MUTATED DEL PEAK  8(4Q22.3) WILD-TYPE 
                           49                            60 
$`DEL PEAK  8(4Q22.3) MUTATED`
TCGA-2Y-A9GS TCGA-2Y-A9GV TCGA-2Y-A9GY TCGA-2Y-A9H0 TCGA-2Y-A9H2 TCGA-2Y-A9H3 
       23.80        83.24        24.89       120.82        56.91        41.33 
TCGA-2Y-A9H8 TCGA-2Y-A9HA TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD 
       20.81         1.18        13.02        10.78        10.59         0.66 
TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A112 TCGA-BC-A217 
       27.52        27.52        23.34         1.12         5.03        13.84 
TCGA-BC-A3KF TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5258 
        0.26        17.98        14.60        13.45         0.66         0.07 
TCGA-CC-5261 TCGA-CC-5263 TCGA-CC-A3M9 TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 
        3.19         4.24         0.10         0.10         0.13        79.73 
TCGA-DD-A114 TCGA-DD-A116 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11C TCGA-DD-A1EB 
       37.78        53.33         7.33         2.60        21.76        66.31 
TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EL 
       12.95        45.11        49.15         6.02        33.04        13.64 
TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A3A0 TCGA-DD-A3A5 TCGA-DD-A3A9 TCGA-DD-A4ND 
       55.69         5.62        25.81       102.74        30.61        90.28 
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-A73G TCGA-DD-AAC8 TCGA-DD-AACB TCGA-DD-AACC 
        9.30        35.67       114.35         0.53        76.41        55.40 
TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN 
       63.48        12.00        15.42         3.52        58.16        42.81 
TCGA-DD-AACP TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACZ 
       13.64        59.31        51.52        50.33        46.82         5.62 
TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD8 TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD 
       42.58        44.22        40.08        40.83        13.97        40.47 
TCGA-DD-AADI TCGA-DD-AADL TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADR TCGA-DD-AADV 
       35.67        20.91        14.89        15.06        66.67        18.87 
TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE6 TCGA-DD-AAE8 TCGA-DD-AAEA 
       18.25        18.25        18.15         4.64        21.83        18.90 
TCGA-DD-AAED TCGA-DD-AAEK TCGA-DD-AAVQ TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW 
       25.08        35.08        89.69        59.93        72.39        76.18 
TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-ED-A459 TCGA-ED-A66X TCGA-ED-A7PX TCGA-ED-A7PY 
       62.47        66.25        13.41        13.35         0.20        12.82 
TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A8O5 TCGA-ED-A97K TCGA-EP-A2KB 
        0.20        14.04        13.15        13.35         0.20        19.59 
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        81.73        13.68 
TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A5SI TCGA-G3-A5SM TCGA-G3-A7M9 
       58.49        14.86        21.53        25.25        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        37.91 
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        13.97 
TCGA-MI-A75G TCGA-O8-A75V TCGA-RC-A7SB TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 
       18.38        17.69        19.33        15.39        15.52        24.13 
TCGA-T1-A6J8 TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7ME TCGA-UB-A7MF TCGA-WQ-A9G7 
        0.76        19.76        16.44        15.98         7.04         0.99 
TCGA-WQ-AB4B TCGA-YA-A8S7 TCGA-ZP-A9D2 TCGA-ZS-A9CE 
       12.99        13.55        24.43        40.80 

$`DEL PEAK  8(4Q22.3) WILD-TYPE`
TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GZ TCGA-2Y-A9H1 
       53.39        63.75        41.79        80.28        27.88        40.41 
TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-2Y-A9H9 TCGA-2Y-A9HB 
       47.74        18.25        11.74        37.25        14.99         8.55 
TCGA-4R-AA8I TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-4073 
        8.61        11.97        11.08         1.51        48.99        27.91 
TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A110 
       37.32        10.13        46.78         2.99        25.32        69.57 
TCGA-BC-A216 TCGA-BC-A3KG TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3ER 
       44.42        22.36        12.72        18.48        44.81        36.66 
TCGA-CC-5260 TCGA-CC-5262 TCGA-CC-A1HT TCGA-CC-A3MA TCGA-DD-A115 TCGA-DD-A118 
        2.86         3.39         3.32         0.07        83.57       113.00 
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-A1EK TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39Z TCGA-DD-A3A1 
       11.47        18.35        21.14        27.19        19.76         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-A4NA TCGA-DD-A4NB TCGA-DD-A4NF TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NP 
       33.14        32.52        30.97        39.78        56.25       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        23.93        23.05        22.78 
TCGA-DD-A73E TCGA-DD-AA3A TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACD TCGA-DD-AACH 
        1.45        13.48        11.41        75.65        12.53         6.41 
TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACO TCGA-DD-AACQ TCGA-DD-AACT 
       53.19        69.11         0.30        61.68        14.20        51.35 
TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD6 
        5.59        47.67         4.50        18.54        21.63        22.09 
TCGA-DD-AADA TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADJ TCGA-DD-AADK 
       40.54        39.52         3.78        37.64        35.05        34.49 
TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADQ TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW 
        0.39        29.52        14.33        15.58        18.21        19.30 
TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE7 TCGA-DD-AAE9 TCGA-DD-AAEB 
       20.98        18.61        19.99        21.17        23.74        15.72 
TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAVP TCGA-DD-AAVR 
       16.37        23.64        25.78        50.33        79.07        82.62 
TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A4XI 
       56.48        64.77        65.39        49.48        53.69        12.69 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66Y TCGA-ED-A82E TCGA-ED-A8O6 TCGA-EP-A12J 
       15.85        13.91         9.73        13.41         1.84        18.74 
TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT 
       19.99        20.61         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 
       60.89        19.10        27.88         6.38        12.03         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        22.95        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-G3-AAV5 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-K7-A5RF TCGA-K7-A6G5 
        8.75         1.02         2.20         2.99        20.75        16.83 
TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75H 
        3.72         2.14        12.03         9.57        16.67        12.85 
TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-PD-A5DF 
       20.71         0.62        10.85        58.88        19.92        21.01 
TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SF TCGA-UB-A7MA TCGA-UB-A7MD TCGA-UB-AA0U 
        3.09        21.04        19.04        17.59         1.71        10.75 
TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WX-AA46 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ 
       10.32        11.34        24.85        35.77        25.71        23.21 
TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CF TCGA-ZS-A9CG 
       23.57         0.69        12.99        45.57        79.30        11.21 

  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 
                       120.82                        113.00 
  DEL PEAK  8(4Q22.3) MUTATED DEL PEAK  8(4Q22.3) WILD-TYPE 
                       18.200                        19.955 
[1] "0.1 - 120.8 (18.2)" "0.0 - 113.0 (20.0)"
[1] "hr=" "1"  
D37V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IIIA
  DEL PEAK  8(4Q22.3) MUTATED        74       43         2         28
  DEL PEAK  8(4Q22.3) WILD-TYPE      94       41         1         31
                               vv
clus                            STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK  8(4Q22.3) MUTATED            4          2        3         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                             74                            94
  STAGE II                            43                            41
  STAGE III                            2                             1
  STAGE IIIA                          28                            31
  STAGE IIIB                           4                             4
  STAGE IIIC                           2                             5
  STAGE IV                             3                             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      78  46  36   5
  DEL PEAK  8(4Q22.3) WILD-TYPE   101  45  37   7
D37V4, multiclass
       clus
vv      DEL PEAK  8(4Q22.3) MUTATED DEL PEAK  8(4Q22.3) WILD-TYPE
  T0+T1                          78                           101
  T2                             46                            45
  T3                             36                            37
  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   119   2
  DEL PEAK  8(4Q22.3) WILD-TYPE 130   1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(4Q22.3) MUTATED    119    2
  DEL PEAK  8(4Q22.3) WILD-TYPE  130    1
   clus
vv  DEL PEAK  8(4Q22.3) MUTATED DEL PEAK  8(4Q22.3) WILD-TYPE
  0                         119                           130
  1                           2                             1
[1] 2 2
[1] FALSE
D37V6, binary
                               cls
clus                              0   1
  DEL PEAK  8(4Q22.3) MUTATED   133   3
  DEL PEAK  8(4Q22.3) WILD-TYPE 127   1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(4Q22.3) MUTATED    133    3
  DEL PEAK  8(4Q22.3) WILD-TYPE  127    1
   clus
vv  DEL PEAK  8(4Q22.3) MUTATED DEL PEAK  8(4Q22.3) WILD-TYPE
  0                         133                           127
  1                           3                             1
[1] 2 2
[1] FALSE
D37V7, binary
                               cls
clus                              0   1
  DEL PEAK  8(4Q22.3) MUTATED    49 117
  DEL PEAK  8(4Q22.3) WILD-TYPE  64 127
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(4Q22.3) MUTATED     49  117
  DEL PEAK  8(4Q22.3) WILD-TYPE   64  127
        clus
vv       DEL PEAK  8(4Q22.3) MUTATED DEL PEAK  8(4Q22.3) WILD-TYPE
  FEMALE                          49                            64
  MALE                           117                           127
[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                        163
  DEL PEAK  8(4Q22.3) WILD-TYPE                      185
                               vv
clus                            HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK  8(4Q22.3) MUTATED                                  3
  DEL PEAK  8(4Q22.3) WILD-TYPE                                4
D37V8, multiclass
                                  clus
vv                                 DEL PEAK  8(4Q22.3) MUTATED
  FIBROLAMELLAR CARCINOMA                                    0
  HEPATOCELLULAR CARCINOMA                                 163
  HEPATOCHOLANGIOCARCINOMA (MIXED)                           3
                                  clus
vv                                 DEL PEAK  8(4Q22.3) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                      2
  HEPATOCELLULAR CARCINOMA                                   185
  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  8(4Q22.3) MUTATED   149   6   1  10
  DEL PEAK  8(4Q22.3) WILD-TYPE 166   9   0   9
D37V9, multiclass
    clus
vv   DEL PEAK  8(4Q22.3) MUTATED DEL PEAK  8(4Q22.3) WILD-TYPE
  R0                         149                           166
  R1                           6                             9
  R2                           1                             0
  RX                          10                             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  8(4Q22.3) MUTATED                                  0    87
  DEL PEAK  8(4Q22.3) WILD-TYPE                                1    69
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  8(4Q22.3) MUTATED                           9    66
  DEL PEAK  8(4Q22.3) WILD-TYPE                         8   107
D37V10, multiclass
                                  clus
vv                                 DEL PEAK  8(4Q22.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                     87
  BLACK OR AFRICAN AMERICAN                                  9
  WHITE                                                     66
                                  clus
vv                                 DEL PEAK  8(4Q22.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                       69
  BLACK OR AFRICAN AMERICAN                                    8
  WHITE                                                      107
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V11, binary
                               cls
clus                              0   1
  DEL PEAK  8(4Q22.3) MUTATED     8 151
  DEL PEAK  8(4Q22.3) WILD-TYPE   3 178
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(4Q22.3) MUTATED      8  151
  DEL PEAK  8(4Q22.3) WILD-TYPE    3  178
                        clus
vv                       DEL PEAK  8(4Q22.3) MUTATED
  HISPANIC OR LATINO                               8
  NOT HISPANIC OR LATINO                         151
                        clus
vv                       DEL PEAK  8(4Q22.3) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           178
[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    98  53
  DEL PEAK  9(4Q35.1) WILD-TYPE 127  56
  DEL PEAK  9(4Q35.1) MUTATED DEL PEAK  9(4Q35.1) WILD-TYPE 
                          151                           183 
  DEL PEAK  9(4Q35.1) MUTATED DEL PEAK  9(4Q35.1) WILD-TYPE 
                           53                            56 
$`DEL PEAK  9(4Q35.1) MUTATED`
TCGA-2Y-A9GS TCGA-2Y-A9GY TCGA-2Y-A9H0 TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H8 
       23.80        24.89       120.82        56.91        41.33        20.81 
TCGA-2Y-A9HA TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-BC-A10R 
        1.18        13.02        10.78        10.59         0.66        10.13 
TCGA-BC-A10T TCGA-BC-A10W TCGA-BC-A10Z TCGA-BC-A112 TCGA-BC-A217 TCGA-BC-A3KF 
       27.52         2.99         1.12         5.03        13.84         0.26 
TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5258 
       22.36        17.98        14.60        13.45         0.66         0.07 
TCGA-CC-5261 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC 
        3.19         3.32         0.10         0.07         0.10         0.13 
TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A116 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B 
       79.73        37.78        53.33         7.33         2.60         0.46 
TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EL 
       12.95        45.11        49.15         6.02        33.04        13.64 
TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A3A0 TCGA-DD-A3A2 TCGA-DD-A3A9 
       27.19        55.69         5.62        25.81        70.06        30.61 
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-AAC8 TCGA-DD-AAC9 TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACE TCGA-DD-AACF 
        0.53        11.41        76.41        55.40        63.48        12.00 
TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN 
       15.42         6.41        53.19         3.52        58.16        42.81 
TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW 
       13.64        14.20        59.31        51.52        50.33        46.82 
TCGA-DD-AACZ TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD8 TCGA-DD-AADB 
        5.62        21.63        42.58        44.22        40.08        40.83 
TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADI TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM 
       13.97        40.47        35.67        34.49        20.91         0.39 
TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADR TCGA-DD-AADV TCGA-DD-AADW TCGA-DD-AADY 
       14.89        15.06        66.67        18.87        19.30        18.25 
TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE6 TCGA-DD-AAE8 TCGA-DD-AAEB TCGA-DD-AAEE 
       18.25        18.15         4.64        21.83        15.72        16.37 
TCGA-DD-AAEK TCGA-DD-AAVQ TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVY 
       35.08        89.69        59.93        72.39        76.18        64.77 
TCGA-DD-AAW0 TCGA-ED-A459 TCGA-ED-A66X TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO 
       66.25        13.41        13.35        12.82         0.20        14.04 
TCGA-ED-A7XP TCGA-ED-A8O5 TCGA-ED-A97K TCGA-EP-A2KB TCGA-EP-A2KC TCGA-FV-A2QQ 
       13.15        13.35         0.20        19.59         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        81.73        13.68        58.49 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A5SI TCGA-G3-A5SM TCGA-G3-A7M9 TCGA-G3-AAV1 
       14.86        21.53        25.25        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-A7SB 
       13.97        18.38        20.71        58.88        19.92        19.33 
TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-T1-A6J8 TCGA-UB-A7MB TCGA-UB-A7MC 
       15.39        15.52        24.13         0.76        19.76        16.44 
TCGA-UB-A7ME TCGA-UB-A7MF TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-YA-A8S7 TCGA-ZP-A9D2 
       15.98         7.04         0.99        12.99        13.55        24.43 
TCGA-ZS-A9CE 
       40.80 

$`DEL PEAK  9(4Q35.1) WILD-TYPE`
TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GV TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GZ 
       53.39        63.75        83.24        41.79        80.28        27.88 
TCGA-2Y-A9H1 TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-2Y-A9H9 
       40.41        47.74        18.25        11.74        37.25        14.99 
TCGA-2Y-A9HB TCGA-4R-AA8I TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4072 
        8.55         8.61        11.97        11.08         1.51        48.99 
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10S TCGA-BC-A10U TCGA-BC-A10X TCGA-BC-A10Y 
       27.91        37.32        46.78        27.52        25.32        23.34 
TCGA-BC-A110 TCGA-BC-A216 TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3ER 
       69.57        44.42        12.72        18.48        44.81        36.66 
TCGA-CC-5260 TCGA-CC-5262 TCGA-CC-5263 TCGA-DD-A115 TCGA-DD-A118 TCGA-DD-A11C 
        2.86         3.39         4.24        83.57       113.00        21.76 
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-A1EK TCGA-DD-A39V TCGA-DD-A39Z TCGA-DD-A3A1 TCGA-DD-A3A3 
       11.47        18.35        21.14        19.76         7.66        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-A4ND TCGA-DD-A4NF TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NP 
       32.52        90.28        30.97        39.78        56.25       108.76 
TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73C 
       12.26         0.30        80.75        78.84        23.93        23.05 
TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AACA 
       22.78         1.45        35.67       114.35        13.48        75.65 
TCGA-DD-AACD TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACO TCGA-DD-AACT TCGA-DD-AACX 
       12.53        69.11         0.30        61.68        51.35         5.59 
TCGA-DD-AACY TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD6 TCGA-DD-AADA TCGA-DD-AADE 
       47.67         4.50        18.54        22.09        40.54        39.52 
TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADJ TCGA-DD-AADN TCGA-DD-AADQ TCGA-DD-AADS 
        3.78        37.64        35.05        29.52        14.33        15.58 
TCGA-DD-AADU TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE7 TCGA-DD-AAE9 
       18.21        20.98        18.61        19.99        21.17        23.74 
TCGA-DD-AAEA TCGA-DD-AAED TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAVP 
       18.90        25.08        23.64        25.78        50.33        79.07 
TCGA-DD-AAVR TCGA-DD-AAVX TCGA-DD-AAVZ TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 
       82.62        56.48        62.47        65.39        49.48        53.69 
TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A82E 
       12.69        15.85        13.91         9.73         0.20        13.41 
TCGA-ED-A8O6 TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A3JL TCGA-EP-A3RK 
        1.84        18.74        19.99        20.61         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        60.89        27.88         6.38        12.03 
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        22.95 
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-G3-AAV5 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ 
        9.70         9.17         8.75         1.02         2.20         2.99 
TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K8 
       37.91        20.75        16.83         3.72         2.14        24.36 
TCGA-LG-A6GG TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75H TCGA-MR-A520 
       12.72        12.03         9.57        16.67        12.85         0.62 
TCGA-MR-A8JO TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SF 
       10.85        17.69        21.01         3.09        21.04        19.04 
TCGA-UB-A7MA TCGA-UB-A7MD TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WX-AA46 
       17.59         1.71        10.75        10.32        11.34        24.85 
TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D4 
       35.77        25.71        23.21        23.57         0.69        12.99 
TCGA-ZS-A9CD TCGA-ZS-A9CF TCGA-ZS-A9CG 
       45.57        79.30        11.21 

  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 
                       120.82                        114.35 
  DEL PEAK  9(4Q35.1) MUTATED DEL PEAK  9(4Q35.1) WILD-TYPE 
                        17.06                         20.75 
[1] "0.1 - 120.8 (17.1)" "0.0 - 114.3 (20.8)"
[1] "hr=" "1.4"
D38V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IIIA
  DEL PEAK  9(4Q35.1) MUTATED        71       46         2         31
  DEL PEAK  9(4Q35.1) WILD-TYPE      97       38         1         28
                               vv
clus                            STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK  9(4Q35.1) MUTATED            3          2        3         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                             71                            97
  STAGE II                            46                            38
  STAGE III                            2                             1
  STAGE IIIA                          31                            28
  STAGE IIIB                           3                             5
  STAGE IIIC                           2                             5
  STAGE IV                             3                             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      75  49  40   4
  DEL PEAK  9(4Q35.1) WILD-TYPE   104  42  33   8
D38V4, multiclass
       clus
vv      DEL PEAK  9(4Q35.1) MUTATED DEL PEAK  9(4Q35.1) WILD-TYPE
  T0+T1                          75                           104
  T2                             49                            42
  T3                             40                            33
  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   123   2
  DEL PEAK  9(4Q35.1) WILD-TYPE 126   1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(4Q35.1) MUTATED    123    2
  DEL PEAK  9(4Q35.1) WILD-TYPE  126    1
   clus
vv  DEL PEAK  9(4Q35.1) MUTATED DEL PEAK  9(4Q35.1) WILD-TYPE
  0                         123                           126
  1                           2                             1
[1] 2 2
[1] FALSE
D38V6, binary
                               cls
clus                              0   1
  DEL PEAK  9(4Q35.1) MUTATED   134   3
  DEL PEAK  9(4Q35.1) WILD-TYPE 126   1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(4Q35.1) MUTATED    134    3
  DEL PEAK  9(4Q35.1) WILD-TYPE  126    1
   clus
vv  DEL PEAK  9(4Q35.1) MUTATED DEL PEAK  9(4Q35.1) WILD-TYPE
  0                         134                           126
  1                           3                             1
[1] 2 2
[1] FALSE
D38V7, binary
                               cls
clus                              0   1
  DEL PEAK  9(4Q35.1) MUTATED    45 123
  DEL PEAK  9(4Q35.1) WILD-TYPE  68 121
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(4Q35.1) MUTATED     45  123
  DEL PEAK  9(4Q35.1) WILD-TYPE   68  121
        clus
vv       DEL PEAK  9(4Q35.1) MUTATED DEL PEAK  9(4Q35.1) WILD-TYPE
  FEMALE                          45                            68
  MALE                           123                           121
[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                        165
  DEL PEAK  9(4Q35.1) WILD-TYPE                      183
                               vv
clus                            HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK  9(4Q35.1) MUTATED                                  3
  DEL PEAK  9(4Q35.1) WILD-TYPE                                4
D38V8, multiclass
                                  clus
vv                                 DEL PEAK  9(4Q35.1) MUTATED
  FIBROLAMELLAR CARCINOMA                                    0
  HEPATOCELLULAR CARCINOMA                                 165
  HEPATOCHOLANGIOCARCINOMA (MIXED)                           3
                                  clus
vv                                 DEL PEAK  9(4Q35.1) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                      2
  HEPATOCELLULAR CARCINOMA                                   183
  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  9(4Q35.1) MUTATED   151   5   1  10
  DEL PEAK  9(4Q35.1) WILD-TYPE 164  10   0   9
D38V9, multiclass
    clus
vv   DEL PEAK  9(4Q35.1) MUTATED DEL PEAK  9(4Q35.1) WILD-TYPE
  R0                         151                           164
  R1                           5                            10
  R2                           1                             0
  RX                          10                             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  9(4Q35.1) MUTATED                                  0    95
  DEL PEAK  9(4Q35.1) WILD-TYPE                                1    61
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  9(4Q35.1) MUTATED                          10    63
  DEL PEAK  9(4Q35.1) WILD-TYPE                         7   110
D38V10, multiclass
                                  clus
vv                                 DEL PEAK  9(4Q35.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                     95
  BLACK OR AFRICAN AMERICAN                                 10
  WHITE                                                     63
                                  clus
vv                                 DEL PEAK  9(4Q35.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                       61
  BLACK OR AFRICAN AMERICAN                                    7
  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"
D38V11, binary
                               cls
clus                              0   1
  DEL PEAK  9(4Q35.1) MUTATED     6 158
  DEL PEAK  9(4Q35.1) WILD-TYPE   5 171
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(4Q35.1) MUTATED      6  158
  DEL PEAK  9(4Q35.1) WILD-TYPE    5  171
                        clus
vv                       DEL PEAK  9(4Q35.1) MUTATED
  HISPANIC OR LATINO                               6
  NOT HISPANIC OR LATINO                         158
                        clus
vv                       DEL PEAK  9(4Q35.1) WILD-TYPE
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                           171
[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    83  44
  DEL PEAK 10(6Q27) WILD-TYPE 142  65
  DEL PEAK 10(6Q27) MUTATED DEL PEAK 10(6Q27) WILD-TYPE 
                        127                         207 
  DEL PEAK 10(6Q27) MUTATED DEL PEAK 10(6Q27) WILD-TYPE 
                         44                          65 
$`DEL PEAK 10(6Q27) MUTATED`
TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H2 TCGA-2Y-A9H5 TCGA-2Y-A9H6 TCGA-2Y-A9H7 
       27.88       120.82        56.91        18.25        11.74        37.25 
TCGA-2Y-A9H8 TCGA-2Y-A9HA TCGA-4R-AA8I TCGA-5R-AA1C TCGA-5R-AAAM TCGA-BC-A10Q 
       20.81         1.18         8.61        11.97         1.51        37.32 
TCGA-BC-A3KF TCGA-BC-A5W4 TCGA-BC-A69I TCGA-BD-A3ER TCGA-CC-5260 TCGA-CC-A1HT 
        0.26        17.98        12.72        36.66         2.86         3.32 
TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MC TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A118 
        0.10         0.07         0.13        37.78        83.57       113.00 
TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11C TCGA-DD-A1E9 TCGA-DD-A1EE TCGA-DD-A1EG 
        7.33         2.60        21.76        90.71        11.47        45.11 
TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A39X TCGA-DD-A39Z 
       49.15         6.02        33.04        18.35        55.69        19.76 
TCGA-DD-A3A0 TCGA-DD-A3A8 TCGA-DD-A4NA TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK 
       25.81         0.36        33.14        30.15        30.51        39.78 
TCGA-DD-A4NN TCGA-DD-A4NS TCGA-DD-A73E TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AACB 
       29.56        80.75         1.45        13.48         0.53        76.41 
TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACP TCGA-DD-AACU 
       12.53        63.48         6.41        53.19        13.64        51.52 
TCGA-DD-AACW TCGA-DD-AACY TCGA-DD-AAD0 TCGA-DD-AAD3 TCGA-DD-AAD8 TCGA-DD-AADF 
       46.82        47.67         4.50        42.58        40.08         3.78 
TCGA-DD-AADG TCGA-DD-AADJ TCGA-DD-AADL TCGA-DD-AADN TCGA-DD-AADP TCGA-DD-AADQ 
       37.64        35.05        20.91        29.52        15.06        14.33 
TCGA-DD-AADR TCGA-DD-AADV TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE2 TCGA-DD-AAE3 
       66.67        18.87        19.30        18.25        20.98        18.61 
TCGA-DD-AAE9 TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAEK TCGA-DD-AAVS 
       23.74        16.37        23.64        25.78        35.08        59.93 
TCGA-DD-AAVU TCGA-DD-AAVY TCGA-DD-AAW0 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 
       72.39        64.77        66.25        49.48        53.69        13.41 
TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PZ TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 
        9.73         0.20         0.20        13.41        13.35         1.84 
TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A3RK TCGA-ES-A2HS TCGA-FV-A23B TCGA-FV-A2QR 
        0.20        18.74        11.93        22.85        60.89        19.10 
TCGA-FV-A3I0 TCGA-FV-A3R2 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-G3-A25S TCGA-G3-A25T 
       27.88         6.38         0.33        81.73        13.68        51.06 
TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A3CG TCGA-G3-A5SL TCGA-G3-A6UC TCGA-G3-A7M9 
       58.49        14.86        22.13        20.42         7.76         1.84 
TCGA-G3-AAV1 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV6 TCGA-HP-A5N0 TCGA-LG-A6GG 
       11.80         9.17         0.89         2.14        37.91        12.72 
TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-NI-A8LF TCGA-RC-A7SK 
       16.67        18.38        12.85        20.71        19.92        15.52 
TCGA-T1-A6J8 TCGA-UB-A7MB TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WJ-A86L TCGA-ZS-A9CE 
        0.76        19.76        15.98        10.75        11.34        40.80 
TCGA-ZS-A9CF 
       79.30 

$`DEL PEAK 10(6Q27) WILD-TYPE`
TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GV TCGA-2Y-A9GW TCGA-2Y-A9GX 
       23.80        53.39        63.75        83.24        41.79        80.28 
TCGA-2Y-A9GY TCGA-2Y-A9H1 TCGA-2Y-A9H3 TCGA-2Y-A9H4 TCGA-2Y-A9H9 TCGA-2Y-A9HB 
       24.89        40.41        41.33        47.74        14.99         8.55 
TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1D TCGA-BC-4072 
       13.02        10.78        10.59         0.66        11.08        48.99 
TCGA-BC-4073 TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W 
       27.91        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-A217 TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP 
       13.84        22.36        14.60        18.48        44.81        13.45 
TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A3MB 
        0.66         0.07         3.19         3.39         4.24         0.10 
TCGA-DD-A113 TCGA-DD-A116 TCGA-DD-A11B TCGA-DD-A11D TCGA-DD-A1EA TCGA-DD-A1EB 
       79.73        53.33         0.46        51.29        79.40        66.31 
TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EF TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W 
       19.79        75.65        12.95        13.64        21.14        27.19 
TCGA-DD-A39Y TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 
        5.62         7.66        70.06        17.59        20.12       102.74 
TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NF 
      107.11        13.78        30.61        32.52        90.28        30.97 
TCGA-DD-A4NI TCGA-DD-A4NL TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR 
       26.83        56.25        73.81       108.76        12.26         0.30 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73F 
       78.84        23.93         9.30        23.05        22.78        35.67 
TCGA-DD-A73G TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACC TCGA-DD-AACF TCGA-DD-AACG 
      114.35        11.41        75.65        55.40        12.00        15.42 
TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO 
       69.11         0.30         3.52        58.16        42.81        61.68 
TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACV TCGA-DD-AACX TCGA-DD-AACZ 
       14.20        59.31        51.35        50.33         5.59         5.62 
TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AADA TCGA-DD-AADB 
       18.54        21.63        44.22        22.09        40.54        40.83 
TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADI TCGA-DD-AADK TCGA-DD-AADM 
       13.97        40.47        39.52        35.67        34.49         0.39 
TCGA-DD-AADO TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE4 
       14.89        15.58        18.21        18.25        18.15        19.99 
TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAED 
        4.64        21.17        21.83        18.90        15.72        25.08 
TCGA-DD-AAEI TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVW TCGA-DD-AAVX 
       50.33        79.07        89.69        82.62        76.18        56.48 
TCGA-DD-AAVZ TCGA-DD-AAW1 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X 
       62.47        65.39        12.69        15.85        13.91        13.35 
TCGA-ED-A7PY TCGA-ED-A7XO TCGA-ED-A7XP TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB 
       12.82        14.04        13.15        19.99        20.61        19.59 
TCGA-EP-A2KC TCGA-EP-A3JL TCGA-ES-A2HT TCGA-FV-A2QQ TCGA-FV-A3I1 TCGA-FV-A3R3 
        0.62         9.96        14.40        23.97         8.12        12.03 
TCGA-FV-A495 TCGA-FV-A4ZQ TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Z 
        0.03         0.39        53.79        28.27        30.74        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        25.25        22.95 
TCGA-G3-A5SM TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV2 
       17.10        12.03         5.98        11.24         8.55         9.70 
TCGA-G3-AAV5 TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-K7-A5RF 
        8.75         3.02         1.02         2.20         2.99        20.75 
TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 
       17.06        16.83         3.72         2.14        11.84        13.38 
TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MR-A520 TCGA-MR-A8JO 
       24.36        13.97        12.03         9.57         0.62        10.85 
TCGA-NI-A4U2 TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SB 
       58.88        17.69        21.01         3.09        21.04        19.33 
TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MC TCGA-UB-A7MD 
       19.04        15.39        24.13        17.59        16.44         1.71 
TCGA-UB-A7MF TCGA-UB-AA0V TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA46 TCGA-YA-A8S7 
        7.04        10.32         0.99        12.99        24.85        13.55 
TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D2 
       35.77        25.71        23.21        23.57         0.69        24.43 
TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CG 
       12.99        45.57        11.21 

  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 
                     120.82                      114.35 
  DEL PEAK 10(6Q27) MUTATED DEL PEAK 10(6Q27) WILD-TYPE 
                      19.10                       19.33 
[1] "0.1 - 120.8 (19.1)" "0.0 - 114.3 (19.3)"
[1] "hr=" "1.1"
D39V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 10(6Q27) MUTATED        61       32         1         23          3
  DEL PEAK 10(6Q27) WILD-TYPE     107       52         2         36          5
                             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        1         1         1
D39V3, multiclass
            clus
vv           DEL PEAK 10(6Q27) MUTATED DEL PEAK 10(6Q27) WILD-TYPE
  STAGE I                           61                         107
  STAGE II                          32                          52
  STAGE III                          1                           2
  STAGE IIIA                        23                          36
  STAGE IIIB                         3                           5
  STAGE IIIC                         5                           2
  STAGE IV                           2                           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 10(6Q27) MUTATED      64  35  28   4
  DEL PEAK 10(6Q27) WILD-TYPE   115  56  45   8
D39V4, multiclass
       clus
vv      DEL PEAK 10(6Q27) MUTATED DEL PEAK 10(6Q27) WILD-TYPE
  T0+T1                        64                         115
  T2                           35                          56
  T3                           28                          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"
D39V5, binary
                             cls
clus                            0   1
  DEL PEAK 10(6Q27) MUTATED    93   2
  DEL PEAK 10(6Q27) WILD-TYPE 156   1
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 10(6Q27) MUTATED     93    2
  DEL PEAK 10(6Q27) WILD-TYPE  156    1
   clus
vv  DEL PEAK 10(6Q27) MUTATED DEL PEAK 10(6Q27) WILD-TYPE
  0                        93                         156
  1                         2                           1
[1] 2 2
[1] FALSE
D39V6, binary
                             cls
clus                            0   1
  DEL PEAK 10(6Q27) MUTATED   103   3
  DEL PEAK 10(6Q27) WILD-TYPE 157   1
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 10(6Q27) MUTATED    103    3
  DEL PEAK 10(6Q27) WILD-TYPE  157    1
   clus
vv  DEL PEAK 10(6Q27) MUTATED DEL PEAK 10(6Q27) WILD-TYPE
  0                       103                         157
  1                         3                           1
[1] 2 2
[1] FALSE
D39V7, binary
                             cls
clus                            0   1
  DEL PEAK 10(6Q27) MUTATED    47  86
  DEL PEAK 10(6Q27) WILD-TYPE  66 158
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 10(6Q27) MUTATED     47   86
  DEL PEAK 10(6Q27) WILD-TYPE   66  158
        clus
vv       DEL PEAK 10(6Q27) MUTATED DEL PEAK 10(6Q27) WILD-TYPE
  FEMALE                        47                          66
  MALE                          86                         158
[1] 2 2
[1] FALSE
                             vv
clus                          FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  DEL PEAK 10(6Q27) MUTATED                         0                      130
  DEL PEAK 10(6Q27) WILD-TYPE                       2                      218
                             vv
clus                          HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK 10(6Q27) MUTATED                                  3
  DEL PEAK 10(6Q27) WILD-TYPE                                4
D39V8, multiclass
                                  clus
vv                                 DEL PEAK 10(6Q27) MUTATED
  FIBROLAMELLAR CARCINOMA                                  0
  HEPATOCELLULAR CARCINOMA                               130
  HEPATOCHOLANGIOCARCINOMA (MIXED)                         3
                                  clus
vv                                 DEL PEAK 10(6Q27) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                    2
  HEPATOCELLULAR CARCINOMA                                 218
  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 10(6Q27) MUTATED   119   6   1   5
  DEL PEAK 10(6Q27) WILD-TYPE 196   9   0  14
D39V9, multiclass
    clus
vv   DEL PEAK 10(6Q27) MUTATED DEL PEAK 10(6Q27) WILD-TYPE
  R0                       119                         196
  R1                         6                           9
  R2                         1                           0
  RX                         5                          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 10(6Q27) MUTATED                                  0    62
  DEL PEAK 10(6Q27) WILD-TYPE                                1    94
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 10(6Q27) MUTATED                           4    65
  DEL PEAK 10(6Q27) WILD-TYPE                        13   108
D39V10, multiclass
                                  clus
vv                                 DEL PEAK 10(6Q27) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         0
  ASIAN                                                   62
  BLACK OR AFRICAN AMERICAN                                4
  WHITE                                                   65
                                  clus
vv                                 DEL PEAK 10(6Q27) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                     94
  BLACK OR AFRICAN AMERICAN                                 13
  WHITE                                                    108
[1] 4 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     2 126
  DEL PEAK 10(6Q27) WILD-TYPE   9 203
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 10(6Q27) MUTATED      2  126
  DEL PEAK 10(6Q27) WILD-TYPE    9  203
                        clus
vv                       DEL PEAK 10(6Q27) MUTATED DEL PEAK 10(6Q27) WILD-TYPE
  HISPANIC OR LATINO                             2                           9
  NOT HISPANIC OR LATINO                       126                         203
[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   152  73
  DEL PEAK 11(8P23.2) WILD-TYPE  73  36
  DEL PEAK 11(8P23.2) MUTATED DEL PEAK 11(8P23.2) WILD-TYPE 
                          225                           109 
  DEL PEAK 11(8P23.2) MUTATED DEL PEAK 11(8P23.2) WILD-TYPE 
                           73                            36 
$`DEL PEAK 11(8P23.2) MUTATED`
TCGA-2Y-A9GS TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GY TCGA-2Y-A9H1 
       23.80        63.75        41.79        80.28        24.89        40.41 
TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H6 TCGA-2Y-A9H7 
       56.91        41.33        47.74        18.25        11.74        37.25 
TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-5C-A9VH TCGA-5R-AA1C 
       14.99         1.18         8.55        13.02        10.59        11.97 
TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
        1.51        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         3.19         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        11.47 
TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL 
       12.95        45.11         6.02        33.04        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        90.28        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        23.93        23.05        22.78 
TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD 
        1.45        35.67       114.35        76.41        55.40        12.53 
TCGA-DD-AACE TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACJ TCGA-DD-AACM TCGA-DD-AACN 
       63.48        15.42         6.41        69.11        58.16        42.81 
TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACY 
       61.68        13.64        14.20        59.31        51.52        47.67 
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        42.58        44.22 
TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE 
       40.08        40.54        40.83        13.97        40.47        39.52 
TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADK TCGA-DD-AADM TCGA-DD-AADN 
        3.78        37.64        35.67        34.49         0.39        29.52 
TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADV TCGA-DD-AAE0 
       14.89        15.06        14.33        66.67        18.87        18.25 
TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAE9 TCGA-DD-AAEB 
       19.99         4.64        21.17        21.83        23.74        15.72 
TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAVP 
       25.08        16.37        23.64        25.78        50.33        79.07 
TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVY TCGA-DD-AAVZ 
       89.69        82.62        59.93        72.39        64.77        62.47 
TCGA-DD-AAW0 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A66X TCGA-ED-A7PY 
       66.25        49.48        53.69        13.41        13.35        12.82 
TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A8O6 TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
        0.20        14.04         1.84        18.74        19.99        20.61 
TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A2QQ 
        0.62         9.96        11.93        22.85        14.40        23.97 
TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A495 TCGA-FV-A4ZP 
       19.10        27.88         8.12         6.38         0.03        81.73 
TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y 
        0.39        13.68        28.27        30.74        58.49        14.86 
TCGA-G3-A3CG TCGA-G3-A3CJ TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A6UC TCGA-G3-A7M6 
       22.13        19.53        22.95        20.42         7.76        12.03 
TCGA-G3-A7M7 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV4 TCGA-G3-AAV5 
        5.98        11.24         8.55         9.70         0.89         8.75 
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         2.99        37.91 
TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-LG-A9QC TCGA-LG-A9QD 
       16.83         3.72        11.84        13.38        13.97        12.03 
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-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SF 
       19.92        17.69        21.01         3.09        21.04        19.04 
TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-T1-A6J8 TCGA-UB-A7MB TCGA-UB-A7MD TCGA-UB-A7ME 
       15.52        24.13         0.76        19.76         1.71        15.98 
TCGA-UB-A7MF TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-YA-A8S7 
        7.04        10.75        11.34         0.99        12.99        13.55 
TCGA-ZP-A9CV TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD 
       35.77        23.21        23.57        24.43        12.99        45.57 
TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       40.80        79.30        11.21 

$`DEL PEAK 11(8P23.2) WILD-TYPE`
TCGA-2Y-A9GT TCGA-2Y-A9GV TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H8 TCGA-4R-AA8I 
       53.39        83.24        27.88       120.82        20.81         8.61 
TCGA-5C-A9VG TCGA-5C-AAPD TCGA-5R-AA1D TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10W 
       10.78         0.66        11.08        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        17.98        18.48 
TCGA-BD-A2L6 TCGA-BD-A3ER TCGA-CC-5260 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-DD-A114 
       44.81        36.66         2.86         0.07         0.10        37.78 
TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11D TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC 
        2.60         0.46        51.29        79.40        66.31        19.79 
TCGA-DD-A1ED TCGA-DD-A1EH TCGA-DD-A39W TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A4 
       75.65        49.15        27.19         7.66        70.06        20.12 
TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A4NB TCGA-DD-A4NL TCGA-DD-A4NP TCGA-DD-A4NQ 
      102.74       107.11        32.52        56.25       108.76        12.26 
TCGA-DD-A73B TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACF 
        9.30        13.48         0.53        11.41        75.65        12.00 
TCGA-DD-AACI TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACT TCGA-DD-AACV TCGA-DD-AACW 
       53.19         0.30         3.52        51.35        50.33        46.82 
TCGA-DD-AACX TCGA-DD-AAD6 TCGA-DD-AADJ TCGA-DD-AADL TCGA-DD-AADS TCGA-DD-AADU 
        5.59        22.09        35.05        20.91        15.58        18.21 
TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAEA 
       19.30        18.25        18.15        20.98        18.61        18.90 
TCGA-DD-AAEK TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAW1 TCGA-ED-A4XI TCGA-ED-A5KG 
       35.08        76.18        56.48        65.39        12.69        15.85 
TCGA-ED-A627 TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 
       13.91         9.73         0.20        13.15        13.41        13.35 
TCGA-ED-A97K TCGA-EP-A2KB TCGA-FV-A23B TCGA-FV-A3R3 TCGA-FV-A496 TCGA-G3-A25T 
        0.20        19.59        60.89        12.03         0.33        51.06 
TCGA-G3-A25U TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CK TCGA-G3-A5SI 
       53.79        21.53        25.64         5.92        19.23        25.25 
TCGA-G3-A5SM TCGA-G3-A7M9 TCGA-G3-AAV1 TCGA-G3-AAV3 TCGA-K7-A5RF TCGA-K7-A5RG 
       17.10         1.84        11.80         9.17        20.75        17.06 
TCGA-KR-A7K0 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-MI-A75G TCGA-MR-A520 TCGA-RC-A7SB 
        2.14        24.36        12.72        18.38         0.62        19.33 
TCGA-RC-A7SH TCGA-UB-A7MA TCGA-UB-A7MC TCGA-UB-AA0V TCGA-WX-AA46 TCGA-ZP-A9CY 
       15.39        17.59        16.44        10.32        24.85        25.71 
TCGA-ZP-A9D1 
        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 
                       114.35                        120.82 
  DEL PEAK 11(8P23.2) MUTATED DEL PEAK 11(8P23.2) WILD-TYPE 
                        19.76                         18.90 
[1] "0.0 - 114.3 (19.8)" "0.1 - 120.8 (18.9)"
[1] "hr=" "1"  
D40V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IIIA
  DEL PEAK 11(8P23.2) MUTATED       118       55         0         36
  DEL PEAK 11(8P23.2) WILD-TYPE      50       29         3         23
                               vv
clus                            STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 11(8P23.2) MUTATED            6          4        3         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                            118                            50
  STAGE II                            55                            29
  STAGE III                            0                             3
  STAGE IIIA                          36                            23
  STAGE IIIB                           6                             2
  STAGE IIIC                           4                             3
  STAGE IV                             3                             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     125  61  46   6
  DEL PEAK 11(8P23.2) WILD-TYPE    54  30  27   6
D40V4, multiclass
       clus
vv      DEL PEAK 11(8P23.2) MUTATED DEL PEAK 11(8P23.2) WILD-TYPE
  T0+T1                         125                            54
  T2                             61                            30
  T3                             46                            27
  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   162   3
  DEL PEAK 11(8P23.2) WILD-TYPE  87   0
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(8P23.2) MUTATED    162    3
  DEL PEAK 11(8P23.2) WILD-TYPE   87    0
   clus
vv  DEL PEAK 11(8P23.2) MUTATED DEL PEAK 11(8P23.2) WILD-TYPE
  0                         162                            87
  1                           3                             0
[1] 2 2
[1] FALSE
D40V6, binary
                               cls
clus                              0   1
  DEL PEAK 11(8P23.2) MUTATED   171   4
  DEL PEAK 11(8P23.2) WILD-TYPE  89   0
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(8P23.2) MUTATED    171    4
  DEL PEAK 11(8P23.2) WILD-TYPE   89    0
   clus
vv  DEL PEAK 11(8P23.2) MUTATED DEL PEAK 11(8P23.2) WILD-TYPE
  0                         171                            89
  1                           4                             0
[1] 2 2
[1] FALSE
D40V7, binary
                               cls
clus                              0   1
  DEL PEAK 11(8P23.2) MUTATED    72 168
  DEL PEAK 11(8P23.2) WILD-TYPE  41  76
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(8P23.2) MUTATED     72  168
  DEL PEAK 11(8P23.2) WILD-TYPE   41   76
        clus
vv       DEL PEAK 11(8P23.2) MUTATED DEL PEAK 11(8P23.2) WILD-TYPE
  FEMALE                          72                            41
  MALE                           168                            76
[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                        236
  DEL PEAK 11(8P23.2) WILD-TYPE                      112
                               vv
clus                            HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK 11(8P23.2) MUTATED                                  3
  DEL PEAK 11(8P23.2) WILD-TYPE                                4
D40V8, multiclass
                                  clus
vv                                 DEL PEAK 11(8P23.2) MUTATED
  FIBROLAMELLAR CARCINOMA                                    1
  HEPATOCELLULAR CARCINOMA                                 236
  HEPATOCHOLANGIOCARCINOMA (MIXED)                           3
                                  clus
vv                                 DEL PEAK 11(8P23.2) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                      1
  HEPATOCELLULAR CARCINOMA                                   112
  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   209  10   1  14
  DEL PEAK 11(8P23.2) WILD-TYPE 106   5   0   5
D40V9, multiclass
    clus
vv   DEL PEAK 11(8P23.2) MUTATED DEL PEAK 11(8P23.2) WILD-TYPE
  R0                         209                           106
  R1                          10                             5
  R2                           1                             0
  RX                          14                             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   101
  DEL PEAK 11(8P23.2) WILD-TYPE                                0    55
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 11(8P23.2) MUTATED                          13   118
  DEL PEAK 11(8P23.2) WILD-TYPE                         4    55
D40V10, multiclass
                                  clus
vv                                 DEL PEAK 11(8P23.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                    101
  BLACK OR AFRICAN AMERICAN                                 13
  WHITE                                                    118
                                  clus
vv                                 DEL PEAK 11(8P23.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                       55
  BLACK OR AFRICAN AMERICAN                                    4
  WHITE                                                       55
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V11, binary
                               cls
clus                              0   1
  DEL PEAK 11(8P23.2) MUTATED     8 220
  DEL PEAK 11(8P23.2) WILD-TYPE   3 109
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(8P23.2) MUTATED      8  220
  DEL PEAK 11(8P23.2) WILD-TYPE    3  109
                        clus
vv                       DEL PEAK 11(8P23.2) MUTATED
  HISPANIC OR LATINO                               8
  NOT HISPANIC OR LATINO                         220
                        clus
vv                       DEL PEAK 11(8P23.2) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           109
[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   151  69
  DEL PEAK 12(8P12) WILD-TYPE  74  40
  DEL PEAK 12(8P12) MUTATED DEL PEAK 12(8P12) WILD-TYPE 
                        220                         114 
  DEL PEAK 12(8P12) MUTATED DEL PEAK 12(8P12) WILD-TYPE 
                         69                          40 
$`DEL PEAK 12(8P12) MUTATED`
TCGA-2Y-A9GS TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GZ TCGA-2Y-A9H1 
       23.80        63.75        41.79        80.28        27.88        40.41 
TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H6 TCGA-2Y-A9H7 
       56.91        41.33        47.74        18.25        11.74        37.25 
TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-5C-A9VH TCGA-5R-AA1C 
       14.99         1.18         8.55        13.02        10.59        11.97 
TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T 
        1.51        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         3.19         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        11.47 
TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL 
       12.95        45.11         6.02        33.04        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        90.28        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 
       23.93         9.30        23.05        22.78         1.45        35.67 
TCGA-DD-A73G TCGA-DD-AAC8 TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE 
      114.35         0.53        76.41        55.40        12.53        63.48 
TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACJ TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO 
       15.42         6.41        69.11        58.16        42.81        61.68 
TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 
       13.64        14.20        59.31         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        42.58        44.22        40.08        40.54        40.83 
TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI 
       13.97        40.47        39.52         3.78        37.64        35.67 
TCGA-DD-AADK TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR 
       34.49        29.52        14.89        15.06        14.33        66.67 
TCGA-DD-AADV TCGA-DD-AAE0 TCGA-DD-AAE4 TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAE9 
       18.87        18.25        19.99        21.17        21.83        23.74 
TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAEI 
       15.72        25.08        16.37        23.64        25.78        50.33 
TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW 
       79.07        89.69        82.62        59.93        72.39        76.18 
TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 
       64.77        62.47        66.25        49.48        53.69        13.41 
TCGA-ED-A4XI TCGA-ED-A66X TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A8O6 
       12.69        13.35        12.82         0.20        14.04         1.84 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK 
       18.74        19.99        20.61         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        81.73         0.39        13.68        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-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-HP-A5MZ TCGA-K7-A6G5 
        0.89         8.75         2.14         3.02         2.99        16.83 
TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD 
        3.72        11.84        13.38        24.36        13.97        12.03 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A8JO TCGA-NI-A8LF 
        9.57        16.67        12.85        20.71        10.85        19.92 
TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SF TCGA-RC-A7SH 
       17.69        21.01         3.09        21.04        19.04        15.39 
TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-T1-A6J8 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MD 
       15.52        24.13         0.76        17.59        19.76         1.71 
TCGA-UB-A7ME TCGA-UB-A7MF TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B 
       15.98         7.04        10.75        11.34         0.99        12.99 
TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 
       13.55        35.77        23.21        23.57        24.43        12.99 
TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       45.57        40.80        79.30        11.21 

$`DEL PEAK 12(8P12) WILD-TYPE`
TCGA-2Y-A9GT TCGA-2Y-A9GV TCGA-2Y-A9GY TCGA-2Y-A9H0 TCGA-2Y-A9H8 TCGA-4R-AA8I 
       53.39        83.24        24.89       120.82        20.81         8.61 
TCGA-5C-A9VG TCGA-5C-AAPD TCGA-5R-AA1D TCGA-BC-4073 TCGA-BC-A10U TCGA-BC-A10W 
       10.78         0.66        11.08        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        17.98        18.48 
TCGA-BD-A2L6 TCGA-BD-A3ER TCGA-CC-5260 TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A114 
       44.81        36.66         2.86         0.10         0.13        37.78 
TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11D TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC 
        2.60         0.46        51.29        79.40        66.31        19.79 
TCGA-DD-A1ED TCGA-DD-A1EH TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A3A0 TCGA-DD-A3A1 
       75.65        49.15        27.19        55.69        25.81         7.66 
TCGA-DD-A3A2 TCGA-DD-A3A4 TCGA-DD-A3A6 TCGA-DD-A4NB TCGA-DD-A4NF TCGA-DD-A4NI 
       70.06        20.12       107.11        32.52        30.97        26.83 
TCGA-DD-A4NL TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-AA3A TCGA-DD-AAC9 TCGA-DD-AACA 
       56.25       108.76        12.26        13.48        11.41        75.65 
TCGA-DD-AACF TCGA-DD-AACI TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACT TCGA-DD-AACU 
       12.00        53.19         0.30         3.52        51.35        51.52 
TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AAD6 TCGA-DD-AADJ 
       50.33        46.82         5.59        47.67        22.09        35.05 
TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY 
       20.91         0.39        15.58        18.21        19.30        18.25 
TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE6 TCGA-DD-AAEA TCGA-DD-AAEK 
       18.15        20.98        18.61         4.64        18.90        35.08 
TCGA-DD-AAVX TCGA-DD-AAW1 TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66Y TCGA-ED-A7PX 
       56.48        65.39        15.85        13.91         9.73         0.20 
TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A97K TCGA-EP-A2KB TCGA-FV-A23B 
       13.15        13.41        13.35         0.20        19.59        60.89 
TCGA-FV-A3R3 TCGA-FV-A496 TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25Y TCGA-G3-A25Z 
       12.03         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        25.25        22.95        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        37.91        20.75 
TCGA-K7-A5RG TCGA-KR-A7K0 TCGA-LG-A6GG TCGA-MI-A75G TCGA-MR-A520 TCGA-NI-A4U2 
       17.06         2.14        12.72        18.38         0.62        58.88 
TCGA-RC-A7SB TCGA-UB-A7MC TCGA-UB-AA0V TCGA-WX-AA46 TCGA-ZP-A9CY TCGA-ZP-A9D1 
       19.33        16.44        10.32        24.85        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 
                     114.35                      120.82 
  DEL PEAK 12(8P12) MUTATED DEL PEAK 12(8P12) WILD-TYPE 
                     18.955                      19.460 
[1] "0.0 - 114.3 (19.0)" "0.1 - 120.8 (19.5)"
[1] "hr=" "1.1"
D41V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 12(8P12) MUTATED       113       55         1         34          7
  DEL PEAK 12(8P12) WILD-TYPE      55       29         2         25          1
                             vv
clus                          STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 12(8P12) MUTATED            4        3         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                          113                          55
  STAGE II                          55                          29
  STAGE III                          1                           2
  STAGE IIIA                        34                          25
  STAGE IIIB                         7                           1
  STAGE IIIC                         4                           3
  STAGE IV                           3                           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     120  61  46   6
  DEL PEAK 12(8P12) WILD-TYPE    59  30  27   6
D41V4, multiclass
       clus
vv      DEL PEAK 12(8P12) MUTATED DEL PEAK 12(8P12) WILD-TYPE
  T0+T1                       120                          59
  T2                           61                          30
  T3                           46                          27
  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   162   3
  DEL PEAK 12(8P12) WILD-TYPE  87   0
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 12(8P12) MUTATED    162    3
  DEL PEAK 12(8P12) WILD-TYPE   87    0
   clus
vv  DEL PEAK 12(8P12) MUTATED DEL PEAK 12(8P12) WILD-TYPE
  0                       162                          87
  1                         3                           0
[1] 2 2
[1] FALSE
D41V6, binary
                             cls
clus                            0   1
  DEL PEAK 12(8P12) MUTATED   167   4
  DEL PEAK 12(8P12) WILD-TYPE  93   0
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 12(8P12) MUTATED    167    4
  DEL PEAK 12(8P12) WILD-TYPE   93    0
   clus
vv  DEL PEAK 12(8P12) MUTATED DEL PEAK 12(8P12) WILD-TYPE
  0                       167                          93
  1                         4                           0
[1] 2 2
[1] FALSE
D41V7, binary
                             cls
clus                            0   1
  DEL PEAK 12(8P12) MUTATED    71 163
  DEL PEAK 12(8P12) WILD-TYPE  42  81
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 12(8P12) MUTATED     71  163
  DEL PEAK 12(8P12) WILD-TYPE   42   81
        clus
vv       DEL PEAK 12(8P12) MUTATED DEL PEAK 12(8P12) WILD-TYPE
  FEMALE                        71                          42
  MALE                         163                          81
[1] 2 2
[1] FALSE
                             vv
clus                          FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  DEL PEAK 12(8P12) MUTATED                         1                      229
  DEL PEAK 12(8P12) WILD-TYPE                       1                      119
                             vv
clus                          HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK 12(8P12) MUTATED                                  4
  DEL PEAK 12(8P12) WILD-TYPE                                3
D41V8, multiclass
                                  clus
vv                                 DEL PEAK 12(8P12) MUTATED
  FIBROLAMELLAR CARCINOMA                                  1
  HEPATOCELLULAR CARCINOMA                               229
  HEPATOCHOLANGIOCARCINOMA (MIXED)                         4
                                  clus
vv                                 DEL PEAK 12(8P12) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                    1
  HEPATOCELLULAR CARCINOMA                                 119
  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   203  11   1  13
  DEL PEAK 12(8P12) WILD-TYPE 112   4   0   6
D41V9, multiclass
    clus
vv   DEL PEAK 12(8P12) MUTATED DEL PEAK 12(8P12) WILD-TYPE
  R0                       203                         112
  R1                        11                           4
  R2                         1                           0
  RX                        13                           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    99
  DEL PEAK 12(8P12) WILD-TYPE                                0    57
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 12(8P12) MUTATED                          13   114
  DEL PEAK 12(8P12) WILD-TYPE                         4    59
D41V10, multiclass
                                  clus
vv                                 DEL PEAK 12(8P12) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         1
  ASIAN                                                   99
  BLACK OR AFRICAN AMERICAN                               13
  WHITE                                                  114
                                  clus
vv                                 DEL PEAK 12(8P12) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                     57
  BLACK OR AFRICAN AMERICAN                                  4
  WHITE                                                     59
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V11, binary
                             cls
clus                            0   1
  DEL PEAK 12(8P12) MUTATED     9 213
  DEL PEAK 12(8P12) WILD-TYPE   2 116
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 12(8P12) MUTATED      9  213
  DEL PEAK 12(8P12) WILD-TYPE    2  116
                        clus
vv                       DEL PEAK 12(8P12) MUTATED DEL PEAK 12(8P12) WILD-TYPE
  HISPANIC OR LATINO                             9                           2
  NOT HISPANIC OR LATINO                       213                         116
[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    87  45
  DEL PEAK 13(9P21.3) WILD-TYPE 138  64
  DEL PEAK 13(9P21.3) MUTATED DEL PEAK 13(9P21.3) WILD-TYPE 
                          132                           202 
  DEL PEAK 13(9P21.3) MUTATED DEL PEAK 13(9P21.3) WILD-TYPE 
                           45                            64 
$`DEL PEAK 13(9P21.3) MUTATED`
TCGA-2Y-A9GS TCGA-2Y-A9GU TCGA-2Y-A9GV TCGA-2Y-A9GY TCGA-2Y-A9H2 TCGA-2Y-A9H3 
       23.80        63.75        83.24        24.89        56.91        41.33 
TCGA-2Y-A9H5 TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-2Y-A9H8 TCGA-3K-AAZ8 TCGA-5C-A9VG 
       18.25        11.74        37.25        20.81        13.02        10.78 
TCGA-5C-A9VH TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S 
       10.59        48.99        27.91        37.32        10.13        46.78 
TCGA-BC-A10U TCGA-BC-A112 TCGA-BC-A3KF TCGA-BC-A5W4 TCGA-BC-A69H TCGA-CC-5258 
       27.52         5.03         0.26        17.98        14.60         0.07 
TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 
        4.24         3.32         0.10         0.10         0.13        79.73 
TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C 
       83.57        53.33         7.33         2.60         0.46        21.76 
TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39X 
       12.95        45.11         6.02        33.04        13.64        55.69 
TCGA-DD-A39Y TCGA-DD-A3A0 TCGA-DD-A3A9 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-A4NO 
        5.62        25.81        30.61        90.28        26.83        73.81 
TCGA-DD-A73F TCGA-DD-AA3A TCGA-DD-AACA TCGA-DD-AACC TCGA-DD-AACE TCGA-DD-AACG 
       35.67        13.48        75.65        55.40        63.48        15.42 
TCGA-DD-AACH TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACW 
        6.41        61.68        13.64        59.31        51.52        46.82 
TCGA-DD-AACZ TCGA-DD-AAD3 TCGA-DD-AADC TCGA-DD-AADE TCGA-DD-AADJ TCGA-DD-AADK 
        5.62        42.58        13.97        39.52        35.05        34.49 
TCGA-DD-AADL TCGA-DD-AADN TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADS TCGA-DD-AADV 
       20.91        29.52        15.06        14.33        15.58        18.87 
TCGA-DD-AAE1 TCGA-DD-AAE3 TCGA-DD-AAE6 TCGA-DD-AAE8 TCGA-DD-AAED TCGA-DD-AAEE 
       18.15        18.61         4.64        21.83        25.08        16.37 
TCGA-DD-AAEK TCGA-DD-AAVQ TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVZ 
       35.08        89.69        59.93        72.39        76.18        62.47 
TCGA-DD-AAW0 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A66X TCGA-ED-A7PZ TCGA-ED-A7XP 
       66.25        13.41        12.69        13.35         0.20        13.15 
TCGA-ED-A82E TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC 
       13.41         1.84         0.20        20.61        19.59         0.62 
TCGA-EP-A3RK TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 
       11.93        60.89        23.97        27.88         8.12         6.38 
TCGA-FV-A4ZP TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A3CJ TCGA-G3-A7M7 TCGA-G3-AAV1 
       81.73        13.68        51.06        19.53         5.98        11.80 
TCGA-G3-AAV3 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A9DB TCGA-KR-A7K7 TCGA-KR-A7K8 
        9.17         2.14         3.02         2.20        13.38        24.36 
TCGA-MI-A75G TCGA-MI-A75I TCGA-NI-A8LF TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF 
       18.38        20.71        19.92        21.04        19.33        19.04 
TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-T1-A6J8 TCGA-UB-A7ME TCGA-UB-A7MF 
       15.39        15.52        24.13         0.76        15.98         7.04 
TCGA-UB-AA0U TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D2 
       10.75         0.99        12.99        23.57         0.69        24.43 

$`DEL PEAK 13(9P21.3) WILD-TYPE`
TCGA-2Y-A9GT TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 
       53.39        41.79        80.28        27.88       120.82        40.41 
TCGA-2Y-A9H4 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-4R-AA8I TCGA-5C-AAPD 
       47.74        14.99         1.18         8.55         8.61         0.66 
TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-A10T TCGA-BC-A10W TCGA-BC-A10X 
       11.97        11.08         1.51        27.52         2.99        25.32 
TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KG 
       23.34         1.12        69.57        44.42        13.84        22.36 
TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BD-A3ER TCGA-BW-A5NO 
       12.72        18.48        44.81        13.45        36.66         0.66 
TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-A3MA TCGA-DD-A114 TCGA-DD-A118 
        2.86         3.19         3.39         0.07        37.78       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-A1EK TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39Z 
       11.47        49.15        18.35        21.14        27.19        19.76 
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-A4NA TCGA-DD-A4NB TCGA-DD-A4NF TCGA-DD-A4NH 
       13.78         0.36        33.14        32.52        30.97        30.15 
TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NP TCGA-DD-A4NQ 
       30.51        39.78        56.25        29.56       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        23.93         9.30        23.05 
TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73G TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACB 
       22.78         1.45       114.35         0.53        11.41        76.41 
TCGA-DD-AACD TCGA-DD-AACF TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL 
       12.53        12.00        53.19        69.11         0.30         3.52 
TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACQ TCGA-DD-AACT TCGA-DD-AACV TCGA-DD-AACX 
       58.16        42.81        14.20        51.35        50.33         5.59 
TCGA-DD-AACY TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD5 TCGA-DD-AAD6 
       47.67         4.50        18.54        21.63        44.22        22.09 
TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADD TCGA-DD-AADF TCGA-DD-AADG 
       40.08        40.54        40.83        40.47         3.78        37.64 
TCGA-DD-AADI TCGA-DD-AADM TCGA-DD-AADO TCGA-DD-AADR TCGA-DD-AADU TCGA-DD-AADW 
       35.67         0.39        14.89        66.67        18.21        19.30 
TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE2 TCGA-DD-AAE4 TCGA-DD-AAE7 TCGA-DD-AAE9 
       18.25        18.25        20.98        19.99        21.17        23.74 
TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAVP 
       18.90        15.72        23.64        25.78        50.33        79.07 
TCGA-DD-AAVR TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 
       82.62        56.48        64.77        65.39        49.48        53.69 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7XO 
       15.85        13.91         9.73         0.20        12.82        14.04 
TCGA-ED-A8O5 TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A3JL TCGA-ES-A2HS TCGA-ES-A2HT 
       13.35        18.74        19.99         9.96        22.85        14.40 
TCGA-FV-A2QR TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25U 
       19.10        12.03         0.03         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-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL 
       25.64         5.92        19.23        25.25        22.95        20.42 
TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV0 
       17.10         7.76        12.03         1.84        11.24         8.55 
TCGA-G3-AAV2 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-HP-A5N0 
        9.70         0.89         8.75         1.02         2.99        37.91 
TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K2 
       20.75        17.06        16.83         3.72         2.14        11.84 
TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75H 
       12.72        13.97        12.03         9.57        16.67        12.85 
TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 
        0.62        10.85        58.88        17.69        21.01         3.09 
TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-AA0V TCGA-WJ-A86L 
       17.59        19.76        16.44         1.71        10.32        11.34 
TCGA-WX-AA46 TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D4 
       24.85        13.55        35.77        25.71        23.21        12.99 
TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       45.57        40.80        79.30        11.21 

  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 
                        90.28                        120.82 
  DEL PEAK 13(9P21.3) MUTATED DEL PEAK 13(9P21.3) WILD-TYPE 
                        18.74                         19.76 
[1] "0.1 - 90.3 (18.7)"  "0.0 - 120.8 (19.8)"
[1] "hr=" "1.2"
D42V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IIIA
  DEL PEAK 13(9P21.3) MUTATED        64       35         0         28
  DEL PEAK 13(9P21.3) WILD-TYPE     104       49         3         31
                               vv
clus                            STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 13(9P21.3) MUTATED            2          2        2         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                             64                           104
  STAGE II                            35                            49
  STAGE III                            0                             3
  STAGE IIIA                          28                            31
  STAGE IIIB                           2                             6
  STAGE IIIC                           2                             5
  STAGE IV                             2                             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      70  39  34   3
  DEL PEAK 13(9P21.3) WILD-TYPE   109  52  39   9
D42V4, multiclass
       clus
vv      DEL PEAK 13(9P21.3) MUTATED DEL PEAK 13(9P21.3) WILD-TYPE
  T0+T1                          70                           109
  T2                             39                            52
  T3                             34                            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"
D42V5, binary
                               cls
clus                              0   1
  DEL PEAK 13(9P21.3) MUTATED   101   2
  DEL PEAK 13(9P21.3) WILD-TYPE 148   1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(9P21.3) MUTATED    101    2
  DEL PEAK 13(9P21.3) WILD-TYPE  148    1
   clus
vv  DEL PEAK 13(9P21.3) MUTATED DEL PEAK 13(9P21.3) WILD-TYPE
  0                         101                           148
  1                           2                             1
[1] 2 2
[1] FALSE
D42V6, binary
                               cls
clus                              0   1
  DEL PEAK 13(9P21.3) MUTATED   106   2
  DEL PEAK 13(9P21.3) WILD-TYPE 154   2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(9P21.3) MUTATED    106    2
  DEL PEAK 13(9P21.3) WILD-TYPE  154    2
   clus
vv  DEL PEAK 13(9P21.3) MUTATED DEL PEAK 13(9P21.3) WILD-TYPE
  0                         106                           154
  1                           2                             2
[1] 2 2
[1] FALSE
D42V7, binary
                               cls
clus                              0   1
  DEL PEAK 13(9P21.3) MUTATED    42 104
  DEL PEAK 13(9P21.3) WILD-TYPE  71 140
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(9P21.3) MUTATED     42  104
  DEL PEAK 13(9P21.3) WILD-TYPE   71  140
        clus
vv       DEL PEAK 13(9P21.3) MUTATED DEL PEAK 13(9P21.3) WILD-TYPE
  FEMALE                          42                            71
  MALE                           104                           140
[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                        143
  DEL PEAK 13(9P21.3) WILD-TYPE                      205
                               vv
clus                            HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK 13(9P21.3) MUTATED                                  3
  DEL PEAK 13(9P21.3) WILD-TYPE                                4
D42V8, multiclass
                                  clus
vv                                 DEL PEAK 13(9P21.3) MUTATED
  FIBROLAMELLAR CARCINOMA                                    0
  HEPATOCELLULAR CARCINOMA                                 143
  HEPATOCHOLANGIOCARCINOMA (MIXED)                           3
                                  clus
vv                                 DEL PEAK 13(9P21.3) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                      2
  HEPATOCELLULAR CARCINOMA                                   205
  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 13(9P21.3) MUTATED   128   8   1   7
  DEL PEAK 13(9P21.3) WILD-TYPE 187   7   0  12
D42V9, multiclass
    clus
vv   DEL PEAK 13(9P21.3) MUTATED DEL PEAK 13(9P21.3) WILD-TYPE
  R0                         128                           187
  R1                           8                             7
  R2                           1                             0
  RX                           7                            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 13(9P21.3) MUTATED                                  1    74
  DEL PEAK 13(9P21.3) WILD-TYPE                                0    82
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 13(9P21.3) MUTATED                           7    63
  DEL PEAK 13(9P21.3) WILD-TYPE                        10   110
D42V10, multiclass
                                  clus
vv                                 DEL PEAK 13(9P21.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                     74
  BLACK OR AFRICAN AMERICAN                                  7
  WHITE                                                     63
                                  clus
vv                                 DEL PEAK 13(9P21.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                       82
  BLACK OR AFRICAN AMERICAN                                   10
  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"
D42V11, binary
                               cls
clus                              0   1
  DEL PEAK 13(9P21.3) MUTATED     2 140
  DEL PEAK 13(9P21.3) WILD-TYPE   9 189
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(9P21.3) MUTATED      2  140
  DEL PEAK 13(9P21.3) WILD-TYPE    9  189
                        clus
vv                       DEL PEAK 13(9P21.3) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                         140
                        clus
vv                       DEL PEAK 13(9P21.3) WILD-TYPE
  HISPANIC OR LATINO                                 9
  NOT HISPANIC OR LATINO                           189
[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    71  37
  DEL PEAK 14(9Q31.3) WILD-TYPE 154  72
  DEL PEAK 14(9Q31.3) MUTATED DEL PEAK 14(9Q31.3) WILD-TYPE 
                          108                           226 
  DEL PEAK 14(9Q31.3) MUTATED DEL PEAK 14(9Q31.3) WILD-TYPE 
                           37                            72 
$`DEL PEAK 14(9Q31.3) MUTATED`
TCGA-2Y-A9GS TCGA-2Y-A9GU TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H5 TCGA-2Y-A9H6 
       23.80        63.75        56.91        41.33        18.25        11.74 
TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-5C-A9VH 
       20.81        14.99         1.18        13.02        10.78        10.59 
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10U TCGA-BC-A112 
       27.91        37.32        10.13        46.78        27.52         5.03 
TCGA-BC-A217 TCGA-BC-A5W4 TCGA-BC-A69H TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-A1HT 
       13.84        17.98        14.60         0.07         2.86         3.32 
TCGA-CC-A3M9 TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A116 TCGA-DD-A119 
        0.10         0.10         0.13        79.73        53.33         7.33 
TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EI 
        2.60         0.46        21.76        12.95        45.11         6.02 
TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A3A9 TCGA-DD-A4NA 
       33.04        18.35        55.69         5.62        30.61        33.14 
TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-AA3A TCGA-DD-AACB 
       26.83        30.51        29.56        73.81        13.48        76.41 
TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACU TCGA-DD-AACZ 
       12.53        63.48        61.68        13.64        51.52         5.62 
TCGA-DD-AAD3 TCGA-DD-AAD8 TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADO 
       42.58        40.08        35.05        34.49        20.91        14.89 
TCGA-DD-AADV TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAED TCGA-DD-AAEK TCGA-DD-AAVQ 
       18.87        21.83        18.90        25.08        35.08        89.69 
TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-ED-A459 TCGA-ED-A66X 
       72.39        76.18        62.47        66.25        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        12.03        81.73        13.68 
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-A7SB TCGA-RC-A7SH TCGA-RC-A7SK 
       18.38        20.71        21.01        19.33        15.39        15.52 
TCGA-RG-A7D4 TCGA-T1-A6J8 TCGA-UB-A7MB TCGA-UB-A7ME TCGA-UB-A7MF TCGA-UB-AA0U 
       24.13         0.76        19.76        15.98         7.04        10.75 
TCGA-WQ-AB4B TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZS-A9CE TCGA-ZS-A9CF 
       12.99        23.21        23.57        24.43        40.80        79.30 

$`DEL PEAK 14(9Q31.3) WILD-TYPE`
TCGA-2Y-A9GT TCGA-2Y-A9GV TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GY TCGA-2Y-A9GZ 
       53.39        83.24        41.79        80.28        24.89        27.88 
TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H4 TCGA-2Y-A9H7 TCGA-2Y-A9HB TCGA-4R-AA8I 
      120.82        40.41        47.74        37.25         8.55         8.61 
TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-A10T 
        0.66        11.97        11.08         1.51        48.99        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-A3KF TCGA-BC-A3KG TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP 
        0.26        22.36        12.72        18.48        44.81        13.45 
TCGA-BD-A3ER TCGA-BW-A5NO TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A3MA 
       36.66         0.66         3.19         3.39         4.24         0.07 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A118 TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA 
       37.78        83.57       113.00        51.29        90.71        79.40 
TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EH TCGA-DD-A1EL 
       66.31        19.79        75.65        11.47        49.15        13.64 
TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 
       21.14        27.19        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-A4NB TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NK TCGA-DD-A4NL 
       32.52        90.28        30.97        30.15        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        23.93 
TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G 
        9.30        23.05        22.78         1.45        35.67       114.35 
TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACC TCGA-DD-AACF TCGA-DD-AACG 
        0.53        11.41        75.65        55.40        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        69.11         0.30         3.52        58.16 
TCGA-DD-AACN TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACV TCGA-DD-AACW 
       42.81        14.20        59.31        51.35        50.33        46.82 
TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD5 
        5.59        47.67         4.50        18.54        21.63        44.22 
TCGA-DD-AAD6 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE 
       22.09        40.54        40.83        13.97        40.47        39.52 
TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADP 
        3.78        37.64        35.67         0.39        29.52        15.06 
TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY 
       14.33        66.67        15.58        18.21        19.30        18.25 
TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 
       18.25        18.15        20.98        18.61        19.99         4.64 
TCGA-DD-AAE7 TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEH 
       21.17        23.74        15.72        16.37        23.64        25.78 
TCGA-DD-AAEI TCGA-DD-AAVP TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVX TCGA-DD-AAVY 
       50.33        79.07        82.62        59.93        56.48        64.77 
TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 
       65.39        49.48        53.69        12.69        15.85        13.91 
TCGA-ED-A66Y TCGA-ED-A7PY TCGA-ED-A7XO TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 
        9.73        12.82        14.04        13.41        13.35         1.84 
TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A3JL 
        0.20        18.74        19.99        20.61        19.59         9.96 
TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A495 TCGA-FV-A496 
       22.85        14.40        60.89        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        25.25 
TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 
       22.95        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-AAV5 TCGA-G3-AAV6 TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG 
        8.75         2.14         2.99        37.91        20.75        17.06 
TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-KR-A7K8 
       16.83         3.72         2.14        11.84        13.38        24.36 
TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75H 
       12.72        13.97        12.03         9.57        16.67        12.85 
TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-QA-A7B7 
        0.62        10.85        58.88        19.92        17.69         3.09 
TCGA-RC-A7S9 TCGA-RC-A7SF TCGA-UB-A7MA TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-AA0V 
       21.04        19.04        17.59        16.44         1.71        10.32 
TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WX-AA46 TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY 
       11.34         0.99        24.85        13.55        35.77        25.71 
TCGA-ZP-A9D1 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CG 
        0.69        12.99        45.57        11.21 

  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 
                        89.69                        120.82 
  DEL PEAK 14(9Q31.3) MUTATED DEL PEAK 14(9Q31.3) WILD-TYPE 
                       18.885                        19.415 
[1] "0.1 - 89.7 (18.9)"  "0.0 - 120.8 (19.4)"
[1] "hr=" "1.2"
D43V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IIIA
  DEL PEAK 14(9Q31.3) MUTATED        46       31         0         17
  DEL PEAK 14(9Q31.3) WILD-TYPE     122       53         3         42
                               vv
clus                            STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 14(9Q31.3) MUTATED            3          4        2         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                             46                           122
  STAGE II                            31                            53
  STAGE III                            0                             3
  STAGE IIIA                          17                            42
  STAGE IIIB                           3                             5
  STAGE IIIC                           4                             3
  STAGE IV                             2                             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      52  36  22   6
  DEL PEAK 14(9Q31.3) WILD-TYPE   127  55  51   6
D43V4, multiclass
       clus
vv      DEL PEAK 14(9Q31.3) MUTATED DEL PEAK 14(9Q31.3) WILD-TYPE
  T0+T1                          52                           127
  T2                             36                            55
  T3                             22                            51
  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    72   3
  DEL PEAK 14(9Q31.3) WILD-TYPE 177   0
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(9Q31.3) MUTATED     72    3
  DEL PEAK 14(9Q31.3) WILD-TYPE  177    0
   clus
vv  DEL PEAK 14(9Q31.3) MUTATED DEL PEAK 14(9Q31.3) WILD-TYPE
  0                          72                           177
  1                           3                             0
[1] 2 2
[1] FALSE
D43V6, binary
                               cls
clus                              0   1
  DEL PEAK 14(9Q31.3) MUTATED    76   3
  DEL PEAK 14(9Q31.3) WILD-TYPE 184   1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(9Q31.3) MUTATED     76    3
  DEL PEAK 14(9Q31.3) WILD-TYPE  184    1
   clus
vv  DEL PEAK 14(9Q31.3) MUTATED DEL PEAK 14(9Q31.3) WILD-TYPE
  0                          76                           184
  1                           3                             1
[1] 2 2
[1] FALSE
D43V7, binary
                               cls
clus                              0   1
  DEL PEAK 14(9Q31.3) MUTATED    35  81
  DEL PEAK 14(9Q31.3) WILD-TYPE  78 163
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(9Q31.3) MUTATED     35   81
  DEL PEAK 14(9Q31.3) WILD-TYPE   78  163
        clus
vv       DEL PEAK 14(9Q31.3) MUTATED DEL PEAK 14(9Q31.3) WILD-TYPE
  FEMALE                          35                            78
  MALE                            81                           163
[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                        114
  DEL PEAK 14(9Q31.3) WILD-TYPE                      234
                               vv
clus                            HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK 14(9Q31.3) MUTATED                                  2
  DEL PEAK 14(9Q31.3) WILD-TYPE                                5
D43V8, multiclass
                                  clus
vv                                 DEL PEAK 14(9Q31.3) MUTATED
  FIBROLAMELLAR CARCINOMA                                    0
  HEPATOCELLULAR CARCINOMA                                 114
  HEPATOCHOLANGIOCARCINOMA (MIXED)                           2
                                  clus
vv                                 DEL PEAK 14(9Q31.3) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                      2
  HEPATOCELLULAR CARCINOMA                                   234
  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 14(9Q31.3) MUTATED    97   7   1   8
  DEL PEAK 14(9Q31.3) WILD-TYPE 218   8   0  11
D43V9, multiclass
    clus
vv   DEL PEAK 14(9Q31.3) MUTATED DEL PEAK 14(9Q31.3) WILD-TYPE
  R0                          97                           218
  R1                           7                             8
  R2                           1                             0
  RX                           8                            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 14(9Q31.3) MUTATED                                  0    53
  DEL PEAK 14(9Q31.3) WILD-TYPE                                1   103
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 14(9Q31.3) MUTATED                           6    57
  DEL PEAK 14(9Q31.3) WILD-TYPE                        11   116
D43V10, multiclass
                                  clus
vv                                 DEL PEAK 14(9Q31.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                     53
  BLACK OR AFRICAN AMERICAN                                  6
  WHITE                                                     57
                                  clus
vv                                 DEL PEAK 14(9Q31.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                      103
  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"
D43V11, binary
                               cls
clus                              0   1
  DEL PEAK 14(9Q31.3) MUTATED     2 113
  DEL PEAK 14(9Q31.3) WILD-TYPE   9 216
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(9Q31.3) MUTATED      2  113
  DEL PEAK 14(9Q31.3) WILD-TYPE    9  216
                        clus
vv                       DEL PEAK 14(9Q31.3) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                         113
                        clus
vv                       DEL PEAK 14(9Q31.3) WILD-TYPE
  HISPANIC OR LATINO                                 9
  NOT HISPANIC OR LATINO                           216
[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    58  30
  DEL PEAK 15(10Q23.31) WILD-TYPE 167  79
  DEL PEAK 15(10Q23.31) MUTATED DEL PEAK 15(10Q23.31) WILD-TYPE 
                             88                             246 
  DEL PEAK 15(10Q23.31) MUTATED DEL PEAK 15(10Q23.31) WILD-TYPE 
                             30                              79 
$`DEL PEAK 15(10Q23.31) MUTATED`
TCGA-2Y-A9GS TCGA-2Y-A9H2 TCGA-2Y-A9H4 TCGA-2Y-A9H9 TCGA-5C-AAPD TCGA-BC-4073 
       23.80        56.91        47.74        14.99         0.66        27.91 
TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10W TCGA-BC-A10Y TCGA-BC-A216 TCGA-BC-A217 
       37.32        10.13         2.99        23.34        44.42        13.84 
TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BW-A5NO 
       22.36        17.98        18.48        44.81        13.45         0.66 
TCGA-CC-5260 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC 
        2.86         4.24         3.32         0.07         0.10         0.13 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A118 TCGA-DD-A11A TCGA-DD-A11C TCGA-DD-A1EG 
       37.78        83.57       113.00         2.60        21.76        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-AACG TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACM TCGA-DD-AACO TCGA-DD-AACQ 
       15.42         6.41        53.19        58.16        61.68        14.20 
TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD3 TCGA-DD-AAD5 
       51.52        50.33         5.62         4.50        42.58        44.22 
TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADL TCGA-DD-AADN TCGA-DD-AADR TCGA-DD-AADY 
       40.08        40.54        20.91        29.52        66.67        18.25 
TCGA-DD-AAE2 TCGA-DD-AAE8 TCGA-ED-A459 TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7XO 
       20.98        21.83        13.41         9.73         0.20        14.04 
TCGA-ED-A8O6 TCGA-ED-A97K TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A496 
        1.84         0.20        23.97        19.10        27.88         0.33 
TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25X TCGA-G3-A5SJ TCGA-G3-AAV1 TCGA-G3-AAV4 
       51.06        53.79        58.49        22.95        11.80         0.89 
TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-NI-A4U2 TCGA-PD-A5DF 
       37.91        17.06        11.84        13.38        58.88        21.01 
TCGA-QA-A7B7 TCGA-RC-A7SB TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MB TCGA-UB-A7MD 
        3.09        19.33        15.52        24.13        19.76         1.71 
TCGA-WJ-A86L TCGA-YA-A8S7 TCGA-ZP-A9D1 TCGA-ZS-A9CE 
       11.34        13.55         0.69        40.80 

$`DEL PEAK 15(10Q23.31) WILD-TYPE`
TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GV TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GY 
       53.39        63.75        83.24        41.79        80.28        24.89 
TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H3 TCGA-2Y-A9H5 TCGA-2Y-A9H6 
       27.88       120.82        40.41        41.33        18.25        11.74 
TCGA-2Y-A9H7 TCGA-2Y-A9H8 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-4R-AA8I 
       37.25        20.81         1.18         8.55        13.02         8.61 
TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4072 
       10.78        10.59        11.97        11.08         1.51        48.99 
TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10X TCGA-BC-A10Z TCGA-BC-A110 
       46.78        27.52        27.52        25.32         1.12        69.57 
TCGA-BC-A112 TCGA-BC-A3KF TCGA-BC-A69H TCGA-BC-A69I TCGA-BD-A3ER TCGA-CC-5258 
        5.03         0.26        14.60        12.72        36.66         0.07 
TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-A3M9 TCGA-DD-A113 TCGA-DD-A116 TCGA-DD-A119 
        3.19         3.39         0.10        79.73        53.33         7.33 
TCGA-DD-A11B TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC 
        0.46        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-A1EJ 
       75.65        11.47        12.95        49.15         6.02        33.04 
TCGA-DD-A1EK TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Z TCGA-DD-A3A1 
       18.35        21.14        27.19        55.69        19.76         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-A4NB TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH 
        0.36        30.61        32.52        90.28        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-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C 
        0.30        80.75        78.84        23.93         9.30        23.05 
TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 
       22.78         1.45        35.67       114.35        13.48         0.53 
TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE 
       11.41        75.65        76.41        55.40        12.53        63.48 
TCGA-DD-AACF TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACN TCGA-DD-AACP 
       12.00        69.11         0.30         3.52        42.81        13.64 
TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AAD1 
       59.31        51.35        46.82         5.59        47.67        18.54 
TCGA-DD-AAD2 TCGA-DD-AAD6 TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE 
       21.63        22.09        40.83        13.97        40.47        39.52 
TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADM 
        3.78        37.64        35.67        35.05        34.49         0.39 
TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADV 
       14.89        15.06        14.33        15.58        18.21        18.87 
TCGA-DD-AADW TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 
       19.30        18.25        18.15        18.61        19.99         4.64 
TCGA-DD-AAE7 TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE 
       21.17        23.74        18.90        15.72        25.08        16.37 
TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ 
       23.64        25.78        50.33        35.08        79.07        89.69 
TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY 
       82.62        59.93        72.39        76.18        56.48        64.77 
TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A4XI 
       62.47        66.25        65.39        49.48        53.69        12.69 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XP 
       15.85        13.91        13.35        12.82         0.20        13.15 
TCGA-ED-A82E TCGA-ED-A8O5 TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB 
       13.41        13.35        18.74        19.99        20.61        19.59 
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        60.89 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A4ZP TCGA-FV-A4ZQ 
        8.12         6.38        12.03         0.03        81.73         0.39 
TCGA-G3-A25S TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG 
       13.68        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-A5SL 
       25.64         5.92        19.53        19.23        25.25        20.42 
TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-G3-AAUZ 
       17.10         7.76        12.03         5.98         1.84        11.24 
TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 
        8.55         9.70         9.17         8.75         2.14         3.02 
TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-K7-A5RF TCGA-K7-A6G5 TCGA-K7-AAU7 
        1.02         2.20         2.99        20.75        16.83         3.72 
TCGA-KR-A7K0 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C 
        2.14        24.36        12.72        13.97        12.03         9.57 
TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO 
       16.67        18.38        12.85        20.71         0.62        10.85 
TCGA-NI-A8LF TCGA-O8-A75V TCGA-RC-A7S9 TCGA-RC-A7SF TCGA-RC-A7SH TCGA-T1-A6J8 
       19.92        17.69        21.04        19.04        15.39         0.76 
TCGA-UB-A7MA TCGA-UB-A7MC TCGA-UB-A7ME TCGA-UB-A7MF TCGA-UB-AA0U TCGA-UB-AA0V 
       17.59        16.44        15.98         7.04        10.75        10.32 
TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA46 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ 
        0.99        12.99        24.85        35.77        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        79.30        11.21 

  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                          120.82 
  DEL PEAK 15(10Q23.31) MUTATED DEL PEAK 15(10Q23.31) WILD-TYPE 
                         19.215                          19.265 
[1] "0.1 - 113.0 (19.2)" "0.0 - 120.8 (19.3)"
[1] "hr=" "1.2"
D44V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE III STAGE IIIA
  DEL PEAK 15(10Q23.31) MUTATED        36       23         0         21
  DEL PEAK 15(10Q23.31) WILD-TYPE     132       61         3         38
                                 vv
clus                              STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 15(10Q23.31) MUTATED            2          4        1         1
  DEL PEAK 15(10Q23.31) WILD-TYPE          6          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                               36                             132
  STAGE II                              23                              61
  STAGE III                              0                               3
  STAGE IIIA                            21                              38
  STAGE IIIB                             2                               6
  STAGE IIIC                             4                               3
  STAGE IV                               1                               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      38  27  22   7
  DEL PEAK 15(10Q23.31) WILD-TYPE   141  64  51   5
D44V4, multiclass
       clus
vv      DEL PEAK 15(10Q23.31) MUTATED DEL PEAK 15(10Q23.31) WILD-TYPE
  T0+T1                            38                             141
  T2                               27                              64
  T3                               22                              51
  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    64   2
  DEL PEAK 15(10Q23.31) WILD-TYPE 185   1
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 15(10Q23.31) MUTATED     64    2
  DEL PEAK 15(10Q23.31) WILD-TYPE  185    1
   clus
vv  DEL PEAK 15(10Q23.31) MUTATED DEL PEAK 15(10Q23.31) WILD-TYPE
  0                            64                             185
  1                             2                               1
[1] 2 2
[1] FALSE
D44V6, binary
                                 cls
clus                                0   1
  DEL PEAK 15(10Q23.31) MUTATED    71   0
  DEL PEAK 15(10Q23.31) WILD-TYPE 189   4
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 15(10Q23.31) MUTATED     71    0
  DEL PEAK 15(10Q23.31) WILD-TYPE  189    4
   clus
vv  DEL PEAK 15(10Q23.31) MUTATED DEL PEAK 15(10Q23.31) WILD-TYPE
  0                            71                             189
  1                             0                               4
[1] 2 2
[1] FALSE
D44V7, binary
                                 cls
clus                                0   1
  DEL PEAK 15(10Q23.31) MUTATED    30  65
  DEL PEAK 15(10Q23.31) WILD-TYPE  83 179
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 15(10Q23.31) MUTATED     30   65
  DEL PEAK 15(10Q23.31) WILD-TYPE   83  179
        clus
vv       DEL PEAK 15(10Q23.31) MUTATED DEL PEAK 15(10Q23.31) WILD-TYPE
  FEMALE                            30                              83
  MALE                              65                             179
[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                         91
  DEL PEAK 15(10Q23.31) WILD-TYPE                      257
                                 vv
clus                              HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK 15(10Q23.31) MUTATED                                  4
  DEL PEAK 15(10Q23.31) WILD-TYPE                                3
D44V8, multiclass
                                  clus
vv                                 DEL PEAK 15(10Q23.31) MUTATED
  FIBROLAMELLAR CARCINOMA                                      0
  HEPATOCELLULAR CARCINOMA                                    91
  HEPATOCHOLANGIOCARCINOMA (MIXED)                             4
                                  clus
vv                                 DEL PEAK 15(10Q23.31) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                        2
  HEPATOCELLULAR CARCINOMA                                     257
  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 15(10Q23.31) MUTATED    81   4   0   8
  DEL PEAK 15(10Q23.31) WILD-TYPE 234  11   1  11
D44V9, multiclass
    clus
vv   DEL PEAK 15(10Q23.31) MUTATED DEL PEAK 15(10Q23.31) WILD-TYPE
  R0                            81                             234
  R1                             4                              11
  R2                             0                               1
  RX                             8                              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 15(10Q23.31) MUTATED                                  0    46
  DEL PEAK 15(10Q23.31) WILD-TYPE                                1   110
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 15(10Q23.31) MUTATED                          10    38
  DEL PEAK 15(10Q23.31) WILD-TYPE                         7   135
D44V10, multiclass
                                  clus
vv                                 DEL PEAK 15(10Q23.31) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                       46
  BLACK OR AFRICAN AMERICAN                                   10
  WHITE                                                       38
                                  clus
vv                                 DEL PEAK 15(10Q23.31) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               1
  ASIAN                                                        110
  BLACK OR AFRICAN AMERICAN                                      7
  WHITE                                                        135
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V11, binary
                                 cls
clus                                0   1
  DEL PEAK 15(10Q23.31) MUTATED     3  85
  DEL PEAK 15(10Q23.31) WILD-TYPE   8 244
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 15(10Q23.31) MUTATED      3   85
  DEL PEAK 15(10Q23.31) WILD-TYPE    8  244
                        clus
vv                       DEL PEAK 15(10Q23.31) MUTATED
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                            85
                        clus
vv                       DEL PEAK 15(10Q23.31) WILD-TYPE
  HISPANIC OR LATINO                                   8
  NOT HISPANIC OR LATINO                             244
[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    60  32
  DEL PEAK 16(10Q26.13) WILD-TYPE 165  77
  DEL PEAK 16(10Q26.13) MUTATED DEL PEAK 16(10Q26.13) WILD-TYPE 
                             92                             242 
  DEL PEAK 16(10Q26.13) MUTATED DEL PEAK 16(10Q26.13) WILD-TYPE 
                             32                              77 
$`DEL PEAK 16(10Q26.13) MUTATED`
TCGA-2Y-A9GS TCGA-2Y-A9GU TCGA-2Y-A9GV TCGA-2Y-A9H2 TCGA-2Y-A9H4 TCGA-2Y-A9H9 
       23.80        63.75        83.24        56.91        47.74        14.99 
TCGA-5C-AAPD TCGA-5R-AAAM TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10W 
        0.66         1.51        27.91        37.32        10.13         2.99 
TCGA-BC-A10Y TCGA-BC-A112 TCGA-BC-A217 TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A8YO 
       23.34         5.03        13.84        22.36        17.98        18.48 
TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5260 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA 
       13.45         0.66         2.86         3.32         0.10         0.07 
TCGA-CC-A3MC TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A11A TCGA-DD-A11C TCGA-DD-A1EB 
        0.13        37.78        83.57         2.60        21.76        66.31 
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-A73F TCGA-DD-AACG TCGA-DD-AACI TCGA-DD-AACM TCGA-DD-AACO 
       12.26        35.67        15.42        53.19        58.16        61.68 
TCGA-DD-AACQ TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACZ TCGA-DD-AAD3 TCGA-DD-AAD5 
       14.20        51.52        50.33         5.62        42.58        44.22 
TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADR 
       40.08        40.54        20.91         0.39        29.52        66.67 
TCGA-DD-AADY TCGA-DD-AAE2 TCGA-DD-AAE8 TCGA-ED-A459 TCGA-ED-A66Y TCGA-ED-A7PX 
       18.25        20.98        21.83        13.41         9.73         0.20 
TCGA-ED-A7XO TCGA-ED-A8O6 TCGA-ED-A97K TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 
       14.04         1.84         0.20        23.97        19.10        27.88 
TCGA-FV-A496 TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A5SJ 
        0.33        51.06        53.79        58.49        14.86        22.95 
TCGA-G3-AAV1 TCGA-G3-AAV4 TCGA-K7-A5RG TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-KR-A7K8 
       11.80         0.89        17.06        11.84        13.38        24.36 
TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7SB TCGA-RC-A7SK 
       10.85        58.88        21.01         3.09        19.33        15.52 
TCGA-RG-A7D4 TCGA-UB-A7MB TCGA-UB-A7MD TCGA-UB-AA0U TCGA-WQ-A9G7 TCGA-YA-A8S7 
       24.13        19.76         1.71        10.75         0.99        13.55 
TCGA-ZP-A9D1 TCGA-ZS-A9CE 
        0.69        40.80 

$`DEL PEAK 16(10Q26.13) WILD-TYPE`
TCGA-2Y-A9GT TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H0 
       53.39        41.79        80.28        24.89        27.88       120.82 
TCGA-2Y-A9H1 TCGA-2Y-A9H3 TCGA-2Y-A9H5 TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-2Y-A9H8 
       40.41        41.33        18.25        11.74        37.25        20.81 
TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-A9VH 
        1.18         8.55        13.02         8.61        10.78        10.59 
TCGA-5R-AA1C TCGA-5R-AA1D TCGA-BC-4072 TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
       11.97        11.08        48.99        46.78        27.52        27.52 
TCGA-BC-A10X TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A216 TCGA-BC-A3KF TCGA-BC-A69H 
       25.32         1.12        69.57        44.42         0.26        14.60 
TCGA-BC-A69I TCGA-BD-A2L6 TCGA-BD-A3ER TCGA-CC-5258 TCGA-CC-5261 TCGA-CC-5262 
       12.72        44.81        36.66         0.07         3.19         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 
       11.47        12.95        49.15         6.02        33.04        18.35 
TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Z TCGA-DD-A3A1 TCGA-DD-A3A2 
       21.14        27.19        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-A4NB TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NJ 
       30.61        32.52        90.28        30.97        30.15        30.51 
TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NR 
       39.78        56.25        29.56        73.81       108.76         0.30 
TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D 
       80.75        78.84        23.93         9.30        23.05        22.78 
TCGA-DD-A73E TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA 
        1.45       114.35        13.48         0.53        11.41        75.65 
TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACH 
       76.41        55.40        12.53        63.48        12.00         6.41 
TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACN TCGA-DD-AACP TCGA-DD-AACS 
       69.11         0.30         3.52        42.81        13.64        59.31 
TCGA-DD-AACT TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AAD0 TCGA-DD-AAD1 
       51.35        46.82         5.59        47.67         4.50        18.54 
TCGA-DD-AAD2 TCGA-DD-AAD6 TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE 
       21.63        22.09        40.83        13.97        40.47        39.52 
TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADO 
        3.78        37.64        35.67        35.05        34.49        14.89 
TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADV TCGA-DD-AADW 
       15.06        14.33        15.58        18.21        18.87        19.30 
TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE7 
       18.25        18.15        18.61        19.99         4.64        21.17 
TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEG 
       23.74        18.90        15.72        25.08        16.37        23.64 
TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR 
       25.78        50.33        35.08        79.07        89.69        82.62 
TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ 
       59.93        72.39        76.18        56.48        64.77        62.47 
TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A4XI TCGA-ED-A5KG 
       66.25        65.39        49.48        53.69        12.69        15.85 
TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-ED-A82E 
       13.91        13.35        12.82         0.20        13.15        13.41 
TCGA-ED-A8O5 TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC 
       13.35        18.74        19.99        20.61        19.59         0.62 
TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A3I1 
        9.96        11.93        22.85        14.40        60.89         8.12 
TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S 
        6.38        12.03         0.03        81.73         0.39        13.68 
TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI 
       28.27        30.74        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        25.25        20.42        17.10         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-AAV3 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB 
        9.17         8.75         2.14         3.02         1.02         2.20 
TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 
        2.99        37.91        20.75        16.83         3.72         2.14 
TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G 
       12.72        13.97        12.03         9.57        16.67        18.38 
TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A520 TCGA-NI-A8LF TCGA-O8-A75V TCGA-RC-A7S9 
       12.85        20.71         0.62        19.92        17.69        21.04 
TCGA-RC-A7SF TCGA-RC-A7SH TCGA-T1-A6J8 TCGA-UB-A7MA TCGA-UB-A7MC TCGA-UB-A7ME 
       19.04        15.39         0.76        17.59        16.44        15.98 
TCGA-UB-A7MF TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-AB4B TCGA-WX-AA46 TCGA-ZP-A9CV 
        7.04        10.32        11.34        12.99        24.85        35.77 
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 
       79.30        11.21 

  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                          120.82 
  DEL PEAK 16(10Q26.13) MUTATED DEL PEAK 16(10Q26.13) WILD-TYPE 
                         18.790                          19.415 
[1] "0.1 - 83.6 (18.8)"  "0.0 - 120.8 (19.4)"
[1] "hr=" "1.3"
D45V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE III STAGE IIIA
  DEL PEAK 16(10Q26.13) MUTATED        41       26         0         20
  DEL PEAK 16(10Q26.13) WILD-TYPE     127       58         3         39
                                 vv
clus                              STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 16(10Q26.13) MUTATED            2          4        1         1
  DEL PEAK 16(10Q26.13) WILD-TYPE          6          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                               41                             127
  STAGE II                              26                              58
  STAGE III                              0                               3
  STAGE IIIA                            20                              39
  STAGE IIIB                             2                               6
  STAGE IIIC                             4                               3
  STAGE IV                               1                               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      43  29  23   7
  DEL PEAK 16(10Q26.13) WILD-TYPE   136  62  50   5
D45V4, multiclass
       clus
vv      DEL PEAK 16(10Q26.13) MUTATED DEL PEAK 16(10Q26.13) WILD-TYPE
  T0+T1                            43                             136
  T2                               29                              62
  T3                               23                              50
  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    70   2
  DEL PEAK 16(10Q26.13) WILD-TYPE 179   1
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 16(10Q26.13) MUTATED     70    2
  DEL PEAK 16(10Q26.13) WILD-TYPE  179    1
   clus
vv  DEL PEAK 16(10Q26.13) MUTATED DEL PEAK 16(10Q26.13) WILD-TYPE
  0                            70                             179
  1                             2                               1
[1] 2 2
[1] FALSE
D45V6, binary
                                 cls
clus                                0   1
  DEL PEAK 16(10Q26.13) MUTATED    75   0
  DEL PEAK 16(10Q26.13) WILD-TYPE 185   4
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 16(10Q26.13) MUTATED     75    0
  DEL PEAK 16(10Q26.13) WILD-TYPE  185    4
   clus
vv  DEL PEAK 16(10Q26.13) MUTATED DEL PEAK 16(10Q26.13) WILD-TYPE
  0                            75                             185
  1                             0                               4
[1] 2 2
[1] FALSE
D45V7, binary
                                 cls
clus                                0   1
  DEL PEAK 16(10Q26.13) MUTATED    33  69
  DEL PEAK 16(10Q26.13) WILD-TYPE  80 175
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 16(10Q26.13) MUTATED     33   69
  DEL PEAK 16(10Q26.13) WILD-TYPE   80  175
        clus
vv       DEL PEAK 16(10Q26.13) MUTATED DEL PEAK 16(10Q26.13) WILD-TYPE
  FEMALE                            33                              80
  MALE                              69                             175
[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                         97
  DEL PEAK 16(10Q26.13) WILD-TYPE                      251
                                 vv
clus                              HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK 16(10Q26.13) MUTATED                                  4
  DEL PEAK 16(10Q26.13) WILD-TYPE                                3
D45V8, multiclass
                                  clus
vv                                 DEL PEAK 16(10Q26.13) MUTATED
  FIBROLAMELLAR CARCINOMA                                      1
  HEPATOCELLULAR CARCINOMA                                    97
  HEPATOCHOLANGIOCARCINOMA (MIXED)                             4
                                  clus
vv                                 DEL PEAK 16(10Q26.13) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                        1
  HEPATOCELLULAR CARCINOMA                                     251
  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 16(10Q26.13) MUTATED    87   5   0   8
  DEL PEAK 16(10Q26.13) WILD-TYPE 228  10   1  11
D45V9, multiclass
    clus
vv   DEL PEAK 16(10Q26.13) MUTATED DEL PEAK 16(10Q26.13) WILD-TYPE
  R0                            87                             228
  R1                             5                              10
  R2                             0                               1
  RX                             8                              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 16(10Q26.13) MUTATED                                  0    48
  DEL PEAK 16(10Q26.13) WILD-TYPE                                1   108
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 16(10Q26.13) MUTATED                          10    42
  DEL PEAK 16(10Q26.13) WILD-TYPE                         7   131
D45V10, multiclass
                                  clus
vv                                 DEL PEAK 16(10Q26.13) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                       48
  BLACK OR AFRICAN AMERICAN                                   10
  WHITE                                                       42
                                  clus
vv                                 DEL PEAK 16(10Q26.13) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               1
  ASIAN                                                        108
  BLACK OR AFRICAN AMERICAN                                      7
  WHITE                                                        131
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V11, binary
                                 cls
clus                                0   1
  DEL PEAK 16(10Q26.13) MUTATED     3  92
  DEL PEAK 16(10Q26.13) WILD-TYPE   8 237
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 16(10Q26.13) MUTATED      3   92
  DEL PEAK 16(10Q26.13) WILD-TYPE    8  237
                        clus
vv                       DEL PEAK 16(10Q26.13) MUTATED
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                            92
                        clus
vv                       DEL PEAK 16(10Q26.13) WILD-TYPE
  HISPANIC OR LATINO                                   8
  NOT HISPANIC OR LATINO                             237
[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    44  19
  DEL PEAK 17(11Q14.1) WILD-TYPE 181  90
  DEL PEAK 17(11Q14.1) MUTATED DEL PEAK 17(11Q14.1) WILD-TYPE 
                            63                            271 
  DEL PEAK 17(11Q14.1) MUTATED DEL PEAK 17(11Q14.1) WILD-TYPE 
                            19                             90 
$`DEL PEAK 17(11Q14.1) MUTATED`
TCGA-2Y-A9GS TCGA-2Y-A9GY TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-3K-AAZ8 TCGA-5C-A9VG 
       23.80        24.89        56.91        41.33        13.02        10.78 
TCGA-5C-AAPD TCGA-5R-AA1D TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10S TCGA-BC-A112 
        0.66        11.08        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        33.04        55.69        32.52 
TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-A73B TCGA-DD-AACB TCGA-DD-AACP TCGA-DD-AACV 
       90.28        26.83         9.30        76.41        13.64        50.33 
TCGA-DD-AACY TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADD TCGA-DD-AADO 
       47.67        44.22        22.09        40.08        40.47        14.89 
TCGA-DD-AADP TCGA-DD-AADY TCGA-DD-AAE3 TCGA-DD-AAE6 TCGA-DD-AAED TCGA-DD-AAEK 
       15.06        18.25        18.61         4.64        25.08        35.08 
TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A8O6 TCGA-EP-A2KC TCGA-FV-A2QQ TCGA-FV-A4ZP 
        0.20        14.04         1.84         0.62        23.97        81.73 
TCGA-G3-A25S TCGA-G3-A5SJ TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV6 TCGA-K7-A5RG 
       13.68        22.95        11.80         9.70         2.14        17.06 
TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RG-A7D4 TCGA-UB-A7MA 
       11.84        13.38        19.33        19.04        24.13        17.59 
TCGA-UB-A7MC TCGA-UB-A7MF TCGA-YA-A8S7 
       16.44         7.04        13.55 

$`DEL PEAK 17(11Q14.1) WILD-TYPE`
TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GV TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GZ 
       53.39        63.75        83.24        41.79        80.28        27.88 
TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H6 TCGA-2Y-A9H7 
      120.82        40.41        47.74        18.25        11.74        37.25 
TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-4R-AA8I TCGA-5C-A9VH 
       20.81        14.99         1.18         8.55         8.61        10.59 
TCGA-5R-AA1C TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U 
       11.97         1.51        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-A2L6 
       22.36        17.98        14.60        12.72        18.48        44.81 
TCGA-BD-A3EP TCGA-BD-A3ER TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 
       13.45        36.66         0.66         0.07         2.86         3.19 
TCGA-CC-5262 TCGA-CC-A1HT TCGA-CC-A3MA TCGA-CC-A3MB TCGA-DD-A114 TCGA-DD-A115 
        3.39         3.32         0.07         0.10        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-A1EG 
       79.40        66.31        19.79        75.65        11.47        45.11 
TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W 
       49.15         6.02        18.35        13.64        21.14        27.19 
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-A4NA TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL 
       33.14        30.97        30.15        30.51        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        23.93        23.05        22.78         1.45        35.67 
TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACC 
      114.35        13.48         0.53        11.41        75.65        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-AACN TCGA-DD-AACO 
       69.11         0.30         3.52        58.16        42.81        61.68 
TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACW TCGA-DD-AACX 
       14.20        59.31        51.35        51.52        46.82         5.59 
TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AADA 
        5.62         4.50        18.54        21.63        42.58        40.54 
TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI 
       40.83        13.97        39.52         3.78        37.64        35.67 
TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADQ 
       35.05        34.49        20.91         0.39        29.52        14.33 
TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADV TCGA-DD-AADW TCGA-DD-AAE0 
       66.67        15.58        18.21        18.87        19.30        18.25 
TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE4 TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAE9 
       18.15        20.98        19.99        21.17        21.83        23.74 
TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAEI 
       18.90        15.72        16.37        23.64        25.78        50.33 
TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW 
       79.07        89.69        82.62        59.93        72.39        76.18 
TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 
       56.48        64.77        62.47        66.25        65.39        49.48 
TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X 
       53.69        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 
        9.73         0.20        12.82        13.15        13.41        13.35 
TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A3JL 
        0.20        18.74        19.99        20.61        19.59         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        60.89        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        12.03         0.03         0.33         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-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 
       25.25        20.42        17.10         7.76        12.03         5.98 
TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 
        1.84        11.24         8.55         9.17         0.89         8.75 
TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF 
        3.02         1.02         2.20         2.99        37.91        20.75 
TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC 
       16.83         3.72         2.14        24.36        12.72        13.97 
TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I 
       12.03         9.57        16.67        18.38        12.85        20.71 
TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF 
        0.62        10.85        58.88        19.92        17.69        21.01 
TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SH TCGA-RC-A7SK TCGA-T1-A6J8 TCGA-UB-A7MB 
        3.09        21.04        15.39        15.52         0.76        19.76 
TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-A9G7 
        1.71        15.98        10.75        10.32        11.34         0.99 
TCGA-WQ-AB4B TCGA-WX-AA46 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 
       12.99        24.85        35.77        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        40.80        79.30 
TCGA-ZS-A9CG 
       11.21 

  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                         120.82 
  DEL PEAK 17(11Q14.1) MUTATED DEL PEAK 17(11Q14.1) WILD-TYPE 
                         17.59                          19.76 
[1] "0.1 - 90.7 (17.6)"  "0.0 - 120.8 (19.8)"
[1] "hr=" "1"  
D46V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IIIA
  DEL PEAK 17(11Q14.1) MUTATED        29       15         0         19
  DEL PEAK 17(11Q14.1) WILD-TYPE     139       69         3         40
                                vv
clus                             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 17(11Q14.1) MUTATED            1          2        2         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                              29                            139
  STAGE II                             15                             69
  STAGE III                             0                              3
  STAGE IIIA                           19                             40
  STAGE IIIB                            1                              7
  STAGE IIIC                            2                              5
  STAGE IV                              2                              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      31  18  22   1
  DEL PEAK 17(11Q14.1) WILD-TYPE   148  73  51  11
D46V4, multiclass
       clus
vv      DEL PEAK 17(11Q14.1) MUTATED DEL PEAK 17(11Q14.1) WILD-TYPE
  T0+T1                           31                            148
  T2                              18                             73
  T3                              22                             51
  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    53   2
  DEL PEAK 17(11Q14.1) WILD-TYPE 196   1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 17(11Q14.1) MUTATED     53    2
  DEL PEAK 17(11Q14.1) WILD-TYPE  196    1
   clus
vv  DEL PEAK 17(11Q14.1) MUTATED DEL PEAK 17(11Q14.1) WILD-TYPE
  0                           53                            196
  1                            2                              1
[1] 2 2
[1] FALSE
D46V6, binary
                                cls
clus                               0   1
  DEL PEAK 17(11Q14.1) MUTATED    56   1
  DEL PEAK 17(11Q14.1) WILD-TYPE 204   3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 17(11Q14.1) MUTATED     56    1
  DEL PEAK 17(11Q14.1) WILD-TYPE  204    3
   clus
vv  DEL PEAK 17(11Q14.1) MUTATED DEL PEAK 17(11Q14.1) WILD-TYPE
  0                           56                            204
  1                            1                              3
[1] 2 2
[1] FALSE
D46V7, binary
                                cls
clus                               0   1
  DEL PEAK 17(11Q14.1) MUTATED    23  49
  DEL PEAK 17(11Q14.1) WILD-TYPE  90 195
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 17(11Q14.1) MUTATED     23   49
  DEL PEAK 17(11Q14.1) WILD-TYPE   90  195
        clus
vv       DEL PEAK 17(11Q14.1) MUTATED DEL PEAK 17(11Q14.1) WILD-TYPE
  FEMALE                           23                             90
  MALE                             49                            195
[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                         68
  DEL PEAK 17(11Q14.1) WILD-TYPE                      280
                                vv
clus                             HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK 17(11Q14.1) MUTATED                                  3
  DEL PEAK 17(11Q14.1) WILD-TYPE                                4
D46V8, multiclass
                                  clus
vv                                 DEL PEAK 17(11Q14.1) MUTATED
  FIBROLAMELLAR CARCINOMA                                     1
  HEPATOCELLULAR CARCINOMA                                   68
  HEPATOCHOLANGIOCARCINOMA (MIXED)                            3
                                  clus
vv                                 DEL PEAK 17(11Q14.1) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                       1
  HEPATOCELLULAR CARCINOMA                                    280
  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 17(11Q14.1) MUTATED    63   5   0   4
  DEL PEAK 17(11Q14.1) WILD-TYPE 252  10   1  15
D46V9, multiclass
    clus
vv   DEL PEAK 17(11Q14.1) MUTATED DEL PEAK 17(11Q14.1) WILD-TYPE
  R0                           63                            252
  R1                            5                             10
  R2                            0                              1
  RX                            4                             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 17(11Q14.1) MUTATED                                  0    33
  DEL PEAK 17(11Q14.1) WILD-TYPE                                1   123
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 17(11Q14.1) MUTATED                           5    34
  DEL PEAK 17(11Q14.1) WILD-TYPE                        12   139
D46V10, multiclass
                                  clus
vv                                 DEL PEAK 17(11Q14.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                      33
  BLACK OR AFRICAN AMERICAN                                   5
  WHITE                                                      34
                                  clus
vv                                 DEL PEAK 17(11Q14.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                       123
  BLACK OR AFRICAN AMERICAN                                    12
  WHITE                                                       139
[1] 4 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     5  63
  DEL PEAK 17(11Q14.1) WILD-TYPE   6 266
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 17(11Q14.1) MUTATED      5   63
  DEL PEAK 17(11Q14.1) WILD-TYPE    6  266
                        clus
vv                       DEL PEAK 17(11Q14.1) MUTATED
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                           63
                        clus
vv                       DEL PEAK 17(11Q14.1) WILD-TYPE
  HISPANIC OR LATINO                                  6
  NOT HISPANIC OR LATINO                            266
[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    58  22
  DEL PEAK 18(11Q24.2) WILD-TYPE 167  87
  DEL PEAK 18(11Q24.2) MUTATED DEL PEAK 18(11Q24.2) WILD-TYPE 
                            80                            254 
  DEL PEAK 18(11Q24.2) MUTATED DEL PEAK 18(11Q24.2) WILD-TYPE 
                            22                             87 
$`DEL PEAK 18(11Q24.2) MUTATED`
TCGA-2Y-A9GS TCGA-2Y-A9GY TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-3K-AAZ8 TCGA-5C-A9VG 
       23.80        24.89        56.91        41.33        13.02        10.78 
TCGA-5C-AAPD TCGA-5R-AA1D TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10S TCGA-BC-A112 
        0.66        11.08        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 
       33.04        55.69        32.52        90.28        26.83        29.56 
TCGA-DD-A73B TCGA-DD-A73E TCGA-DD-AACB TCGA-DD-AACI TCGA-DD-AACO TCGA-DD-AACP 
        9.30         1.45        76.41        53.19        61.68        13.64 
TCGA-DD-AACV TCGA-DD-AACY TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADD 
       50.33        47.67        44.22        22.09        40.08        40.47 
TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADY TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE6 
       14.89        15.06        18.25        20.98        18.61         4.64 
TCGA-DD-AAED TCGA-DD-AAEK TCGA-DD-AAVP TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A8O6 
       25.08        35.08        79.07         0.20        14.04         1.84 
TCGA-EP-A2KC TCGA-FV-A2QQ TCGA-FV-A4ZP TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A5SJ 
        0.62        23.97        81.73        13.68        53.79        22.95 
TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV6 TCGA-GJ-A6C0 TCGA-K7-A5RG 
        8.55        11.80         9.70         2.14         1.02        17.06 
TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-PD-A5DF TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RG-A7D4 
       11.84        13.38        21.01        19.33        19.04        24.13 
TCGA-UB-A7MA TCGA-UB-A7MC TCGA-UB-A7ME TCGA-UB-A7MF TCGA-WQ-AB4B TCGA-YA-A8S7 
       17.59        16.44        15.98         7.04        12.99        13.55 
TCGA-ZP-A9CZ TCGA-ZP-A9D0 
       23.21        23.57 

$`DEL PEAK 18(11Q24.2) WILD-TYPE`
TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GV TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GZ 
       53.39        63.75        83.24        41.79        80.28        27.88 
TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H6 TCGA-2Y-A9H7 
      120.82        40.41        47.74        18.25        11.74        37.25 
TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-4R-AA8I TCGA-5C-A9VH 
       20.81        14.99         1.18         8.55         8.61        10.59 
TCGA-5R-AA1C TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U 
       11.97         1.51        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-A2L6 TCGA-BD-A3EP 
       22.36        17.98        12.72        18.48        44.81        13.45 
TCGA-BD-A3ER TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-A1HT 
       36.66         0.07         2.86         3.19         3.39         3.32 
TCGA-CC-A3MB TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 
        0.10        37.78        83.57        53.33       113.00         7.33 
TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC 
        0.46        21.76        51.29        79.40        66.31        19.79 
TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EK 
       75.65        11.47        45.11        49.15         6.02        18.35 
TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 
       13.64        21.14        27.19         5.62        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-A3A9 TCGA-DD-A4NA TCGA-DD-A4NF TCGA-DD-A4NH 
       13.78         0.36        30.61        33.14        30.97        30.15 
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-A4NV TCGA-DD-A73A TCGA-DD-A73C TCGA-DD-A73D 
        0.30        80.75        78.84        23.93        23.05        22.78 
TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA 
       35.67       114.35        13.48         0.53        11.41        75.65 
TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH 
       55.40        12.53        63.48        12.00        15.42         6.41 
TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACQ 
       69.11         0.30         3.52        58.16        42.81        14.20 
TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACZ 
       59.31        51.35        51.52        46.82         5.59         5.62 
TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AADA TCGA-DD-AADB 
        4.50        18.54        21.63        42.58        40.54        40.83 
TCGA-DD-AADC TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ 
       13.97        39.52         3.78        37.64        35.67        35.05 
TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADQ TCGA-DD-AADR 
       34.49        20.91         0.39        29.52        14.33        66.67 
TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADV TCGA-DD-AADW TCGA-DD-AAE0 TCGA-DD-AAE1 
       15.58        18.21        18.87        19.30        18.25        18.15 
TCGA-DD-AAE4 TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB 
       19.99        21.17        21.83        23.74        18.90        15.72 
TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAVQ TCGA-DD-AAVR 
       16.37        23.64        25.78        50.33        89.69        82.62 
TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ 
       59.93        72.39        76.18        56.48        64.77        62.47 
TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI 
       66.25        65.39        49.48        53.69        13.41        12.69 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY 
       15.85        13.91        13.35         9.73         0.20        12.82 
TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S 
       13.15        13.41        13.35         0.20        18.74        19.99 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT 
       20.61        19.59         9.96        11.93        22.85        14.40 
TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 
       60.89        19.10        27.88         8.12         6.38        12.03 
TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25V TCGA-G3-A25W 
        0.03         0.33         0.39        51.06        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        25.25        20.42        17.10         7.76 
TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV3 TCGA-G3-AAV4 
       12.03         5.98         1.84        11.24         9.17         0.89 
TCGA-G3-AAV5 TCGA-G3-AAV7 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF 
        8.75         3.02         2.20         2.99        37.91        20.75 
TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC 
       16.83         3.72         2.14        24.36        12.72        13.97 
TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I 
       12.03         9.57        16.67        18.38        12.85        20.71 
TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-QA-A7B7 
        0.62        10.85        58.88        19.92        17.69         3.09 
TCGA-RC-A7S9 TCGA-RC-A7SH TCGA-RC-A7SK TCGA-T1-A6J8 TCGA-UB-A7MB TCGA-UB-A7MD 
       21.04        15.39        15.52         0.76        19.76         1.71 
TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WX-AA46 TCGA-ZP-A9CV 
       10.75        10.32        11.34         0.99        24.85        35.77 
TCGA-ZP-A9CY TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE 
       25.71         0.69        24.43        12.99        45.57        40.80 
TCGA-ZS-A9CF TCGA-ZS-A9CG 
       79.30        11.21 

  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                         120.82 
  DEL PEAK 18(11Q24.2) MUTATED DEL PEAK 18(11Q24.2) WILD-TYPE 
                        17.920                         19.675 
[1] "0.1 - 90.7 (17.9)"  "0.0 - 120.8 (19.7)"
[1] "hr=" "1.1"
D47V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IIIA
  DEL PEAK 18(11Q24.2) MUTATED        37       20         0         21
  DEL PEAK 18(11Q24.2) WILD-TYPE     131       64         3         38
                                vv
clus                             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 18(11Q24.2) MUTATED            2          2        2         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                              37                            131
  STAGE II                             20                             64
  STAGE III                             0                              3
  STAGE IIIA                           21                             38
  STAGE IIIB                            2                              6
  STAGE IIIC                            2                              5
  STAGE IV                              2                              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      41  23  24   2
  DEL PEAK 18(11Q24.2) WILD-TYPE   138  68  49  10
D47V4, multiclass
       clus
vv      DEL PEAK 18(11Q24.2) MUTATED DEL PEAK 18(11Q24.2) WILD-TYPE
  T0+T1                           41                            138
  T2                              23                             68
  T3                              24                             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"
D47V5, binary
                                cls
clus                               0   1
  DEL PEAK 18(11Q24.2) MUTATED    64   2
  DEL PEAK 18(11Q24.2) WILD-TYPE 185   1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(11Q24.2) MUTATED     64    2
  DEL PEAK 18(11Q24.2) WILD-TYPE  185    1
   clus
vv  DEL PEAK 18(11Q24.2) MUTATED DEL PEAK 18(11Q24.2) WILD-TYPE
  0                           64                            185
  1                            2                              1
[1] 2 2
[1] FALSE
D47V6, binary
                                cls
clus                               0   1
  DEL PEAK 18(11Q24.2) MUTATED    69   1
  DEL PEAK 18(11Q24.2) WILD-TYPE 191   3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(11Q24.2) MUTATED     69    1
  DEL PEAK 18(11Q24.2) WILD-TYPE  191    3
   clus
vv  DEL PEAK 18(11Q24.2) MUTATED DEL PEAK 18(11Q24.2) WILD-TYPE
  0                           69                            191
  1                            1                              3
[1] 2 2
[1] FALSE
D47V7, binary
                                cls
clus                               0   1
  DEL PEAK 18(11Q24.2) MUTATED    29  61
  DEL PEAK 18(11Q24.2) WILD-TYPE  84 183
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(11Q24.2) MUTATED     29   61
  DEL PEAK 18(11Q24.2) WILD-TYPE   84  183
        clus
vv       DEL PEAK 18(11Q24.2) MUTATED DEL PEAK 18(11Q24.2) WILD-TYPE
  FEMALE                           29                             84
  MALE                             61                            183
[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                         86
  DEL PEAK 18(11Q24.2) WILD-TYPE                      262
                                vv
clus                             HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK 18(11Q24.2) MUTATED                                  3
  DEL PEAK 18(11Q24.2) WILD-TYPE                                4
D47V8, multiclass
                                  clus
vv                                 DEL PEAK 18(11Q24.2) MUTATED
  FIBROLAMELLAR CARCINOMA                                     1
  HEPATOCELLULAR CARCINOMA                                   86
  HEPATOCHOLANGIOCARCINOMA (MIXED)                            3
                                  clus
vv                                 DEL PEAK 18(11Q24.2) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                       1
  HEPATOCELLULAR CARCINOMA                                    262
  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 18(11Q24.2) MUTATED    78   5   0   6
  DEL PEAK 18(11Q24.2) WILD-TYPE 237  10   1  13
D47V9, multiclass
    clus
vv   DEL PEAK 18(11Q24.2) MUTATED DEL PEAK 18(11Q24.2) WILD-TYPE
  R0                           78                            237
  R1                            5                             10
  R2                            0                              1
  RX                            6                             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 18(11Q24.2) MUTATED                                  0    43
  DEL PEAK 18(11Q24.2) WILD-TYPE                                1   113
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 18(11Q24.2) MUTATED                           7    40
  DEL PEAK 18(11Q24.2) WILD-TYPE                        10   133
D47V10, multiclass
                                  clus
vv                                 DEL PEAK 18(11Q24.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                      43
  BLACK OR AFRICAN AMERICAN                                   7
  WHITE                                                      40
                                  clus
vv                                 DEL PEAK 18(11Q24.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                       113
  BLACK OR AFRICAN AMERICAN                                    10
  WHITE                                                       133
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V11, binary
                                cls
clus                               0   1
  DEL PEAK 18(11Q24.2) MUTATED     5  81
  DEL PEAK 18(11Q24.2) WILD-TYPE   6 248
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(11Q24.2) MUTATED      5   81
  DEL PEAK 18(11Q24.2) WILD-TYPE    6  248
                        clus
vv                       DEL PEAK 18(11Q24.2) MUTATED
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                           81
                        clus
vv                       DEL PEAK 18(11Q24.2) WILD-TYPE
  HISPANIC OR LATINO                                  6
  NOT HISPANIC OR LATINO                            248
[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    46  20
  DEL PEAK 19(12P12.1) WILD-TYPE 179  89
  DEL PEAK 19(12P12.1) MUTATED DEL PEAK 19(12P12.1) WILD-TYPE 
                            66                            268 
  DEL PEAK 19(12P12.1) MUTATED DEL PEAK 19(12P12.1) WILD-TYPE 
                            20                             89 
$`DEL PEAK 19(12P12.1) MUTATED`
TCGA-2Y-A9GS TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-BC-4073 TCGA-BC-A10Y TCGA-BC-A217 
       23.80         8.55        13.02        27.91        23.34        13.84 
TCGA-BC-A3KF TCGA-BC-A5W4 TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-CC-A1HT TCGA-CC-A3MA 
        0.26        17.98        44.81        13.45         3.32         0.07 
TCGA-CC-A3MC TCGA-DD-A119 TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EJ TCGA-DD-A1EL 
        0.13         7.33        45.11        49.15        33.04        13.64 
TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A3A1 TCGA-DD-A3A7 TCGA-DD-A4NA TCGA-DD-A4NH 
       55.69         5.62         7.66        13.78        33.14        30.15 
TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NO TCGA-DD-A73F TCGA-DD-AACE TCGA-DD-AACG 
       26.83        30.51        73.81        35.67        63.48        15.42 
TCGA-DD-AACN TCGA-DD-AACU TCGA-DD-AACY TCGA-DD-AAD5 TCGA-DD-AAD8 TCGA-DD-AADD 
       42.81        51.52        47.67        44.22        40.08        40.47 
TCGA-DD-AADJ TCGA-DD-AADM TCGA-DD-AADO TCGA-DD-AAE3 TCGA-DD-AAEE TCGA-DD-AAEI 
       35.05         0.39        14.89        18.61        16.37        50.33 
TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVU TCGA-ED-A7XP TCGA-EP-A2KC TCGA-FV-A3I1 
       35.08        79.07        72.39        13.15         0.62         8.12 
TCGA-FV-A3R2 TCGA-FV-A496 TCGA-G3-A25S TCGA-G3-A25Z TCGA-G3-A7M6 TCGA-G3-AAV0 
        6.38         0.33        13.68        21.53        12.03         8.55 
TCGA-G3-AAV3 TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-K7-AAU7 TCGA-MI-A75G TCGA-MI-A75I 
        9.17         3.02         1.02         3.72        18.38        20.71 
TCGA-MR-A8JO TCGA-PD-A5DF TCGA-RC-A7SK TCGA-T1-A6J8 TCGA-UB-AA0U TCGA-ZP-A9D1 
       10.85        21.01        15.52         0.76        10.75         0.69 

$`DEL PEAK 19(12P12.1) WILD-TYPE`
TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GV TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GY 
       53.39        63.75        83.24        41.79        80.28        24.89 
TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H4 
       27.88       120.82        40.41        56.91        41.33        47.74 
TCGA-2Y-A9H5 TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA 
       18.25        11.74        37.25        20.81        14.99         1.18 
TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D 
        8.61        10.78        10.59         0.66        11.97        11.08 
TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T 
        1.51        48.99        37.32        10.13        46.78        27.52 
TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 
       27.52         2.99        25.32         1.12        69.57         5.03 
TCGA-BC-A216 TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A3ER 
       44.42        22.36        14.60        12.72        18.48        36.66 
TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 
        0.66         0.07         2.86         3.19         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-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 
      113.00         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        11.47        12.95 
TCGA-DD-A1EI TCGA-DD-A1EK TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39Z TCGA-DD-A3A0 
        6.02        18.35        21.14        27.19        19.76        25.81 
TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A8 
       70.06        17.59        20.12       102.74       107.11         0.36 
TCGA-DD-A3A9 TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NK TCGA-DD-A4NL 
       30.61        32.52        90.28        30.97        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 
       23.93         9.30        23.05        22.78         1.45       114.35 
TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC 
       13.48         0.53        11.41        75.65        76.41        55.40 
TCGA-DD-AACD TCGA-DD-AACF TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK 
       12.53        12.00         6.41        53.19        69.11         0.30 
TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS 
        3.52        58.16        61.68        13.64        14.20        59.31 
TCGA-DD-AACT TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACZ TCGA-DD-AAD0 
       51.35        50.33        46.82         5.59         5.62         4.50 
TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD6 TCGA-DD-AADA TCGA-DD-AADB 
       18.54        21.63        42.58        22.09        40.54        40.83 
TCGA-DD-AADC TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADK 
       13.97        39.52         3.78        37.64        35.67        34.49 
TCGA-DD-AADL TCGA-DD-AADN TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS 
       20.91        29.52        15.06        14.33        66.67        15.58 
TCGA-DD-AADU TCGA-DD-AADV TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 
       18.21        18.87        19.30        18.25        18.25        18.15 
TCGA-DD-AAE2 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAE9 
       20.98        19.99         4.64        21.17        21.83        23.74 
TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAVQ 
       18.90        15.72        25.08        23.64        25.78        89.69 
TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ 
       82.62        59.93        76.18        56.48        64.77        62.47 
TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI 
       66.25        65.39        49.48        53.69        13.41        12.69 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY 
       15.85        13.91        13.35         9.73         0.20        12.82 
TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K 
        0.20        14.04        13.41        13.35         1.84         0.20 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A3JL TCGA-EP-A3RK 
       18.74        19.99        20.61        19.59         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        60.89        23.97        19.10        27.88 
TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25U 
       12.03         0.03        81.73         0.39        51.06        53.79 
TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A3CG TCGA-G3-A3CH 
       28.27        30.74        58.49        14.86        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        25.25        22.95        20.42 
TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV1 
       17.10         7.76         5.98         1.84        11.24        11.80 
TCGA-G3-AAV2 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-GJ-A9DB TCGA-HP-A5MZ 
        9.70         0.89         8.75         2.14         2.20         2.99 
TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 
       37.91        20.75        17.06        16.83         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        13.97        12.03         9.57 
TCGA-MI-A75E TCGA-MI-A75H TCGA-MR-A520 TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V 
       16.67        12.85         0.62        58.88        19.92        17.69 
TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RG-A7D4 
        3.09        21.04        19.33        19.04        15.39        24.13 
TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-A7MF 
       17.59        19.76        16.44         1.71        15.98         7.04 
TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA46 TCGA-YA-A8S7 
       10.32        11.34         0.99        12.99        24.85        13.55 
TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 
       35.77        25.71        23.21        23.57        24.43        12.99 
TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       45.57        40.80        79.30        11.21 

  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                         120.82 
  DEL PEAK 19(12P12.1) MUTATED DEL PEAK 19(12P12.1) WILD-TYPE 
                        15.945                         19.675 
[1] "0.1 - 79.1 (15.9)"  "0.0 - 120.8 (19.7)"
[1] "hr=" "1.1"
D48V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IIIA
  DEL PEAK 19(12P12.1) MUTATED        30       17         1         10
  DEL PEAK 19(12P12.1) WILD-TYPE     138       67         2         49
                                vv
clus                             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 19(12P12.1) MUTATED            5          2        3         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                              30                            138
  STAGE II                             17                             67
  STAGE III                             1                              2
  STAGE IIIA                           10                             49
  STAGE IIIB                            5                              3
  STAGE IIIC                            2                              5
  STAGE IV                              3                              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      33  22  15   3
  DEL PEAK 19(12P12.1) WILD-TYPE   146  69  58   9
D48V4, multiclass
       clus
vv      DEL PEAK 19(12P12.1) MUTATED DEL PEAK 19(12P12.1) WILD-TYPE
  T0+T1                           33                            146
  T2                              22                             69
  T3                              15                             58
  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    50   2
  DEL PEAK 19(12P12.1) WILD-TYPE 199   1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(12P12.1) MUTATED     50    2
  DEL PEAK 19(12P12.1) WILD-TYPE  199    1
   clus
vv  DEL PEAK 19(12P12.1) MUTATED DEL PEAK 19(12P12.1) WILD-TYPE
  0                           50                            199
  1                            2                              1
[1] 2 2
[1] FALSE
D48V6, binary
                                cls
clus                               0   1
  DEL PEAK 19(12P12.1) MUTATED    55   2
  DEL PEAK 19(12P12.1) WILD-TYPE 205   2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(12P12.1) MUTATED     55    2
  DEL PEAK 19(12P12.1) WILD-TYPE  205    2
   clus
vv  DEL PEAK 19(12P12.1) MUTATED DEL PEAK 19(12P12.1) WILD-TYPE
  0                           55                            205
  1                            2                              2
[1] 2 2
[1] FALSE
D48V7, binary
                                cls
clus                               0   1
  DEL PEAK 19(12P12.1) MUTATED    22  51
  DEL PEAK 19(12P12.1) WILD-TYPE  91 193
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(12P12.1) MUTATED     22   51
  DEL PEAK 19(12P12.1) WILD-TYPE   91  193
        clus
vv       DEL PEAK 19(12P12.1) MUTATED DEL PEAK 19(12P12.1) WILD-TYPE
  FEMALE                           22                             91
  MALE                             51                            193
[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                         71
  DEL PEAK 19(12P12.1) WILD-TYPE                      277
                                vv
clus                             HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK 19(12P12.1) MUTATED                                  1
  DEL PEAK 19(12P12.1) WILD-TYPE                                6
D48V8, multiclass
                                  clus
vv                                 DEL PEAK 19(12P12.1) MUTATED
  FIBROLAMELLAR CARCINOMA                                     1
  HEPATOCELLULAR CARCINOMA                                   71
  HEPATOCHOLANGIOCARCINOMA (MIXED)                            1
                                  clus
vv                                 DEL PEAK 19(12P12.1) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                       1
  HEPATOCELLULAR CARCINOMA                                    277
  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    60   4   1   6
  DEL PEAK 19(12P12.1) WILD-TYPE 255  11   0  13
D48V9, multiclass
    clus
vv   DEL PEAK 19(12P12.1) MUTATED DEL PEAK 19(12P12.1) WILD-TYPE
  R0                           60                            255
  R1                            4                             11
  R2                            1                              0
  RX                            6                             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    33
  DEL PEAK 19(12P12.1) WILD-TYPE                                1   123
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 19(12P12.1) MUTATED                           5    32
  DEL PEAK 19(12P12.1) WILD-TYPE                        12   141
D48V10, multiclass
                                  clus
vv                                 DEL PEAK 19(12P12.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                      33
  BLACK OR AFRICAN AMERICAN                                   5
  WHITE                                                      32
                                  clus
vv                                 DEL PEAK 19(12P12.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                       123
  BLACK OR AFRICAN AMERICAN                                    12
  WHITE                                                       141
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V11, binary
                                cls
clus                               0   1
  DEL PEAK 19(12P12.1) MUTATED     3  64
  DEL PEAK 19(12P12.1) WILD-TYPE   8 265
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(12P12.1) MUTATED      3   64
  DEL PEAK 19(12P12.1) WILD-TYPE    8  265
                        clus
vv                       DEL PEAK 19(12P12.1) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           64
                        clus
vv                       DEL PEAK 19(12P12.1) WILD-TYPE
  HISPANIC OR LATINO                                  8
  NOT HISPANIC OR LATINO                            265
[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    29  20
  DEL PEAK 20(12Q24.33) WILD-TYPE 196  89
  DEL PEAK 20(12Q24.33) MUTATED DEL PEAK 20(12Q24.33) WILD-TYPE 
                             49                             285 
  DEL PEAK 20(12Q24.33) MUTATED DEL PEAK 20(12Q24.33) WILD-TYPE 
                             20                              89 
$`DEL PEAK 20(12Q24.33) MUTATED`
TCGA-2Y-A9GS TCGA-2Y-A9GY TCGA-2Y-A9H2 TCGA-2Y-A9H8 TCGA-3K-AAZ8 TCGA-BC-A217 
       23.80        24.89        56.91        20.81        13.02        13.84 
TCGA-BC-A5W4 TCGA-CC-5260 TCGA-CC-A1HT TCGA-CC-A3MA TCGA-CC-A3MC TCGA-DD-A1EG 
       17.98         2.86         3.32         0.07         0.13        45.11 
TCGA-DD-A1EH TCGA-DD-A1EL TCGA-DD-A39X TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A5 
       49.15        13.64        55.69        19.76        25.81       102.74 
TCGA-DD-A3A9 TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NO TCGA-DD-AAC8 TCGA-DD-AACA 
       30.61        26.83        30.51        73.81         0.53        75.65 
TCGA-DD-AACE TCGA-DD-AACG TCGA-DD-AACN TCGA-DD-AACU TCGA-DD-AAD3 TCGA-DD-AAD8 
       63.48        15.42        42.81        51.52        42.58        40.08 
TCGA-DD-AADF TCGA-DD-AADM TCGA-DD-AADY TCGA-DD-AAE3 TCGA-DD-AAEK TCGA-DD-AAVU 
        3.78         0.39        18.25        18.61        35.08        72.39 
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-A7SB TCGA-RC-A7SK 
       30.74        14.86        18.38        19.92        19.33        15.52 
TCGA-ZP-A9D1 
        0.69 

$`DEL PEAK 20(12Q24.33) WILD-TYPE`
TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GV TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GZ 
       53.39        63.75        83.24        41.79        80.28        27.88 
TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H3 TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H6 
      120.82        40.41        41.33        47.74        18.25        11.74 
TCGA-2Y-A9H7 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-4R-AA8I TCGA-5C-A9VG 
       37.25        14.99         1.18         8.55         8.61        10.78 
TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4072 
       10.59         0.66        11.97        11.08         1.51        48.99 
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
       27.91        37.32        10.13        46.78        27.52        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-A3KF TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A69I TCGA-BC-A8YO 
       44.42         0.26        22.36        14.60        12.72        18.48 
TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BD-A3ER TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5261 
       44.81        13.45        36.66         0.66         0.07         3.19 
TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A3M9 TCGA-CC-A3MB TCGA-DD-A113 TCGA-DD-A114 
        3.39         4.24         0.10         0.10        79.73        37.78 
TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B 
       83.57        53.33       113.00         7.33         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-A1EJ TCGA-DD-A1EK 
       75.65        11.47        12.95         6.02        33.04        18.35 
TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39Y TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 
       21.14        27.19         5.62         7.66        70.06        17.59 
TCGA-DD-A3A4 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A4NA TCGA-DD-A4NB 
       20.12       107.11        13.78         0.36        33.14        32.52 
TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN 
       90.28        30.97        30.15        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        23.93 
TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G 
        9.30        23.05        22.78         1.45        35.67       114.35 
TCGA-DD-AA3A TCGA-DD-AAC9 TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACF 
       13.48        11.41        76.41        55.40        12.53        12.00 
TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM 
        6.41        53.19        69.11         0.30         3.52        58.16 
TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACV 
       61.68        13.64        14.20        59.31        51.35        50.33 
TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 
       46.82         5.59        47.67         5.62         4.50        18.54 
TCGA-DD-AAD2 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC 
       21.63        44.22        22.09        40.54        40.83        13.97 
TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK 
       40.47        39.52        37.64        35.67        35.05        34.49 
TCGA-DD-AADL TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR 
       20.91        29.52        14.89        15.06        14.33        66.67 
TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADV TCGA-DD-AADW TCGA-DD-AAE0 TCGA-DD-AAE1 
       15.58        18.21        18.87        19.30        18.25        18.15 
TCGA-DD-AAE2 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAE9 
       20.98        19.99         4.64        21.17        21.83        23.74 
TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEH 
       18.90        15.72        25.08        16.37        23.64        25.78 
TCGA-DD-AAEI TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVW 
       50.33        79.07        89.69        82.62        59.93        76.18 
TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 
       56.48        64.77        62.47        66.25        65.39        49.48 
TCGA-DD-AAW3 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y 
       53.69        12.69        15.85        13.91        13.35         9.73 
TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A8O5 
        0.20        12.82         0.20        14.04        13.15        13.35 
TCGA-ED-A8O6 TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A3JL 
        1.84        18.74        19.99        20.61        19.59         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        60.89        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        12.03         0.03        81.73         0.39 
TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25X TCGA-G3-A25Z 
       13.68        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        25.25 
TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 
       22.95        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-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB 
        0.89         8.75         2.14         3.02         1.02         2.20 
TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 
        2.99        37.91        20.75        17.06        16.83         3.72 
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        13.97 
TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A520 
       12.03         9.57        16.67        12.85        20.71         0.62 
TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 
       10.85        58.88        17.69        21.01         3.09        21.04 
TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RG-A7D4 TCGA-T1-A6J8 TCGA-UB-A7MA TCGA-UB-A7MB 
       19.04        15.39        24.13         0.76        17.59        19.76 
TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-A7MF TCGA-UB-AA0U TCGA-UB-AA0V 
       16.44         1.71        15.98         7.04        10.75        10.32 
TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA46 TCGA-YA-A8S7 TCGA-ZP-A9CV 
       11.34         0.99        12.99        24.85        13.55        35.77 
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-A9CF TCGA-ZS-A9CG 
       40.80        79.30        11.21 

  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                          120.82 
  DEL PEAK 20(12Q24.33) MUTATED DEL PEAK 20(12Q24.33) WILD-TYPE 
                          19.33                           19.23 
[1] "0.1 - 102.7 (19.3)" "0.0 - 120.8 (19.2)"
[1] "hr=" "1.4"
D49V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE III STAGE IIIA
  DEL PEAK 20(12Q24.33) MUTATED        20       15         2          9
  DEL PEAK 20(12Q24.33) WILD-TYPE     148       69         1         50
                                 vv
clus                              STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 20(12Q24.33) MUTATED            3          1        2         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                               20                             148
  STAGE II                              15                              69
  STAGE III                              2                               1
  STAGE IIIA                             9                              50
  STAGE IIIB                             3                               5
  STAGE IIIC                             1                               6
  STAGE IV                               2                               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      22  16  13   3
  DEL PEAK 20(12Q24.33) WILD-TYPE   157  75  60   9
D49V4, multiclass
       clus
vv      DEL PEAK 20(12Q24.33) MUTATED DEL PEAK 20(12Q24.33) WILD-TYPE
  T0+T1                            22                             157
  T2                               16                              75
  T3                               13                              60
  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    40   0
  DEL PEAK 20(12Q24.33) WILD-TYPE 209   3
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 20(12Q24.33) MUTATED     40    0
  DEL PEAK 20(12Q24.33) WILD-TYPE  209    3
   clus
vv  DEL PEAK 20(12Q24.33) MUTATED DEL PEAK 20(12Q24.33) WILD-TYPE
  0                            40                             209
  1                             0                               3
[1] 2 2
[1] FALSE
D49V6, binary
                                 cls
clus                                0   1
  DEL PEAK 20(12Q24.33) MUTATED    43   2
  DEL PEAK 20(12Q24.33) WILD-TYPE 217   2
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 20(12Q24.33) MUTATED     43    2
  DEL PEAK 20(12Q24.33) WILD-TYPE  217    2
   clus
vv  DEL PEAK 20(12Q24.33) MUTATED DEL PEAK 20(12Q24.33) WILD-TYPE
  0                            43                             217
  1                             2                               2
[1] 2 2
[1] FALSE
D49V7, binary
                                 cls
clus                                0   1
  DEL PEAK 20(12Q24.33) MUTATED    21  33
  DEL PEAK 20(12Q24.33) WILD-TYPE  92 211
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 20(12Q24.33) MUTATED     21   33
  DEL PEAK 20(12Q24.33) WILD-TYPE   92  211
        clus
vv       DEL PEAK 20(12Q24.33) MUTATED DEL PEAK 20(12Q24.33) WILD-TYPE
  FEMALE                            21                              92
  MALE                              33                             211
[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                         53
  DEL PEAK 20(12Q24.33) WILD-TYPE                      295
                                 vv
clus                              HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK 20(12Q24.33) MUTATED                                  1
  DEL PEAK 20(12Q24.33) WILD-TYPE                                6
D49V8, multiclass
                                  clus
vv                                 DEL PEAK 20(12Q24.33) MUTATED
  FIBROLAMELLAR CARCINOMA                                      0
  HEPATOCELLULAR CARCINOMA                                    53
  HEPATOCHOLANGIOCARCINOMA (MIXED)                             1
                                  clus
vv                                 DEL PEAK 20(12Q24.33) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                        2
  HEPATOCELLULAR CARCINOMA                                     295
  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 20(12Q24.33) MUTATED    49   1   0   3
  DEL PEAK 20(12Q24.33) WILD-TYPE 266  14   1  16
D49V9, multiclass
    clus
vv   DEL PEAK 20(12Q24.33) MUTATED DEL PEAK 20(12Q24.33) WILD-TYPE
  R0                            49                             266
  R1                             1                              14
  R2                             0                               1
  RX                             3                              16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 20(12Q24.33) MUTATED                                  0    28
  DEL PEAK 20(12Q24.33) WILD-TYPE                                1   128
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 20(12Q24.33) MUTATED                           3    22
  DEL PEAK 20(12Q24.33) WILD-TYPE                        14   151
D49V10, multiclass
                                  clus
vv                                 DEL PEAK 20(12Q24.33) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                       28
  BLACK OR AFRICAN AMERICAN                                    3
  WHITE                                                       22
                                  clus
vv                                 DEL PEAK 20(12Q24.33) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               1
  ASIAN                                                        128
  BLACK OR AFRICAN AMERICAN                                     14
  WHITE                                                        151
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V11, binary
                                 cls
clus                                0   1
  DEL PEAK 20(12Q24.33) MUTATED     2  50
  DEL PEAK 20(12Q24.33) WILD-TYPE   9 279
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 20(12Q24.33) MUTATED      2   50
  DEL PEAK 20(12Q24.33) WILD-TYPE    9  279
                        clus
vv                       DEL PEAK 20(12Q24.33) MUTATED
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                            50
                        clus
vv                       DEL PEAK 20(12Q24.33) WILD-TYPE
  HISPANIC OR LATINO                                   9
  NOT HISPANIC OR LATINO                             279
[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    97  56
  DEL PEAK 21(13Q14.2) WILD-TYPE 128  53
  DEL PEAK 21(13Q14.2) MUTATED DEL PEAK 21(13Q14.2) WILD-TYPE 
                           153                            181 
  DEL PEAK 21(13Q14.2) MUTATED DEL PEAK 21(13Q14.2) WILD-TYPE 
                            56                             53 
$`DEL PEAK 21(13Q14.2) MUTATED`
TCGA-2Y-A9GS TCGA-2Y-A9GV TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H2 
       23.80        83.24        24.89        27.88       120.82        56.91 
TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-2Y-A9HA TCGA-3K-AAZ8 TCGA-4R-AA8I 
       47.74        18.25        20.81         1.18        13.02         8.61 
TCGA-5C-A9VG TCGA-5C-A9VH TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10W 
       10.78        10.59        37.32        10.13        27.52         2.99 
TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A112 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG 
       23.34         1.12         5.03        13.84         0.26        22.36 
TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A8YO TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5260 
       17.98        14.60        18.48         0.66         0.07         2.86 
TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA 
        3.19         3.39         4.24         3.32         0.10         0.07 
TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 
        0.13        79.73        37.78        83.57        53.33       113.00 
TCGA-DD-A11A TCGA-DD-A11C TCGA-DD-A1EF TCGA-DD-A1EI TCGA-DD-A1EK TCGA-DD-A39X 
        2.60        21.76        12.95         6.02        18.35        55.69 
TCGA-DD-A39Y TCGA-DD-A3A0 TCGA-DD-A3A5 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NH 
        5.62        25.81       102.74        30.61        33.14        30.15 
TCGA-DD-A4NJ TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A73E 
       30.51        29.56        73.81        12.26         0.30         1.45 
TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AACF TCGA-DD-AACG 
       35.67       114.35        13.48         0.53        12.00        15.42 
TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO 
        6.41        53.19         3.52        58.16        42.81        61.68 
TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AAD1 
       13.64        14.20        59.31        51.52        50.33        18.54 
TCGA-DD-AAD8 TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADF TCGA-DD-AADI TCGA-DD-AADK 
       40.08        13.97        40.47         3.78        35.67        34.49 
TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADO TCGA-DD-AADR TCGA-DD-AADV TCGA-DD-AADW 
       20.91         0.39        14.89        66.67        18.87        19.30 
TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE8 
       18.25        18.25        20.98        18.61        19.99        21.83 
TCGA-DD-AAEA TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEI TCGA-DD-AAEK 
       18.90        25.08        16.37        23.64        50.33        35.08 
TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A66Y TCGA-ED-A7PX 
       79.07        89.69        13.41        12.69         9.73         0.20 
TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-EP-A3RK TCGA-FV-A3I0 TCGA-FV-A3I1 
        0.20        14.04        13.15        11.93        27.88         8.12 
TCGA-FV-A3R2 TCGA-FV-A495 TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25X TCGA-G3-A25Y 
        6.38         0.03        13.68        51.06        58.49        14.86 
TCGA-G3-A3CH TCGA-G3-A5SI TCGA-G3-A5SM TCGA-G3-A7M6 TCGA-G3-AAUZ TCGA-G3-AAV4 
       25.64        25.25        17.10        12.03        11.24         0.89 
TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-K7-A5RG TCGA-KR-A7K2 TCGA-KR-A7K8 
        3.02         1.02         2.20        17.06        11.84        24.36 
TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A8JO TCGA-NI-A8LF TCGA-PD-A5DF TCGA-RC-A7S9 
       18.38        20.71        10.85        19.92        21.01        21.04 
TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MC 
       19.04        15.39        15.52        24.13        17.59        16.44 
TCGA-UB-A7MF TCGA-UB-AA0U TCGA-WJ-A86L TCGA-YA-A8S7 TCGA-ZP-A9CY TCGA-ZP-A9CZ 
        7.04        10.75        11.34        13.55        25.71        23.21 
TCGA-ZP-A9D0 TCGA-ZS-A9CE TCGA-ZS-A9CG 
       23.57        40.80        11.21 

$`DEL PEAK 21(13Q14.2) WILD-TYPE`
TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9H1 TCGA-2Y-A9H3 
       53.39        63.75        41.79        80.28        40.41        41.33 
TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-2Y-A9H9 TCGA-2Y-A9HB TCGA-5C-AAPD TCGA-5R-AA1C 
       11.74        37.25        14.99         8.55         0.66        11.97 
TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10S TCGA-BC-A10U 
       11.08         1.51        48.99        27.91        46.78        27.52 
TCGA-BC-A10X TCGA-BC-A110 TCGA-BC-A216 TCGA-BC-A69I TCGA-BD-A2L6 TCGA-BD-A3EP 
       25.32        69.57        44.42        12.72        44.81        13.45 
TCGA-BD-A3ER TCGA-CC-A3MB TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11D TCGA-DD-A1E9 
       36.66         0.10         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-A1EG 
       79.40        66.31        19.79        75.65        11.47        45.11 
TCGA-DD-A1EH TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39Z 
       49.15        33.04        13.64        21.14        27.19        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-A4NB TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NI TCGA-DD-A4NK 
        0.36        32.52        90.28        30.97        26.83        39.78 
TCGA-DD-A4NL TCGA-DD-A4NP TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B 
       56.25       108.76        80.75        78.84        23.93         9.30 
TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC 
       23.05        22.78        11.41        75.65        76.41        55.40 
TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACT TCGA-DD-AACW 
       12.53        63.48        69.11         0.30        51.35        46.82 
TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD2 TCGA-DD-AAD3 
        5.59        47.67         5.62         4.50        21.63        42.58 
TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADE TCGA-DD-AADG 
       44.22        22.09        40.54        40.83        39.52        37.64 
TCGA-DD-AADJ TCGA-DD-AADN TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADS TCGA-DD-AADU 
       35.05        29.52        15.06        14.33        15.58        18.21 
TCGA-DD-AAE1 TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAEH 
       18.15         4.64        21.17        23.74        15.72        25.78 
TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY 
       82.62        59.93        72.39        76.18        56.48        64.77 
TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A5KG 
       62.47        66.25        65.39        49.48        53.69        15.85 
TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A7PY TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 
       13.91        13.35        12.82        13.41        13.35         1.84 
TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC 
        0.20        18.74        19.99        20.61        19.59         0.62 
TCGA-EP-A3JL TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR 
        9.96        22.85        14.40        60.89        23.97        19.10 
TCGA-FV-A3R3 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25U TCGA-G3-A25V 
       12.03         0.33        81.73         0.39        53.79        28.27 
TCGA-G3-A25W TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
       30.74        21.53        22.13         5.92        19.53        19.23 
TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-G3-AAV0 
       22.95        20.42         7.76         5.98         1.84         8.55 
TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-HP-A5MZ 
       11.80         9.70         9.17         8.75         2.14         2.99 
TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K7 
       37.91        20.75        16.83         3.72         2.14        13.38 
TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75H 
       12.72        13.97        12.03         9.57        16.67        12.85 
TCGA-MR-A520 TCGA-NI-A4U2 TCGA-O8-A75V TCGA-QA-A7B7 TCGA-RC-A7SB TCGA-T1-A6J8 
        0.62        58.88        17.69         3.09        19.33         0.76 
TCGA-UB-A7MB TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0V TCGA-WQ-A9G7 TCGA-WQ-AB4B 
       19.76         1.71        15.98        10.32         0.99        12.99 
TCGA-WX-AA46 TCGA-ZP-A9CV TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD 
       24.85        35.77         0.69        24.43        12.99        45.57 
TCGA-ZS-A9CF 
       79.30 

  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 
                        120.82                         108.76 
  DEL PEAK 21(13Q14.2) MUTATED DEL PEAK 21(13Q14.2) WILD-TYPE 
                         18.25                          20.61 
[1] "0.0 - 120.8 (18.2)" "0.1 - 108.8 (20.6)"
[1] "hr=" "1.4"
D50V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IIIA
  DEL PEAK 21(13Q14.2) MUTATED        71       48         1         28
  DEL PEAK 21(13Q14.2) WILD-TYPE      97       36         2         31
                                vv
clus                             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 21(13Q14.2) MUTATED            4          4        1         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                              71                             97
  STAGE II                             48                             36
  STAGE III                             1                              2
  STAGE IIIA                           28                             31
  STAGE IIIB                            4                              4
  STAGE IIIC                            4                              3
  STAGE IV                              1                              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      75  51  33  10
  DEL PEAK 21(13Q14.2) WILD-TYPE   104  40  40   2
D50V4, multiclass
       clus
vv      DEL PEAK 21(13Q14.2) MUTATED DEL PEAK 21(13Q14.2) WILD-TYPE
  T0+T1                           75                            104
  T2                              51                             40
  T3                              33                             40
  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   123   1
  DEL PEAK 21(13Q14.2) WILD-TYPE 126   2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(13Q14.2) MUTATED    123    1
  DEL PEAK 21(13Q14.2) WILD-TYPE  126    2
   clus
vv  DEL PEAK 21(13Q14.2) MUTATED DEL PEAK 21(13Q14.2) WILD-TYPE
  0                          123                            126
  1                            1                              2
[1] 2 2
[1] FALSE
D50V6, binary
                                cls
clus                               0   1
  DEL PEAK 21(13Q14.2) MUTATED   125   2
  DEL PEAK 21(13Q14.2) WILD-TYPE 135   2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(13Q14.2) MUTATED    125    2
  DEL PEAK 21(13Q14.2) WILD-TYPE  135    2
   clus
vv  DEL PEAK 21(13Q14.2) MUTATED DEL PEAK 21(13Q14.2) WILD-TYPE
  0                          125                            135
  1                            2                              2
[1] 2 2
[1] FALSE
D50V7, binary
                                cls
clus                               0   1
  DEL PEAK 21(13Q14.2) MUTATED    60 109
  DEL PEAK 21(13Q14.2) WILD-TYPE  53 135
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(13Q14.2) MUTATED     60  109
  DEL PEAK 21(13Q14.2) WILD-TYPE   53  135
        clus
vv       DEL PEAK 21(13Q14.2) MUTATED DEL PEAK 21(13Q14.2) WILD-TYPE
  FEMALE                           60                             53
  MALE                            109                            135
[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                        164
  DEL PEAK 21(13Q14.2) WILD-TYPE                      184
                                vv
clus                             HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK 21(13Q14.2) MUTATED                                  4
  DEL PEAK 21(13Q14.2) WILD-TYPE                                3
D50V8, multiclass
                                  clus
vv                                 DEL PEAK 21(13Q14.2) MUTATED
  FIBROLAMELLAR CARCINOMA                                     1
  HEPATOCELLULAR CARCINOMA                                  164
  HEPATOCHOLANGIOCARCINOMA (MIXED)                            4
                                  clus
vv                                 DEL PEAK 21(13Q14.2) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                       1
  HEPATOCELLULAR CARCINOMA                                    184
  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 21(13Q14.2) MUTATED   146   8   0  11
  DEL PEAK 21(13Q14.2) WILD-TYPE 169   7   1   8
D50V9, multiclass
    clus
vv   DEL PEAK 21(13Q14.2) MUTATED DEL PEAK 21(13Q14.2) WILD-TYPE
  R0                          146                            169
  R1                            8                              7
  R2                            0                              1
  RX                           11                              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 21(13Q14.2) MUTATED                                  0    86
  DEL PEAK 21(13Q14.2) WILD-TYPE                                1    70
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 21(13Q14.2) MUTATED                           9    72
  DEL PEAK 21(13Q14.2) WILD-TYPE                         8   101
D50V10, multiclass
                                  clus
vv                                 DEL PEAK 21(13Q14.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                      86
  BLACK OR AFRICAN AMERICAN                                   9
  WHITE                                                      72
                                  clus
vv                                 DEL PEAK 21(13Q14.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        70
  BLACK OR AFRICAN AMERICAN                                     8
  WHITE                                                       101
[1] 4 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     5 158
  DEL PEAK 21(13Q14.2) WILD-TYPE   6 171
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(13Q14.2) MUTATED      5  158
  DEL PEAK 21(13Q14.2) WILD-TYPE    6  171
                        clus
vv                       DEL PEAK 21(13Q14.2) MUTATED
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                          158
                        clus
vv                       DEL PEAK 21(13Q14.2) WILD-TYPE
  HISPANIC OR LATINO                                  6
  NOT HISPANIC OR LATINO                            171
[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    77  36
  DEL PEAK 22(14Q23.3) WILD-TYPE 148  73
  DEL PEAK 22(14Q23.3) MUTATED DEL PEAK 22(14Q23.3) WILD-TYPE 
                           113                            221 
  DEL PEAK 22(14Q23.3) MUTATED DEL PEAK 22(14Q23.3) WILD-TYPE 
                            36                             73 
$`DEL PEAK 22(14Q23.3) MUTATED`
TCGA-2Y-A9GS TCGA-2Y-A9GX TCGA-2Y-A9GY TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 
       23.80        80.28        24.89        40.41        56.91        41.33 
TCGA-2Y-A9H4 TCGA-2Y-A9H9 TCGA-5C-A9VG TCGA-5C-AAPD TCGA-BC-4073 TCGA-BC-A10Q 
       47.74        14.99        10.78         0.66        27.91        37.32 
TCGA-BC-A10Z TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BD-A3EP 
        1.12         5.03        44.42         0.26        22.36        13.45 
TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-A1HT TCGA-CC-A3MA TCGA-CC-A3MB 
        0.07         2.86         3.19         3.32         0.07         0.10 
TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A115 TCGA-DD-A118 TCGA-DD-A11A TCGA-DD-A11C 
        0.13        79.73        83.57       113.00         2.60        21.76 
TCGA-DD-A1E9 TCGA-DD-A1EG TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39X 
       90.71        45.11         6.02        33.04        13.64        55.69 
TCGA-DD-A39Y TCGA-DD-A3A1 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NB TCGA-DD-A4NH 
        5.62         7.66        13.78        30.61        32.52        30.15 
TCGA-DD-A4NI TCGA-DD-A4NO TCGA-DD-A4NQ TCGA-DD-A73F TCGA-DD-AA3A TCGA-DD-AAC8 
       26.83        73.81        12.26        35.67        13.48         0.53 
TCGA-DD-AACA TCGA-DD-AACE TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACN TCGA-DD-AACS 
       75.65        63.48        15.42         6.41        42.81        59.31 
TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACX TCGA-DD-AACZ TCGA-DD-AAD5 TCGA-DD-AAD6 
       51.52        50.33         5.59         5.62        44.22        22.09 
TCGA-DD-AADB TCGA-DD-AADD TCGA-DD-AADF TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN 
       40.83        40.47         3.78        20.91         0.39        29.52 
TCGA-DD-AADO TCGA-DD-AADR TCGA-DD-AADV TCGA-DD-AADW TCGA-DD-AAE0 TCGA-DD-AAE3 
       14.89        66.67        18.87        19.30        18.25        18.61 
TCGA-DD-AAE6 TCGA-DD-AAE8 TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAVP 
        4.64        21.83        25.08        16.37        23.64        79.07 
TCGA-DD-AAVU TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A7PX TCGA-ED-A7PZ TCGA-ED-A7XP 
       72.39        53.69        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         1.84         0.20        18.74        19.59        11.93 
TCGA-FV-A3I0 TCGA-FV-A4ZP TCGA-G3-A25S TCGA-G3-A25X TCGA-G3-A3CH TCGA-G3-A5SM 
       27.88        81.73        13.68        58.49        25.64        17.10 
TCGA-G3-A7M9 TCGA-G3-AAV1 TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-K7-A5RG TCGA-KR-A7K7 
        1.84        11.80         3.02         1.02        17.06        13.38 
TCGA-NI-A8LF TCGA-PD-A5DF TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 
       19.92        21.01        19.04        15.39        15.52        24.13 
TCGA-UB-A7MC TCGA-UB-A7MF TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-ZP-A9D2 
       16.44         7.04         0.99        12.99        24.43 

$`DEL PEAK 22(14Q23.3) WILD-TYPE`
TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GV TCGA-2Y-A9GW TCGA-2Y-A9GZ TCGA-2Y-A9H0 
       53.39        63.75        83.24        41.79        27.88       120.82 
TCGA-2Y-A9H5 TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-2Y-A9H8 TCGA-2Y-A9HA TCGA-2Y-A9HB 
       18.25        11.74        37.25        20.81         1.18         8.55 
TCGA-3K-AAZ8 TCGA-4R-AA8I TCGA-5C-A9VH TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM 
       13.02         8.61        10.59        11.97        11.08         1.51 
TCGA-BC-4072 TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W 
       48.99        10.13        46.78        27.52        27.52         2.99 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A110 TCGA-BC-A217 TCGA-BC-A5W4 TCGA-BC-A69H 
       25.32        23.34        69.57        13.84        17.98        14.60 
TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3ER TCGA-BW-A5NO TCGA-CC-5262 
       12.72        18.48        44.81        36.66         0.66         3.39 
TCGA-CC-5263 TCGA-CC-A3M9 TCGA-DD-A114 TCGA-DD-A116 TCGA-DD-A119 TCGA-DD-A11B 
        4.24         0.10        37.78        53.33         7.33         0.46 
TCGA-DD-A11D TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE 
       51.29        79.40        66.31        19.79        75.65        11.47 
TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EK TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39Z 
       12.95        49.15        18.35        21.14        27.19        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        90.28        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 
       23.93         9.30        23.05        22.78         1.45       114.35 
TCGA-DD-AAC9 TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACF TCGA-DD-AACI 
       11.41        76.41        55.40        12.53        12.00        53.19 
TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACO TCGA-DD-AACP 
       69.11         0.30         3.52        58.16        61.68        13.64 
TCGA-DD-AACQ TCGA-DD-AACT TCGA-DD-AACW TCGA-DD-AACY TCGA-DD-AAD0 TCGA-DD-AAD1 
       14.20        51.35        46.82        47.67         4.50        18.54 
TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADC TCGA-DD-AADE 
       21.63        42.58        40.08        40.54        13.97        39.52 
TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADP TCGA-DD-AADQ 
       37.64        35.67        35.05        34.49        15.06        14.33 
TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADY TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE4 
       15.58        18.21        18.25        18.15        20.98        19.99 
TCGA-DD-AAE7 TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAEH TCGA-DD-AAEI 
       21.17        23.74        18.90        15.72        25.78        50.33 
TCGA-DD-AAEK TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVW TCGA-DD-AAVX 
       35.08        89.69        82.62        59.93        76.18        56.48 
TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-ED-A4XI 
       64.77        62.47        66.25        65.39        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         9.73        12.82        14.04 
TCGA-ED-A8O5 TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3JL TCGA-ES-A2HS 
       13.35        19.99        20.61         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        60.89        23.97        19.10         8.12         6.38 
TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25U 
       12.03         0.03         0.33         0.39        51.06        53.79 
TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CI 
       28.27        30.74        14.86        21.53        22.13         5.92 
TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A6UC 
       19.53        19.23        25.25        22.95        20.42         7.76 
TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV3 
       12.03         5.98        11.24         8.55         9.70         9.17 
TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 
        0.89         8.75         2.14         2.20         2.99        37.91 
TCGA-K7-A5RF TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K8 
       20.75        16.83         3.72         2.14        11.84        24.36 
TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G 
       12.72        13.97        12.03         9.57        16.67        18.38 
TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-O8-A75V 
       12.85        20.71         0.62        10.85        58.88        17.69 
TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-T1-A6J8 TCGA-UB-A7MA TCGA-UB-A7MB 
        3.09        21.04        19.33         0.76        17.59        19.76 
TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WX-AA46 
        1.71        15.98        10.75        10.32        11.34        24.85 
TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 
       13.55        35.77        25.71        23.21        23.57         0.69 
TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       12.99        45.57        40.80        79.30        11.21 

  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                         120.82 
  DEL PEAK 22(14Q23.3) MUTATED DEL PEAK 22(14Q23.3) WILD-TYPE 
                         18.74                          19.76 
[1] "0.1 - 113.0 (18.7)" "0.0 - 120.8 (19.8)"
[1] "hr=" "1"  
D51V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IIIA
  DEL PEAK 22(14Q23.3) MUTATED        53       33         0         25
  DEL PEAK 22(14Q23.3) WILD-TYPE     115       51         3         34
                                vv
clus                             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 22(14Q23.3) MUTATED            5          3        2         0
  DEL PEAK 22(14Q23.3) WILD-TYPE          3          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                              53                            115
  STAGE II                             33                             51
  STAGE III                             0                              3
  STAGE IIIA                           25                             34
  STAGE IIIB                            5                              3
  STAGE IIIC                            3                              4
  STAGE IV                              2                              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      54  37  30   5
  DEL PEAK 22(14Q23.3) WILD-TYPE   125  54  43   7
D51V4, multiclass
       clus
vv      DEL PEAK 22(14Q23.3) MUTATED DEL PEAK 22(14Q23.3) WILD-TYPE
  T0+T1                           54                            125
  T2                              37                             54
  T3                              30                             43
  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    95   1
  DEL PEAK 22(14Q23.3) WILD-TYPE 154   2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 22(14Q23.3) MUTATED     95    1
  DEL PEAK 22(14Q23.3) WILD-TYPE  154    2
   clus
vv  DEL PEAK 22(14Q23.3) MUTATED DEL PEAK 22(14Q23.3) WILD-TYPE
  0                           95                            154
  1                            1                              2
[1] 2 2
[1] FALSE
D51V6, binary
                                cls
clus                               0   1
  DEL PEAK 22(14Q23.3) MUTATED    99   2
  DEL PEAK 22(14Q23.3) WILD-TYPE 161   2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 22(14Q23.3) MUTATED     99    2
  DEL PEAK 22(14Q23.3) WILD-TYPE  161    2
   clus
vv  DEL PEAK 22(14Q23.3) MUTATED DEL PEAK 22(14Q23.3) WILD-TYPE
  0                           99                            161
  1                            2                              2
[1] 2 2
[1] FALSE
D51V7, binary
                                cls
clus                               0   1
  DEL PEAK 22(14Q23.3) MUTATED    36  90
  DEL PEAK 22(14Q23.3) WILD-TYPE  77 154
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 22(14Q23.3) MUTATED     36   90
  DEL PEAK 22(14Q23.3) WILD-TYPE   77  154
        clus
vv       DEL PEAK 22(14Q23.3) MUTATED DEL PEAK 22(14Q23.3) WILD-TYPE
  FEMALE                           36                             77
  MALE                             90                            154
[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                        121
  DEL PEAK 22(14Q23.3) WILD-TYPE                      227
                                vv
clus                             HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK 22(14Q23.3) MUTATED                                  4
  DEL PEAK 22(14Q23.3) WILD-TYPE                                3
D51V8, multiclass
                                  clus
vv                                 DEL PEAK 22(14Q23.3) MUTATED
  FIBROLAMELLAR CARCINOMA                                     1
  HEPATOCELLULAR CARCINOMA                                  121
  HEPATOCHOLANGIOCARCINOMA (MIXED)                            4
                                  clus
vv                                 DEL PEAK 22(14Q23.3) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                       1
  HEPATOCELLULAR CARCINOMA                                    227
  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 22(14Q23.3) MUTATED   110   5   0   8
  DEL PEAK 22(14Q23.3) WILD-TYPE 205  10   1  11
D51V9, multiclass
    clus
vv   DEL PEAK 22(14Q23.3) MUTATED DEL PEAK 22(14Q23.3) WILD-TYPE
  R0                          110                            205
  R1                            5                             10
  R2                            0                              1
  RX                            8                             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 22(14Q23.3) MUTATED                                  0    68
  DEL PEAK 22(14Q23.3) WILD-TYPE                                1    88
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 22(14Q23.3) MUTATED                           7    49
  DEL PEAK 22(14Q23.3) WILD-TYPE                        10   124
D51V10, multiclass
                                  clus
vv                                 DEL PEAK 22(14Q23.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                      68
  BLACK OR AFRICAN AMERICAN                                   7
  WHITE                                                      49
                                  clus
vv                                 DEL PEAK 22(14Q23.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        88
  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"
D51V11, binary
                                cls
clus                               0   1
  DEL PEAK 22(14Q23.3) MUTATED     4 116
  DEL PEAK 22(14Q23.3) WILD-TYPE   7 213
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 22(14Q23.3) MUTATED      4  116
  DEL PEAK 22(14Q23.3) WILD-TYPE    7  213
                        clus
vv                       DEL PEAK 22(14Q23.3) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                          116
                        clus
vv                       DEL PEAK 22(14Q23.3) WILD-TYPE
  HISPANIC OR LATINO                                  7
  NOT HISPANIC OR LATINO                            213
[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    83  35
  DEL PEAK 23(14Q32.33) WILD-TYPE 142  74
  DEL PEAK 23(14Q32.33) MUTATED DEL PEAK 23(14Q32.33) WILD-TYPE 
                            118                             216 
  DEL PEAK 23(14Q32.33) MUTATED DEL PEAK 23(14Q32.33) WILD-TYPE 
                             35                              74 
$`DEL PEAK 23(14Q32.33) MUTATED`
TCGA-2Y-A9GS TCGA-2Y-A9GX TCGA-2Y-A9GY TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 
       23.80        80.28        24.89        40.41        56.91        41.33 
TCGA-2Y-A9H4 TCGA-2Y-A9H6 TCGA-2Y-A9H9 TCGA-5C-A9VG TCGA-5C-AAPD TCGA-BC-A10Q 
       47.74        11.74        14.99        10.78         0.66        37.32 
TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10Z TCGA-BC-A112 TCGA-BC-A217 TCGA-BC-A3KF 
       10.13        27.52         1.12         5.03        13.84         0.26 
TCGA-BC-A3KG TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-A1HT TCGA-CC-A3MA 
       22.36         0.07         2.86         3.19         3.32         0.07 
TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A115 TCGA-DD-A11A TCGA-DD-A11C 
        0.10         0.13        79.73        83.57         2.60        21.76 
TCGA-DD-A1E9 TCGA-DD-A1EG TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39X TCGA-DD-A39Y 
       90.71        45.11        33.04        13.64        55.69         5.62 
TCGA-DD-A3A1 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NB TCGA-DD-A4NH TCGA-DD-A4NI 
        7.66        13.78        30.61        32.52        30.15        26.83 
TCGA-DD-A4NJ TCGA-DD-A4NO TCGA-DD-A4NQ TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AACA 
       30.51        73.81        12.26       114.35        13.48        75.65 
TCGA-DD-AACE TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACN TCGA-DD-AACO 
       63.48        15.42         6.41        53.19        42.81        61.68 
TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACX TCGA-DD-AACZ TCGA-DD-AAD5 TCGA-DD-AAD6 
       59.31        51.52         5.59         5.62        44.22        22.09 
TCGA-DD-AADB TCGA-DD-AADD TCGA-DD-AADF TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN 
       40.83        40.47         3.78        20.91         0.39        29.52 
TCGA-DD-AADO TCGA-DD-AADR TCGA-DD-AADV TCGA-DD-AADW TCGA-DD-AAE0 TCGA-DD-AAE6 
       14.89        66.67        18.87        19.30        18.25         4.64 
TCGA-DD-AAE8 TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEK TCGA-DD-AAVP 
       21.83        25.08        16.37        23.64        35.08        79.07 
TCGA-DD-AAVU TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A7PX TCGA-ED-A7PZ TCGA-ED-A7XP 
       72.39        53.69        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         1.84         0.20        18.74        19.59        11.93 
TCGA-FV-A3I0 TCGA-FV-A495 TCGA-FV-A4ZP TCGA-G3-A25S TCGA-G3-A25X TCGA-G3-A3CH 
       27.88         0.03        81.73        13.68        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        19.92         3.09        15.39        15.52 
TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MF TCGA-WJ-A86L 
       24.13        17.59        19.76        16.44         7.04        11.34 
TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-ZP-A9D0 TCGA-ZP-A9D2 
        0.99        12.99        23.57        24.43 

$`DEL PEAK 23(14Q32.33) WILD-TYPE`
TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GV TCGA-2Y-A9GW TCGA-2Y-A9GZ TCGA-2Y-A9H0 
       53.39        63.75        83.24        41.79        27.88       120.82 
TCGA-2Y-A9H5 TCGA-2Y-A9H7 TCGA-2Y-A9H8 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 
       18.25        37.25        20.81         1.18         8.55        13.02 
TCGA-4R-AA8I TCGA-5C-A9VH TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4072 
        8.61        10.59        11.97        11.08         1.51        48.99 
TCGA-BC-4073 TCGA-BC-A10S TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y 
       27.91        46.78        27.52         2.99        25.32        23.34 
TCGA-BC-A110 TCGA-BC-A216 TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I TCGA-BC-A8YO 
       69.57        44.42        17.98        14.60        12.72        18.48 
TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BD-A3ER TCGA-BW-A5NO TCGA-CC-5262 TCGA-CC-5263 
       44.81        13.45        36.66         0.66         3.39         4.24 
TCGA-CC-A3M9 TCGA-DD-A114 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11B 
        0.10        37.78        53.33       113.00         7.33         0.46 
TCGA-DD-A11D TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE 
       51.29        79.40        66.31        19.79        75.65        11.47 
TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EK TCGA-DD-A39V TCGA-DD-A39W 
       12.95        49.15         6.02        18.35        21.14        27.19 
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-A4NA TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NK 
      107.11         0.36        33.14        90.28        30.97        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-A73F 
       23.93         9.30        23.05        22.78         1.45        35.67 
TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACF 
        0.53        11.41        76.41        55.40        12.53        12.00 
TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACP TCGA-DD-AACQ 
       69.11         0.30         3.52        58.16        13.64        14.20 
TCGA-DD-AACT TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACY TCGA-DD-AAD0 TCGA-DD-AAD1 
       51.35        50.33        46.82        47.67         4.50        18.54 
TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADC TCGA-DD-AADE 
       21.63        42.58        40.08        40.54        13.97        39.52 
TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADP TCGA-DD-AADQ 
       37.64        35.67        35.05        34.49        15.06        14.33 
TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADY TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 
       15.58        18.21        18.25        18.15        20.98        18.61 
TCGA-DD-AAE4 TCGA-DD-AAE7 TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAEH 
       19.99        21.17        23.74        18.90        15.72        25.78 
TCGA-DD-AAEI TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVW TCGA-DD-AAVX 
       50.33        89.69        82.62        59.93        76.18        56.48 
TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-ED-A4XI 
       64.77        62.47        66.25        65.39        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         9.73        12.82        14.04 
TCGA-ED-A8O5 TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3JL TCGA-ES-A2HS 
       13.35        19.99        20.61         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        60.89        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 
       12.03         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        25.25        22.95        20.42         7.76        12.03 
TCGA-G3-A7M7 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV4 TCGA-G3-AAV5 
        5.98        11.24         8.55         9.70         0.89         8.75 
TCGA-G3-AAV6 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF 
        2.14         1.02         2.20         2.99        37.91        20.75 
TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-LG-A6GG TCGA-LG-A9QC 
       16.83         3.72         2.14        11.84        12.72        13.97 
TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I 
       12.03         9.57        16.67        18.38        12.85        20.71 
TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-O8-A75V TCGA-PD-A5DF TCGA-RC-A7S9 
        0.62        10.85        58.88        17.69        21.01        21.04 
TCGA-RC-A7SB TCGA-RC-A7SF TCGA-T1-A6J8 TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0U 
       19.33        19.04         0.76         1.71        15.98        10.75 
TCGA-UB-AA0V TCGA-WX-AA46 TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ 
       10.32        24.85        13.55        35.77        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        40.80        79.30        11.21 

  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 
                         114.35                          120.82 
  DEL PEAK 23(14Q32.33) MUTATED DEL PEAK 23(14Q32.33) WILD-TYPE 
                         18.495                          19.645 
[1] "0.0 - 114.3 (18.5)" "0.1 - 120.8 (19.6)"
[1] "hr=" "1.1"
D52V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE III STAGE IIIA
  DEL PEAK 23(14Q32.33) MUTATED        51       39         0         22
  DEL PEAK 23(14Q32.33) WILD-TYPE     117       45         3         37
                                 vv
clus                              STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 23(14Q32.33) MUTATED            4          3        2         0
  DEL PEAK 23(14Q32.33) WILD-TYPE          4          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                               51                             117
  STAGE II                              39                              45
  STAGE III                              0                               3
  STAGE IIIA                            22                              37
  STAGE IIIB                             4                               4
  STAGE IIIC                             3                               4
  STAGE IV                               2                               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      53  43  28   5
  DEL PEAK 23(14Q32.33) WILD-TYPE   126  48  45   7
D52V4, multiclass
       clus
vv      DEL PEAK 23(14Q32.33) MUTATED DEL PEAK 23(14Q32.33) WILD-TYPE
  T0+T1                            53                             126
  T2                               43                              48
  T3                               28                              45
  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    91   1
  DEL PEAK 23(14Q32.33) WILD-TYPE 158   2
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 23(14Q32.33) MUTATED     91    1
  DEL PEAK 23(14Q32.33) WILD-TYPE  158    2
   clus
vv  DEL PEAK 23(14Q32.33) MUTATED DEL PEAK 23(14Q32.33) WILD-TYPE
  0                            91                             158
  1                             1                               2
[1] 2 2
[1] FALSE
D52V6, binary
                                 cls
clus                                0   1
  DEL PEAK 23(14Q32.33) MUTATED    97   2
  DEL PEAK 23(14Q32.33) WILD-TYPE 163   2
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 23(14Q32.33) MUTATED     97    2
  DEL PEAK 23(14Q32.33) WILD-TYPE  163    2
   clus
vv  DEL PEAK 23(14Q32.33) MUTATED DEL PEAK 23(14Q32.33) WILD-TYPE
  0                            97                             163
  1                             2                               2
[1] 2 2
[1] FALSE
D52V7, binary
                                 cls
clus                                0   1
  DEL PEAK 23(14Q32.33) MUTATED    40  89
  DEL PEAK 23(14Q32.33) WILD-TYPE  73 155
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 23(14Q32.33) MUTATED     40   89
  DEL PEAK 23(14Q32.33) WILD-TYPE   73  155
        clus
vv       DEL PEAK 23(14Q32.33) MUTATED DEL PEAK 23(14Q32.33) WILD-TYPE
  FEMALE                            40                              73
  MALE                              89                             155
[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                        123
  DEL PEAK 23(14Q32.33) WILD-TYPE                      225
                                 vv
clus                              HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK 23(14Q32.33) MUTATED                                  5
  DEL PEAK 23(14Q32.33) WILD-TYPE                                2
D52V8, multiclass
                                  clus
vv                                 DEL PEAK 23(14Q32.33) MUTATED
  FIBROLAMELLAR CARCINOMA                                      1
  HEPATOCELLULAR CARCINOMA                                   123
  HEPATOCHOLANGIOCARCINOMA (MIXED)                             5
                                  clus
vv                                 DEL PEAK 23(14Q32.33) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                        1
  HEPATOCELLULAR CARCINOMA                                     225
  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 23(14Q32.33) MUTATED   113   6   0   8
  DEL PEAK 23(14Q32.33) WILD-TYPE 202   9   1  11
D52V9, multiclass
    clus
vv   DEL PEAK 23(14Q32.33) MUTATED DEL PEAK 23(14Q32.33) WILD-TYPE
  R0                           113                             202
  R1                             6                               9
  R2                             0                               1
  RX                             8                              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 23(14Q32.33) MUTATED                                  0    64
  DEL PEAK 23(14Q32.33) WILD-TYPE                                1    92
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 23(14Q32.33) MUTATED                           8    54
  DEL PEAK 23(14Q32.33) WILD-TYPE                         9   119
D52V10, multiclass
                                  clus
vv                                 DEL PEAK 23(14Q32.33) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                       64
  BLACK OR AFRICAN AMERICAN                                    8
  WHITE                                                       54
                                  clus
vv                                 DEL PEAK 23(14Q32.33) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               1
  ASIAN                                                         92
  BLACK OR AFRICAN AMERICAN                                      9
  WHITE                                                        119
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V11, binary
                                 cls
clus                                0   1
  DEL PEAK 23(14Q32.33) MUTATED     4 118
  DEL PEAK 23(14Q32.33) WILD-TYPE   7 211
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 23(14Q32.33) MUTATED      4  118
  DEL PEAK 23(14Q32.33) WILD-TYPE    7  211
                        clus
vv                       DEL PEAK 23(14Q32.33) MUTATED
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           118
                        clus
vv                       DEL PEAK 23(14Q32.33) WILD-TYPE
  HISPANIC OR LATINO                                   7
  NOT HISPANIC OR LATINO                             211
[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    38  27
  DEL PEAK 24(15Q26.3) WILD-TYPE 187  82
  DEL PEAK 24(15Q26.3) MUTATED DEL PEAK 24(15Q26.3) WILD-TYPE 
                            65                            269 
  DEL PEAK 24(15Q26.3) MUTATED DEL PEAK 24(15Q26.3) WILD-TYPE 
                            27                             82 
$`DEL PEAK 24(15Q26.3) MUTATED`
TCGA-2Y-A9GZ TCGA-2Y-A9H8 TCGA-3K-AAZ8 TCGA-5C-A9VH TCGA-5C-AAPD TCGA-BC-A112 
       27.88        20.81        13.02        10.59         0.66         5.03 
TCGA-BC-A216 TCGA-BC-A5W4 TCGA-BC-A69H TCGA-CC-5258 TCGA-CC-A3MA TCGA-DD-A113 
       44.42        17.98        14.60         0.07         0.07        79.73 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A11C TCGA-DD-A1E9 TCGA-DD-A1EI TCGA-DD-A1EJ 
       37.78        83.57        21.76        90.71         6.02        33.04 
TCGA-DD-A1EL TCGA-DD-A39Y TCGA-DD-A3A5 TCGA-DD-A4NA TCGA-DD-A4NQ TCGA-DD-A73B 
       13.64         5.62       102.74        33.14        12.26         9.30 
TCGA-DD-A73F TCGA-DD-AAC8 TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACL TCGA-DD-AACS 
       35.67         0.53        15.42         6.41         3.52        59.31 
TCGA-DD-AADB TCGA-DD-AADF TCGA-DD-AADK TCGA-DD-AADV TCGA-DD-AAE1 TCGA-DD-AAE4 
       40.83         3.78        34.49        18.87        18.15        19.99 
TCGA-DD-AAE7 TCGA-DD-AAEK TCGA-DD-AAVQ TCGA-DD-AAVX TCGA-ED-A459 TCGA-ED-A66Y 
       21.17        35.08        89.69        56.48        13.41         9.73 
TCGA-ED-A7PX TCGA-ED-A82E TCGA-EP-A2KB TCGA-FV-A3I0 TCGA-FV-A496 TCGA-FV-A4ZP 
        0.20        13.41        19.59        27.88         0.33        81.73 
TCGA-G3-A25Z TCGA-G3-A5SI TCGA-G3-A5SM TCGA-G3-A7M9 TCGA-G3-AAV0 TCGA-G3-AAV1 
       21.53        25.25        17.10         1.84         8.55        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-NI-A8LF TCGA-RG-A7D4 TCGA-WQ-A9G7 TCGA-YA-A8S7 TCGA-ZS-A9CF 
       19.92        24.13         0.99        13.55        79.30 

$`DEL PEAK 24(15Q26.3) WILD-TYPE`
TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GV TCGA-2Y-A9GW TCGA-2Y-A9GX 
       23.80        53.39        63.75        83.24        41.79        80.28 
TCGA-2Y-A9GY TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H4 
       24.89       120.82        40.41        56.91        41.33        47.74 
TCGA-2Y-A9H5 TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB 
       18.25        11.74        37.25        14.99         1.18         8.55 
TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4072 
        8.61        10.78        11.97        11.08         1.51        48.99 
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
       27.91        37.32        10.13        46.78        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A217 
        2.99        25.32        23.34         1.12        69.57        13.84 
TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP 
        0.26        22.36        12.72        18.48        44.81        13.45 
TCGA-BD-A3ER TCGA-BW-A5NO TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 
       36.66         0.66         2.86         3.19         3.39         4.24 
TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A116 TCGA-DD-A118 
        3.32         0.10         0.10         0.13        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        11.47        12.95        45.11        49.15 
TCGA-DD-A1EK TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Z TCGA-DD-A3A0 
       18.35        21.14        27.19        55.69        19.76        25.81 
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-A3A9 TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH 
        0.36        30.61        32.52        90.28        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-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73C 
      108.76         0.30        80.75        78.84        23.93        23.05 
TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC9 TCGA-DD-AACA 
       22.78         1.45       114.35        13.48        11.41        75.65 
TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACI 
       76.41        55.40        12.53        63.48        12.00        53.19 
TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP 
       69.11         0.30        58.16        42.81        61.68        13.64 
TCGA-DD-AACQ TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX 
       14.20        51.35        51.52        50.33        46.82         5.59 
TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 
       47.67         5.62         4.50        18.54        21.63        42.58 
TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADC TCGA-DD-AADD 
       44.22        22.09        40.08        40.54        13.97        40.47 
TCGA-DD-AADE TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADL TCGA-DD-AADM 
       39.52        37.64        35.67        35.05        20.91         0.39 
TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS 
       29.52        14.89        15.06        14.33        66.67        15.58 
TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE2 TCGA-DD-AAE3 
       18.21        19.30        18.25        18.25        20.98        18.61 
TCGA-DD-AAE6 TCGA-DD-AAE8 TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAED 
        4.64        21.83        23.74        18.90        15.72        25.08 
TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAVP TCGA-DD-AAVR 
       16.37        23.64        25.78        50.33        79.07        82.62 
TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 
       59.93        72.39        76.18        64.77        62.47        66.25 
TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 
       65.39        49.48        53.69        12.69        15.85        13.91 
TCGA-ED-A66X TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A8O5 
       13.35        12.82         0.20        14.04        13.15        13.35 
TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC 
        1.84         0.20        18.74        19.99        20.61         0.62 
TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ 
        9.96        11.93        22.85        14.40        60.89        23.97 
TCGA-FV-A2QR TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A4ZQ 
       19.10         8.12         6.38        12.03         0.03         0.39 
TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X 
       13.68        51.06        53.79        28.27        30.74        58.49 
TCGA-G3-A25Y TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
       14.86        22.13        25.64         5.92        19.53        19.23 
TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-AAUZ 
       22.95        20.42         7.76        12.03         5.98        11.24 
TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV5 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ 
        9.70         9.17         8.75         1.02         2.20         2.99 
TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K8 
       37.91        20.75        16.83         3.72         2.14        24.36 
TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G 
       12.72        13.97        12.03         9.57        16.67        18.38 
TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-O8-A75V 
       12.85        20.71         0.62        10.85        58.88        17.69 
TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH 
       21.01         3.09        21.04        19.33        19.04        15.39 
TCGA-RC-A7SK TCGA-T1-A6J8 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD 
       15.52         0.76        17.59        19.76        16.44         1.71 
TCGA-UB-A7ME TCGA-UB-A7MF TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-AB4B 
       15.98         7.04        10.75        10.32        11.34        12.99 
TCGA-WX-AA46 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 
       24.85        35.77        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        40.80        11.21 

  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                         120.82 
  DEL PEAK 24(15Q26.3) MUTATED DEL PEAK 24(15Q26.3) WILD-TYPE 
                         17.06                          19.76 
[1] "0.1 - 102.7 (17.1)" "0.0 - 120.8 (19.8)"
[1] "hr=" "1.5"
D53V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IIIA
  DEL PEAK 24(15Q26.3) MUTATED        26       26         1         15
  DEL PEAK 24(15Q26.3) WILD-TYPE     142       58         2         44
                                vv
clus                             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 24(15Q26.3) MUTATED            2          3        0         0
  DEL PEAK 24(15Q26.3) WILD-TYPE          6          4        3         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                              26                            142
  STAGE II                             26                             58
  STAGE III                             1                              2
  STAGE IIIA                           15                             44
  STAGE IIIB                            2                              6
  STAGE IIIC                            3                              4
  STAGE IV                              0                              3
  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      28  26  20   1
  DEL PEAK 24(15Q26.3) WILD-TYPE   151  65  53  11
D53V4, multiclass
       clus
vv      DEL PEAK 24(15Q26.3) MUTATED DEL PEAK 24(15Q26.3) WILD-TYPE
  T0+T1                           28                            151
  T2                              26                             65
  T3                              20                             53
  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    52   2
  DEL PEAK 24(15Q26.3) WILD-TYPE 197   1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(15Q26.3) MUTATED     52    2
  DEL PEAK 24(15Q26.3) WILD-TYPE  197    1
   clus
vv  DEL PEAK 24(15Q26.3) MUTATED DEL PEAK 24(15Q26.3) WILD-TYPE
  0                           52                            197
  1                            2                              1
[1] 2 2
[1] FALSE
D53V6, binary
                                cls
clus                               0   1
  DEL PEAK 24(15Q26.3) MUTATED    64   0
  DEL PEAK 24(15Q26.3) WILD-TYPE 196   4
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(15Q26.3) MUTATED     64    0
  DEL PEAK 24(15Q26.3) WILD-TYPE  196    4
   clus
vv  DEL PEAK 24(15Q26.3) MUTATED DEL PEAK 24(15Q26.3) WILD-TYPE
  0                           64                            196
  1                            0                              4
[1] 2 2
[1] FALSE
D53V7, binary
                                cls
clus                               0   1
  DEL PEAK 24(15Q26.3) MUTATED    25  50
  DEL PEAK 24(15Q26.3) WILD-TYPE  88 194
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(15Q26.3) MUTATED     25   50
  DEL PEAK 24(15Q26.3) WILD-TYPE   88  194
        clus
vv       DEL PEAK 24(15Q26.3) MUTATED DEL PEAK 24(15Q26.3) WILD-TYPE
  FEMALE                           25                             88
  MALE                             50                            194
[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                         72
  DEL PEAK 24(15Q26.3) WILD-TYPE                      276
                                vv
clus                             HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK 24(15Q26.3) MUTATED                                  3
  DEL PEAK 24(15Q26.3) WILD-TYPE                                4
D53V8, multiclass
                                  clus
vv                                 DEL PEAK 24(15Q26.3) MUTATED
  FIBROLAMELLAR CARCINOMA                                     0
  HEPATOCELLULAR CARCINOMA                                   72
  HEPATOCHOLANGIOCARCINOMA (MIXED)                            3
                                  clus
vv                                 DEL PEAK 24(15Q26.3) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                       2
  HEPATOCELLULAR CARCINOMA                                    276
  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 24(15Q26.3) MUTATED    68   2   0   5
  DEL PEAK 24(15Q26.3) WILD-TYPE 247  13   1  14
D53V9, multiclass
    clus
vv   DEL PEAK 24(15Q26.3) MUTATED DEL PEAK 24(15Q26.3) WILD-TYPE
  R0                           68                            247
  R1                            2                             13
  R2                            0                              1
  RX                            5                             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 24(15Q26.3) MUTATED                                  0    38
  DEL PEAK 24(15Q26.3) WILD-TYPE                                1   118
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 24(15Q26.3) MUTATED                           5    32
  DEL PEAK 24(15Q26.3) WILD-TYPE                        12   141
D53V10, multiclass
                                  clus
vv                                 DEL PEAK 24(15Q26.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                      38
  BLACK OR AFRICAN AMERICAN                                   5
  WHITE                                                      32
                                  clus
vv                                 DEL PEAK 24(15Q26.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                       118
  BLACK OR AFRICAN AMERICAN                                    12
  WHITE                                                       141
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V11, binary
                                cls
clus                               0   1
  DEL PEAK 24(15Q26.3) MUTATED     3  68
  DEL PEAK 24(15Q26.3) WILD-TYPE   8 261
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(15Q26.3) MUTATED      3   68
  DEL PEAK 24(15Q26.3) WILD-TYPE    8  261
                        clus
vv                       DEL PEAK 24(15Q26.3) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           68
                        clus
vv                       DEL PEAK 24(15Q26.3) WILD-TYPE
  HISPANIC OR LATINO                                  8
  NOT HISPANIC OR LATINO                            261
[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    99  44
  DEL PEAK 25(16Q23.1) WILD-TYPE 126  65
  DEL PEAK 25(16Q23.1) MUTATED DEL PEAK 25(16Q23.1) WILD-TYPE 
                           143                            191 
  DEL PEAK 25(16Q23.1) MUTATED DEL PEAK 25(16Q23.1) WILD-TYPE 
                            44                             65 
$`DEL PEAK 25(16Q23.1) MUTATED`
TCGA-2Y-A9GY TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H5 TCGA-2Y-A9H7 TCGA-2Y-A9H8 
       24.89        56.91        41.33        18.25        37.25        20.81 
TCGA-2Y-A9HA TCGA-5C-A9VG TCGA-5C-AAPD TCGA-BC-4073 TCGA-BC-A10R TCGA-BC-A10S 
        1.18        10.78         0.66        27.91        10.13        46.78 
TCGA-BC-A10W TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KG 
        2.99        23.34         1.12        44.42        13.84        22.36 
TCGA-BC-A69H TCGA-BC-A8YO TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5260 
       14.60        18.48        13.45         0.66         0.07         2.86 
TCGA-CC-5261 TCGA-CC-5263 TCGA-CC-A3M9 TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 
        3.19         4.24         0.10         0.10         0.13        79.73 
TCGA-DD-A114 TCGA-DD-A116 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A1EF TCGA-DD-A1EH 
       37.78        53.33         2.60         0.46        12.95        49.15 
TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A8 TCGA-DD-A3A9 
        6.02        33.04         5.62        19.76         0.36        30.61 
TCGA-DD-A4ND TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NN TCGA-DD-A4NO 
       90.28        30.15        26.83        30.51        29.56        73.81 
TCGA-DD-A4NQ TCGA-DD-A73B TCGA-DD-A73F TCGA-DD-AACC TCGA-DD-AACF TCGA-DD-AACG 
       12.26         9.30        35.67        55.40        12.00        15.42 
TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO 
        6.41        53.19         3.52        58.16        42.81        61.68 
TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW 
       13.64        14.20        59.31        51.52        50.33        46.82 
TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD3 TCGA-DD-AADA TCGA-DD-AADB 
        5.62         4.50        18.54        42.58        40.54        40.83 
TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADO 
       35.67        35.05        34.49        20.91         0.39        14.89 
TCGA-DD-AADP TCGA-DD-AADR TCGA-DD-AADV TCGA-DD-AADW TCGA-DD-AAE0 TCGA-DD-AAE1 
       15.06        66.67        18.87        19.30        18.25        18.15 
TCGA-DD-AAE6 TCGA-DD-AAE8 TCGA-DD-AAED TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAEK 
        4.64        21.83        25.08        23.64        25.78        35.08 
TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVZ 
       79.07        89.69        59.93        72.39        76.18        62.47 
TCGA-DD-AAW0 TCGA-ED-A459 TCGA-ED-A5KG TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PY 
       66.25        13.41        15.85        13.35         9.73        12.82 
TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-EP-A2KB TCGA-ES-A2HS TCGA-FV-A23B TCGA-FV-A2QQ 
       13.35         1.84        19.59        22.85        60.89        23.97 
TCGA-FV-A3I0 TCGA-FV-A3R2 TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25X TCGA-G3-A25Y 
       27.88         6.38        13.68        53.79        58.49        14.86 
TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A5SI TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV6 
       21.53        25.64        25.25         1.84        11.24         2.14 
TCGA-G3-AAV7 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-MI-A75G TCGA-MI-A75I 
        3.02        13.38        24.36        12.72        18.38        20.71 
TCGA-NI-A8LF TCGA-O8-A75V TCGA-QA-A7B7 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH 
       19.92        17.69         3.09        19.33        19.04        15.39 
TCGA-RG-A7D4 TCGA-T1-A6J8 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MF TCGA-UB-AA0U 
       24.13         0.76        17.59        19.76         7.04        10.75 
TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-ZP-A9CZ TCGA-ZP-A9D1 TCGA-ZS-A9CG 
       11.34         0.99        23.21         0.69        11.21 

$`DEL PEAK 25(16Q23.1) WILD-TYPE`
TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GV TCGA-2Y-A9GW TCGA-2Y-A9GX 
       23.80        53.39        63.75        83.24        41.79        80.28 
TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H4 TCGA-2Y-A9H6 TCGA-2Y-A9H9 
       27.88       120.82        40.41        47.74        11.74        14.99 
TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-4R-AA8I TCGA-5C-A9VH TCGA-5R-AA1C TCGA-5R-AA1D 
        8.55        13.02         8.61        10.59        11.97        11.08 
TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-A10Q TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10X 
        1.51        48.99        37.32        27.52        27.52        25.32 
TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A3KF TCGA-BC-A5W4 TCGA-BC-A69I TCGA-BD-A2L6 
       69.57         5.03         0.26        17.98        12.72        44.81 
TCGA-BD-A3ER TCGA-CC-5262 TCGA-CC-A1HT TCGA-CC-A3MA TCGA-DD-A115 TCGA-DD-A118 
       36.66         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        11.47        45.11        18.35        13.64 
TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 
       21.14        27.19        55.69        25.81         7.66        70.06 
TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A4NA 
       17.59        20.12       102.74       107.11        13.78        33.14 
TCGA-DD-A4NB TCGA-DD-A4NF TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NP TCGA-DD-A4NR 
       32.52        30.97        39.78        56.25       108.76         0.30 
TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E 
       80.75        78.84        23.93        23.05        22.78         1.45 
TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB 
      114.35        13.48         0.53        11.41        75.65        76.41 
TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACT TCGA-DD-AACX 
       12.53        63.48        69.11         0.30        51.35         5.59 
TCGA-DD-AACY TCGA-DD-AAD2 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADC 
       47.67        21.63        44.22        22.09        40.08        13.97 
TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADN TCGA-DD-AADQ 
       40.47        39.52         3.78        37.64        29.52        14.33 
TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADY TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 
       15.58        18.21        18.25        20.98        18.61        19.99 
TCGA-DD-AAE7 TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAEE TCGA-DD-AAEI 
       21.17        23.74        18.90        15.72        16.37        50.33 
TCGA-DD-AAVR TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 
       82.62        56.48        64.77        65.39        49.48        53.69 
TCGA-ED-A4XI TCGA-ED-A627 TCGA-ED-A7PX TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP 
       12.69        13.91         0.20         0.20        14.04        13.15 
TCGA-ED-A82E TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC 
       13.41         0.20        18.74        19.99        20.61         0.62 
TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A2QR TCGA-FV-A3I1 TCGA-FV-A3R3 
        9.96        11.93        14.40        19.10         8.12        12.03 
TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25V 
        0.03         0.33        81.73         0.39        51.06        28.27 
TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SJ 
       30.74        22.13         5.92        19.53        19.23        22.95 
TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-AAV0 
       20.42        17.10         7.76        12.03         5.98         8.55 
TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-GJ-A6C0 
       11.80         9.70         9.17         0.89         8.75         1.02 
TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 
        2.20         2.99        37.91        20.75        17.06        16.83 
TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C 
        3.72         2.14        11.84        13.97        12.03         9.57 
TCGA-MI-A75E TCGA-MI-A75H TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-PD-A5DF 
       16.67        12.85         0.62        10.85        58.88        21.01 
TCGA-RC-A7S9 TCGA-RC-A7SK TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0V 
       21.04        15.52        16.44         1.71        15.98        10.32 
TCGA-WQ-AB4B TCGA-WX-AA46 TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9D0 
       12.99        24.85        13.55        35.77        25.71        23.57 
TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CF 
       24.43        12.99        45.57        40.80        79.30 

  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 
                         90.28                         120.82 
  DEL PEAK 25(16Q23.1) MUTATED DEL PEAK 25(16Q23.1) WILD-TYPE 
                         19.04                          19.53 
[1] "0.1 - 90.3 (19.0)"  "0.0 - 120.8 (19.5)"
[1] "hr=" "1.1"
D54V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IIIA
  DEL PEAK 25(16Q23.1) MUTATED        66       49         1         25
  DEL PEAK 25(16Q23.1) WILD-TYPE     102       35         2         34
                                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          5          4        2         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                              66                            102
  STAGE II                             49                             35
  STAGE III                             1                              2
  STAGE IIIA                           25                             34
  STAGE IIIB                            3                              5
  STAGE IIIC                            3                              4
  STAGE IV                              1                              2
  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      72  50  31   6
  DEL PEAK 25(16Q23.1) WILD-TYPE   107  41  42   6
D54V4, multiclass
       clus
vv      DEL PEAK 25(16Q23.1) MUTATED DEL PEAK 25(16Q23.1) WILD-TYPE
  T0+T1                           72                            107
  T2                              50                             41
  T3                              31                             42
  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   119   2
  DEL PEAK 25(16Q23.1) WILD-TYPE 130   1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(16Q23.1) MUTATED    119    2
  DEL PEAK 25(16Q23.1) WILD-TYPE  130    1
   clus
vv  DEL PEAK 25(16Q23.1) MUTATED DEL PEAK 25(16Q23.1) WILD-TYPE
  0                          119                            130
  1                            2                              1
[1] 2 2
[1] FALSE
D54V6, binary
                                cls
clus                               0   1
  DEL PEAK 25(16Q23.1) MUTATED   125   2
  DEL PEAK 25(16Q23.1) WILD-TYPE 135   2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(16Q23.1) MUTATED    125    2
  DEL PEAK 25(16Q23.1) WILD-TYPE  135    2
   clus
vv  DEL PEAK 25(16Q23.1) MUTATED DEL PEAK 25(16Q23.1) WILD-TYPE
  0                          125                            135
  1                            2                              2
[1] 2 2
[1] FALSE
D54V7, binary
                                cls
clus                               0   1
  DEL PEAK 25(16Q23.1) MUTATED    56 103
  DEL PEAK 25(16Q23.1) WILD-TYPE  57 141
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(16Q23.1) MUTATED     56  103
  DEL PEAK 25(16Q23.1) WILD-TYPE   57  141
        clus
vv       DEL PEAK 25(16Q23.1) MUTATED DEL PEAK 25(16Q23.1) WILD-TYPE
  FEMALE                           56                             57
  MALE                            103                            141
[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                        156
  DEL PEAK 25(16Q23.1) WILD-TYPE                      192
                                vv
clus                             HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK 25(16Q23.1) MUTATED                                  3
  DEL PEAK 25(16Q23.1) WILD-TYPE                                4
D54V8, multiclass
                                  clus
vv                                 DEL PEAK 25(16Q23.1) MUTATED
  FIBROLAMELLAR CARCINOMA                                     0
  HEPATOCELLULAR CARCINOMA                                  156
  HEPATOCHOLANGIOCARCINOMA (MIXED)                            3
                                  clus
vv                                 DEL PEAK 25(16Q23.1) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                       2
  HEPATOCELLULAR CARCINOMA                                    192
  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 25(16Q23.1) MUTATED   141   7   0  11
  DEL PEAK 25(16Q23.1) WILD-TYPE 174   8   1   8
D54V9, multiclass
    clus
vv   DEL PEAK 25(16Q23.1) MUTATED DEL PEAK 25(16Q23.1) WILD-TYPE
  R0                          141                            174
  R1                            7                              8
  R2                            0                              1
  RX                           11                              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 25(16Q23.1) MUTATED                                  0    90
  DEL PEAK 25(16Q23.1) WILD-TYPE                                1    66
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 25(16Q23.1) MUTATED                           7    58
  DEL PEAK 25(16Q23.1) WILD-TYPE                        10   115
D54V10, multiclass
                                  clus
vv                                 DEL PEAK 25(16Q23.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                      90
  BLACK OR AFRICAN AMERICAN                                   7
  WHITE                                                      58
                                  clus
vv                                 DEL PEAK 25(16Q23.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        66
  BLACK OR AFRICAN AMERICAN                                    10
  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"
D54V11, binary
                                cls
clus                               0   1
  DEL PEAK 25(16Q23.1) MUTATED     6 148
  DEL PEAK 25(16Q23.1) WILD-TYPE   5 181
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(16Q23.1) MUTATED      6  148
  DEL PEAK 25(16Q23.1) WILD-TYPE    5  181
                        clus
vv                       DEL PEAK 25(16Q23.1) MUTATED
  HISPANIC OR LATINO                                6
  NOT HISPANIC OR LATINO                          148
                        clus
vv                       DEL PEAK 25(16Q23.1) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                            181
[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   126  74
  DEL PEAK 26(17P13.1) WILD-TYPE  99  35
  DEL PEAK 26(17P13.1) MUTATED DEL PEAK 26(17P13.1) WILD-TYPE 
                           200                            134 
  DEL PEAK 26(17P13.1) MUTATED DEL PEAK 26(17P13.1) WILD-TYPE 
                            74                             35 
$`DEL PEAK 26(17P13.1) MUTATED`
TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GV TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H0 
       23.80        53.39        83.24        24.89        27.88       120.82 
TCGA-2Y-A9H2 TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA 
       56.91        47.74        18.25        20.81        14.99         1.18 
TCGA-4R-AA8I TCGA-5C-AAPD TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10R 
        8.61         0.66         1.51        48.99        27.91        10.13 
TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 
       27.52        27.52        23.34         1.12        69.57         5.03 
TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H 
       44.42        13.84         0.26        22.36        17.98        14.60 
TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5260 
       18.48        44.81        13.45         0.66         0.07         2.86 
TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3MA TCGA-CC-A3MB 
        3.19         3.39         4.24         3.32         0.07         0.10 
TCGA-CC-A3MC TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 
        0.13        37.78        83.57        53.33       113.00         7.33 
TCGA-DD-A11A TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EG 
        2.60        21.76        51.29        79.40        66.31        45.11 
TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39Y 
       49.15         6.02        33.04        18.35        13.64         5.62 
TCGA-DD-A3A0 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A7 TCGA-DD-A3A9 
       25.81        17.59        20.12       102.74        13.78        30.61 
TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NO 
       33.14        32.52        30.15        26.83        30.51        73.81 
TCGA-DD-A4NQ TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73E TCGA-DD-AAC9 TCGA-DD-AACA 
       12.26        23.93         9.30         1.45        11.41        75.65 
TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH 
       76.41        55.40        63.48        12.00        15.42         6.41 
TCGA-DD-AACJ TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACU 
       69.11         3.52        58.16        14.20        59.31        51.52 
TCGA-DD-AACV TCGA-DD-AACX TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD3 
       50.33         5.59         5.62         4.50        18.54        42.58 
TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD 
       44.22        22.09        40.08        40.83        13.97        40.47 
TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADL TCGA-DD-AADN TCGA-DD-AADR 
       39.52         3.78        37.64        20.91        29.52        66.67 
TCGA-DD-AADV TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 
       18.87        19.30        18.25        18.25        18.15        20.98 
TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAED 
       19.99         4.64        21.83        18.90        15.72        25.08 
TCGA-DD-AAEE TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR 
       16.37        50.33        35.08        79.07        89.69        82.62 
TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAW1 TCGA-ED-A459 TCGA-ED-A7PX TCGA-ED-A7PZ 
       72.39        76.18        65.39        13.41         0.20         0.20 
TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A2KC 
       14.04        13.15        13.41         1.84         0.20         0.62 
TCGA-ES-A2HS TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 
       22.85        60.89        23.97        19.10        27.88         8.12 
TCGA-FV-A3R2 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-G3-A25S TCGA-G3-A25U 
        6.38         0.03         0.33        81.73        13.68        53.79 
TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A5SI 
       28.27        30.74        14.86        21.53        25.64        25.25 
TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A7M6 TCGA-G3-A7M9 TCGA-G3-AAUZ 
       22.95        20.42        17.10        12.03         1.84        11.24 
TCGA-G3-AAV1 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB 
       11.80         0.89         8.75         3.02         1.02         2.20 
TCGA-HP-A5N0 TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-LG-A6GG TCGA-MI-A75E 
       37.91         3.72         2.14        11.84        12.72        16.67 
TCGA-MI-A75G TCGA-MI-A75I TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF 
       18.38        20.71        58.88        19.92        17.69        21.01 
TCGA-QA-A7B7 TCGA-RC-A7SB TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-T1-A6J8 
        3.09        19.33        15.39        15.52        24.13         0.76 
TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-A7MF TCGA-UB-AA0U 
       19.76        16.44         1.71        15.98         7.04        10.75 
TCGA-WJ-A86L TCGA-WQ-AB4B TCGA-YA-A8S7 TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZP-A9D4 
       11.34        12.99        13.55         0.69        24.43        12.99 
TCGA-ZS-A9CE TCGA-ZS-A9CF 
       40.80        79.30 

$`DEL PEAK 26(17P13.1) WILD-TYPE`
TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9H1 TCGA-2Y-A9H3 TCGA-2Y-A9H6 
       63.75        41.79        80.28        40.41        41.33        11.74 
TCGA-2Y-A9H7 TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5R-AA1C 
       37.25         8.55        13.02        10.78        10.59        11.97 
TCGA-5R-AA1D TCGA-BC-A10Q TCGA-BC-A10S TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A69I 
       11.08        37.32        46.78         2.99        25.32        12.72 
TCGA-BD-A3ER TCGA-CC-A3M9 TCGA-DD-A113 TCGA-DD-A11B TCGA-DD-A1E9 TCGA-DD-A1EC 
       36.66         0.10        79.73         0.46        90.71        19.79 
TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39X 
       75.65        11.47        12.95        21.14        27.19        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        90.28 
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        23.05        22.78        35.67       114.35 
TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AACD TCGA-DD-AACI TCGA-DD-AACK TCGA-DD-AACN 
       13.48         0.53        12.53        53.19         0.30        42.81 
TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACT TCGA-DD-AACW TCGA-DD-AACY TCGA-DD-AAD2 
       61.68        13.64        51.35        46.82        47.67        21.63 
TCGA-DD-AADA TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADM TCGA-DD-AADO 
       40.54        35.67        35.05        34.49         0.39        14.89 
TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AAE3 TCGA-DD-AAE7 
       15.06        14.33        15.58        18.21        18.61        21.17 
TCGA-DD-AAE9 TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAVS TCGA-DD-AAVX TCGA-DD-AAVY 
       23.74        23.64        25.78        59.93        56.48        64.77 
TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A4XI TCGA-ED-A5KG 
       62.47        66.25        49.48        53.69        12.69        15.85 
TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PY TCGA-ED-A8O5 TCGA-EP-A12J 
       13.91        13.35         9.73        12.82        13.35        18.74 
TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HT 
       19.99        20.61        19.59         9.96        11.93        14.40 
TCGA-FV-A3R3 TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25X TCGA-G3-A3CG TCGA-G3-A3CI 
       12.03         0.39        51.06        58.49        22.13         5.92 
TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-AAV0 TCGA-G3-AAV2 
       19.53        19.23         7.76         5.98         8.55         9.70 
TCGA-G3-AAV3 TCGA-G3-AAV6 TCGA-HP-A5MZ TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 
        9.17         2.14         2.99        20.75        17.06        16.83 
TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75H 
       13.38        24.36        13.97        12.03         9.57        12.85 
TCGA-MR-A520 TCGA-MR-A8JO TCGA-RC-A7S9 TCGA-RC-A7SF TCGA-UB-A7MA TCGA-UB-AA0V 
        0.62        10.85        21.04        19.04        17.59        10.32 
TCGA-WQ-A9G7 TCGA-WX-AA46 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 
        0.99        24.85        35.77        25.71        23.21        23.57 
TCGA-ZS-A9CD TCGA-ZS-A9CG 
       45.57        11.21 

  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 
                        120.82                         114.35 
  DEL PEAK 26(17P13.1) MUTATED DEL PEAK 26(17P13.1) WILD-TYPE 
                        18.705                         19.775 
[1] "0.0 - 120.8 (18.7)" "0.1 - 114.3 (19.8)"
[1] "hr=" "1.5"
D55V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IIIA
  DEL PEAK 26(17P13.1) MUTATED        89       56         2         38
  DEL PEAK 26(17P13.1) WILD-TYPE      79       28         1         21
                                vv
clus                             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 26(17P13.1) MUTATED            6          7        3         1
  DEL PEAK 26(17P13.1) WILD-TYPE          2          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                              89                             79
  STAGE II                             56                             28
  STAGE III                             2                              1
  STAGE IIIA                           38                             21
  STAGE IIIB                            6                              2
  STAGE IIIC                            7                              0
  STAGE IV                              3                              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      96 62 47 11
  DEL PEAK 26(17P13.1) WILD-TYPE    83 29 26  1
D55V4, multiclass
       clus
vv      DEL PEAK 26(17P13.1) MUTATED DEL PEAK 26(17P13.1) WILD-TYPE
  T0+T1                           96                             83
  T2                              62                             29
  T3                              47                             26
  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   151   3
  DEL PEAK 26(17P13.1) WILD-TYPE  98   0
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(17P13.1) MUTATED    151    3
  DEL PEAK 26(17P13.1) WILD-TYPE   98    0
   clus
vv  DEL PEAK 26(17P13.1) MUTATED DEL PEAK 26(17P13.1) WILD-TYPE
  0                          151                             98
  1                            3                              0
[1] 2 2
[1] FALSE
D55V6, binary
                                cls
clus                               0   1
  DEL PEAK 26(17P13.1) MUTATED   160   4
  DEL PEAK 26(17P13.1) WILD-TYPE 100   0
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(17P13.1) MUTATED    160    4
  DEL PEAK 26(17P13.1) WILD-TYPE  100    0
   clus
vv  DEL PEAK 26(17P13.1) MUTATED DEL PEAK 26(17P13.1) WILD-TYPE
  0                          160                            100
  1                            4                              0
[1] 2 2
[1] FALSE
D55V7, binary
                                cls
clus                               0   1
  DEL PEAK 26(17P13.1) MUTATED    66 151
  DEL PEAK 26(17P13.1) WILD-TYPE  47  93
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(17P13.1) MUTATED     66  151
  DEL PEAK 26(17P13.1) WILD-TYPE   47   93
        clus
vv       DEL PEAK 26(17P13.1) MUTATED DEL PEAK 26(17P13.1) WILD-TYPE
  FEMALE                           66                             47
  MALE                            151                             93
[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                        211
  DEL PEAK 26(17P13.1) WILD-TYPE                      137
                                vv
clus                             HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK 26(17P13.1) MUTATED                                  5
  DEL PEAK 26(17P13.1) WILD-TYPE                                2
D55V8, multiclass
                                  clus
vv                                 DEL PEAK 26(17P13.1) MUTATED
  FIBROLAMELLAR CARCINOMA                                     1
  HEPATOCELLULAR CARCINOMA                                  211
  HEPATOCHOLANGIOCARCINOMA (MIXED)                            5
                                  clus
vv                                 DEL PEAK 26(17P13.1) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                       1
  HEPATOCELLULAR CARCINOMA                                    137
  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   189  10   1  14
  DEL PEAK 26(17P13.1) WILD-TYPE 126   5   0   5
D55V9, multiclass
    clus
vv   DEL PEAK 26(17P13.1) MUTATED DEL PEAK 26(17P13.1) WILD-TYPE
  R0                          189                            126
  R1                           10                              5
  R2                            1                              0
  RX                           14                              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 26(17P13.1) MUTATED                                  0   103
  DEL PEAK 26(17P13.1) WILD-TYPE                                1    53
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 26(17P13.1) MUTATED                          12    97
  DEL PEAK 26(17P13.1) WILD-TYPE                         5    76
D55V10, multiclass
                                  clus
vv                                 DEL PEAK 26(17P13.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                     103
  BLACK OR AFRICAN AMERICAN                                  12
  WHITE                                                      97
                                  clus
vv                                 DEL PEAK 26(17P13.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        53
  BLACK OR AFRICAN AMERICAN                                     5
  WHITE                                                        76
[1] 4 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     8 199
  DEL PEAK 26(17P13.1) WILD-TYPE   3 130
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(17P13.1) MUTATED      8  199
  DEL PEAK 26(17P13.1) WILD-TYPE    3  130
                        clus
vv                       DEL PEAK 26(17P13.1) MUTATED
  HISPANIC OR LATINO                                8
  NOT HISPANIC OR LATINO                          199
                        clus
vv                       DEL PEAK 26(17P13.1) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            130
[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   105  66
  DEL PEAK 27(17P11.2) WILD-TYPE 120  43
  DEL PEAK 27(17P11.2) MUTATED DEL PEAK 27(17P11.2) WILD-TYPE 
                           171                            163 
  DEL PEAK 27(17P11.2) MUTATED DEL PEAK 27(17P11.2) WILD-TYPE 
                            66                             43 
$`DEL PEAK 27(17P11.2) MUTATED`
TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GV TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H0 
       23.80        53.39        83.24        24.89        27.88       120.82 
TCGA-2Y-A9H2 TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-5C-AAPD 
       56.91        18.25        20.81        14.99         1.18         0.66 
TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U 
        1.51        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-A2L6 TCGA-BD-A3EP 
       22.36        17.98        14.60        18.48        44.81        13.45 
TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT 
        0.66         0.07         3.19         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-A118 TCGA-DD-A119 TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1EA TCGA-DD-A1EB 
      113.00         7.33        21.76        51.29        79.40        66.31 
TCGA-DD-A1EG TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39Y 
       45.11         6.02        33.04        18.35        13.64         5.62 
TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A7 TCGA-DD-A4NA TCGA-DD-A4NB 
       17.59        20.12       102.74        13.78        33.14        32.52 
TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NO TCGA-DD-A4NQ TCGA-DD-A73B 
       30.15        26.83        30.51        73.81        12.26         9.30 
TCGA-DD-A73E TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACC TCGA-DD-AACE TCGA-DD-AACG 
        1.45        11.41        75.65        55.40        63.48        15.42 
TCGA-DD-AACH TCGA-DD-AACJ TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACX TCGA-DD-AACZ 
        6.41        69.11         3.52        58.16         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        42.58        44.22        22.09        40.08 
TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADJ 
       40.83        13.97        39.52         3.78        37.64        35.05 
TCGA-DD-AADL TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADV TCGA-DD-AADW TCGA-DD-AADY 
       20.91        29.52        14.89        18.87        19.30        18.25 
TCGA-DD-AAE0 TCGA-DD-AAE2 TCGA-DD-AAE4 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAEE 
       18.25        20.98        19.99        18.90        15.72        16.37 
TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVU 
       50.33        35.08        79.07        89.69        82.62        72.39 
TCGA-DD-AAW1 TCGA-ED-A459 TCGA-ED-A7PX TCGA-ED-A82E TCGA-ED-A8O6 TCGA-ED-A97K 
       65.39        13.41         0.20        13.41         1.84         0.20 
TCGA-EP-A2KC TCGA-ES-A2HS TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 
        0.62        22.85        60.89        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        81.73        13.68        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-G3-AAV5 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5N0 TCGA-K7-AAU7 TCGA-KR-A7K0 
        8.75         1.02         2.20        37.91         3.72         2.14 
TCGA-KR-A7K2 TCGA-LG-A6GG TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I TCGA-NI-A4U2 
       11.84        12.72        16.67        18.38        20.71        58.88 
TCGA-NI-A8LF TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7SB TCGA-RC-A7SK TCGA-RG-A7D4 
       19.92        21.01         3.09        19.33        15.52        24.13 
TCGA-T1-A6J8 TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-A7MF 
        0.76        19.76        16.44         1.71        15.98         7.04 
TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-AB4B TCGA-YA-A8S7 TCGA-ZP-A9D1 TCGA-ZP-A9D2 
       10.75        11.34        12.99        13.55         0.69        24.43 
TCGA-ZP-A9D4 TCGA-ZS-A9CE TCGA-ZS-A9CF 
       12.99        40.80        79.30 

$`DEL PEAK 27(17P11.2) WILD-TYPE`
TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9H1 TCGA-2Y-A9H3 TCGA-2Y-A9H4 
       63.75        41.79        80.28        40.41        41.33        47.74 
TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-4R-AA8I TCGA-5C-A9VG 
       11.74        37.25         8.55        13.02         8.61        10.78 
TCGA-5C-A9VH TCGA-5R-AA1C TCGA-5R-AA1D TCGA-BC-A10Q TCGA-BC-A10S TCGA-BC-A10W 
       10.59        11.97        11.08        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        36.66         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-A39W TCGA-DD-A39X 
       11.47        12.95        49.15        21.14        27.19        55.69 
TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A6 TCGA-DD-A3A8 
       19.76        25.81         7.66        70.06       107.11         0.36 
TCGA-DD-A3A9 TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN 
       30.61        90.28        30.97        39.78        56.25        29.56 
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        23.93        23.05 
TCGA-DD-A73D TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AACB 
       22.78        35.67       114.35        13.48         0.53        76.41 
TCGA-DD-AACD TCGA-DD-AACF TCGA-DD-AACI TCGA-DD-AACK TCGA-DD-AACN TCGA-DD-AACO 
       12.53        12.00        53.19         0.30        42.81        61.68 
TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACV 
       13.64        14.20        59.31        51.35        51.52        50.33 
TCGA-DD-AACW TCGA-DD-AACY TCGA-DD-AAD2 TCGA-DD-AADA TCGA-DD-AADD TCGA-DD-AADI 
       46.82        47.67        21.63        40.54        40.47        35.67 
TCGA-DD-AADK TCGA-DD-AADM TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS 
       34.49         0.39        15.06        14.33        66.67        15.58 
TCGA-DD-AADU TCGA-DD-AAE1 TCGA-DD-AAE3 TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAE8 
       18.21        18.15        18.61         4.64        21.17        21.83 
TCGA-DD-AAE9 TCGA-DD-AAED TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAVS TCGA-DD-AAVW 
       23.74        25.08        23.64        25.78        59.93        76.18 
TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW2 TCGA-DD-AAW3 
       56.48        64.77        62.47        66.25        49.48        53.69 
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         9.73        12.82 
TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A8O5 TCGA-EP-A12J TCGA-EP-A26S 
        0.20        14.04        13.15        13.35        18.74        19.99 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A3R3 
       20.61        19.59         9.96        11.93        14.40        12.03 
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        25.25        22.95         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         2.99 
TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A9QC 
       20.75        17.06        16.83        13.38        24.36        13.97 
TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75H TCGA-MR-A520 TCGA-MR-A8JO TCGA-O8-A75V 
       12.03         9.57        12.85         0.62        10.85        17.69 
TCGA-RC-A7S9 TCGA-RC-A7SF TCGA-RC-A7SH TCGA-UB-A7MA TCGA-UB-AA0V TCGA-WQ-A9G7 
       21.04        19.04        15.39        17.59        10.32         0.99 
TCGA-WX-AA46 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZS-A9CD 
       24.85        35.77        25.71        23.21        23.57        45.57 
TCGA-ZS-A9CG 
       11.21 

  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 
                        120.82                         114.35 
  DEL PEAK 27(17P11.2) MUTATED DEL PEAK 27(17P11.2) WILD-TYPE 
                         18.54                          19.79 
[1] "0.0 - 120.8 (18.5)" "0.1 - 114.3 (19.8)"
[1] "hr=" "1.6"
D56V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IIIA
  DEL PEAK 27(17P11.2) MUTATED        71       49         1         35
  DEL PEAK 27(17P11.2) WILD-TYPE      97       35         2         24
                                vv
clus                             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 27(17P11.2) MUTATED            6          6        3         1
  DEL PEAK 27(17P11.2) WILD-TYPE          2          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                              71                             97
  STAGE II                             49                             35
  STAGE III                             1                              2
  STAGE IIIA                           35                             24
  STAGE IIIB                            6                              2
  STAGE IIIC                            6                              1
  STAGE IV                              3                              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      78  55  43   9
  DEL PEAK 27(17P11.2) WILD-TYPE   101  36  30   3
D56V4, multiclass
       clus
vv      DEL PEAK 27(17P11.2) MUTATED DEL PEAK 27(17P11.2) WILD-TYPE
  T0+T1                           78                            101
  T2                              55                             36
  T3                              43                             30
  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   128   3
  DEL PEAK 27(17P11.2) WILD-TYPE 121   0
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(17P11.2) MUTATED    128    3
  DEL PEAK 27(17P11.2) WILD-TYPE  121    0
   clus
vv  DEL PEAK 27(17P11.2) MUTATED DEL PEAK 27(17P11.2) WILD-TYPE
  0                          128                            121
  1                            3                              0
[1] 2 2
[1] FALSE
D56V6, binary
                                cls
clus                               0   1
  DEL PEAK 27(17P11.2) MUTATED   134   3
  DEL PEAK 27(17P11.2) WILD-TYPE 126   1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(17P11.2) MUTATED    134    3
  DEL PEAK 27(17P11.2) WILD-TYPE  126    1
   clus
vv  DEL PEAK 27(17P11.2) MUTATED DEL PEAK 27(17P11.2) WILD-TYPE
  0                          134                            126
  1                            3                              1
[1] 2 2
[1] FALSE
D56V7, binary
                                cls
clus                               0   1
  DEL PEAK 27(17P11.2) MUTATED    59 127
  DEL PEAK 27(17P11.2) WILD-TYPE  54 117
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(17P11.2) MUTATED     59  127
  DEL PEAK 27(17P11.2) WILD-TYPE   54  117
        clus
vv       DEL PEAK 27(17P11.2) MUTATED DEL PEAK 27(17P11.2) WILD-TYPE
  FEMALE                           59                             54
  MALE                            127                            117
[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                        180
  DEL PEAK 27(17P11.2) WILD-TYPE                      168
                                vv
clus                             HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK 27(17P11.2) MUTATED                                  5
  DEL PEAK 27(17P11.2) WILD-TYPE                                2
D56V8, multiclass
                                  clus
vv                                 DEL PEAK 27(17P11.2) MUTATED
  FIBROLAMELLAR CARCINOMA                                     1
  HEPATOCELLULAR CARCINOMA                                  180
  HEPATOCHOLANGIOCARCINOMA (MIXED)                            5
                                  clus
vv                                 DEL PEAK 27(17P11.2) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                       1
  HEPATOCELLULAR CARCINOMA                                    168
  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   160  10   1  12
  DEL PEAK 27(17P11.2) WILD-TYPE 155   5   0   7
D56V9, multiclass
    clus
vv   DEL PEAK 27(17P11.2) MUTATED DEL PEAK 27(17P11.2) WILD-TYPE
  R0                          160                            155
  R1                           10                              5
  R2                            1                              0
  RX                           12                              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"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 27(17P11.2) MUTATED                                  0    83
  DEL PEAK 27(17P11.2) WILD-TYPE                                1    73
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 27(17P11.2) MUTATED                          10    89
  DEL PEAK 27(17P11.2) WILD-TYPE                         7    84
D56V10, multiclass
                                  clus
vv                                 DEL PEAK 27(17P11.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                      83
  BLACK OR AFRICAN AMERICAN                                  10
  WHITE                                                      89
                                  clus
vv                                 DEL PEAK 27(17P11.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        73
  BLACK OR AFRICAN AMERICAN                                     7
  WHITE                                                        84
[1] 4 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     7 170
  DEL PEAK 27(17P11.2) WILD-TYPE   4 159
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(17P11.2) MUTATED      7  170
  DEL PEAK 27(17P11.2) WILD-TYPE    4  159
                        clus
vv                       DEL PEAK 27(17P11.2) MUTATED
  HISPANIC OR LATINO                                7
  NOT HISPANIC OR LATINO                          170
                        clus
vv                       DEL PEAK 27(17P11.2) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            159
[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    58  24
  DEL PEAK 28(18Q21.2) WILD-TYPE 167  85
  DEL PEAK 28(18Q21.2) MUTATED DEL PEAK 28(18Q21.2) WILD-TYPE 
                            82                            252 
  DEL PEAK 28(18Q21.2) MUTATED DEL PEAK 28(18Q21.2) WILD-TYPE 
                            24                             85 
$`DEL PEAK 28(18Q21.2) MUTATED`
TCGA-2Y-A9H3 TCGA-2Y-A9H5 TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1D TCGA-BC-A10R 
       41.33        18.25        10.59         0.66        11.08        10.13 
TCGA-BC-A10U TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-CC-A3MB 
       27.52         5.03        44.42        13.84         0.26         0.10 
TCGA-DD-A118 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A1EF TCGA-DD-A1EJ TCGA-DD-A1EL 
      113.00         2.60         0.46        12.95        33.04        13.64 
TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A3A4 TCGA-DD-A3A9 TCGA-DD-A4NB TCGA-DD-A4NI 
       55.69         5.62        20.12        30.61        32.52        26.83 
TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A73B TCGA-DD-A73E TCGA-DD-A73G TCGA-DD-AAC8 
       29.56        73.81         9.30         1.45       114.35         0.53 
TCGA-DD-AACB TCGA-DD-AACE TCGA-DD-AACI TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP 
       76.41        63.48        53.19        42.81        61.68        13.64 
TCGA-DD-AACV TCGA-DD-AACX TCGA-DD-AACZ TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AADA 
       50.33         5.59         5.62        44.22        22.09        40.54 
TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADO TCGA-DD-AADV TCGA-DD-AADW TCGA-DD-AAE0 
       35.67        35.05        14.89        18.87        19.30        18.25 
TCGA-DD-AAE2 TCGA-DD-AAEG TCGA-DD-AAEK TCGA-DD-AAVP TCGA-ED-A459 TCGA-ED-A66X 
       20.98        23.64        35.08        79.07        13.41        13.35 
TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O6 TCGA-ES-A2HS TCGA-FV-A3I0 TCGA-FV-A3R2 
       13.15        13.41         1.84        22.85        27.88         6.38 
TCGA-FV-A496 TCGA-G3-A25S TCGA-G3-AAV1 TCGA-G3-AAV6 TCGA-KR-A7K7 TCGA-MI-A75G 
        0.33        13.68        11.80         2.14        13.38        18.38 
TCGA-MR-A8JO TCGA-NI-A8LF TCGA-QA-A7B7 TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK 
       10.85        19.92         3.09        19.04        15.39        15.52 
TCGA-RG-A7D4 TCGA-T1-A6J8 TCGA-UB-A7MC TCGA-UB-A7MF TCGA-YA-A8S7 TCGA-ZP-A9CZ 
       24.13         0.76        16.44         7.04        13.55        23.21 
TCGA-ZP-A9D0 TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       23.57        40.80        79.30        11.21 

$`DEL PEAK 28(18Q21.2) WILD-TYPE`
TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GV TCGA-2Y-A9GW TCGA-2Y-A9GX 
       23.80        53.39        63.75        83.24        41.79        80.28 
TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H4 
       24.89        27.88       120.82        40.41        56.91        47.74 
TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB 
       11.74        37.25        20.81        14.99         1.18         8.55 
TCGA-3K-AAZ8 TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5R-AA1C TCGA-5R-AAAM TCGA-BC-4072 
       13.02         8.61        10.78        11.97         1.51        48.99 
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10W TCGA-BC-A10X 
       27.91        37.32        46.78        27.52         2.99        25.32 
TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H 
       23.34         1.12        69.57        22.36        17.98        14.60 
TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BD-A3ER TCGA-BW-A5NO 
       12.72        18.48        44.81        13.45        36.66         0.66 
TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT 
        0.07         2.86         3.19         3.39         4.24         3.32 
TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 
        0.10         0.07         0.13        79.73        37.78        83.57 
TCGA-DD-A116 TCGA-DD-A119 TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA 
       53.33         7.33        21.76        51.29        90.71        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        11.47        45.11        49.15 
TCGA-DD-A1EI TCGA-DD-A1EK TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39Z TCGA-DD-A3A0 
        6.02        18.35        21.14        27.19        19.76        25.81 
TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 
        7.66        70.06        17.59       102.74       107.11        13.78 
TCGA-DD-A3A8 TCGA-DD-A4NA TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NJ 
        0.36        33.14        90.28        30.97        30.15        30.51 
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-A73C TCGA-DD-A73D TCGA-DD-A73F TCGA-DD-AA3A 
       78.84        23.93        23.05        22.78        35.67        13.48 
TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACF TCGA-DD-AACG 
       11.41        75.65        55.40        12.53        12.00        15.42 
TCGA-DD-AACH TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACQ 
        6.41        69.11         0.30         3.52        58.16        14.20 
TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACW TCGA-DD-AACY TCGA-DD-AAD0 
       59.31        51.35        51.52        46.82        47.67         4.50 
TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD8 TCGA-DD-AADB TCGA-DD-AADC 
       18.54        21.63        42.58        40.08        40.83        13.97 
TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADK TCGA-DD-AADL 
       40.47        39.52         3.78        37.64        34.49        20.91 
TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS 
        0.39        29.52        15.06        14.33        66.67        15.58 
TCGA-DD-AADU TCGA-DD-AADY TCGA-DD-AAE1 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 
       18.21        18.25        18.15        18.61        19.99         4.64 
TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAED 
       21.17        21.83        23.74        18.90        15.72        25.08 
TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS 
       16.37        25.78        50.33        89.69        82.62        59.93 
TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 
       72.39        76.18        56.48        64.77        62.47        66.25 
TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 
       65.39        49.48        53.69        12.69        15.85        13.91 
TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A8O5 
        9.73         0.20        12.82         0.20        14.04        13.35 
TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC 
        0.20        18.74        19.99        20.61        19.59         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        60.89        23.97        19.10 
TCGA-FV-A3I1 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25T 
        8.12        12.03         0.03        81.73         0.39        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        25.25 
TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 
       22.95        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-AAV5 TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 
        8.75         3.02         1.02         2.20         2.99        37.91 
TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K2 
       20.75        17.06        16.83         3.72         2.14        11.84 
TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E 
       24.36        12.72        13.97        12.03         9.57        16.67 
TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A520 TCGA-NI-A4U2 TCGA-O8-A75V TCGA-PD-A5DF 
       12.85        20.71         0.62        58.88        17.69        21.01 
TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MD TCGA-UB-A7ME 
       21.04        19.33        17.59        19.76         1.71        15.98 
TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA46 
       10.75        10.32        11.34         0.99        12.99        24.85 
TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD 
       35.77        25.71         0.69        24.43        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 
                        114.35                         120.82 
  DEL PEAK 28(18Q21.2) MUTATED DEL PEAK 28(18Q21.2) WILD-TYPE 
                         18.25                          19.76 
[1] "0.1 - 114.3 (18.2)" "0.0 - 120.8 (19.8)"
[1] "hr=" "1"  
D57V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IIIA
  DEL PEAK 28(18Q21.2) MUTATED        42       21         0         15
  DEL PEAK 28(18Q21.2) WILD-TYPE     126       63         3         44
                                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          8          5        2         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                              42                            126
  STAGE II                             21                             63
  STAGE III                             0                              3
  STAGE IIIA                           15                             44
  STAGE IIIB                            0                              8
  STAGE IIIC                            2                              5
  STAGE IV                              1                              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 28(18Q21.2) MUTATED      46  23  17   2
  DEL PEAK 28(18Q21.2) WILD-TYPE   133  68  56  10
D57V4, multiclass
       clus
vv      DEL PEAK 28(18Q21.2) MUTATED DEL PEAK 28(18Q21.2) WILD-TYPE
  T0+T1                           46                            133
  T2                              23                             68
  T3                              17                             56
  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    62   1
  DEL PEAK 28(18Q21.2) WILD-TYPE 187   2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 28(18Q21.2) MUTATED     62    1
  DEL PEAK 28(18Q21.2) WILD-TYPE  187    2
   clus
vv  DEL PEAK 28(18Q21.2) MUTATED DEL PEAK 28(18Q21.2) WILD-TYPE
  0                           62                            187
  1                            1                              2
[1] 2 2
[1] FALSE
D57V6, binary
                                cls
clus                               0   1
  DEL PEAK 28(18Q21.2) MUTATED    66   2
  DEL PEAK 28(18Q21.2) WILD-TYPE 194   2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 28(18Q21.2) MUTATED     66    2
  DEL PEAK 28(18Q21.2) WILD-TYPE  194    2
   clus
vv  DEL PEAK 28(18Q21.2) MUTATED DEL PEAK 28(18Q21.2) WILD-TYPE
  0                           66                            194
  1                            2                              2
[1] 2 2
[1] FALSE
D57V7, binary
                                cls
clus                               0   1
  DEL PEAK 28(18Q21.2) MUTATED    32  56
  DEL PEAK 28(18Q21.2) WILD-TYPE  81 188
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 28(18Q21.2) MUTATED     32   56
  DEL PEAK 28(18Q21.2) WILD-TYPE   81  188
        clus
vv       DEL PEAK 28(18Q21.2) MUTATED DEL PEAK 28(18Q21.2) WILD-TYPE
  FEMALE                           32                             81
  MALE                             56                            188
[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                         84
  DEL PEAK 28(18Q21.2) WILD-TYPE                      264
                                vv
clus                             HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK 28(18Q21.2) MUTATED                                  2
  DEL PEAK 28(18Q21.2) WILD-TYPE                                5
D57V8, multiclass
                                  clus
vv                                 DEL PEAK 28(18Q21.2) MUTATED
  FIBROLAMELLAR CARCINOMA                                     2
  HEPATOCELLULAR CARCINOMA                                   84
  HEPATOCHOLANGIOCARCINOMA (MIXED)                            2
                                  clus
vv                                 DEL PEAK 28(18Q21.2) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                       0
  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
  DEL PEAK 28(18Q21.2) MUTATED    80   2   0   6
  DEL PEAK 28(18Q21.2) WILD-TYPE 235  13   1  13
D57V9, multiclass
    clus
vv   DEL PEAK 28(18Q21.2) MUTATED DEL PEAK 28(18Q21.2) WILD-TYPE
  R0                           80                            235
  R1                            2                             13
  R2                            0                              1
  RX                            6                             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 28(18Q21.2) MUTATED                                  0    40
  DEL PEAK 28(18Q21.2) WILD-TYPE                                1   116
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 28(18Q21.2) MUTATED                           5    43
  DEL PEAK 28(18Q21.2) WILD-TYPE                        12   130
D57V10, multiclass
                                  clus
vv                                 DEL PEAK 28(18Q21.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                      40
  BLACK OR AFRICAN AMERICAN                                   5
  WHITE                                                      43
                                  clus
vv                                 DEL PEAK 28(18Q21.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                       116
  BLACK OR AFRICAN AMERICAN                                    12
  WHITE                                                       130
[1] 4 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     4  79
  DEL PEAK 28(18Q21.2) WILD-TYPE   7 250
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 28(18Q21.2) MUTATED      4   79
  DEL PEAK 28(18Q21.2) WILD-TYPE    7  250
                        clus
vv                       DEL PEAK 28(18Q21.2) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                           79
                        clus
vv                       DEL PEAK 28(18Q21.2) WILD-TYPE
  HISPANIC OR LATINO                                  7
  NOT HISPANIC OR LATINO                            250
[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    48  27
  DEL PEAK 29(19P13.3) WILD-TYPE 177  82
  DEL PEAK 29(19P13.3) MUTATED DEL PEAK 29(19P13.3) WILD-TYPE 
                            75                            259 
  DEL PEAK 29(19P13.3) MUTATED DEL PEAK 29(19P13.3) WILD-TYPE 
                            27                             82 
$`DEL PEAK 29(19P13.3) MUTATED`
TCGA-2Y-A9GS TCGA-2Y-A9GU TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H2 TCGA-2Y-A9H3 
       23.80        63.75        24.89        27.88        56.91        41.33 
TCGA-2Y-A9HA TCGA-4R-AA8I TCGA-BC-A10W TCGA-BC-A112 TCGA-BC-A3KF TCGA-BC-A69H 
        1.18         8.61         2.99         5.03         0.26        14.60 
TCGA-BC-A8YO TCGA-CC-5258 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3MC TCGA-DD-A113 
       18.48         0.07         4.24         3.32         0.13        79.73 
TCGA-DD-A118 TCGA-DD-A11A TCGA-DD-A1EG TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EL 
      113.00         2.60        45.11         6.02        33.04        13.64 
TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A3A9 TCGA-DD-A4NJ TCGA-DD-A4NQ TCGA-DD-A73D 
       55.69         5.62        30.61        30.51        12.26        22.78 
TCGA-DD-AACB TCGA-DD-AACE TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACL TCGA-DD-AACO 
       76.41        63.48        15.42         6.41         3.52        61.68 
TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACZ 
       13.64        14.20        59.31        51.52        50.33         5.62 
TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD 
       44.22        22.09        40.08        40.83        13.97        40.47 
TCGA-DD-AADL TCGA-DD-AADV TCGA-DD-AAE6 TCGA-DD-AAE8 TCGA-DD-AAEG TCGA-DD-AAVR 
       20.91        18.87         4.64        21.83        23.64        82.62 
TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A8O6 TCGA-ED-A97K 
       13.41        12.69         0.20        14.04         1.84         0.20 
TCGA-FV-A3I1 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-G3-A25S TCGA-G3-A25X TCGA-G3-A3CH 
        8.12         0.33        81.73        13.68        58.49        25.64 
TCGA-G3-A5SM TCGA-G3-A7M6 TCGA-G3-AAV1 TCGA-G3-AAV7 TCGA-MI-A75C TCGA-NI-A8LF 
       17.10        12.03        11.80         3.02         9.57        19.92 
TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-T1-A6J8 
       15.52        24.13         0.76 

$`DEL PEAK 29(19P13.3) WILD-TYPE`
TCGA-2Y-A9GT TCGA-2Y-A9GV TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9H0 TCGA-2Y-A9H1 
       53.39        83.24        41.79        80.28       120.82        40.41 
TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-2Y-A9H8 TCGA-2Y-A9H9 
       47.74        18.25        11.74        37.25        20.81        14.99 
TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C 
        8.55        13.02        10.78        10.59         0.66        11.97 
TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R 
       11.08         1.51        48.99        27.91        37.32        10.13 
TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z 
       46.78        27.52        27.52        25.32        23.34         1.12 
TCGA-BC-A110 TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69I 
       69.57        44.42        13.84        22.36        17.98        12.72 
TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BD-A3ER TCGA-BW-A5NO TCGA-CC-5260 TCGA-CC-5261 
       44.81        13.45        36.66         0.66         2.86         3.19 
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        11.47        12.95 
TCGA-DD-A1EH TCGA-DD-A1EK TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39Z TCGA-DD-A3A0 
       49.15        18.35        21.14        27.19        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-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NF 
       13.78         0.36        33.14        32.52        90.28        30.97 
TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO 
       30.15        26.83        39.78        56.25        29.56        73.81 
TCGA-DD-A4NP TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B 
      108.76         0.30        80.75        78.84        23.93         9.30 
TCGA-DD-A73C TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 
       23.05         1.45        35.67       114.35        13.48         0.53 
TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACF TCGA-DD-AACI 
       11.41        75.65        55.40        12.53        12.00        53.19 
TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACT TCGA-DD-AACW 
       69.11         0.30        58.16        42.81        51.35        46.82 
TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 
        5.59        47.67         4.50        18.54        21.63        42.58 
TCGA-DD-AADA TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ 
       40.54        39.52         3.78        37.64        35.67        35.05 
TCGA-DD-AADK TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ 
       34.49         0.39        29.52        14.89        15.06        14.33 
TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 
       66.67        15.58        18.21        19.30        18.25        18.25 
TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE7 TCGA-DD-AAE9 
       18.15        20.98        18.61        19.99        21.17        23.74 
TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAEI 
       18.90        15.72        25.08        16.37        25.78        50.33 
TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW 
       35.08        79.07        89.69        59.93        72.39        76.18 
TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 
       56.48        64.77        62.47        66.25        65.39        49.48 
TCGA-DD-AAW3 TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX 
       53.69        15.85        13.91        13.35         9.73         0.20 
TCGA-ED-A7PY TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-EP-A12J TCGA-EP-A26S 
       12.82        13.15        13.41        13.35        18.74        19.99 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS 
       20.61        19.59         0.62         9.96        11.93        22.85 
TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R2 
       14.40        60.89        23.97        19.10        27.88         6.38 
TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V 
       12.03         0.03         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-A7M7 
       19.23        25.25        22.95        20.42         7.76         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-AAV5 TCGA-G3-AAV6 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 
        8.75         2.14         1.02         2.20         2.99        37.91 
TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K2 
       20.75        17.06        16.83         3.72         2.14        11.84 
TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75E 
       13.38        24.36        12.72        13.97        12.03        16.67 
TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 
       18.38        12.85        20.71         0.62        10.85        58.88 
TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF 
       17.69        21.01         3.09        21.04        19.33        19.04 
TCGA-RC-A7SH TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME 
       15.39        17.59        19.76        16.44         1.71        15.98 
TCGA-UB-A7MF TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B 
        7.04        10.75        10.32        11.34         0.99        12.99 
TCGA-WX-AA46 TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 
       24.85        13.55        35.77        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        40.80        79.30 
TCGA-ZS-A9CG 
       11.21 

  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                         120.82 
  DEL PEAK 29(19P13.3) MUTATED DEL PEAK 29(19P13.3) WILD-TYPE 
                         15.52                          19.59 
[1] "0.1 - 113.0 (15.5)" "0.0 - 120.8 (19.6)"
[1] "hr=" "1.2"
D58V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IIIA
  DEL PEAK 29(19P13.3) MUTATED        35       25         0         15
  DEL PEAK 29(19P13.3) WILD-TYPE     133       59         3         44
                                vv
clus                             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 29(19P13.3) MUTATED            1          3        1         0
  DEL PEAK 29(19P13.3) WILD-TYPE          7          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                              35                            133
  STAGE II                             25                             59
  STAGE III                             0                              3
  STAGE IIIA                           15                             44
  STAGE IIIB                            1                              7
  STAGE IIIC                            3                              4
  STAGE IV                              1                              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      37  26  16   5
  DEL PEAK 29(19P13.3) WILD-TYPE   142  65  57   7
D58V4, multiclass
       clus
vv      DEL PEAK 29(19P13.3) MUTATED DEL PEAK 29(19P13.3) WILD-TYPE
  T0+T1                           37                            142
  T2                              26                             65
  T3                              16                             57
  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    61   1
  DEL PEAK 29(19P13.3) WILD-TYPE 188   2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(19P13.3) MUTATED     61    1
  DEL PEAK 29(19P13.3) WILD-TYPE  188    2
   clus
vv  DEL PEAK 29(19P13.3) MUTATED DEL PEAK 29(19P13.3) WILD-TYPE
  0                           61                            188
  1                            1                              2
[1] 2 2
[1] FALSE
D58V6, binary
                                cls
clus                               0   1
  DEL PEAK 29(19P13.3) MUTATED    68   1
  DEL PEAK 29(19P13.3) WILD-TYPE 192   3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(19P13.3) MUTATED     68    1
  DEL PEAK 29(19P13.3) WILD-TYPE  192    3
   clus
vv  DEL PEAK 29(19P13.3) MUTATED DEL PEAK 29(19P13.3) WILD-TYPE
  0                           68                            192
  1                            1                              3
[1] 2 2
[1] FALSE
D58V7, binary
                                cls
clus                               0   1
  DEL PEAK 29(19P13.3) MUTATED    24  60
  DEL PEAK 29(19P13.3) WILD-TYPE  89 184
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(19P13.3) MUTATED     24   60
  DEL PEAK 29(19P13.3) WILD-TYPE   89  184
        clus
vv       DEL PEAK 29(19P13.3) MUTATED DEL PEAK 29(19P13.3) WILD-TYPE
  FEMALE                           24                             89
  MALE                             60                            184
[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                         83
  DEL PEAK 29(19P13.3) WILD-TYPE                      265
                                vv
clus                             HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK 29(19P13.3) MUTATED                                  1
  DEL PEAK 29(19P13.3) WILD-TYPE                                6
D58V8, multiclass
                                  clus
vv                                 DEL PEAK 29(19P13.3) MUTATED
  FIBROLAMELLAR CARCINOMA                                     0
  HEPATOCELLULAR CARCINOMA                                   83
  HEPATOCHOLANGIOCARCINOMA (MIXED)                            1
                                  clus
vv                                 DEL PEAK 29(19P13.3) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                       2
  HEPATOCELLULAR CARCINOMA                                    265
  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 29(19P13.3) MUTATED    76   3   0   4
  DEL PEAK 29(19P13.3) WILD-TYPE 239  12   1  15
D58V9, multiclass
    clus
vv   DEL PEAK 29(19P13.3) MUTATED DEL PEAK 29(19P13.3) WILD-TYPE
  R0                           76                            239
  R1                            3                             12
  R2                            0                              1
  RX                            4                             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 29(19P13.3) MUTATED                                  0    50
  DEL PEAK 29(19P13.3) WILD-TYPE                                1   106
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 29(19P13.3) MUTATED                           3    31
  DEL PEAK 29(19P13.3) WILD-TYPE                        14   142
D58V10, multiclass
                                  clus
vv                                 DEL PEAK 29(19P13.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                      50
  BLACK OR AFRICAN AMERICAN                                   3
  WHITE                                                      31
                                  clus
vv                                 DEL PEAK 29(19P13.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                       106
  BLACK OR AFRICAN AMERICAN                                    14
  WHITE                                                       142
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V11, binary
                                cls
clus                               0   1
  DEL PEAK 29(19P13.3) MUTATED     3  80
  DEL PEAK 29(19P13.3) WILD-TYPE   8 249
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(19P13.3) MUTATED      3   80
  DEL PEAK 29(19P13.3) WILD-TYPE    8  249
                        clus
vv                       DEL PEAK 29(19P13.3) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           80
                        clus
vv                       DEL PEAK 29(19P13.3) WILD-TYPE
  HISPANIC OR LATINO                                  8
  NOT HISPANIC OR LATINO                            249
[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    15   9
  DEL PEAK 30(20P12.1) WILD-TYPE 210 100
  DEL PEAK 30(20P12.1) MUTATED DEL PEAK 30(20P12.1) WILD-TYPE 
                            24                            310 
  DEL PEAK 30(20P12.1) MUTATED DEL PEAK 30(20P12.1) WILD-TYPE 
                             9                            100 
$`DEL PEAK 30(20P12.1) MUTATED`
TCGA-2Y-A9H6 TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-5R-AA1D TCGA-BC-A10Z TCGA-CC-A3MC 
       11.74        13.02        10.78        11.08         1.12         0.13 
TCGA-DD-A1EK TCGA-DD-A39V TCGA-DD-A39Y TCGA-DD-A3A3 TCGA-DD-A3A5 TCGA-DD-A4NO 
       18.35        21.14         5.62        17.59       102.74        73.81 
TCGA-DD-A4NQ TCGA-DD-A73F TCGA-DD-AACS TCGA-DD-AACX TCGA-DD-AACZ TCGA-DD-AAD5 
       12.26        35.67        59.31         5.59         5.62        44.22 
TCGA-DD-AADA TCGA-DD-AADJ TCGA-DD-AADM TCGA-ED-A7PX TCGA-ED-A97K TCGA-MR-A8JO 
       40.54        35.05         0.39         0.20         0.20        10.85 

$`DEL PEAK 30(20P12.1) WILD-TYPE`
TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GV TCGA-2Y-A9GW TCGA-2Y-A9GX 
       23.80        53.39        63.75        83.24        41.79        80.28 
TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 
       24.89        27.88       120.82        40.41        56.91        41.33 
TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H7 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA 
       47.74        18.25        37.25        20.81        14.99         1.18 
TCGA-2Y-A9HB TCGA-4R-AA8I TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AAAM 
        8.55         8.61        10.59         0.66        11.97         1.51 
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T 
       48.99        27.91        37.32        10.13        46.78        27.52 
TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A110 TCGA-BC-A112 
       27.52         2.99        25.32        23.34        69.57         5.03 
TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H 
       44.42        13.84         0.26        22.36        17.98        14.60 
TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BD-A3ER TCGA-BW-A5NO 
       12.72        18.48        44.81        13.45        36.66         0.66 
TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT 
        0.07         2.86         3.19         3.39         4.24         3.32 
TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 
        0.10         0.07         0.10        79.73        37.78        83.57 
TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C 
       53.33       113.00         7.33         2.60         0.46        21.76 
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-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ 
       11.47        12.95        45.11        49.15         6.02        33.04 
TCGA-DD-A1EL TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 
       13.64        27.19        55.69        19.76        25.81         7.66 
TCGA-DD-A3A2 TCGA-DD-A3A4 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 
       70.06        20.12       107.11        13.78         0.36        30.61 
TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI 
       33.14        32.52        90.28        30.97        30.15        26.83 
TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NP TCGA-DD-A4NR 
       30.51        39.78        56.25        29.56       108.76         0.30 
TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D 
       80.75        78.84        23.93         9.30        23.05        22.78 
TCGA-DD-A73E TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA 
        1.45       114.35        13.48         0.53        11.41        75.65 
TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG 
       76.41        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        69.11         0.30         3.52        58.16 
TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACT TCGA-DD-AACU 
       42.81        61.68        13.64        14.20        51.35        51.52 
TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACY TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 
       50.33        46.82        47.67         4.50        18.54        21.63 
TCGA-DD-AAD3 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD 
       42.58        22.09        40.08        40.83        13.97        40.47 
TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADK TCGA-DD-AADL 
       39.52         3.78        37.64        35.67        34.49        20.91 
TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS 
       29.52        14.89        15.06        14.33        66.67        15.58 
TCGA-DD-AADU TCGA-DD-AADV TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 
       18.21        18.87        19.30        18.25        18.25        18.15 
TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAE8 
       20.98        18.61        19.99         4.64        21.17        21.83 
TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEG 
       23.74        18.90        15.72        25.08        16.37        23.64 
TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR 
       25.78        50.33        35.08        79.07        89.69        82.62 
TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ 
       59.93        72.39        76.18        56.48        64.77        62.47 
TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI 
       66.25        65.39        49.48        53.69        13.41        12.69 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PY TCGA-ED-A7PZ 
       15.85        13.91        13.35         9.73        12.82         0.20 
TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-EP-A12J 
       14.04        13.15        13.41        13.35         1.84        18.74 
TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK 
       19.99        20.61        19.59         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        60.89        23.97        19.10        27.88 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP 
        8.12         6.38        12.03         0.03         0.33        81.73 
TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W 
        0.39        13.68        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        25.25        22.95        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-AAV5 TCGA-G3-AAV6 
       11.80         9.70         9.17         0.89         8.75         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         2.99        37.91        20.75 
TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 
       17.06        16.83         3.72         2.14        11.84        13.38 
TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E 
       24.36        12.72        13.97        12.03         9.57        16.67 
TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A520 TCGA-NI-A4U2 TCGA-NI-A8LF 
       18.38        12.85        20.71         0.62        58.88        19.92 
TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF 
       17.69        21.01         3.09        21.04        19.33        19.04 
TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-T1-A6J8 TCGA-UB-A7MA TCGA-UB-A7MB 
       15.39        15.52        24.13         0.76        17.59        19.76 
TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-A7MF TCGA-UB-AA0U TCGA-UB-AA0V 
       16.44         1.71        15.98         7.04        10.75        10.32 
TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA46 TCGA-YA-A8S7 TCGA-ZP-A9CV 
       11.34         0.99        12.99        24.85        13.55        35.77 
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        40.80        79.30        11.21 

  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                         120.82 
  DEL PEAK 30(20P12.1) MUTATED DEL PEAK 30(20P12.1) WILD-TYPE 
                        12.000                         19.675 
[1] "0.1 - 102.7 (12.0)" "0.0 - 120.8 (19.7)"
[1] "hr=" "1.4"
D59V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IIIA
  DEL PEAK 30(20P12.1) MUTATED        12        7         1          5
  DEL PEAK 30(20P12.1) WILD-TYPE     156       77         2         54
                                vv
clus                             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 30(20P12.1) MUTATED            1          0        0         0
  DEL PEAK 30(20P12.1) WILD-TYPE          7          7        3         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                              12                            156
  STAGE II                              7                             77
  STAGE III                             1                              2
  STAGE IIIA                            5                             54
  STAGE IIIB                            1                              7
  STAGE IIIC                            0                              7
  STAGE IV                              0                              3
  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      12   7   7   1
  DEL PEAK 30(20P12.1) WILD-TYPE   167  84  66  11
D59V4, multiclass
       clus
vv      DEL PEAK 30(20P12.1) MUTATED DEL PEAK 30(20P12.1) WILD-TYPE
  T0+T1                           12                            167
  T2                               7                             84
  T3                               7                             66
  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    22   0
  DEL PEAK 30(20P12.1) WILD-TYPE 227   3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(20P12.1) MUTATED     22    0
  DEL PEAK 30(20P12.1) WILD-TYPE  227    3
   clus
vv  DEL PEAK 30(20P12.1) MUTATED DEL PEAK 30(20P12.1) WILD-TYPE
  0                           22                            227
  1                            0                              3
[1] 2 2
[1] FALSE
D59V6, binary
                                cls
clus                               0   1
  DEL PEAK 30(20P12.1) MUTATED    22   1
  DEL PEAK 30(20P12.1) WILD-TYPE 238   3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(20P12.1) MUTATED     22    1
  DEL PEAK 30(20P12.1) WILD-TYPE  238    3
   clus
vv  DEL PEAK 30(20P12.1) MUTATED DEL PEAK 30(20P12.1) WILD-TYPE
  0                           22                            238
  1                            1                              3
[1] 2 2
[1] FALSE
D59V7, binary
                                cls
clus                               0   1
  DEL PEAK 30(20P12.1) MUTATED    10  17
  DEL PEAK 30(20P12.1) WILD-TYPE 103 227
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(20P12.1) MUTATED     10   17
  DEL PEAK 30(20P12.1) WILD-TYPE  103  227
        clus
vv       DEL PEAK 30(20P12.1) MUTATED DEL PEAK 30(20P12.1) WILD-TYPE
  FEMALE                           10                            103
  MALE                             17                            227
[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                         25
  DEL PEAK 30(20P12.1) WILD-TYPE                      323
                                vv
clus                             HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK 30(20P12.1) MUTATED                                  1
  DEL PEAK 30(20P12.1) WILD-TYPE                                6
D59V8, multiclass
                                  clus
vv                                 DEL PEAK 30(20P12.1) MUTATED
  FIBROLAMELLAR CARCINOMA                                     1
  HEPATOCELLULAR CARCINOMA                                   25
  HEPATOCHOLANGIOCARCINOMA (MIXED)                            1
                                  clus
vv                                 DEL PEAK 30(20P12.1) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                       1
  HEPATOCELLULAR CARCINOMA                                    323
  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 30(20P12.1) MUTATED    25   0   0   2
  DEL PEAK 30(20P12.1) WILD-TYPE 290  15   1  17
D59V9, multiclass
    clus
vv   DEL PEAK 30(20P12.1) MUTATED DEL PEAK 30(20P12.1) WILD-TYPE
  R0                           25                            290
  R1                            0                             15
  R2                            0                              1
  RX                            2                             17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 30(20P12.1) MUTATED                                  0    15
  DEL PEAK 30(20P12.1) WILD-TYPE                                1   141
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 30(20P12.1) MUTATED                           1    11
  DEL PEAK 30(20P12.1) WILD-TYPE                        16   162
D59V10, multiclass
                                  clus
vv                                 DEL PEAK 30(20P12.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                      15
  BLACK OR AFRICAN AMERICAN                                   1
  WHITE                                                      11
                                  clus
vv                                 DEL PEAK 30(20P12.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                       141
  BLACK OR AFRICAN AMERICAN                                    16
  WHITE                                                       162
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V11, binary
                                cls
clus                               0   1
  DEL PEAK 30(20P12.1) MUTATED     1  25
  DEL PEAK 30(20P12.1) WILD-TYPE  10 304
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(20P12.1) MUTATED      1   25
  DEL PEAK 30(20P12.1) WILD-TYPE   10  304
                        clus
vv                       DEL PEAK 30(20P12.1) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           25
                        clus
vv                       DEL PEAK 30(20P12.1) WILD-TYPE
  HISPANIC OR LATINO                                 10
  NOT HISPANIC OR LATINO                            304
[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    45  22
  DEL PEAK 31(22Q12.1) WILD-TYPE 180  87
  DEL PEAK 31(22Q12.1) MUTATED DEL PEAK 31(22Q12.1) WILD-TYPE 
                            67                            267 
  DEL PEAK 31(22Q12.1) MUTATED DEL PEAK 31(22Q12.1) WILD-TYPE 
                            22                             87 
$`DEL PEAK 31(22Q12.1) MUTATED`
TCGA-2Y-A9GS TCGA-2Y-A9H0 TCGA-2Y-A9H3 TCGA-2Y-A9H4 TCGA-2Y-A9HA TCGA-5C-A9VG 
       23.80       120.82        41.33        47.74         1.18        10.78 
TCGA-5R-AA1D TCGA-BC-A10Q TCGA-BC-A10T TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A5W4 
       11.08        37.32        27.52        13.84         0.26        17.98 
TCGA-BC-A69H TCGA-BC-A8YO TCGA-BD-A3EP TCGA-CC-5260 TCGA-CC-A1HT TCGA-DD-A113 
       14.60        18.48        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        44.22         3.78        35.05 
TCGA-DD-AADQ TCGA-DD-AADS TCGA-DD-AAE3 TCGA-DD-AAEE TCGA-DD-AAVR TCGA-ED-A459 
       14.33        15.58        18.61        16.37        82.62        13.41 
TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7XO TCGA-ED-A7XP TCGA-EP-A2KB TCGA-FV-A495 
        9.73         0.20        14.04        13.15        19.59         0.03 
TCGA-FV-A4ZP TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A5SI TCGA-G3-A7M9 TCGA-G3-AAV3 
       81.73        13.68        51.06        25.25         1.84         9.17 
TCGA-K7-A5RG TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-MI-A75G TCGA-MI-A75I 
       17.06         3.72        11.84        13.38        18.38        20.71 
TCGA-MR-A8JO TCGA-QA-A7B7 TCGA-RG-A7D4 TCGA-T1-A6J8 TCGA-UB-A7MC TCGA-WQ-AB4B 
       10.85         3.09        24.13         0.76        16.44        12.99 
TCGA-ZS-A9CF 
       79.30 

$`DEL PEAK 31(22Q12.1) WILD-TYPE`
TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GV TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GY 
       53.39        63.75        83.24        41.79        80.28        24.89 
TCGA-2Y-A9GZ TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H5 TCGA-2Y-A9H6 TCGA-2Y-A9H7 
       27.88        40.41        56.91        18.25        11.74        37.25 
TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-4R-AA8I TCGA-5C-A9VH 
       20.81        14.99         8.55        13.02         8.61        10.59 
TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10R 
        0.66        11.97         1.51        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-A2L6 
       69.57         5.03        44.42        22.36        12.72        44.81 
TCGA-BD-A3ER TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 
       36.66         0.66         0.07         3.19         3.39         4.24 
TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A115 TCGA-DD-A116 
        0.10         0.07         0.10         0.13        83.57        53.33 
TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 
      113.00         7.33         0.46        21.76        51.29        90.71 
TCGA-DD-A1EA TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG 
       79.40        19.79        75.65        11.47        12.95        45.11 
TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V 
       49.15         6.02        33.04        18.35        13.64        21.14 
TCGA-DD-A39W TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 
       27.19        19.76        25.81         7.66        70.06        17.59 
TCGA-DD-A3A5 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4ND 
      102.74        13.78         0.36        30.61        33.14        90.28 
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        23.93        23.05        22.78 
TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC9 TCGA-DD-AACA 
        1.45        35.67       114.35        13.48        11.41        75.65 
TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG 
       76.41        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        69.11         0.30         3.52        58.16 
TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT 
       42.81        61.68        13.64        14.20        59.31        51.35 
TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AAD0 
       51.52        50.33        46.82         5.59        47.67         4.50 
TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA 
       18.54        21.63        42.58        22.09        40.08        40.54 
TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADG TCGA-DD-AADI 
       40.83        13.97        40.47        39.52        37.64        35.67 
TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP 
       34.49        20.91         0.39        29.52        14.89        15.06 
TCGA-DD-AADR TCGA-DD-AADU TCGA-DD-AADV TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 
       66.67        18.21        18.87        19.30        18.25        18.25 
TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAE8 
       18.15        20.98        19.99         4.64        21.17        21.83 
TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEG TCGA-DD-AAEH 
       23.74        18.90        15.72        25.08        23.64        25.78 
TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVS TCGA-DD-AAVU 
       50.33        35.08        79.07        89.69        59.93        72.39 
TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 
       76.18        56.48        64.77        62.47        66.25        65.39 
TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X 
       49.48        53.69        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 
       12.82         0.20        13.41        13.35         1.84         0.20 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK 
       18.74        19.99        20.61         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        60.89        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        12.03         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        22.95        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-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 
       11.80         9.70         0.89         8.75         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         2.99        37.91        20.75        16.83 
TCGA-KR-A7K0 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C 
        2.14        24.36        12.72        13.97        12.03         9.57 
TCGA-MI-A75E TCGA-MI-A75H TCGA-MR-A520 TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V 
       16.67        12.85         0.62        58.88        19.92        17.69 
TCGA-PD-A5DF TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK 
       21.01        21.04        19.33        19.04        15.39        15.52 
TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-A7MF TCGA-UB-AA0U 
       17.59        19.76         1.71        15.98         7.04        10.75 
TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WX-AA46 TCGA-YA-A8S7 TCGA-ZP-A9CV 
       10.32        11.34         0.99        24.85        13.55        35.77 
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        40.80        11.21 

  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 
                        120.82                         114.35 
  DEL PEAK 31(22Q12.1) MUTATED DEL PEAK 31(22Q12.1) WILD-TYPE 
                         16.37                          19.92 
[1] "0.0 - 120.8 (16.4)" "0.1 - 114.3 (19.9)"
[1] "hr=" "1"  
D60V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IIIA
  DEL PEAK 31(22Q12.1) MUTATED        27       25         0         14
  DEL PEAK 31(22Q12.1) WILD-TYPE     141       59         3         45
                                vv
clus                             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 31(22Q12.1) MUTATED            1          2        2         0
  DEL PEAK 31(22Q12.1) WILD-TYPE          7          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                              27                            141
  STAGE II                             25                             59
  STAGE III                             0                              3
  STAGE IIIA                           14                             45
  STAGE IIIB                            1                              7
  STAGE IIIC                            2                              5
  STAGE IV                              2                              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      28  29  15   3
  DEL PEAK 31(22Q12.1) WILD-TYPE   151  62  58   9
D60V4, multiclass
       clus
vv      DEL PEAK 31(22Q12.1) MUTATED DEL PEAK 31(22Q12.1) WILD-TYPE
  T0+T1                           28                            151
  T2                              29                             62
  T3                              15                             58
  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    48   0
  DEL PEAK 31(22Q12.1) WILD-TYPE 201   3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(22Q12.1) MUTATED     48    0
  DEL PEAK 31(22Q12.1) WILD-TYPE  201    3
   clus
vv  DEL PEAK 31(22Q12.1) MUTATED DEL PEAK 31(22Q12.1) WILD-TYPE
  0                           48                            201
  1                            0                              3
[1] 2 2
[1] FALSE
D60V6, binary
                                cls
clus                               0   1
  DEL PEAK 31(22Q12.1) MUTATED    57   1
  DEL PEAK 31(22Q12.1) WILD-TYPE 203   3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(22Q12.1) MUTATED     57    1
  DEL PEAK 31(22Q12.1) WILD-TYPE  203    3
   clus
vv  DEL PEAK 31(22Q12.1) MUTATED DEL PEAK 31(22Q12.1) WILD-TYPE
  0                           57                            203
  1                            1                              3
[1] 2 2
[1] FALSE
D60V7, binary
                                cls
clus                               0   1
  DEL PEAK 31(22Q12.1) MUTATED    27  48
  DEL PEAK 31(22Q12.1) WILD-TYPE  86 196
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(22Q12.1) MUTATED     27   48
  DEL PEAK 31(22Q12.1) WILD-TYPE   86  196
        clus
vv       DEL PEAK 31(22Q12.1) MUTATED DEL PEAK 31(22Q12.1) WILD-TYPE
  FEMALE                           27                             86
  MALE                             48                            196
[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                         71
  DEL PEAK 31(22Q12.1) WILD-TYPE                      277
                                vv
clus                             HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK 31(22Q12.1) MUTATED                                  2
  DEL PEAK 31(22Q12.1) WILD-TYPE                                5
D60V8, multiclass
                                  clus
vv                                 DEL PEAK 31(22Q12.1) MUTATED
  FIBROLAMELLAR CARCINOMA                                     2
  HEPATOCELLULAR CARCINOMA                                   71
  HEPATOCHOLANGIOCARCINOMA (MIXED)                            2
                                  clus
vv                                 DEL PEAK 31(22Q12.1) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                       0
  HEPATOCELLULAR CARCINOMA                                    277
  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    61   5   0   8
  DEL PEAK 31(22Q12.1) WILD-TYPE 254  10   1  11
D60V9, multiclass
    clus
vv   DEL PEAK 31(22Q12.1) MUTATED DEL PEAK 31(22Q12.1) WILD-TYPE
  R0                           61                            254
  R1                            5                             10
  R2                            0                              1
  RX                            8                             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 31(22Q12.1) MUTATED                                  0    25
  DEL PEAK 31(22Q12.1) WILD-TYPE                                1   131
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 31(22Q12.1) MUTATED                           8    41
  DEL PEAK 31(22Q12.1) WILD-TYPE                         9   132
D60V10, multiclass
                                  clus
vv                                 DEL PEAK 31(22Q12.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                      25
  BLACK OR AFRICAN AMERICAN                                   8
  WHITE                                                      41
                                  clus
vv                                 DEL PEAK 31(22Q12.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                       131
  BLACK OR AFRICAN AMERICAN                                     9
  WHITE                                                       132
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V11, binary
                                cls
clus                               0   1
  DEL PEAK 31(22Q12.1) MUTATED     5  64
  DEL PEAK 31(22Q12.1) WILD-TYPE   6 265
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(22Q12.1) MUTATED      5   64
  DEL PEAK 31(22Q12.1) WILD-TYPE    6  265
                        clus
vv                       DEL PEAK 31(22Q12.1) MUTATED
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                           64
                        clus
vv                       DEL PEAK 31(22Q12.1) WILD-TYPE
  HISPANIC OR LATINO                                  6
  NOT HISPANIC OR LATINO                            265
[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    45  27
  DEL PEAK 32(22Q13.32) WILD-TYPE 180  82
  DEL PEAK 32(22Q13.32) MUTATED DEL PEAK 32(22Q13.32) WILD-TYPE 
                             72                             262 
  DEL PEAK 32(22Q13.32) MUTATED DEL PEAK 32(22Q13.32) WILD-TYPE 
                             27                              82 
$`DEL PEAK 32(22Q13.32) MUTATED`
TCGA-2Y-A9GS TCGA-2Y-A9H0 TCGA-2Y-A9H3 TCGA-2Y-A9H4 TCGA-5C-A9VG TCGA-5R-AA1D 
       23.80       120.82        41.33        47.74        10.78        11.08 
TCGA-BC-A10Q TCGA-BC-A10T TCGA-BC-A10Y TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG 
       37.32        27.52        23.34        13.84         0.26        22.36 
TCGA-BC-A5W4 TCGA-BC-A8YO TCGA-BD-A3EP TCGA-CC-5260 TCGA-CC-A1HT TCGA-CC-A3M9 
       17.98        18.48        13.45         2.86         3.32         0.10 
TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A1EB TCGA-DD-A39X TCGA-DD-A39Y 
       79.73        37.78        83.57        66.31        55.69         5.62 
TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NI 
      102.74       107.11        13.78        33.14        32.52        26.83 
TCGA-DD-A4NJ TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A73B TCGA-DD-AAC8 TCGA-DD-AACZ 
       30.51        73.81       108.76         9.30         0.53         5.62 
TCGA-DD-AADD TCGA-DD-AADF TCGA-DD-AADQ TCGA-DD-AADS TCGA-DD-AADV TCGA-DD-AAE3 
       40.47         3.78        14.33        15.58        18.87        18.61 
TCGA-DD-AAEE TCGA-ED-A459 TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7XO TCGA-ED-A7XP 
       16.37        13.41         9.73         0.20        14.04        13.15 
TCGA-EP-A2KB TCGA-FV-A2QR TCGA-FV-A4ZP TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A3CJ 
       19.59        19.10        81.73        13.68        51.06        19.53 
TCGA-G3-A5SI TCGA-G3-A7M9 TCGA-G3-AAV3 TCGA-K7-A5RG TCGA-K7-AAU7 TCGA-KR-A7K2 
       25.25         1.84         9.17        17.06         3.72        11.84 
TCGA-KR-A7K7 TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-PD-A5DF 
       13.38        18.38        20.71        10.85        58.88        21.01 
TCGA-QA-A7B7 TCGA-RG-A7D4 TCGA-T1-A6J8 TCGA-UB-A7MC TCGA-WQ-AB4B TCGA-ZS-A9CF 
        3.09        24.13         0.76        16.44        12.99        79.30 

$`DEL PEAK 32(22Q13.32) WILD-TYPE`
TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GV TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GY 
       53.39        63.75        83.24        41.79        80.28        24.89 
TCGA-2Y-A9GZ TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H5 TCGA-2Y-A9H6 TCGA-2Y-A9H7 
       27.88        40.41        56.91        18.25        11.74        37.25 
TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-4R-AA8I 
       20.81        14.99         1.18         8.55        13.02         8.61 
TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-4073 
       10.59         0.66        11.97         1.51        48.99        27.91 
TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Z 
       10.13        46.78        27.52         2.99        25.32         1.12 
TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A69H TCGA-BC-A69I TCGA-BD-A2L6 
       69.57         5.03        44.42        14.60        12.72        44.81 
TCGA-BD-A3ER TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 
       36.66         0.66         0.07         3.19         3.39         4.24 
TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 
        0.07         0.10         0.13        53.33       113.00         7.33 
TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA 
        2.60         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        11.47        12.95        45.11        49.15 
TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W 
        6.02        33.04        18.35        13.64        21.14        27.19 
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-A3A8 TCGA-DD-A3A9 TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NK 
        0.36        30.61        90.28        30.97        30.15        39.78 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV 
       56.25        29.56        12.26         0.30        80.75        78.84 
TCGA-DD-A73A TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G 
       23.93        23.05        22.78         1.45        35.67       114.35 
TCGA-DD-AA3A TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD 
       13.48        11.41        75.65        76.41        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        69.11 
TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP 
        0.30         3.52        58.16        42.81        61.68        13.64 
TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW 
       14.20        59.31        51.35        51.52        50.33        46.82 
TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 
        5.59        47.67         4.50        18.54        21.63        42.58 
TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC 
       44.22        22.09        40.08        40.54        40.83        13.97 
TCGA-DD-AADE TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL 
       39.52        37.64        35.67        35.05        34.49        20.91 
TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADR TCGA-DD-AADU 
        0.39        29.52        14.89        15.06        66.67        18.21 
TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE4 
       19.30        18.25        18.25        18.15        20.98        19.99 
TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB 
        4.64        21.17        21.83        23.74        18.90        15.72 
TCGA-DD-AAED TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP 
       25.08        23.64        25.78        50.33        35.08        79.07 
TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVX 
       89.69        82.62        59.93        72.39        76.18        56.48 
TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 
       64.77        62.47        66.25        65.39        49.48        53.69 
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        12.82         0.20 
TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S 
       13.41        13.35         1.84         0.20        18.74        19.99 
TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT 
       20.61         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 
       60.89        23.97        27.88         8.12         6.38        12.03 
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        22.95        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-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ 
        8.75         2.14         3.02         1.02         2.20         2.99 
TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K8 TCGA-LG-A6GG 
       37.91        20.75        16.83         2.14        24.36        12.72 
TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75H TCGA-MR-A520 
       13.97        12.03         9.57        16.67        12.85         0.62 
TCGA-NI-A8LF TCGA-O8-A75V TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH 
       19.92        17.69        21.04        19.33        19.04        15.39 
TCGA-RC-A7SK TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-A7MF 
       15.52        17.59        19.76         1.71        15.98         7.04 
TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WX-AA46 TCGA-YA-A8S7 
       10.75        10.32        11.34         0.99        24.85        13.55 
TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D2 
       35.77        25.71        23.21        23.57         0.69        24.43 
TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CG 
       12.99        45.57        40.80        11.21 

  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 
                         120.82                          114.35 
  DEL PEAK 32(22Q13.32) MUTATED DEL PEAK 32(22Q13.32) WILD-TYPE 
                         18.430                          19.775 
[1] "0.1 - 120.8 (18.4)" "0.0 - 114.3 (19.8)"
[1] "hr=" "1.1"
D61V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE III STAGE IIIA
  DEL PEAK 32(22Q13.32) MUTATED        26       23         1         16
  DEL PEAK 32(22Q13.32) WILD-TYPE     142       61         2         43
                                 vv
clus                              STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 32(22Q13.32) MUTATED            3          3        2         0
  DEL PEAK 32(22Q13.32) WILD-TYPE          5          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                               26                             142
  STAGE II                              23                              61
  STAGE III                              1                               2
  STAGE IIIA                            16                              43
  STAGE IIIB                             3                               5
  STAGE IIIC                             3                               4
  STAGE IV                               2                               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      27  28  19   5
  DEL PEAK 32(22Q13.32) WILD-TYPE   152  63  54   7
D61V4, multiclass
       clus
vv      DEL PEAK 32(22Q13.32) MUTATED DEL PEAK 32(22Q13.32) WILD-TYPE
  T0+T1                            27                             152
  T2                               28                              63
  T3                               19                              54
  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    52   1
  DEL PEAK 32(22Q13.32) WILD-TYPE 197   2
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 32(22Q13.32) MUTATED     52    1
  DEL PEAK 32(22Q13.32) WILD-TYPE  197    2
   clus
vv  DEL PEAK 32(22Q13.32) MUTATED DEL PEAK 32(22Q13.32) WILD-TYPE
  0                            52                             197
  1                             1                               2
[1] 2 2
[1] FALSE
D61V6, binary
                                 cls
clus                                0   1
  DEL PEAK 32(22Q13.32) MUTATED    60   1
  DEL PEAK 32(22Q13.32) WILD-TYPE 200   3
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 32(22Q13.32) MUTATED     60    1
  DEL PEAK 32(22Q13.32) WILD-TYPE  200    3
   clus
vv  DEL PEAK 32(22Q13.32) MUTATED DEL PEAK 32(22Q13.32) WILD-TYPE
  0                            60                             200
  1                             1                               3
[1] 2 2
[1] FALSE
D61V7, binary
                                 cls
clus                                0   1
  DEL PEAK 32(22Q13.32) MUTATED    28  51
  DEL PEAK 32(22Q13.32) WILD-TYPE  85 193
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 32(22Q13.32) MUTATED     28   51
  DEL PEAK 32(22Q13.32) WILD-TYPE   85  193
        clus
vv       DEL PEAK 32(22Q13.32) MUTATED DEL PEAK 32(22Q13.32) WILD-TYPE
  FEMALE                            28                              85
  MALE                              51                             193
[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                         75
  DEL PEAK 32(22Q13.32) WILD-TYPE                      273
                                 vv
clus                              HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK 32(22Q13.32) MUTATED                                  2
  DEL PEAK 32(22Q13.32) WILD-TYPE                                5
D61V8, multiclass
                                  clus
vv                                 DEL PEAK 32(22Q13.32) MUTATED
  FIBROLAMELLAR CARCINOMA                                      2
  HEPATOCELLULAR CARCINOMA                                    75
  HEPATOCHOLANGIOCARCINOMA (MIXED)                             2
                                  clus
vv                                 DEL PEAK 32(22Q13.32) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                        0
  HEPATOCELLULAR CARCINOMA                                     273
  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    63   5   0   9
  DEL PEAK 32(22Q13.32) WILD-TYPE 252  10   1  10
D61V9, multiclass
    clus
vv   DEL PEAK 32(22Q13.32) MUTATED DEL PEAK 32(22Q13.32) WILD-TYPE
  R0                            63                             252
  R1                             5                              10
  R2                             0                               1
  RX                             9                              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 32(22Q13.32) MUTATED                                  1    24
  DEL PEAK 32(22Q13.32) WILD-TYPE                                0   132
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 32(22Q13.32) MUTATED                           7    45
  DEL PEAK 32(22Q13.32) WILD-TYPE                        10   128
D61V10, multiclass
                                  clus
vv                                 DEL PEAK 32(22Q13.32) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                       24
  BLACK OR AFRICAN AMERICAN                                    7
  WHITE                                                       45
                                  clus
vv                                 DEL PEAK 32(22Q13.32) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               0
  ASIAN                                                        132
  BLACK OR AFRICAN AMERICAN                                     10
  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"
D61V11, binary
                                 cls
clus                                0   1
  DEL PEAK 32(22Q13.32) MUTATED     5  66
  DEL PEAK 32(22Q13.32) WILD-TYPE   6 263
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 32(22Q13.32) MUTATED      5   66
  DEL PEAK 32(22Q13.32) WILD-TYPE    6  263
                        clus
vv                       DEL PEAK 32(22Q13.32) MUTATED
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                            66
                        clus
vv                       DEL PEAK 32(22Q13.32) WILD-TYPE
  HISPANIC OR LATINO                                   6
  NOT HISPANIC OR LATINO                             263
[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    42  16
  DEL PEAK 33(XQ26.2) WILD-TYPE 183  93
  DEL PEAK 33(XQ26.2) MUTATED DEL PEAK 33(XQ26.2) WILD-TYPE 
                           58                           276 
  DEL PEAK 33(XQ26.2) MUTATED DEL PEAK 33(XQ26.2) WILD-TYPE 
                           16                            93 
$`DEL PEAK 33(XQ26.2) MUTATED`
TCGA-2Y-A9GS TCGA-5C-AAPD TCGA-BC-A10R TCGA-BC-A10Z TCGA-BC-A112 TCGA-BC-A217 
       23.80         0.66        10.13         1.12         5.03        13.84 
TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-A3MA 
        0.26        22.36        17.98         0.07         2.86         0.07 
TCGA-CC-A3MB TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A11B TCGA-DD-A4NA TCGA-DD-A4NO 
        0.10        83.57        53.33         0.46        33.14        73.81 
TCGA-DD-A73B TCGA-DD-A73G TCGA-DD-AACG TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACU 
        9.30       114.35        15.42        42.81        61.68        51.52 
TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AAD5 TCGA-DD-AAD8 TCGA-DD-AADB TCGA-DD-AADC 
       50.33        46.82        44.22        40.08        40.83        13.97 
TCGA-DD-AADL TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADV TCGA-DD-AADY TCGA-DD-AAE2 
       20.91        14.89        15.06        18.87        18.25        20.98 
TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAVU TCGA-ED-A459 TCGA-ED-A7PX TCGA-ED-A7PZ 
       25.08        16.37        72.39        13.41         0.20         0.20 
TCGA-ED-A97K TCGA-FV-A3I0 TCGA-G3-AAV4 TCGA-G3-AAV6 TCGA-GJ-A6C0 TCGA-KR-A7K7 
        0.20        27.88         0.89         2.14         1.02        13.38 
TCGA-LG-A9QC TCGA-QA-A7B7 TCGA-RC-A7SB TCGA-RC-A7SH TCGA-RC-A7SK TCGA-T1-A6J8 
       13.97         3.09        19.33        15.39        15.52         0.76 
TCGA-UB-A7MC TCGA-UB-A7MF TCGA-ZP-A9D2 TCGA-ZS-A9CF 
       16.44         7.04        24.43        79.30 

$`DEL PEAK 33(XQ26.2) WILD-TYPE`
TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GV TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GY 
       53.39        63.75        83.24        41.79        80.28        24.89 
TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H4 
       27.88       120.82        40.41        56.91        41.33        47.74 
TCGA-2Y-A9H5 TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA 
       18.25        11.74        37.25        20.81        14.99         1.18 
TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5R-AA1C 
        8.55        13.02         8.61        10.78        10.59        11.97 
TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10S 
       11.08         1.51        48.99        27.91        37.32        46.78 
TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A110 
       27.52        27.52         2.99        25.32        23.34        69.57 
TCGA-BC-A216 TCGA-BC-A69H TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP 
       44.42        14.60        12.72        18.48        44.81        13.45 
TCGA-BD-A3ER TCGA-BW-A5NO TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT 
       36.66         0.66         3.19         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        11.47        12.95        45.11        49.15 
TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W 
        6.02        33.04        18.35        13.64        21.14        27.19 
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-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-A4NB TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI 
       30.61        32.52        90.28        30.97        30.15        26.83 
TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NP TCGA-DD-A4NQ 
       30.51        39.78        56.25        29.56       108.76        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        23.93        23.05        22.78 
TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA 
        1.45        35.67        13.48         0.53        11.41        75.65 
TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACH 
       76.41        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-AACP 
       53.19        69.11         0.30         3.52        58.16        13.64 
TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AACZ 
       14.20        59.31        51.35         5.59        47.67         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        42.58        22.09        40.54 
TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ 
       40.47        39.52         3.78        37.64        35.67        35.05 
TCGA-DD-AADK TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS 
       34.49         0.39        29.52        14.33        66.67        15.58 
TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE3 TCGA-DD-AAE4 
       18.21        19.30        18.25        18.15        18.61        19.99 
TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB 
        4.64        21.17        21.83        23.74        18.90        15.72 
TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ 
       23.64        25.78        50.33        35.08        79.07        89.69 
TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ 
       82.62        59.93        76.18        56.48        64.77        62.47 
TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A4XI TCGA-ED-A5KG 
       66.25        65.39        49.48        53.69        12.69        15.85 
TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PY TCGA-ED-A7XO TCGA-ED-A7XP 
       13.91        13.35         9.73        12.82        14.04        13.15 
TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
       13.41        13.35         1.84        18.74        19.99        20.61 
TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT 
       19.59         0.62         9.96        11.93        22.85        14.40 
TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 
       60.89        23.97        19.10         8.12         6.38        12.03 
TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T 
        0.03         0.33        81.73         0.39        13.68        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        25.25 
TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 
       22.95        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-AAV5 TCGA-G3-AAV7 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF 
        8.75         3.02         2.20         2.99        37.91        20.75 
TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K8 
       17.06        16.83         3.72         2.14        11.84        24.36 
TCGA-LG-A6GG TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H 
       12.72        12.03         9.57        16.67        18.38        12.85 
TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V 
       20.71         0.62        10.85        58.88        19.92        17.69 
TCGA-PD-A5DF TCGA-RC-A7S9 TCGA-RC-A7SF TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB 
       21.01        21.04        19.04        24.13        17.59        19.76 
TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-A9G7 
        1.71        15.98        10.75        10.32        11.34         0.99 
TCGA-WQ-AB4B TCGA-WX-AA46 TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ 
       12.99        24.85        13.55        35.77        25.71        23.21 
TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CG 
       23.57         0.69        12.99        45.57        40.80        11.21 

  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 
                       114.35                        120.82 
  DEL PEAK 33(XQ26.2) MUTATED DEL PEAK 33(XQ26.2) WILD-TYPE 
                       15.470                        19.855 
[1] "0.1 - 114.3 (15.5)" "0.0 - 120.8 (19.9)"
[1] "hr=" "1"  
D62V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IIIA
  DEL PEAK 33(XQ26.2) MUTATED        27       17         0         14
  DEL PEAK 33(XQ26.2) WILD-TYPE     141       67         3         45
                               vv
clus                            STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 33(XQ26.2) MUTATED            0          2        1         0
  DEL PEAK 33(XQ26.2) WILD-TYPE          8          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                             27                           141
  STAGE II                            17                            67
  STAGE III                            0                             3
  STAGE IIIA                          14                            45
  STAGE IIIB                           0                             8
  STAGE IIIC                           2                             5
  STAGE IV                             1                             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      28  20  16   1
  DEL PEAK 33(XQ26.2) WILD-TYPE   151  71  57  11
D62V4, multiclass
       clus
vv      DEL PEAK 33(XQ26.2) MUTATED DEL PEAK 33(XQ26.2) WILD-TYPE
  T0+T1                          28                           151
  T2                             20                            71
  T3                             16                            57
  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    47   1
  DEL PEAK 33(XQ26.2) WILD-TYPE 202   2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 33(XQ26.2) MUTATED     47    1
  DEL PEAK 33(XQ26.2) WILD-TYPE  202    2
   clus
vv  DEL PEAK 33(XQ26.2) MUTATED DEL PEAK 33(XQ26.2) WILD-TYPE
  0                          47                           202
  1                           1                             2
[1] 2 2
[1] FALSE
D62V6, binary
                               cls
clus                              0   1
  DEL PEAK 33(XQ26.2) MUTATED    54   0
  DEL PEAK 33(XQ26.2) WILD-TYPE 206   4
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 33(XQ26.2) MUTATED     54    0
  DEL PEAK 33(XQ26.2) WILD-TYPE  206    4
   clus
vv  DEL PEAK 33(XQ26.2) MUTATED DEL PEAK 33(XQ26.2) WILD-TYPE
  0                          54                           206
  1                           0                             4
[1] 2 2
[1] FALSE
D62V7, binary
                               cls
clus                              0   1
  DEL PEAK 33(XQ26.2) MUTATED    18  47
  DEL PEAK 33(XQ26.2) WILD-TYPE  95 197
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 33(XQ26.2) MUTATED     18   47
  DEL PEAK 33(XQ26.2) WILD-TYPE   95  197
        clus
vv       DEL PEAK 33(XQ26.2) MUTATED DEL PEAK 33(XQ26.2) WILD-TYPE
  FEMALE                          18                            95
  MALE                            47                           197
[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                         62
  DEL PEAK 33(XQ26.2) WILD-TYPE                      286
                               vv
clus                            HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK 33(XQ26.2) MUTATED                                  3
  DEL PEAK 33(XQ26.2) WILD-TYPE                                4
D62V8, multiclass
                                  clus
vv                                 DEL PEAK 33(XQ26.2) MUTATED
  FIBROLAMELLAR CARCINOMA                                    0
  HEPATOCELLULAR CARCINOMA                                  62
  HEPATOCHOLANGIOCARCINOMA (MIXED)                           3
                                  clus
vv                                 DEL PEAK 33(XQ26.2) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                      2
  HEPATOCELLULAR CARCINOMA                                   286
  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 33(XQ26.2) MUTATED    58   1   0   6
  DEL PEAK 33(XQ26.2) WILD-TYPE 257  14   1  13
D62V9, multiclass
    clus
vv   DEL PEAK 33(XQ26.2) MUTATED DEL PEAK 33(XQ26.2) WILD-TYPE
  R0                          58                           257
  R1                           1                            14
  R2                           0                             1
  RX                           6                            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 33(XQ26.2) MUTATED                                  0    39
  DEL PEAK 33(XQ26.2) WILD-TYPE                                1   117
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 33(XQ26.2) MUTATED                           1    25
  DEL PEAK 33(XQ26.2) WILD-TYPE                        16   148
D62V10, multiclass
                                  clus
vv                                 DEL PEAK 33(XQ26.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                     39
  BLACK OR AFRICAN AMERICAN                                  1
  WHITE                                                     25
                                  clus
vv                                 DEL PEAK 33(XQ26.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                      117
  BLACK OR AFRICAN AMERICAN                                   16
  WHITE                                                      148
[1] 4 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     2  59
  DEL PEAK 33(XQ26.2) WILD-TYPE   9 270
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 33(XQ26.2) MUTATED      2   59
  DEL PEAK 33(XQ26.2) WILD-TYPE    9  270
                        clus
vv                       DEL PEAK 33(XQ26.2) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          59
                        clus
vv                       DEL PEAK 33(XQ26.2) WILD-TYPE
  HISPANIC OR LATINO                                 9
  NOT HISPANIC OR LATINO                           270
[1] 2 2
[1] FALSE
