[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/19775332/LIHC-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/LIHC-TP/19782292/transformed.cor.cli.txt"

nPatients in clinical file=368, in cluster file=370, common to both=362
[1]  62 362
[1] "AMP PEAK  1(1P22.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  1(1P22.3) MUTATED AMP PEAK  1(1P22.3) WILD-TYPE 
                           88                           274 
  AMP PEAK  1(1P22.3) MUTATED AMP PEAK  1(1P22.3) WILD-TYPE 
                           88                           274 
[1] "AMP PEAK  2(1Q22) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  2(1Q22) MUTATED AMP PEAK  2(1Q22) WILD-TYPE 
                        277                          85 
  AMP PEAK  2(1Q22) MUTATED AMP PEAK  2(1Q22) WILD-TYPE 
                        277                          85 
[1] "AMP PEAK  3(1Q42.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  3(1Q42.3) MUTATED AMP PEAK  3(1Q42.3) WILD-TYPE 
                          266                            96 
  AMP PEAK  3(1Q42.3) MUTATED AMP PEAK  3(1Q42.3) WILD-TYPE 
                          266                            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                           298 
  AMP PEAK  4(2P24.1) MUTATED AMP PEAK  4(2P24.1) WILD-TYPE 
                           64                           298 
[1] "AMP PEAK  5(2Q33.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  5(2Q33.1) MUTATED AMP PEAK  5(2Q33.1) WILD-TYPE 
                           62                           300 
  AMP PEAK  5(2Q33.1) MUTATED AMP PEAK  5(2Q33.1) WILD-TYPE 
                           62                           300 
[1] "AMP PEAK  6(3Q26.31) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  6(3Q26.31) MUTATED AMP PEAK  6(3Q26.31) WILD-TYPE 
                            76                            286 
  AMP PEAK  6(3Q26.31) MUTATED AMP PEAK  6(3Q26.31) WILD-TYPE 
                            76                            286 
[1] "AMP PEAK  7(4P14) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  7(4P14) MUTATED AMP PEAK  7(4P14) WILD-TYPE 
                         52                         310 
  AMP PEAK  7(4P14) MUTATED AMP PEAK  7(4P14) WILD-TYPE 
                         52                         310 
[1] "AMP PEAK  8(5P15.33) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  8(5P15.33) MUTATED AMP PEAK  8(5P15.33) WILD-TYPE 
                           161                            201 
  AMP PEAK  8(5P15.33) MUTATED AMP PEAK  8(5P15.33) WILD-TYPE 
                           161                            201 
[1] "AMP PEAK  9(5Q35.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  9(5Q35.3) MUTATED AMP PEAK  9(5Q35.3) WILD-TYPE 
                          134                           228 
  AMP PEAK  9(5Q35.3) MUTATED AMP PEAK  9(5Q35.3) WILD-TYPE 
                          134                           228 
[1] "AMP PEAK 10(6P25.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 10(6P25.2) MUTATED AMP PEAK 10(6P25.2) WILD-TYPE 
                          153                           209 
  AMP PEAK 10(6P25.2) MUTATED AMP PEAK 10(6P25.2) WILD-TYPE 
                          153                           209 
[1] "AMP PEAK 11(6P21.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 11(6P21.1) MUTATED AMP PEAK 11(6P21.1) WILD-TYPE 
                          154                           208 
  AMP PEAK 11(6P21.1) MUTATED AMP PEAK 11(6P21.1) WILD-TYPE 
                          154                           208 
[1] "AMP PEAK 12(6Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 12(6Q12) MUTATED AMP PEAK 12(6Q12) WILD-TYPE 
                        104                         258 
  AMP PEAK 12(6Q12) MUTATED AMP PEAK 12(6Q12) WILD-TYPE 
                        104                         258 
[1] "AMP PEAK 13(6Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 13(6Q12) MUTATED AMP PEAK 13(6Q12) WILD-TYPE 
                         80                         282 
  AMP PEAK 13(6Q12) MUTATED AMP PEAK 13(6Q12) WILD-TYPE 
                         80                         282 
[1] "AMP PEAK 14(7Q31.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 14(7Q31.2) MUTATED AMP PEAK 14(7Q31.2) WILD-TYPE 
                          117                           245 
  AMP PEAK 14(7Q31.2) MUTATED AMP PEAK 14(7Q31.2) WILD-TYPE 
                          117                           245 
[1] "AMP PEAK 15(8Q13.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 15(8Q13.3) MUTATED AMP PEAK 15(8Q13.3) WILD-TYPE 
                          203                           159 
  AMP PEAK 15(8Q13.3) MUTATED AMP PEAK 15(8Q13.3) WILD-TYPE 
                          203                           159 
[1] "AMP PEAK 16(8Q24.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 16(8Q24.21) MUTATED AMP PEAK 16(8Q24.21) WILD-TYPE 
                           227                            135 
  AMP PEAK 16(8Q24.21) MUTATED AMP PEAK 16(8Q24.21) WILD-TYPE 
                           227                            135 
[1] "AMP PEAK 17(9Q34.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 17(9Q34.2) MUTATED AMP PEAK 17(9Q34.2) WILD-TYPE 
                           45                           317 
  AMP PEAK 17(9Q34.2) MUTATED AMP PEAK 17(9Q34.2) WILD-TYPE 
                           45                           317 
[1] "AMP PEAK 18(11Q13.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 18(11Q13.3) MUTATED AMP PEAK 18(11Q13.3) WILD-TYPE 
                            56                            306 
  AMP PEAK 18(11Q13.3) MUTATED AMP PEAK 18(11Q13.3) WILD-TYPE 
                            56                            306 
[1] "AMP PEAK 19(13Q32.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 19(13Q32.3) MUTATED AMP PEAK 19(13Q32.3) WILD-TYPE 
                            65                            297 
  AMP PEAK 19(13Q32.3) MUTATED AMP PEAK 19(13Q32.3) WILD-TYPE 
                            65                            297 
[1] "AMP PEAK 20(13Q33.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 20(13Q33.3) MUTATED AMP PEAK 20(13Q33.3) WILD-TYPE 
                            66                            296 
  AMP PEAK 20(13Q33.3) MUTATED AMP PEAK 20(13Q33.3) WILD-TYPE 
                            66                            296 
[1] "AMP PEAK 21(15Q26.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 21(15Q26.3) MUTATED AMP PEAK 21(15Q26.3) WILD-TYPE 
                            54                            308 
  AMP PEAK 21(15Q26.3) MUTATED AMP PEAK 21(15Q26.3) WILD-TYPE 
                            54                            308 
[1] "AMP PEAK 22(17P11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 22(17P11.2) MUTATED AMP PEAK 22(17P11.2) WILD-TYPE 
                            46                            316 
  AMP PEAK 22(17P11.2) MUTATED AMP PEAK 22(17P11.2) WILD-TYPE 
                            46                            316 
[1] "AMP PEAK 23(17Q25.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 23(17Q25.3) MUTATED AMP PEAK 23(17Q25.3) WILD-TYPE 
                           142                            220 
  AMP PEAK 23(17Q25.3) MUTATED AMP PEAK 23(17Q25.3) WILD-TYPE 
                           142                            220 
[1] "AMP PEAK 24(19P13.12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 24(19P13.12) MUTATED AMP PEAK 24(19P13.12) WILD-TYPE 
                             67                             295 
  AMP PEAK 24(19P13.12) MUTATED AMP PEAK 24(19P13.12) WILD-TYPE 
                             67                             295 
[1] "AMP PEAK 25(19Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 25(19Q12) MUTATED AMP PEAK 25(19Q12) WILD-TYPE 
                          77                          285 
  AMP PEAK 25(19Q12) MUTATED AMP PEAK 25(19Q12) WILD-TYPE 
                          77                          285 
[1] "AMP PEAK 26(19Q13.11) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 26(19Q13.11) MUTATED AMP PEAK 26(19Q13.11) WILD-TYPE 
                             89                             273 
  AMP PEAK 26(19Q13.11) MUTATED AMP PEAK 26(19Q13.11) WILD-TYPE 
                             89                             273 
[1] "AMP PEAK 27(20Q13.13) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 27(20Q13.13) MUTATED AMP PEAK 27(20Q13.13) WILD-TYPE 
                            120                             242 
  AMP PEAK 27(20Q13.13) MUTATED AMP PEAK 27(20Q13.13) WILD-TYPE 
                            120                             242 
[1] "AMP PEAK 28(20Q13.33) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 28(20Q13.33) MUTATED AMP PEAK 28(20Q13.33) WILD-TYPE 
                            125                             237 
  AMP PEAK 28(20Q13.33) MUTATED AMP PEAK 28(20Q13.33) WILD-TYPE 
                            125                             237 
[1] "AMP PEAK 29(XQ28) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 29(XQ28) MUTATED AMP PEAK 29(XQ28) WILD-TYPE 
                         83                         279 
  AMP PEAK 29(XQ28) MUTATED AMP PEAK 29(XQ28) WILD-TYPE 
                         83                         279 
[1] "DEL PEAK  1(1P36.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                           161                            201 
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                           161                            201 
[1] "DEL PEAK  2(1P36.11) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  2(1P36.11) MUTATED DEL PEAK  2(1P36.11) WILD-TYPE 
                           141                            221 
  DEL PEAK  2(1P36.11) MUTATED DEL PEAK  2(1P36.11) WILD-TYPE 
                           141                            221 
[1] "DEL PEAK  3(2Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                           51                           311 
  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                           51                           311 
[1] "DEL PEAK  4(2Q37.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                           60                           302 
  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                           60                           302 
[1] "DEL PEAK  5(3P13) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  5(3P13) MUTATED DEL PEAK  5(3P13) WILD-TYPE 
                         69                         293 
  DEL PEAK  5(3P13) MUTATED DEL PEAK  5(3P13) WILD-TYPE 
                         69                         293 
[1] "DEL PEAK  6(4P16.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  6(4P16.3) MUTATED DEL PEAK  6(4P16.3) WILD-TYPE 
                           84                           278 
  DEL PEAK  6(4P16.3) MUTATED DEL PEAK  6(4P16.3) WILD-TYPE 
                           84                           278 
[1] "DEL PEAK  7(4Q21.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  7(4Q21.3) MUTATED DEL PEAK  7(4Q21.3) WILD-TYPE 
                          169                           193 
  DEL PEAK  7(4Q21.3) MUTATED DEL PEAK  7(4Q21.3) WILD-TYPE 
                          169                           193 
[1] "DEL PEAK  8(4Q22.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  8(4Q22.3) MUTATED DEL PEAK  8(4Q22.3) WILD-TYPE 
                          170                           192 
  DEL PEAK  8(4Q22.3) MUTATED DEL PEAK  8(4Q22.3) WILD-TYPE 
                          170                           192 
[1] "DEL PEAK  9(4Q35.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  9(4Q35.1) MUTATED DEL PEAK  9(4Q35.1) WILD-TYPE 
                          171                           191 
  DEL PEAK  9(4Q35.1) MUTATED DEL PEAK  9(4Q35.1) WILD-TYPE 
                          171                           191 
[1] "DEL PEAK 10(6Q27) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 10(6Q27) MUTATED DEL PEAK 10(6Q27) WILD-TYPE 
                        133                         229 
  DEL PEAK 10(6Q27) MUTATED DEL PEAK 10(6Q27) WILD-TYPE 
                        133                         229 
[1] "DEL PEAK 11(8P23.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 11(8P23.2) MUTATED DEL PEAK 11(8P23.2) WILD-TYPE 
                          241                           121 
  DEL PEAK 11(8P23.2) MUTATED DEL PEAK 11(8P23.2) WILD-TYPE 
                          241                           121 
[1] "DEL PEAK 12(8P12) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 12(8P12) MUTATED DEL PEAK 12(8P12) WILD-TYPE 
                        236                         126 
  DEL PEAK 12(8P12) MUTATED DEL PEAK 12(8P12) WILD-TYPE 
                        236                         126 
[1] "DEL PEAK 13(9P21.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 13(9P21.3) MUTATED DEL PEAK 13(9P21.3) WILD-TYPE 
                          147                           215 
  DEL PEAK 13(9P21.3) MUTATED DEL PEAK 13(9P21.3) WILD-TYPE 
                          147                           215 
[1] "DEL PEAK 14(9Q31.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 14(9Q31.3) MUTATED DEL PEAK 14(9Q31.3) WILD-TYPE 
                          116                           246 
  DEL PEAK 14(9Q31.3) MUTATED DEL PEAK 14(9Q31.3) WILD-TYPE 
                          116                           246 
[1] "DEL PEAK 15(10Q23.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 15(10Q23.31) MUTATED DEL PEAK 15(10Q23.31) WILD-TYPE 
                             95                             267 
  DEL PEAK 15(10Q23.31) MUTATED DEL PEAK 15(10Q23.31) WILD-TYPE 
                             95                             267 
[1] "DEL PEAK 16(10Q26.13) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 16(10Q26.13) MUTATED DEL PEAK 16(10Q26.13) WILD-TYPE 
                            102                             260 
  DEL PEAK 16(10Q26.13) MUTATED DEL PEAK 16(10Q26.13) WILD-TYPE 
                            102                             260 
[1] "DEL PEAK 17(11Q14.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 17(11Q14.1) MUTATED DEL PEAK 17(11Q14.1) WILD-TYPE 
                            72                            290 
  DEL PEAK 17(11Q14.1) MUTATED DEL PEAK 17(11Q14.1) WILD-TYPE 
                            72                            290 
[1] "DEL PEAK 18(11Q24.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 18(11Q24.2) MUTATED DEL PEAK 18(11Q24.2) WILD-TYPE 
                            92                            270 
  DEL PEAK 18(11Q24.2) MUTATED DEL PEAK 18(11Q24.2) WILD-TYPE 
                            92                            270 
[1] "DEL PEAK 19(12P12.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 19(12P12.1) MUTATED DEL PEAK 19(12P12.1) WILD-TYPE 
                            74                            288 
  DEL PEAK 19(12P12.1) MUTATED DEL PEAK 19(12P12.1) WILD-TYPE 
                            74                            288 
[1] "DEL PEAK 20(12Q24.33) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 20(12Q24.33) MUTATED DEL PEAK 20(12Q24.33) WILD-TYPE 
                             54                             308 
  DEL PEAK 20(12Q24.33) MUTATED DEL PEAK 20(12Q24.33) WILD-TYPE 
                             54                             308 
[1] "DEL PEAK 21(13Q14.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 21(13Q14.2) MUTATED DEL PEAK 21(13Q14.2) WILD-TYPE 
                           174                            188 
  DEL PEAK 21(13Q14.2) MUTATED DEL PEAK 21(13Q14.2) WILD-TYPE 
                           174                            188 
[1] "DEL PEAK 22(14Q23.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 22(14Q23.3) MUTATED DEL PEAK 22(14Q23.3) WILD-TYPE 
                           129                            233 
  DEL PEAK 22(14Q23.3) MUTATED DEL PEAK 22(14Q23.3) WILD-TYPE 
                           129                            233 
[1] "DEL PEAK 23(14Q32.33) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 23(14Q32.33) MUTATED DEL PEAK 23(14Q32.33) WILD-TYPE 
                            131                             231 
  DEL PEAK 23(14Q32.33) MUTATED DEL PEAK 23(14Q32.33) WILD-TYPE 
                            131                             231 
[1] "DEL PEAK 24(15Q26.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 24(15Q26.3) MUTATED DEL PEAK 24(15Q26.3) WILD-TYPE 
                            77                            285 
  DEL PEAK 24(15Q26.3) MUTATED DEL PEAK 24(15Q26.3) WILD-TYPE 
                            77                            285 
[1] "DEL PEAK 25(16Q23.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 25(16Q23.1) MUTATED DEL PEAK 25(16Q23.1) WILD-TYPE 
                           161                            201 
  DEL PEAK 25(16Q23.1) MUTATED DEL PEAK 25(16Q23.1) WILD-TYPE 
                           161                            201 
[1] "DEL PEAK 26(17P13.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 26(17P13.1) MUTATED DEL PEAK 26(17P13.1) WILD-TYPE 
                           220                            142 
  DEL PEAK 26(17P13.1) MUTATED DEL PEAK 26(17P13.1) WILD-TYPE 
                           220                            142 
[1] "DEL PEAK 27(17P11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 27(17P11.2) MUTATED DEL PEAK 27(17P11.2) WILD-TYPE 
                           189                            173 
  DEL PEAK 27(17P11.2) MUTATED DEL PEAK 27(17P11.2) WILD-TYPE 
                           189                            173 
[1] "DEL PEAK 28(18Q21.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 28(18Q21.2) MUTATED DEL PEAK 28(18Q21.2) WILD-TYPE 
                            92                            270 
  DEL PEAK 28(18Q21.2) MUTATED DEL PEAK 28(18Q21.2) WILD-TYPE 
                            92                            270 
[1] "DEL PEAK 29(19P13.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 29(19P13.3) MUTATED DEL PEAK 29(19P13.3) WILD-TYPE 
                            85                            277 
  DEL PEAK 29(19P13.3) MUTATED DEL PEAK 29(19P13.3) WILD-TYPE 
                            85                            277 
[1] "DEL PEAK 30(20P12.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 30(20P12.1) MUTATED DEL PEAK 30(20P12.1) WILD-TYPE 
                            27                            335 
  DEL PEAK 30(20P12.1) MUTATED DEL PEAK 30(20P12.1) WILD-TYPE 
                            27                            335 
[1] "DEL PEAK 31(22Q12.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 31(22Q12.1) MUTATED DEL PEAK 31(22Q12.1) WILD-TYPE 
                            75                            287 
  DEL PEAK 31(22Q12.1) MUTATED DEL PEAK 31(22Q12.1) WILD-TYPE 
                            75                            287 
[1] "DEL PEAK 32(22Q13.32) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 32(22Q13.32) MUTATED DEL PEAK 32(22Q13.32) WILD-TYPE 
                             79                             283 
  DEL PEAK 32(22Q13.32) MUTATED DEL PEAK 32(22Q13.32) WILD-TYPE 
                             79                             283 
[1] "DEL PEAK 33(XQ26.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 33(XQ26.2) MUTATED DEL PEAK 33(XQ26.2) WILD-TYPE 
                           66                           296 
  DEL PEAK 33(XQ26.2) MUTATED DEL PEAK 33(XQ26.2) WILD-TYPE 
                           66                           296 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                      
 [2] "VITAL_STATUS"                        
 [3] "DAYS_TO_DEATH"                       
 [4] "DAYS_TO_LAST_FOLLOWUP"               
 [5] "TUMOR_TISSUE_SITE"                   
 [6] "PATHOLOGIC_STAGE"                    
 [7] "PATHOLOGY_T_STAGE"                   
 [8] "PATHOLOGY_N_STAGE"                   
 [9] "PATHOLOGY_M_STAGE"                   
[10] "GENDER"                              
[11] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"
[12] "DAYS_TO_LAST_KNOWN_ALIVE"            
[13] "RADIATION_THERAPY"                   
[14] "HISTOLOGICAL_TYPE"                   
[15] "RESIDUAL_TUMOR"                      
[16] "RACE"                                
[17] "ETHNICITY"                           

Input Data has 17 rows and 362 columns.

[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=62,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=122,	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=231,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'TUMOR_TISSUE_SITE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "TUMOR_TISSUE_SITE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'PATHOLOGIC_STAGE':	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:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'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 12:'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 13:'RADIATION_THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'HISTOLOGICAL_TYPE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'RESIDUAL_TUMOR':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'RACE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[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 362 columns, 1 survival variables, and 11 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
 [1] "YEARS_TO_BIRTH"    "PATHOLOGIC_STAGE"  "PATHOLOGY_T_STAGE"
 [4] "PATHOLOGY_N_STAGE" "PATHOLOGY_M_STAGE" "GENDER"           
 [7] "RADIATION_THERAPY" "HISTOLOGICAL_TYPE" "RESIDUAL_TUMOR"   
[10] "RACE"              "ETHNICITY"        
YEARS_TO_BIRTH, nv=62, binary=FALSE, numeric=TRUE
PATHOLOGIC_STAGE, 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 
  1 181  92  74  12 
[1] "table(vv)"
vv
T0+T1    T2    T3    T4 
  182    92    74    12 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T0  T1  T2  T3  T4 
  1 181  92  74  12 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


T0+T1    T2    T3    T4 
  182    92    74    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
RADIATION_THERAPY, nv=2, binary=FALSE, numeric=FALSE
HISTOLOGICAL_TYPE, nv=3, binary=FALSE, numeric=FALSE
RESIDUAL_TUMOR, 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    51  34
  AMP PEAK  1(1P22.3) WILD-TYPE 178  95
  AMP PEAK  1(1P22.3) MUTATED AMP PEAK  1(1P22.3) WILD-TYPE 
                           85                           273 
  AMP PEAK  1(1P22.3) MUTATED AMP PEAK  1(1P22.3) WILD-TYPE 
                           34                            95 
$`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        17.10        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        45.93        18.48 
TCGA-BW-A5NO TCGA-CC-5261 TCGA-CC-5263 TCGA-CC-A3MB TCGA-CC-A5UE TCGA-CC-A7II 
        0.66         3.19         4.24        10.36         8.94        13.12 
TCGA-CC-A7IK TCGA-CC-A7IL TCGA-CC-A8HU TCGA-CC-A8HV TCGA-DD-A113 TCGA-DD-A114 
        8.61         9.14        11.31         9.17        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-AAVV TCGA-DD-AAVY TCGA-DD-AAVZ 
       18.25        21.17        23.64        80.71        64.77        62.47 
TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A7PY TCGA-ED-A7XO 
       66.25        65.39        29.92        26.93        12.82        14.04 
TCGA-ED-A8O5 TCGA-EP-A2KB TCGA-FV-A496 TCGA-FV-A4ZP TCGA-G3-A25S TCGA-G3-A25W 
       13.35        19.59         0.33        81.73        13.68        30.74 
TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A7M6 TCGA-G3-A7M9 TCGA-G3-AAV1 
       19.23        25.25        22.95        20.78         1.84        11.80 
TCGA-KR-A7K2 TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MF TCGA-UB-AA0U TCGA-WX-AA44 
       21.60        19.76        16.44         7.04        10.75        20.22 
TCGA-XR-A8TF 
       22.78 

$`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        49.84        47.74        18.25        11.74 
TCGA-2Y-A9H7 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 
       38.40        20.81        22.92         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        14.76         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        23.38         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         4.24         2.86 
TCGA-CC-5262 TCGA-CC-5264 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MC 
        3.39         3.35         3.32         9.86         9.96        11.93 
TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7IH 
       11.41         9.99         7.13        21.34         9.83        12.00 
TCGA-CC-A7IJ TCGA-CC-A8HT TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A115 TCGA-DD-A116 
       12.56         4.60         6.94         8.15        83.57        53.33 
TCGA-DD-A118 TCGA-DD-A11B TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB 
      113.00         0.46        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-A1EI 
       19.79        75.65        11.47        12.95        45.11         6.02 
TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39Z TCGA-DD-A3A0 
       18.35        13.64        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-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-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ 
       39.78        56.25        29.56        73.81       108.76        12.26 
TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C 
        0.30        80.75        78.84        23.93         9.30        23.05 
TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-AA3A TCGA-DD-AAC9 TCGA-DD-AACA 
       22.78         1.45        35.67        13.48        11.41        75.65 
TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACK 
       55.40        12.53        63.48        12.00        15.42         0.30 
TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACU TCGA-DD-AACV 
        3.52        58.16        13.64        14.20        51.52        50.33 
TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD1 TCGA-DD-AAD2 
       46.82         5.59        47.67         5.62        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-AADE TCGA-DD-AADG TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADN 
       13.97        39.52        37.64        35.05        34.49        29.52 
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-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE8 
       18.15        20.98        18.61        19.99         4.64        21.83 
TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEH 
       23.74        18.90        15.72        25.08        26.63        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-AAW2 TCGA-DD-AAW3 TCGA-ED-A5KG 
       72.39        76.18        56.48        49.48        53.69        28.08 
TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PZ TCGA-ED-A7XP 
       13.91        13.35         9.73         0.20         0.20        13.15 
TCGA-ED-A82E TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
       13.41         1.84         0.20        18.74        19.99        20.61 
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-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-A4ZQ TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25X 
        0.03         0.39        51.06        53.79        28.27        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-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M5 TCGA-G3-A7M7 TCGA-G3-A7M8 
       20.42        17.10        22.06        14.70        11.87        14.14 
TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 
       15.78        15.65        12.23        13.55         0.89         8.75 
TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ 
        2.14        11.87        22.92         1.02         2.20         2.99 
TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 
       37.71        20.75        17.06        16.83        11.80         2.14 
TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C 
       31.27        29.79        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        22.95        24.56        20.71         7.53        10.85 
TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 
       58.88        26.27        17.69        21.01         3.09        21.04 
TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-T1-A6J8 
       19.33        19.04        15.39        15.52        36.10         0.76 
TCGA-UB-A7MA TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-A9G7 
       17.59         1.71        15.98        10.32        11.34         0.99 
TCGA-WQ-AB4B TCGA-WX-AA46 TCGA-WX-AA47 TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY 
       12.99        24.85        18.28        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        35.87         0.69        25.15        12.99        45.57 
TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       40.80        79.30        11.21 

  AMP PEAK  1(1P22.3) MUTATED AMP PEAK  1(1P22.3) WILD-TYPE 
                         0.33                          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 
                        20.91                         19.10 
[1] "0.3 - 114.3 (20.9)" "0.0 - 120.8 (19.1)"
[1] "hr=" "1.1"
D1V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IIIA
  AMP PEAK  1(1P22.3) MUTATED        36       19         1         18
  AMP PEAK  1(1P22.3) WILD-TYPE     135       66         2         42
                               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                             36                           135
  STAGE II                            19                            66
  STAGE III                            1                             2
  STAGE IIIA                          18                            42
  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      37  22  24   5
  AMP PEAK  1(1P22.3) WILD-TYPE   145  70  50   7
D1V4, multiclass
       clus
vv      AMP PEAK  1(1P22.3) MUTATED AMP PEAK  1(1P22.3) WILD-TYPE
  T0+T1                          37                           145
  T2                             22                            70
  T3                             24                            50
  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    62   1
  AMP PEAK  1(1P22.3) WILD-TYPE 188   2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1P22.3) MUTATED     62    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                          62                           188
  1                           1                             2
[1] 2 2
[1] FALSE
D1V6, binary
                               cls
clus                              0   1
  AMP PEAK  1(1P22.3) MUTATED    67   3
  AMP PEAK  1(1P22.3) WILD-TYPE 194   1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1P22.3) MUTATED     67    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                          67                           194
  1                           3                             1
[1] 2 2
[1] FALSE
D1V7, binary
                               cls
clus                              0   1
  AMP PEAK  1(1P22.3) MUTATED    31  57
  AMP PEAK  1(1P22.3) WILD-TYPE  84 190
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1P22.3) MUTATED     31   57
  AMP PEAK  1(1P22.3) WILD-TYPE   84  190
        clus
vv       AMP PEAK  1(1P22.3) MUTATED AMP PEAK  1(1P22.3) WILD-TYPE
  FEMALE                          31                            84
  MALE                            57                           190
[1] 2 2
[1] FALSE
D1V8, binary
                               cls
clus                              0   1
  AMP PEAK  1(1P22.3) MUTATED    80   2
  AMP PEAK  1(1P22.3) WILD-TYPE 256   5
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1P22.3) MUTATED     80    2
  AMP PEAK  1(1P22.3) WILD-TYPE  256    5
     clus
vv    AMP PEAK  1(1P22.3) MUTATED AMP PEAK  1(1P22.3) WILD-TYPE
  NO                           80                           256
  YES                           2                             5
[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                         87
  AMP PEAK  1(1P22.3) WILD-TYPE                      266
                               vv
clus                            HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK  1(1P22.3) MUTATED                                  1
  AMP PEAK  1(1P22.3) WILD-TYPE                                6
D1V9, multiclass
                                  clus
vv                                 AMP PEAK  1(1P22.3) MUTATED
  FIBROLAMELLAR CARCINOMA                                    0
  HEPATOCELLULAR CARCINOMA                                  87
  HEPATOCHOLANGIOCARCINOMA (MIXED)                           1
                                  clus
vv                                 AMP PEAK  1(1P22.3) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                      2
  HEPATOCELLULAR CARCINOMA                                   266
  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    73   7   1   7
  AMP PEAK  1(1P22.3) WILD-TYPE 245   8   0  14
D1V10, multiclass
    clus
vv   AMP PEAK  1(1P22.3) MUTATED AMP PEAK  1(1P22.3) WILD-TYPE
  R0                          73                           245
  R1                           7                             8
  R2                           1                             0
  RX                           7                            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  1(1P22.3) MUTATED                                  0    47
  AMP PEAK  1(1P22.3) WILD-TYPE                                1   110
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  1(1P22.3) MUTATED                           3    36
  AMP PEAK  1(1P22.3) WILD-TYPE                        14   141
D1V11, multiclass
                                  clus
vv                                 AMP PEAK  1(1P22.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                     47
  BLACK OR AFRICAN AMERICAN                                  3
  WHITE                                                     36
                                  clus
vv                                 AMP PEAK  1(1P22.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                      110
  BLACK OR AFRICAN AMERICAN                                   14
  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"
D1V12, binary
                               cls
clus                              0   1
  AMP PEAK  1(1P22.3) MUTATED     3  80
  AMP PEAK  1(1P22.3) WILD-TYPE  10 252
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1P22.3) MUTATED      3   80
  AMP PEAK  1(1P22.3) WILD-TYPE   10  252
                        clus
vv                       AMP PEAK  1(1P22.3) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                          80
                        clus
vv                       AMP PEAK  1(1P22.3) WILD-TYPE
  HISPANIC OR LATINO                                10
  NOT HISPANIC OR LATINO                           252
[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   170 104
  AMP PEAK  2(1Q22) WILD-TYPE  59  25
  AMP PEAK  2(1Q22) MUTATED AMP PEAK  2(1Q22) WILD-TYPE 
                        274                          84 
  AMP PEAK  2(1Q22) MUTATED AMP PEAK  2(1Q22) WILD-TYPE 
                        104                          25 
$`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        49.84        18.25        11.74        38.40 
TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-5C-A9VG 
       20.81        22.92         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        17.10        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        23.38         1.12         5.03        44.42 
TCGA-BC-A217 TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I TCGA-BC-A8YO 
       45.93        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         4.24         3.19         3.39         4.24 
TCGA-CC-5264 TCGA-CC-A1HT TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UC 
        3.35         3.32         9.96        10.36        11.93        11.41 
TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7IH 
        9.99         8.94         7.13        21.34         9.83        12.00 
TCGA-CC-A7IK TCGA-CC-A7IL TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FW 
        8.61         9.14         4.60        11.31         9.17         8.15 
TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A 
       79.73        37.78        83.57       113.00         7.33         2.60 
TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB 
        0.46        21.76        51.29        90.71        79.40        66.31 
TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EJ TCGA-DD-A1EK 
       11.47        12.95        45.11        49.15        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-A3A3 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 
       25.81         7.66        17.59        13.78         0.36        30.61 
TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NN 
       30.97        30.15        26.83        30.51        39.78        29.56 
TCGA-DD-A4NO TCGA-DD-A4NR TCGA-DD-A4NV TCGA-DD-A73B TCGA-DD-A73D TCGA-DD-A73F 
       73.81         0.30        78.84         9.30        22.78        35.67 
TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACB TCGA-DD-AACC 
      114.35        13.48         0.53        11.41        76.41        55.40 
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-AADC TCGA-DD-AADD TCGA-DD-AADF TCGA-DD-AADG 
       40.08        40.54        13.97        40.47         3.78        37.64 
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-AADU TCGA-DD-AADV TCGA-DD-AADW TCGA-DD-AADY 
       15.06        66.67        18.21        18.87        19.30        18.25 
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-AAE8 TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEG 
       21.83        23.74        18.90        15.72        25.08        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-AAVV TCGA-DD-AAVW TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 
       80.71        76.18        64.77        62.47        66.25        65.39 
TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A66X TCGA-ED-A66Y 
       49.48        53.69        29.92        26.93        13.35         9.73 
TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 
       12.82         0.20        14.04        13.15        13.41        13.35 
TCGA-ED-A8O6 TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC 
        1.84        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-A496 TCGA-FV-A4ZP TCGA-G3-A25S 
        8.12        12.03         0.03         0.33        81.73        13.68 
TCGA-G3-A25U TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG 
       53.79        30.74        58.49        14.86        21.53        22.13 
TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC 
       19.53        19.23        25.25        20.42        17.10        22.06 
TCGA-G3-A7M6 TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 
       20.78         1.84        15.78        15.65        11.80        12.23 
TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A3OU 
       13.55         0.89         8.75         2.14        11.87        22.92 
TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 
        1.02         2.99        37.71        16.83         2.14        21.60 
TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC TCGA-MI-A75C TCGA-MI-A75E 
       31.27        29.79        12.72        13.97         9.57        16.67 
TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-NI-A8LF TCGA-O8-A75V TCGA-QA-A7B7 
       22.95        24.56        20.71        26.27        17.69         3.09 
TCGA-RC-A7S9 TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-T1-A6J8 TCGA-UB-A7MA 
       21.04        15.39        15.52        36.10         0.76        17.59 
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-A9G7 TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-WX-AA47 TCGA-XR-A8TF 
       11.34         0.99        12.99        20.22        18.28        22.78 
TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D2 
       13.55        35.77        23.21        35.87         0.69        25.15 
TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CG 
       12.99        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        14.76 
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-CC-A7II 
        0.26        44.81        13.45         2.86         9.86        13.12 
TCGA-CC-A7IJ TCGA-CC-A9FS TCGA-DD-A116 TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EI 
       12.56         6.94        53.33        19.79        75.65         6.02 
TCGA-DD-A3A2 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A4NA TCGA-DD-A4NB 
       70.06        20.12       102.74       107.11        33.14        32.52 
TCGA-DD-A4ND TCGA-DD-A4NL TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NS TCGA-DD-A73A 
       90.28        56.25       108.76        12.26        80.75        23.93 
TCGA-DD-A73C TCGA-DD-A73E TCGA-DD-AACA TCGA-DD-AACD TCGA-DD-AACG TCGA-DD-AACK 
       23.05         1.45        75.65        12.53        15.42         0.30 
TCGA-DD-AAD6 TCGA-DD-AADB TCGA-DD-AADE TCGA-DD-AADN TCGA-DD-AADQ TCGA-DD-AADS 
       22.09        40.83        39.52        29.52        14.33        15.58 
TCGA-DD-AAE2 TCGA-DD-AAEE TCGA-DD-AAEI TCGA-DD-AAVU TCGA-DD-AAVX TCGA-ED-A5KG 
       20.98        26.63        50.33        72.39        56.48        28.08 
TCGA-ED-A627 TCGA-ED-A7PX TCGA-ED-A97K TCGA-ES-A2HS TCGA-FV-A3I0 TCGA-FV-A3R2 
       13.91         0.20         0.20        22.85        27.88         6.38 
TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25V TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A5SJ 
        0.39        51.06        28.27        25.64         5.92        22.95 
TCGA-G3-A7M5 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-GJ-A9DB TCGA-K7-A5RF TCGA-K7-A5RG 
       14.70        11.87        14.14         2.20        20.75        17.06 
TCGA-K7-AAU7 TCGA-LG-A9QD TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-PD-A5DF 
       11.80        12.03         7.53        10.85        58.88        21.01 
TCGA-RC-A7SB TCGA-RC-A7SF TCGA-UB-AA0V TCGA-WX-AA46 TCGA-ZP-A9CY TCGA-ZS-A9CF 
       19.33        19.04        10.32        24.85        25.71        79.30 

  AMP PEAK  2(1Q22) MUTATED AMP PEAK  2(1Q22) WILD-TYPE 
                       0.03                        0.20 
  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 
                      19.00                       22.47 
[1] "0.0 - 120.8 (19.0)" "0.2 - 108.8 (22.5)"
[1] "hr=" "1.5"
D2V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  2(1Q22) MUTATED       128       68         2         44          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                          128                          43
  STAGE II                          68                          17
  STAGE III                          2                           1
  STAGE IIIA                        44                          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     137  72  56  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                       137                          45
  T2                           72                          20
  T3                           56                          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   194   2
  AMP PEAK  2(1Q22) WILD-TYPE  56   1
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  2(1Q22) MUTATED    194    2
  AMP PEAK  2(1Q22) WILD-TYPE   56    1
   clus
vv  AMP PEAK  2(1Q22) MUTATED AMP PEAK  2(1Q22) WILD-TYPE
  0                       194                          56
  1                         2                           1
[1] 2 2
[1] FALSE
D2V6, binary
                             cls
clus                            0   1
  AMP PEAK  2(1Q22) MUTATED   203   4
  AMP PEAK  2(1Q22) WILD-TYPE  58   0
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  2(1Q22) MUTATED    203    4
  AMP PEAK  2(1Q22) WILD-TYPE   58    0
   clus
vv  AMP PEAK  2(1Q22) MUTATED AMP PEAK  2(1Q22) WILD-TYPE
  0                       203                          58
  1                         4                           0
[1] 2 2
[1] FALSE
D2V7, binary
                             cls
clus                            0   1
  AMP PEAK  2(1Q22) MUTATED    91 186
  AMP PEAK  2(1Q22) WILD-TYPE  24  61
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  2(1Q22) MUTATED     91  186
  AMP PEAK  2(1Q22) WILD-TYPE   24   61
        clus
vv       AMP PEAK  2(1Q22) MUTATED AMP PEAK  2(1Q22) WILD-TYPE
  FEMALE                        91                          24
  MALE                         186                          61
[1] 2 2
[1] FALSE
D2V8, binary
                             cls
clus                            0   1
  AMP PEAK  2(1Q22) MUTATED   259   5
  AMP PEAK  2(1Q22) WILD-TYPE  77   2
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  2(1Q22) MUTATED    259    5
  AMP PEAK  2(1Q22) WILD-TYPE   77    2
     clus
vv    AMP PEAK  2(1Q22) MUTATED AMP PEAK  2(1Q22) WILD-TYPE
  NO                        259                          77
  YES                         5                           2
[1] 2 2
[1] FALSE
                             vv
clus                          FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  AMP PEAK  2(1Q22) MUTATED                         0                      273
  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
D2V9, multiclass
                                  clus
vv                                 AMP PEAK  2(1Q22) MUTATED
  FIBROLAMELLAR CARCINOMA                                  0
  HEPATOCELLULAR CARCINOMA                               273
  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   241  13   1  17
  AMP PEAK  2(1Q22) WILD-TYPE  77   2   0   4
D2V10, multiclass
    clus
vv   AMP PEAK  2(1Q22) MUTATED AMP PEAK  2(1Q22) WILD-TYPE
  R0                       241                          77
  R1                        13                           2
  R2                         1                           0
  RX                        17                           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   126
  AMP PEAK  2(1Q22) WILD-TYPE                                0    31
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  2(1Q22) MUTATED                          13   127
  AMP PEAK  2(1Q22) WILD-TYPE                         4    50
D2V11, multiclass
                                  clus
vv                                 AMP PEAK  2(1Q22) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         1
  ASIAN                                                  126
  BLACK OR AFRICAN AMERICAN                               13
  WHITE                                                  127
                                  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"
D2V12, binary
                             cls
clus                            0   1
  AMP PEAK  2(1Q22) MUTATED    10 253
  AMP PEAK  2(1Q22) WILD-TYPE   3  79
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  2(1Q22) MUTATED     10  253
  AMP PEAK  2(1Q22) WILD-TYPE    3   79
                        clus
vv                       AMP PEAK  2(1Q22) MUTATED AMP PEAK  2(1Q22) WILD-TYPE
  HISPANIC OR LATINO                            10                           3
  NOT HISPANIC OR LATINO                       253                          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   168  95
  AMP PEAK  3(1Q42.3) WILD-TYPE  61  34
  AMP PEAK  3(1Q42.3) MUTATED AMP PEAK  3(1Q42.3) WILD-TYPE 
                          263                            95 
  AMP PEAK  3(1Q42.3) MUTATED AMP PEAK  3(1Q42.3) WILD-TYPE 
                           95                            34 
$`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        49.84        18.25        11.74        38.40 
TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-5C-A9VH 
       20.81        22.92         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        17.10        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 
       23.38         5.03        44.42        45.93        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-5264 TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MC 
        3.39         4.24         3.35         9.86         9.96        11.93 
TCGA-CC-A5UC TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7IH 
       11.41         8.94         7.13        21.34         9.83        12.00 
TCGA-CC-A7IK TCGA-CC-A7IL TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FW 
        8.61         9.14         4.60        11.31         9.17         8.15 
TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B 
       79.73        37.78       113.00         7.33         2.60         0.46 
TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG 
       51.29        90.71        79.40        11.47        12.95        45.11 
TCGA-DD-A1EH TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W 
       49.15        33.04        18.35        13.64        21.14        27.19 
TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A3 TCGA-DD-A3A5 
        5.62        19.76        25.81         7.66        17.59       102.74 
TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NF 
       13.78         0.36        30.61        33.14        32.52        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-A4NQ TCGA-DD-A4NR TCGA-DD-A4NV TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F 
       12.26         0.30        78.84        22.78         1.45        35.67 
TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACB TCGA-DD-AACC 
      114.35        13.48         0.53        11.41        76.41        55.40 
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-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-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 
       47.67         5.62         4.50        18.54        21.63        42.58 
TCGA-DD-AAD5 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADD TCGA-DD-AADF TCGA-DD-AADG 
       44.22        40.08        40.54        40.47         3.78        37.64 
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-AADU TCGA-DD-AADV TCGA-DD-AADW TCGA-DD-AADY 
       15.06        66.67        18.21        18.87        19.30        18.25 
TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAE9 
       18.25        18.15         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-AAVV TCGA-DD-AAVW 
       79.07        89.69        82.62        59.93        80.71        76.18 
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-A66X TCGA-ED-A66Y TCGA-ED-A7PY 
       29.92        26.93        28.08        13.35         9.73        12.82 
TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 
        0.20        14.04        13.15        13.41        13.35         1.84 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL 
       18.74        19.99        20.61        19.59         0.62         9.96 
TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I1 
       11.93        14.40        60.89        23.97        19.10         8.12 
TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-G3-A25S TCGA-G3-A25W TCGA-G3-A25X 
       12.03         0.03         0.33        13.68        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-AAV0 
       20.42        17.10        22.06        20.78         1.84        15.65 
TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 
       11.80        12.23        13.55         0.89         8.75         2.14 
TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A6G5 TCGA-KR-A7K0 
       11.87        22.92         2.99        37.71        16.83         2.14 
TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC TCGA-MI-A75C 
       21.60        31.27        29.79        12.72        13.97         9.57 
TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A8JO TCGA-O8-A75V 
       16.67        22.95        24.56        20.71        10.85        17.69 
TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RG-A7D4 
       21.01         3.09        21.04        19.04        15.39        36.10 
TCGA-T1-A6J8 TCGA-UB-A7MA TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-A7MF 
        0.76        17.59        16.44         1.71        15.98         7.04 
TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-WX-AA47 
       10.75        11.34         0.99        12.99        20.22        18.28 
TCGA-XR-A8TF TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 
       22.78        35.77        25.71        23.21        35.87         0.69 
TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CG 
       25.15        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 
       14.76         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-CC-A5UD TCGA-CC-A7II 
        4.24         2.86         3.32        10.36         9.99        13.12 
TCGA-CC-A7IJ TCGA-CC-A9FS TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A11C TCGA-DD-A1EB 
       12.56         6.94        83.57        53.33        21.76        66.31 
TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EI TCGA-DD-A39X TCGA-DD-A3A2 TCGA-DD-A3A4 
       19.79        75.65         6.02        55.69        70.06        20.12 
TCGA-DD-A3A6 TCGA-DD-A4ND TCGA-DD-A4NL TCGA-DD-A4NP TCGA-DD-A4NS TCGA-DD-A73A 
      107.11        90.28        56.25       108.76        80.75        23.93 
TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-AACA TCGA-DD-AACG TCGA-DD-AACK TCGA-DD-AAD6 
        9.30        23.05        75.65        15.42         0.30        22.09 
TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADE TCGA-DD-AADN TCGA-DD-AADQ TCGA-DD-AADS 
       40.83        13.97        39.52        29.52        14.33        15.58 
TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAEE TCGA-DD-AAEI TCGA-DD-AAVU 
       20.98        18.61        19.99        26.63        50.33        72.39 
TCGA-DD-AAVX TCGA-ED-A627 TCGA-ED-A7PX TCGA-ED-A97K TCGA-ES-A2HS TCGA-FV-A3I0 
       56.48        13.91         0.20         0.20        22.85        27.88 
TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V 
        6.38        81.73         0.39        51.06        53.79        28.27 
TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A5SJ TCGA-G3-A7M5 TCGA-G3-A7M7 TCGA-G3-A7M8 
       25.64         5.92        22.95        14.70        11.87        14.14 
TCGA-G3-AAUZ TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-AAU7 
       15.78         1.02         2.20        20.75        17.06        11.80 
TCGA-LG-A9QD TCGA-MR-A520 TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-RC-A7SB TCGA-RC-A7SK 
       12.03         7.53        58.88        26.27        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                          0.20 
  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 
                        19.53                         19.99 
[1] "0.0 - 120.8 (19.5)" "0.2 - 108.8 (20.0)"
[1] "hr=" "1.1"
D3V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IIIA
  AMP PEAK  3(1Q42.3) MUTATED       121       65         3         39
  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                            121                            50
  STAGE II                            65                            20
  STAGE III                            3                             0
  STAGE IIIA                          39                            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     131  72  52   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                         131                            51
  T2                             72                            20
  T3                             52                            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   187   3
  AMP PEAK  3(1Q42.3) WILD-TYPE  63   0
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(1Q42.3) MUTATED    187    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                         187                            63
  1                           3                             0
[1] 2 2
[1] FALSE
D3V6, binary
                               cls
clus                              0   1
  AMP PEAK  3(1Q42.3) MUTATED   196   4
  AMP PEAK  3(1Q42.3) WILD-TYPE  65   0
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(1Q42.3) MUTATED    196    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                         196                            65
  1                           4                             0
[1] 2 2
[1] FALSE
D3V7, binary
                               cls
clus                              0   1
  AMP PEAK  3(1Q42.3) MUTATED    87 179
  AMP PEAK  3(1Q42.3) WILD-TYPE  28  68
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(1Q42.3) MUTATED     87  179
  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                          87                            28
  MALE                           179                            68
[1] 2 2
[1] FALSE
D3V8, binary
                               cls
clus                              0   1
  AMP PEAK  3(1Q42.3) MUTATED   248   5
  AMP PEAK  3(1Q42.3) WILD-TYPE  88   2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(1Q42.3) MUTATED    248    5
  AMP PEAK  3(1Q42.3) WILD-TYPE   88    2
     clus
vv    AMP PEAK  3(1Q42.3) MUTATED AMP PEAK  3(1Q42.3) WILD-TYPE
  NO                          248                            88
  YES                           5                             2
[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                        260
  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
D3V9, multiclass
                                  clus
vv                                 AMP PEAK  3(1Q42.3) MUTATED
  FIBROLAMELLAR CARCINOMA                                    2
  HEPATOCELLULAR CARCINOMA                                 260
  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   234  11   1  15
  AMP PEAK  3(1Q42.3) WILD-TYPE  84   4   0   6
D3V10, multiclass
    clus
vv   AMP PEAK  3(1Q42.3) MUTATED AMP PEAK  3(1Q42.3) WILD-TYPE
  R0                         234                            84
  R1                          11                             4
  R2                           1                             0
  RX                          15                             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   120
  AMP PEAK  3(1Q42.3) WILD-TYPE                                0    37
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  3(1Q42.3) MUTATED                          13   124
  AMP PEAK  3(1Q42.3) WILD-TYPE                         4    53
D3V11, multiclass
                                  clus
vv                                 AMP PEAK  3(1Q42.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                    120
  BLACK OR AFRICAN AMERICAN                                 13
  WHITE                                                    124
                                  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"
D3V12, binary
                               cls
clus                              0   1
  AMP PEAK  3(1Q42.3) MUTATED     9 243
  AMP PEAK  3(1Q42.3) WILD-TYPE   4  89
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(1Q42.3) MUTATED      9  243
  AMP PEAK  3(1Q42.3) WILD-TYPE    4   89
                        clus
vv                       AMP PEAK  3(1Q42.3) MUTATED
  HISPANIC OR LATINO                               9
  NOT HISPANIC OR LATINO                         243
                        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  31
  AMP PEAK  4(2P24.1) WILD-TYPE 198  98
  AMP PEAK  4(2P24.1) MUTATED AMP PEAK  4(2P24.1) WILD-TYPE 
                           62                           296 
  AMP PEAK  4(2P24.1) MUTATED AMP PEAK  4(2P24.1) WILD-TYPE 
                           31                            98 
$`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 
       17.10        48.99        37.32        10.13        27.52         5.03 
TCGA-BC-A5W4 TCGA-BW-A5NO TCGA-CC-5263 TCGA-CC-5264 TCGA-CC-A3M9 TCGA-CC-A7IE 
       17.98         0.66         4.24         3.35         9.86         7.13 
TCGA-CC-A7IG TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-DD-A113 TCGA-DD-A115 TCGA-DD-A11A 
        9.83        12.56         8.61        79.73        83.57         2.60 
TCGA-DD-A1E9 TCGA-DD-A1EG TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39X TCGA-DD-A3A9 
       90.71        45.11        33.04        13.64        55.69        30.61 
TCGA-DD-A4NA TCGA-DD-A4NO TCGA-DD-A73B TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F 
       33.14        73.81         9.30        22.78         1.45        35.67 
TCGA-DD-AA3A TCGA-DD-AACB TCGA-DD-AACI TCGA-DD-AAD6 TCGA-DD-AADF TCGA-DD-AADN 
       13.48        76.41        53.19        22.09         3.78        29.52 
TCGA-DD-AADO TCGA-DD-AADR TCGA-DD-AAE2 TCGA-ED-A7PY TCGA-ED-A82E TCGA-ED-A8O6 
       14.89        66.67        20.98        12.82        13.41         1.84 
TCGA-EP-A2KA TCGA-ES-A2HS TCGA-G3-A25T TCGA-G3-A25W TCGA-G3-A25Z TCGA-G3-A7M9 
       20.61        22.85        51.06        30.74        21.53         1.84 
TCGA-G3-AAV0 TCGA-G3-AAV4 TCGA-G3-AAV6 TCGA-LG-A6GG TCGA-UB-A7MA TCGA-UB-A7MB 
       15.65         0.89         2.14        12.72        17.59        19.76 
TCGA-WJ-A86L TCGA-ZS-A9CF 
       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        49.84        11.74        38.40        20.81        22.92 
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        14.76         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        23.38         1.12        69.57        44.42 
TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A69I TCGA-BC-A8YO 
       45.93         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         4.24         2.86         3.19 
TCGA-CC-5262 TCGA-CC-A1HT TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UC 
        3.39         3.32         9.96        10.36        11.93        11.41 
TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IF TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IL 
        9.99         8.94        21.34        12.00        13.12         9.14 
TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A114 
        4.60        11.31         9.17         6.94         8.15        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        26.63        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-AAVV TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ 
       72.39        80.71        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        29.92        26.93 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PZ 
       28.08        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-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25U 
        0.03         0.33        81.73         0.39        13.68        53.79 
TCGA-G3-A25V TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI 
       28.27        58.49        14.86        22.13        25.64         5.92 
TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM 
       19.53        19.23        25.25        22.95        20.42        17.10 
TCGA-G3-A6UC TCGA-G3-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ 
       22.06        14.70        20.78        11.87        14.14        15.78 
TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV5 TCGA-G3-AAV7 TCGA-GJ-A3OU 
       11.80        12.23        13.55         8.75        11.87        22.92 
TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG 
        1.02         2.20         2.99        37.71        20.75        17.06 
TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-KR-A7K8 
       16.83        11.80         2.14        21.60        31.27        29.79 
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        22.95        24.56 
TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V 
       20.71         7.53        10.85        58.88        26.27        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-RG-A7D4 TCGA-T1-A6J8 TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME 
       15.52        36.10         0.76        16.44         1.71        15.98 
TCGA-UB-A7MF TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA44 
        7.04        10.75        10.32         0.99        12.99        20.22 
TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY 
       24.85        18.28        22.78        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        35.87         0.69        25.15        12.99        45.57 
TCGA-ZS-A9CE TCGA-ZS-A9CG 
       40.80        11.21 

  AMP PEAK  4(2P24.1) MUTATED AMP PEAK  4(2P24.1) WILD-TYPE 
                         0.66                          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 
                       20.185                        19.675 
[1] "0.7 - 90.7 (20.2)"  "0.0 - 120.8 (19.7)"
[1] "hr=" "1.5"
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     147       71         3         44
                               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                           147
  STAGE II                            14                            71
  STAGE III                            0                             3
  STAGE IIIA                          16                            44
  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   157  75  54  10
D4V4, multiclass
       clus
vv      AMP PEAK  4(2P24.1) MUTATED AMP PEAK  4(2P24.1) WILD-TYPE
  T0+T1                          25                           157
  T2                             17                            75
  T3                             20                            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"
D4V5, binary
                               cls
clus                              0   1
  AMP PEAK  4(2P24.1) MUTATED    42   2
  AMP PEAK  4(2P24.1) WILD-TYPE 208   1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(2P24.1) MUTATED     42    2
  AMP PEAK  4(2P24.1) WILD-TYPE  208    1
   clus
vv  AMP PEAK  4(2P24.1) MUTATED AMP PEAK  4(2P24.1) WILD-TYPE
  0                          42                           208
  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 219   2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(2P24.1) MUTATED     42    2
  AMP PEAK  4(2P24.1) WILD-TYPE  219    2
   clus
vv  AMP PEAK  4(2P24.1) MUTATED AMP PEAK  4(2P24.1) WILD-TYPE
  0                          42                           219
  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  83 215
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(2P24.1) MUTATED     32   32
  AMP PEAK  4(2P24.1) WILD-TYPE   83  215
        clus
vv       AMP PEAK  4(2P24.1) MUTATED AMP PEAK  4(2P24.1) WILD-TYPE
  FEMALE                          32                            83
  MALE                            32                           215
[1] 2 2
[1] FALSE
D4V8, binary
                               cls
clus                              0   1
  AMP PEAK  4(2P24.1) MUTATED    60   0
  AMP PEAK  4(2P24.1) WILD-TYPE 276   7
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(2P24.1) MUTATED     60    0
  AMP PEAK  4(2P24.1) WILD-TYPE  276    7
     clus
vv    AMP PEAK  4(2P24.1) MUTATED AMP PEAK  4(2P24.1) WILD-TYPE
  NO                           60                           276
  YES                           0                             7
[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                      291
                               vv
clus                            HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK  4(2P24.1) MUTATED                                  2
  AMP PEAK  4(2P24.1) WILD-TYPE                                5
D4V9, 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                                   291
  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 263  10   1  17
D4V10, multiclass
    clus
vv   AMP PEAK  4(2P24.1) MUTATED AMP PEAK  4(2P24.1) WILD-TYPE
  R0                          55                           263
  R1                           5                            10
  R2                           0                             1
  RX                           4                            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  4(2P24.1) MUTATED                                  0    21
  AMP PEAK  4(2P24.1) WILD-TYPE                                1   136
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  4(2P24.1) MUTATED                           4    39
  AMP PEAK  4(2P24.1) WILD-TYPE                        13   138
D4V11, 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                                                      136
  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"
D4V12, binary
                               cls
clus                              0   1
  AMP PEAK  4(2P24.1) MUTATED     2  61
  AMP PEAK  4(2P24.1) WILD-TYPE  11 271
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(2P24.1) MUTATED      2   61
  AMP PEAK  4(2P24.1) WILD-TYPE   11  271
                        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                                11
  NOT HISPANIC OR LATINO                           271
[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  29
  AMP PEAK  5(2Q33.1) WILD-TYPE 198 100
  AMP PEAK  5(2Q33.1) MUTATED AMP PEAK  5(2Q33.1) WILD-TYPE 
                           60                           298 
  AMP PEAK  5(2Q33.1) MUTATED AMP PEAK  5(2Q33.1) WILD-TYPE 
                           29                           100 
$`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        17.10        48.99        37.32 
TCGA-BC-A10R TCGA-BC-A10Y TCGA-BC-A217 TCGA-BC-A8YO TCGA-CC-A7IE TCGA-CC-A7IJ 
       10.13        23.38        45.93        18.48         7.13        12.56 
TCGA-CC-A7IK TCGA-CC-A8HV TCGA-DD-A113 TCGA-DD-A11C TCGA-DD-A1E9 TCGA-DD-A1EJ 
        8.61         9.17        79.73        21.76        90.71        33.04 
TCGA-DD-A1EL TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A3A5 TCGA-DD-A3A7 TCGA-DD-A3A9 
       13.64        27.19        55.69       102.74        13.78        30.61 
TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-AA3A TCGA-DD-AACB TCGA-DD-AACH TCGA-DD-AACI 
       22.78         1.45        13.48        76.41         6.41        53.19 
TCGA-DD-AACZ TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADC TCGA-DD-AADF 
        5.62        44.22        22.09        40.08        13.97         3.78 
TCGA-DD-AADJ TCGA-DD-AADO TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AAE6 TCGA-DD-AAEE 
       35.05        14.89        18.21        19.30         4.64        26.63 
TCGA-DD-AAVS TCGA-ED-A7PY TCGA-ED-A82E TCGA-ED-A8O6 TCGA-EP-A2KA TCGA-ES-A2HS 
       59.93        12.82        13.41         1.84        20.61        22.85 
TCGA-FV-A495 TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25W TCGA-G3-A25Z TCGA-G3-A5SM 
        0.03        13.68        51.06        30.74        21.53        17.10 
TCGA-G3-AAV6 TCGA-LG-A6GG TCGA-RC-A7SK TCGA-UB-A7MA TCGA-YA-A8S7 TCGA-ZS-A9CF 
        2.14        12.72        15.52        17.59        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        49.84        47.74        11.74 
TCGA-2Y-A9H7 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 
       38.40        20.81        22.92         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        14.76         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         4.24         2.86         3.19         3.39         4.24 
TCGA-CC-5264 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC 
        3.35         3.32         9.86         9.96        10.36        11.93 
TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7IH 
       11.41         9.99         8.94        21.34         9.83        12.00 
TCGA-CC-A7II TCGA-CC-A7IL TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A9FS TCGA-CC-A9FW 
       13.12         9.14         4.60        11.31         6.94         8.15 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A 
       37.78        83.57        53.33       113.00         7.33         2.60 
TCGA-DD-A11B TCGA-DD-A11D TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED 
        0.46        51.29        79.40        66.31        19.79        75.65 
TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EK 
       11.47        12.95        45.11        49.15         6.02        18.35 
TCGA-DD-A39V TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 
       21.14         5.62        19.76        25.81         7.66        70.06 
TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A6 TCGA-DD-A3A8 TCGA-DD-A4NA TCGA-DD-A4NB 
       17.59        20.12       107.11         0.36        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-A73F 
       80.75        78.84        23.93         9.30        23.05        35.67 
TCGA-DD-A73G TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACC TCGA-DD-AACD 
      114.35         0.53        11.41        75.65        55.40        12.53 
TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL 
       63.48        12.00        15.42        69.11         0.30         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-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-AADD TCGA-DD-AADE TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADK TCGA-DD-AADL 
       40.47        39.52        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-AADV TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 
       18.87        18.25        18.25        18.15        20.98        18.61 
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-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-AAVU TCGA-DD-AAVV TCGA-DD-AAVW TCGA-DD-AAVX 
       89.69        82.62        72.39        80.71        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-A66X TCGA-ED-A66Y 
       29.92        26.93        28.08        13.91        13.35         9.73 
TCGA-ED-A7PX TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A8O5 TCGA-ED-A97K 
        0.20         0.20        14.04        13.15        13.35         0.20 
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-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-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25U 
        6.38        12.03         0.33        81.73         0.39        53.79 
TCGA-G3-A25V TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI 
       28.27        58.49        14.86        22.13        25.64         5.92 
TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A6UC 
       19.53        19.23        25.25        22.95        20.42        22.06 
TCGA-G3-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-A7M9 TCGA-G3-AAUZ 
       14.70        20.78        11.87        14.14         1.84        15.78 
TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 
       15.65        11.80        12.23        13.55         0.89         8.75 
TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 
       11.87        22.92         1.02         2.20         2.99        37.71 
TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K2 
       20.75        17.06        16.83        11.80         2.14        21.60 
TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E 
       31.27        29.79        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 
       22.95        24.56        20.71         7.53        10.85        58.88 
TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SB 
       26.27        17.69        21.01         3.09        21.04        19.33 
TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RG-A7D4 TCGA-T1-A6J8 TCGA-UB-A7MB TCGA-UB-A7MC 
       19.04        15.39        36.10         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-AA44 TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TF 
        0.99        12.99        20.22        24.85        18.28        22.78 
TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D2 
       35.77        25.71        23.21        35.87         0.69        25.15 
TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CG 
       12.99        45.57        40.80        11.21 

  AMP PEAK  5(2Q33.1) MUTATED AMP PEAK  5(2Q33.1) WILD-TYPE 
                         0.03                          0.20 
  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 
                       18.890                        19.775 
[1] "0.0 - 120.8 (18.9)" "0.2 - 114.3 (19.8)"
[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     149       68         1         48
                               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                           149
  STAGE II                            17                            68
  STAGE III                            2                             1
  STAGE IIIA                          12                            48
  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   159  73  57   9
D5V4, multiclass
       clus
vv      AMP PEAK  5(2Q33.1) MUTATED AMP PEAK  5(2Q33.1) WILD-TYPE
  T0+T1                          23                           159
  T2                             19                            73
  T3                             17                            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"
D5V5, binary
                               cls
clus                              0   1
  AMP PEAK  5(2Q33.1) MUTATED    47   1
  AMP PEAK  5(2Q33.1) WILD-TYPE 203   2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(2Q33.1) MUTATED     47    1
  AMP PEAK  5(2Q33.1) WILD-TYPE  203    2
   clus
vv  AMP PEAK  5(2Q33.1) MUTATED AMP PEAK  5(2Q33.1) WILD-TYPE
  0                          47                           203
  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 212   2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(2Q33.1) MUTATED     49    2
  AMP PEAK  5(2Q33.1) WILD-TYPE  212    2
   clus
vv  AMP PEAK  5(2Q33.1) MUTATED AMP PEAK  5(2Q33.1) WILD-TYPE
  0                          49                           212
  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  81 219
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(2Q33.1) MUTATED     34   28
  AMP PEAK  5(2Q33.1) WILD-TYPE   81  219
        clus
vv       AMP PEAK  5(2Q33.1) MUTATED AMP PEAK  5(2Q33.1) WILD-TYPE
  FEMALE                          34                            81
  MALE                            28                           219
[1] 2 2
[1] FALSE
D5V8, binary
                               cls
clus                              0   1
  AMP PEAK  5(2Q33.1) MUTATED    57   0
  AMP PEAK  5(2Q33.1) WILD-TYPE 279   7
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(2Q33.1) MUTATED     57    0
  AMP PEAK  5(2Q33.1) WILD-TYPE  279    7
     clus
vv    AMP PEAK  5(2Q33.1) MUTATED AMP PEAK  5(2Q33.1) WILD-TYPE
  NO                           57                           279
  YES                           0                             7
[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                      293
                               vv
clus                            HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK  5(2Q33.1) MUTATED                                  2
  AMP PEAK  5(2Q33.1) WILD-TYPE                                5
D5V9, 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                                   293
  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 262  11   1  19
D5V10, multiclass
    clus
vv   AMP PEAK  5(2Q33.1) MUTATED AMP PEAK  5(2Q33.1) WILD-TYPE
  R0                          56                           262
  R1                           4                            11
  R2                           0                             1
  RX                           2                            19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  5(2Q33.1) MUTATED                                  0    26
  AMP PEAK  5(2Q33.1) WILD-TYPE                                1   131
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  5(2Q33.1) MUTATED                           1    34
  AMP PEAK  5(2Q33.1) WILD-TYPE                        16   143
D5V11, 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                                                      131
  BLACK OR AFRICAN AMERICAN                                   16
  WHITE                                                      143
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V12, binary
                               cls
clus                              0   1
  AMP PEAK  5(2Q33.1) MUTATED     3  57
  AMP PEAK  5(2Q33.1) WILD-TYPE  10 275
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(2Q33.1) MUTATED      3   57
  AMP PEAK  5(2Q33.1) WILD-TYPE   10  275
                        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                                10
  NOT HISPANIC OR LATINO                           275
[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    43  32
  AMP PEAK  6(3Q26.31) WILD-TYPE 186  97
  AMP PEAK  6(3Q26.31) MUTATED AMP PEAK  6(3Q26.31) WILD-TYPE 
                            75                            283 
  AMP PEAK  6(3Q26.31) MUTATED AMP PEAK  6(3Q26.31) WILD-TYPE 
                            32                             97 
$`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        17.10        10.13        27.52        23.38         1.12 
TCGA-BC-A217 TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BD-A3EP TCGA-BW-A5NO 
       45.93        22.36        17.98        14.60        13.45         0.66 
TCGA-CC-A3MA TCGA-CC-A7IE TCGA-CC-A7IG TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-DD-A114 
        9.96         7.13         9.83        12.56         8.61        37.78 
TCGA-DD-A115 TCGA-DD-A11C TCGA-DD-A1EF TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39Y 
       83.57        21.76        12.95        33.04        13.64         5.62 
TCGA-DD-A3A5 TCGA-DD-A4NI TCGA-DD-A4NV TCGA-DD-A73E TCGA-DD-A73G TCGA-DD-AA3A 
      102.74        26.83        78.84         1.45       114.35        13.48 
TCGA-DD-AACG TCGA-DD-AACL TCGA-DD-AACS TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACZ 
       15.42         3.52        59.31        50.33        46.82         5.62 
TCGA-DD-AAD5 TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADL TCGA-DD-AADN TCGA-DD-AADR 
       44.22        13.97        40.47        20.91        29.52        66.67 
TCGA-DD-AADU TCGA-DD-AAE1 TCGA-DD-AAE6 TCGA-DD-AAE9 TCGA-DD-AAEK TCGA-DD-AAVS 
       18.21        18.15         4.64        23.74        35.08        59.93 
TCGA-DD-AAVV TCGA-DD-AAW0 TCGA-ED-A7PX TCGA-ED-A7PZ TCGA-ED-A82E TCGA-EP-A2KA 
       80.71        66.25         0.20         0.20        13.41        20.61 
TCGA-ES-A2HS TCGA-FV-A3R2 TCGA-FV-A495 TCGA-G3-A25X TCGA-G3-A7M9 TCGA-GJ-A6C0 
       22.85         6.38         0.03        58.49         1.84         1.02 
TCGA-KR-A7K8 TCGA-LG-A9QD TCGA-MI-A75G TCGA-PD-A5DF TCGA-UB-A7MC TCGA-UB-A7MD 
       29.79        12.03        22.95        21.01        16.44         1.71 
TCGA-WJ-A86L TCGA-WX-AA44 TCGA-ZS-A9CF 
       11.34        20.22        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        49.84        18.25        11.74        38.40 
TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-A9VH 
       22.92         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 
       14.76         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         4.24 
TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-5264 TCGA-CC-A1HT 
        2.86         3.19         3.39         4.24         3.35         3.32 
TCGA-CC-A3M9 TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A5UE 
        9.86        10.36        11.93        11.41         9.99         8.94 
TCGA-CC-A7IF TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IL TCGA-CC-A8HT TCGA-CC-A8HU 
       21.34        12.00        13.12         9.14         4.60        11.31 
TCGA-CC-A8HV TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A116 TCGA-DD-A118 
        9.17         6.94         8.15        79.73        53.33       113.00 
TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA 
        7.33         2.60         0.46        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-A39X TCGA-DD-A39Z 
        6.02        18.35        21.14        27.19        55.69        19.76 
TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A6 
       25.81         7.66        70.06        17.59        20.12       107.11 
TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND 
       13.78         0.36        30.61        33.14        32.52        90.28 
TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN 
       30.97        30.15        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-A73F TCGA-DD-AAC8 TCGA-DD-AAC9 
        9.30        23.05        22.78        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-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-AACT TCGA-DD-AACU TCGA-DD-AACX 
       61.68        13.64        14.20        51.35        51.52         5.59 
TCGA-DD-AACY TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD6 
       47.67         4.50        18.54        21.63        42.58        22.09 
TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG 
       40.08        40.54        40.83        39.52         3.78        37.64 
TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADM TCGA-DD-AADO TCGA-DD-AADP 
       35.67        35.05        34.49         0.39        14.89        15.06 
TCGA-DD-AADQ TCGA-DD-AADS TCGA-DD-AADV TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 
       14.33        15.58        18.87        19.30        18.25        18.25 
TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEA 
       20.98        18.61        19.99        21.17        21.83        18.90 
TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAEI 
       15.72        25.08        26.63        23.64        25.78        50.33 
TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVX 
       79.07        89.69        82.62        72.39        76.18        56.48 
TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 
       64.77        62.47        65.39        49.48        53.69        29.92 
TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PY 
       26.93        28.08        13.91        13.35         9.73        12.82 
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-A2HT 
       19.99        19.59         0.62         9.96        11.93        14.40 
TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R3 
       60.89        23.97        19.10        27.88         8.12        12.03 
TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U 
        0.33        81.73         0.39        13.68        51.06        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-A5SM TCGA-G3-A6UC TCGA-G3-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 
       17.10        22.06        14.70        20.78        11.87        14.14 
TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 
       15.78        15.65        11.80        12.23        13.55         0.89 
TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A9DB TCGA-HP-A5MZ 
        8.75         2.14        11.87        22.92         2.20         2.99 
TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 
       37.71        20.75        17.06        16.83        11.80         2.14 
TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-LG-A9QC TCGA-MI-A75C TCGA-MI-A75E 
       21.60        31.27        12.72        13.97         9.57        16.67 
TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF 
       24.56        20.71         7.53        10.85        58.88        26.27 
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-RG-A7D4 TCGA-T1-A6J8 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7ME 
       15.52        36.10         0.76        17.59        19.76        15.98 
TCGA-UB-A7MF TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA46 
        7.04        10.75        10.32         0.99        12.99        24.85 
TCGA-WX-AA47 TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ 
       18.28        22.78        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 
       35.87         0.69        25.15        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                           0.20 
  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 
                         20.22                          19.76 
[1] "0.0 - 120.8 (20.2)" "0.2 - 113.0 (19.8)"
[1] "hr=" "1.2"
D6V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IIIA
  AMP PEAK  6(3Q26.31) MUTATED        32       23         1         12
  AMP PEAK  6(3Q26.31) WILD-TYPE     139       62         2         48
                                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                              32                            139
  STAGE II                             23                             62
  STAGE III                             1                              2
  STAGE IIIA                           12                             48
  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      34  23  16   3
  AMP PEAK  6(3Q26.31) WILD-TYPE   148  69  58   9
D6V4, multiclass
       clus
vv      AMP PEAK  6(3Q26.31) MUTATED AMP PEAK  6(3Q26.31) WILD-TYPE
  T0+T1                           34                            148
  T2                              23                             69
  T3                              16                             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"
D6V5, binary
                                cls
clus                               0   1
  AMP PEAK  6(3Q26.31) MUTATED    48   1
  AMP PEAK  6(3Q26.31) WILD-TYPE 202   2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  6(3Q26.31) MUTATED     48    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                           48                            202
  1                            1                              2
[1] 2 2
[1] FALSE
D6V6, binary
                                cls
clus                               0   1
  AMP PEAK  6(3Q26.31) MUTATED    53   0
  AMP PEAK  6(3Q26.31) WILD-TYPE 208   4
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  6(3Q26.31) MUTATED     53    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                           53                            208
  1                            0                              4
[1] 2 2
[1] FALSE
D6V7, binary
                                cls
clus                               0   1
  AMP PEAK  6(3Q26.31) MUTATED    23  53
  AMP PEAK  6(3Q26.31) WILD-TYPE  92 194
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  6(3Q26.31) MUTATED     23   53
  AMP PEAK  6(3Q26.31) WILD-TYPE   92  194
        clus
vv       AMP PEAK  6(3Q26.31) MUTATED AMP PEAK  6(3Q26.31) WILD-TYPE
  FEMALE                           23                             92
  MALE                             53                            194
[1] 2 2
[1] FALSE
D6V8, binary
                                cls
clus                               0   1
  AMP PEAK  6(3Q26.31) MUTATED    71   1
  AMP PEAK  6(3Q26.31) WILD-TYPE 265   6
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  6(3Q26.31) MUTATED     71    1
  AMP PEAK  6(3Q26.31) WILD-TYPE  265    6
     clus
vv    AMP PEAK  6(3Q26.31) MUTATED AMP PEAK  6(3Q26.31) WILD-TYPE
  NO                            71                            265
  YES                            1                              6
[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                         74
  AMP PEAK  6(3Q26.31) WILD-TYPE                      279
                                vv
clus                             HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK  6(3Q26.31) MUTATED                                  2
  AMP PEAK  6(3Q26.31) WILD-TYPE                                5
D6V9, multiclass
                                  clus
vv                                 AMP PEAK  6(3Q26.31) MUTATED
  FIBROLAMELLAR CARCINOMA                                     0
  HEPATOCELLULAR CARCINOMA                                   74
  HEPATOCHOLANGIOCARCINOMA (MIXED)                            2
                                  clus
vv                                 AMP PEAK  6(3Q26.31) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                       2
  HEPATOCELLULAR CARCINOMA                                    279
  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    67   2   0   6
  AMP PEAK  6(3Q26.31) WILD-TYPE 251  13   1  15
D6V10, multiclass
    clus
vv   AMP PEAK  6(3Q26.31) MUTATED AMP PEAK  6(3Q26.31) WILD-TYPE
  R0                           67                            251
  R1                            2                             13
  R2                            0                              1
  RX                            6                             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  6(3Q26.31) MUTATED                                  0    31
  AMP PEAK  6(3Q26.31) WILD-TYPE                                1   126
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  6(3Q26.31) MUTATED                           7    37
  AMP PEAK  6(3Q26.31) WILD-TYPE                        10   140
D6V11, multiclass
                                  clus
vv                                 AMP PEAK  6(3Q26.31) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                      31
  BLACK OR AFRICAN AMERICAN                                   7
  WHITE                                                      37
                                  clus
vv                                 AMP PEAK  6(3Q26.31) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                       126
  BLACK OR AFRICAN AMERICAN                                    10
  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"
D6V12, binary
                                cls
clus                               0   1
  AMP PEAK  6(3Q26.31) MUTATED     4  69
  AMP PEAK  6(3Q26.31) WILD-TYPE   9 263
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  6(3Q26.31) MUTATED      4   69
  AMP PEAK  6(3Q26.31) WILD-TYPE    9  263
                        clus
vv                       AMP PEAK  6(3Q26.31) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                           69
                        clus
vv                       AMP PEAK  6(3Q26.31) WILD-TYPE
  HISPANIC OR LATINO                                  9
  NOT HISPANIC OR LATINO                            263
[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    36  15
  AMP PEAK  7(4P14) WILD-TYPE 193 114
  AMP PEAK  7(4P14) MUTATED AMP PEAK  7(4P14) WILD-TYPE 
                         51                         307 
  AMP PEAK  7(4P14) MUTATED AMP PEAK  7(4P14) WILD-TYPE 
                         15                         114 
$`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        49.84        11.74        20.81 
TCGA-BC-A10R TCGA-BC-A217 TCGA-BC-A5W4 TCGA-BD-A3EP TCGA-CC-5261 TCGA-CC-A3M9 
       10.13        45.93        17.98        13.45         3.19         9.86 
TCGA-CC-A3MB TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A8HV TCGA-CC-A9FS TCGA-DD-A113 
       10.36         9.83        12.00         9.17         6.94        79.73 
TCGA-DD-A118 TCGA-DD-A11A TCGA-DD-A1EC TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A4NN 
      113.00         2.60        19.79        49.15         6.02        29.56 
TCGA-DD-A73G TCGA-DD-AACG TCGA-DD-AACI TCGA-DD-AACM TCGA-DD-AAD3 TCGA-DD-AADB 
      114.35        15.42        53.19        58.16        42.58        40.83 
TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADR TCGA-DD-AAED TCGA-DD-AAVR TCGA-DD-AAVS 
       14.89        15.06        66.67        25.08        82.62        59.93 
TCGA-ED-A66X TCGA-ED-A7PZ TCGA-ED-A82E TCGA-ED-A8O5 TCGA-EP-A2KA TCGA-FV-A2QR 
       13.35         0.20        13.41        13.35        20.61        19.10 
TCGA-G3-A3CG TCGA-G3-A7M9 TCGA-K7-AAU7 TCGA-LG-A6GG TCGA-QA-A7B7 TCGA-RC-A7SK 
       22.13         1.84        11.80        12.72         3.09        15.52 
TCGA-T1-A6J8 TCGA-WQ-A9G7 TCGA-ZS-A9CF 
        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        38.40        22.92 
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        17.10        14.76         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 
       23.38         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-5264 
        0.66         4.24         2.86         3.39         4.24         3.35 
TCGA-CC-A1HT TCGA-CC-A3MA TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A5UE 
        3.32         9.96        11.93        11.41         9.99         8.94 
TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A7IL 
        7.13        21.34        13.12        12.56         8.61         9.14 
TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A9FW TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 
        4.60        11.31         8.15        37.78        83.57        53.33 
TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA 
        7.33         0.46        21.76        51.29        90.71        79.40 
TCGA-DD-A1EB TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EJ 
       66.31        75.65        11.47        12.95        45.11        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-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-A4NJ 
       32.52        90.28        30.97        30.15        26.83        30.51 
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-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-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-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP 
       69.11         0.30         3.52        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-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 
        5.59        47.67         5.62         4.50        18.54        21.63 
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-AADF TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK 
       39.52         3.78        37.64        35.67        35.05        34.49 
TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADQ TCGA-DD-AADS TCGA-DD-AADU 
       20.91         0.39        29.52        14.33        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-AAEG TCGA-DD-AAEH TCGA-DD-AAEI 
       18.90        15.72        26.63        23.64        25.78        50.33 
TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVU TCGA-DD-AAVV TCGA-DD-AAVW 
       35.08        79.07        89.69        72.39        80.71        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-A66Y 
       53.69        29.92        26.93        28.08        13.91         9.73 
TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A8O6 TCGA-ED-A97K 
        0.20        12.82        14.04        13.15         1.84         0.20 
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-A3I0 TCGA-FV-A3I1 
       22.85        14.40        60.89        23.97        27.88         8.12 
TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ 
        6.38        12.03         0.03         0.33        81.73         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-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
       14.86        21.53        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-A7M5 
       25.25        22.95        20.42        17.10        22.06        14.70 
TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 
       20.78        11.87        14.14        15.78        15.65        11.80 
TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 
       12.23        13.55         0.89         8.75         2.14        11.87 
TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF 
       22.92         1.02         2.20         2.99        37.71        20.75 
TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-KR-A7K8 
       17.06        16.83         2.14        21.60        31.27        29.79 
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        22.95        24.56 
TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V 
       20.71         7.53        10.85        58.88        26.27        17.69 
TCGA-PD-A5DF TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RG-A7D4 
       21.01        21.04        19.33        19.04        15.39        36.10 
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-AA0U TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-WX-AA46 
       10.75        10.32        11.34        12.99        20.22        24.85 
TCGA-WX-AA47 TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ 
       18.28        22.78        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 
       35.87         0.69        25.15        12.99        45.57        40.80 
TCGA-ZS-A9CG 
       11.21 

  AMP PEAK  7(4P14) MUTATED AMP PEAK  7(4P14) WILD-TYPE 
                       0.20                        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 
                      15.52                       19.99 
[1] "0.2 - 114.3 (15.5)" "0.0 - 120.8 (20.0)"
[1] "hr=" "1.4"
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     151       67         2         51          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                         151
  STAGE II                          18                          67
  STAGE III                          1                           2
  STAGE IIIA                         9                          51
  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   160  75  61  12
D7V4, multiclass
       clus
vv      AMP PEAK  7(4P14) MUTATED AMP PEAK  7(4P14) WILD-TYPE
  T0+T1                        22                         160
  T2                           17                          75
  T3                           13                          61
  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 215   3
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  7(4P14) MUTATED     35    0
  AMP PEAK  7(4P14) WILD-TYPE  215    3
   clus
vv  AMP PEAK  7(4P14) MUTATED AMP PEAK  7(4P14) WILD-TYPE
  0                        35                         215
  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 221   4
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  7(4P14) MUTATED     40    0
  AMP PEAK  7(4P14) WILD-TYPE  221    4
   clus
vv  AMP PEAK  7(4P14) MUTATED AMP PEAK  7(4P14) WILD-TYPE
  0                        40                         221
  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  95 215
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  7(4P14) MUTATED     20   32
  AMP PEAK  7(4P14) WILD-TYPE   95  215
        clus
vv       AMP PEAK  7(4P14) MUTATED AMP PEAK  7(4P14) WILD-TYPE
  FEMALE                        20                          95
  MALE                          32                         215
[1] 2 2
[1] FALSE
D7V8, binary
                             cls
clus                            0   1
  AMP PEAK  7(4P14) MUTATED    48   0
  AMP PEAK  7(4P14) WILD-TYPE 288   7
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  7(4P14) MUTATED     48    0
  AMP PEAK  7(4P14) WILD-TYPE  288    7
     clus
vv    AMP PEAK  7(4P14) MUTATED AMP PEAK  7(4P14) WILD-TYPE
  NO                         48                         288
  YES                         0                           7
[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                      302
                             vv
clus                          HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK  7(4P14) MUTATED                                  1
  AMP PEAK  7(4P14) WILD-TYPE                                6
D7V9, 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                                 302
  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 273  13   1  16
D7V10, multiclass
    clus
vv   AMP PEAK  7(4P14) MUTATED AMP PEAK  7(4P14) WILD-TYPE
  R0                        45                         273
  R1                         2                          13
  R2                         0                           1
  RX                         5                          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  7(4P14) MUTATED                                  0    25
  AMP PEAK  7(4P14) WILD-TYPE                                1   132
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  7(4P14) MUTATED                           3    24
  AMP PEAK  7(4P14) WILD-TYPE                        14   153
D7V11, 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                                                    132
  BLACK OR AFRICAN AMERICAN                                 14
  WHITE                                                    153
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V12, binary
                             cls
clus                            0   1
  AMP PEAK  7(4P14) MUTATED     1  50
  AMP PEAK  7(4P14) WILD-TYPE  12 282
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  7(4P14) MUTATED      1   50
  AMP PEAK  7(4P14) WILD-TYPE   12  282
                        clus
vv                       AMP PEAK  7(4P14) MUTATED AMP PEAK  7(4P14) WILD-TYPE
  HISPANIC OR LATINO                             1                          12
  NOT HISPANIC OR LATINO                        50                         282
[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  67
  AMP PEAK  8(5P15.33) WILD-TYPE 137  62
  AMP PEAK  8(5P15.33) MUTATED AMP PEAK  8(5P15.33) WILD-TYPE 
                           159                            199 
  AMP PEAK  8(5P15.33) MUTATED AMP PEAK  8(5P15.33) WILD-TYPE 
                            67                             62 
$`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 
       49.84        47.74        20.81        22.92         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        45.93        22.36        18.48        13.45 
TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5263 TCGA-CC-5264 TCGA-CC-A1HT TCGA-CC-A3M9 
        0.66         4.24         4.24         3.35         3.32         9.86 
TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A7IG TCGA-CC-A7II 
       10.36        11.93        11.41         9.99         9.83        13.12 
TCGA-CC-A7IJ TCGA-CC-A7IL TCGA-CC-A8HU TCGA-CC-A9FW TCGA-DD-A115 TCGA-DD-A116 
       12.56         9.14        11.31         8.15        83.57        53.33 
TCGA-DD-A118 TCGA-DD-A11A TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EE 
      113.00         2.60        51.29        90.71        79.40        11.47 
TCGA-DD-A1EF TCGA-DD-A1EI TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y 
       12.95         6.02        13.64        21.14        55.69         5.62 
TCGA-DD-A3A1 TCGA-DD-A3A3 TCGA-DD-A3A5 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A4ND 
        7.66        17.59       102.74        13.78         0.36        90.28 
TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NO TCGA-DD-A4NV TCGA-DD-A73C TCGA-DD-A73G 
       30.51        39.78        73.81        78.84        23.05       114.35 
TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AACA TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACI 
       13.48         0.53        75.65        12.00        15.42        53.19 
TCGA-DD-AACJ TCGA-DD-AACP TCGA-DD-AACT TCGA-DD-AACV TCGA-DD-AACY TCGA-DD-AACZ 
       69.11        13.64        51.35        50.33        47.67         5.62 
TCGA-DD-AAD2 TCGA-DD-AAD5 TCGA-DD-AAD8 TCGA-DD-AADC TCGA-DD-AADF TCGA-DD-AADG 
       21.63        44.22        40.08        13.97         3.78        37.64 
TCGA-DD-AADN TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADU TCGA-DD-AADV TCGA-DD-AAE2 
       29.52        14.33        66.67        18.21        18.87        20.98 
TCGA-DD-AAE3 TCGA-DD-AAE6 TCGA-DD-AAEA TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEK 
       18.61         4.64        18.90        26.63        23.64        35.08 
TCGA-DD-AAVU TCGA-DD-AAVV TCGA-DD-AAVY TCGA-DD-AAW2 TCGA-ED-A459 TCGA-ED-A66X 
       72.39        80.71        64.77        49.48        29.92        13.35 
TCGA-ED-A66Y TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O6 TCGA-EP-A2KB 
        9.73        14.04        13.15        13.41         1.84        19.59 
TCGA-EP-A2KC TCGA-EP-A3JL TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR 
        0.62         9.96        14.40        60.89        23.97        19.10 
TCGA-FV-A3I0 TCGA-FV-A495 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T 
       27.88         0.03        81.73         0.39        13.68        51.06 
TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A3CG TCGA-G3-A3CJ TCGA-G3-A5SI TCGA-G3-A5SM 
       30.74        58.49        22.13        19.53        25.25        17.10 
TCGA-G3-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV1 TCGA-G3-AAV2 
       14.70        20.78         1.84        15.78        11.80        12.23 
TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-KR-A7K2 
        8.75         2.14        11.87         2.20         2.99        21.60 
TCGA-LG-A6GG TCGA-LG-A9QC TCGA-MI-A75G TCGA-MI-A75I TCGA-NI-A4U2 TCGA-O8-A75V 
       12.72        13.97        22.95        20.71        58.88        17.69 
TCGA-PD-A5DF TCGA-RC-A7SF TCGA-RG-A7D4 TCGA-UB-A7ME TCGA-UB-A7MF TCGA-UB-AA0U 
       21.01        19.04        36.10        15.98         7.04        10.75 
TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA47 TCGA-XR-A8TF TCGA-ZP-A9CZ TCGA-ZP-A9D1 
        0.99        12.99        18.28        22.78        23.21         0.69 
TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CE 
       25.15        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        38.40         8.61        10.59         0.66        17.10 
TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10S TCGA-BC-A10T 
       14.76         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        23.38        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-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IH 
        3.39         9.96         8.94         7.13        21.34        12.00 
TCGA-CC-A7IK TCGA-CC-A8HT TCGA-CC-A8HV TCGA-CC-A9FS TCGA-DD-A113 TCGA-DD-A114 
        8.61         4.60         9.17         6.94        79.73        37.78 
TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED 
        7.33         0.46        21.76        66.31        19.79        75.65 
TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A39W TCGA-DD-A39Z 
       45.11        49.15        33.04        18.35        27.19        19.76 
TCGA-DD-A3A0 TCGA-DD-A3A2 TCGA-DD-A3A4 TCGA-DD-A3A6 TCGA-DD-A3A9 TCGA-DD-A4NA 
       25.81        70.06        20.12       107.11        30.61        33.14 
TCGA-DD-A4NB TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NL TCGA-DD-A4NN 
       32.52        30.97        30.15        26.83        56.25        29.56 
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-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-AAC9 TCGA-DD-AACB TCGA-DD-AACC 
       22.78         1.45        35.67        11.41        76.41        55.40 
TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACH TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM 
       12.53        63.48         6.41         0.30         3.52        58.16 
TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACW 
       42.81        61.68        14.20        59.31        51.52        46.82 
TCGA-DD-AACX TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD3 TCGA-DD-AAD6 TCGA-DD-AADA 
        5.59         4.50        18.54        42.58        22.09        40.54 
TCGA-DD-AADB TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK 
       40.83        40.47        39.52        35.67        35.05        34.49 
TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADS TCGA-DD-AADW 
       20.91         0.39        14.89        15.06        15.58        19.30 
TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE4 TCGA-DD-AAE7 TCGA-DD-AAE8 
       18.25        18.25        18.15        19.99        21.17        21.83 
TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAVP 
       23.74        15.72        25.08        25.78        50.33        79.07 
TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVZ 
       89.69        82.62        59.93        76.18        56.48        62.47 
TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW3 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 
       66.25        65.39        53.69        26.93        28.08        13.91 
TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A8O5 TCGA-ED-A97K TCGA-EP-A12J 
        0.20        12.82         0.20        13.35         0.20        18.74 
TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A3RK TCGA-ES-A2HS TCGA-FV-A3I1 TCGA-FV-A3R2 
       19.99        20.61        11.93        22.85         8.12         6.38 
TCGA-FV-A3R3 TCGA-FV-A496 TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25Y TCGA-G3-A25Z 
       12.03         0.33        53.79        28.27        14.86        21.53 
TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CK TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A6UC 
       25.64         5.92        19.23        22.95        20.42        22.06 
TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAV0 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-GJ-A3OU 
       11.87        14.14        15.65        13.55         0.89        22.92 
TCGA-GJ-A6C0 TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 
        1.02        37.71        20.75        17.06        16.83        11.80 
TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E 
        2.14        31.27        29.79        12.03         9.57        16.67 
TCGA-MI-A75H TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A8LF TCGA-QA-A7B7 TCGA-RC-A7S9 
       24.56         7.53        10.85        26.27         3.09        21.04 
TCGA-RC-A7SB TCGA-RC-A7SH TCGA-RC-A7SK TCGA-T1-A6J8 TCGA-UB-A7MA TCGA-UB-A7MB 
       19.33        15.39        15.52         0.76        17.59        19.76 
TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WX-AA44 TCGA-WX-AA46 
       16.44         1.71        10.32        11.34        20.22        24.85 
TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9D0 TCGA-ZS-A9CD TCGA-ZS-A9CF 
       13.55        35.77        25.71        35.87        45.57        79.30 
TCGA-ZS-A9CG 
       11.21 

  AMP PEAK  8(5P15.33) MUTATED AMP PEAK  8(5P15.33) WILD-TYPE 
                          0.03                           0.20 
  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 
                         18.28                          20.75 
[1] "0.0 - 120.8 (18.3)" "0.2 - 108.8 (20.8)"
[1] "hr=" "1.4"
D8V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IIIA
  AMP PEAK  8(5P15.33) MUTATED        64       42         1         35
  AMP PEAK  8(5P15.33) WILD-TYPE     107       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                              64                            107
  STAGE II                             42                             43
  STAGE III                             1                              2
  STAGE IIIA                           35                             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      69  45  43   4
  AMP PEAK  8(5P15.33) WILD-TYPE   113  47  31   8
D8V4, multiclass
       clus
vv      AMP PEAK  8(5P15.33) MUTATED AMP PEAK  8(5P15.33) WILD-TYPE
  T0+T1                           69                            113
  T2                              45                             47
  T3                              43                             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   110   1
  AMP PEAK  8(5P15.33) WILD-TYPE 140   2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  8(5P15.33) MUTATED    110    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                          110                            140
  1                            1                              2
[1] 2 2
[1] FALSE
D8V6, binary
                                cls
clus                               0   1
  AMP PEAK  8(5P15.33) MUTATED   117   1
  AMP PEAK  8(5P15.33) WILD-TYPE 144   3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  8(5P15.33) MUTATED    117    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                          117                            144
  1                            1                              3
[1] 2 2
[1] FALSE
D8V7, binary
                                cls
clus                               0   1
  AMP PEAK  8(5P15.33) MUTATED    50 111
  AMP PEAK  8(5P15.33) WILD-TYPE  65 136
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  8(5P15.33) MUTATED     50  111
  AMP PEAK  8(5P15.33) WILD-TYPE   65  136
        clus
vv       AMP PEAK  8(5P15.33) MUTATED AMP PEAK  8(5P15.33) WILD-TYPE
  FEMALE                           50                             65
  MALE                            111                            136
[1] 2 2
[1] FALSE
D8V8, binary
                                cls
clus                               0   1
  AMP PEAK  8(5P15.33) MUTATED   148   5
  AMP PEAK  8(5P15.33) WILD-TYPE 188   2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  8(5P15.33) MUTATED    148    5
  AMP PEAK  8(5P15.33) WILD-TYPE  188    2
     clus
vv    AMP PEAK  8(5P15.33) MUTATED AMP PEAK  8(5P15.33) WILD-TYPE
  NO                           148                            188
  YES                            5                              2
[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                        158
  AMP PEAK  8(5P15.33) WILD-TYPE                      195
                                vv
clus                             HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK  8(5P15.33) MUTATED                                  3
  AMP PEAK  8(5P15.33) WILD-TYPE                                4
D8V9, multiclass
                                  clus
vv                                 AMP PEAK  8(5P15.33) MUTATED
  FIBROLAMELLAR CARCINOMA                                     0
  HEPATOCELLULAR CARCINOMA                                  158
  HEPATOCHOLANGIOCARCINOMA (MIXED)                            3
                                  clus
vv                                 AMP PEAK  8(5P15.33) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                       2
  HEPATOCELLULAR CARCINOMA                                    195
  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   143   7   0   8
  AMP PEAK  8(5P15.33) WILD-TYPE 175   8   1  13
D8V10, multiclass
    clus
vv   AMP PEAK  8(5P15.33) MUTATED AMP PEAK  8(5P15.33) WILD-TYPE
  R0                          143                            175
  R1                            7                              8
  R2                            0                              1
  RX                            8                             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  8(5P15.33) MUTATED                                  1    69
  AMP PEAK  8(5P15.33) WILD-TYPE                                0    88
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  8(5P15.33) MUTATED                          10    75
  AMP PEAK  8(5P15.33) WILD-TYPE                         7   102
D8V11, multiclass
                                  clus
vv                                 AMP PEAK  8(5P15.33) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                      69
  BLACK OR AFRICAN AMERICAN                                  10
  WHITE                                                      75
                                  clus
vv                                 AMP PEAK  8(5P15.33) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                        88
  BLACK OR AFRICAN AMERICAN                                     7
  WHITE                                                       102
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V12, binary
                                cls
clus                               0   1
  AMP PEAK  8(5P15.33) MUTATED     7 147
  AMP PEAK  8(5P15.33) WILD-TYPE   6 185
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  8(5P15.33) MUTATED      7  147
  AMP PEAK  8(5P15.33) WILD-TYPE    6  185
                        clus
vv                       AMP PEAK  8(5P15.33) MUTATED
  HISPANIC OR LATINO                                7
  NOT HISPANIC OR LATINO                          147
                        clus
vv                       AMP PEAK  8(5P15.33) WILD-TYPE
  HISPANIC OR LATINO                                  6
  NOT HISPANIC OR LATINO                            185
[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    78  54
  AMP PEAK  9(5Q35.3) WILD-TYPE 151  75
  AMP PEAK  9(5Q35.3) MUTATED AMP PEAK  9(5Q35.3) WILD-TYPE 
                          132                           226 
  AMP PEAK  9(5Q35.3) MUTATED AMP PEAK  9(5Q35.3) WILD-TYPE 
                           54                            75 
$`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        49.84        47.74        11.74 
TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-BC-A10Q 
       22.92         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        45.93         3.32 
TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A7IG TCGA-CC-A7IL TCGA-CC-A8HU 
       10.36        11.93        11.41         9.83         9.14        11.31 
TCGA-CC-A9FW TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11D 
        8.15        83.57        53.33       113.00         7.33        51.29 
TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EE TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39X 
       90.71        79.40        11.47        21.14        27.19        55.69 
TCGA-DD-A39Y TCGA-DD-A3A1 TCGA-DD-A3A3 TCGA-DD-A3A5 TCGA-DD-A3A7 TCGA-DD-A3A8 
        5.62         7.66        17.59       102.74        13.78         0.36 
TCGA-DD-A4ND TCGA-DD-A4NK TCGA-DD-A4NO TCGA-DD-A4NR TCGA-DD-A4NV TCGA-DD-A73A 
       90.28        39.78        73.81         0.30        78.84        23.93 
TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACF 
      114.35        13.48         0.53        55.40        12.53        12.00 
TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACP TCGA-DD-AACT 
       15.42         6.41        53.19        69.11        13.64        51.35 
TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AADC TCGA-DD-AADE 
       47.67         5.62        18.54        21.63        13.97        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-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADV TCGA-DD-AAE0 
       14.33        66.67        15.58        18.21        18.87        18.25 
TCGA-DD-AAE1 TCGA-DD-AAE3 TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEK TCGA-DD-AAVP 
       18.15        18.61        26.63        23.64        35.08        79.07 
TCGA-DD-AAVR TCGA-DD-AAVU TCGA-DD-AAVV TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAW0 
       82.62        72.39        80.71        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-A7M5 
       13.68        51.06        30.74        22.13        17.10        14.70 
TCGA-G3-AAV1 TCGA-G3-AAV5 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-K7-AAU7 TCGA-KR-A7K2 
       11.80         8.75         2.20         2.99        11.80        21.60 
TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75G TCGA-MI-A75I 
       12.72        13.97        12.03         9.57        22.95        20.71 
TCGA-NI-A8LF TCGA-O8-A75V TCGA-RC-A7SF TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-WQ-A9G7 
       26.27        17.69        19.04        36.10        17.59         0.99 
TCGA-WQ-AB4B TCGA-WX-AA47 TCGA-XR-A8TF TCGA-ZP-A9CZ TCGA-ZP-A9D1 TCGA-ZS-A9CE 
       12.99        18.28        22.78        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        38.40        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        17.10        14.76         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        23.38 
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-5264 
        4.24         2.86         3.19         3.39         4.24         3.35 
TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IF 
        9.86         9.96         9.99         8.94         7.13        21.34 
TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A8HT TCGA-CC-A8HV 
       12.00        13.12        12.56         8.61         4.60         9.17 
TCGA-CC-A9FS TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C 
        6.94        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 
       29.92        26.93        28.08        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-A7M8 TCGA-G3-A7M9 TCGA-G3-AAUZ 
       22.06        20.78        11.87        14.14         1.84        15.78 
TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV6 TCGA-G3-AAV7 
       15.65        12.23        13.55         0.89         2.14        11.87 
TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 
       22.92         1.02        37.71        20.75        17.06        16.83 
TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-MI-A75E TCGA-MI-A75H TCGA-MR-A520 
        2.14        31.27        29.79        16.67        24.56         7.53 
TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SB 
       10.85        58.88        21.01         3.09        21.04        19.33 
TCGA-RC-A7SH TCGA-RC-A7SK TCGA-T1-A6J8 TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD 
       15.39        15.52         0.76        19.76        16.44         1.71 
TCGA-UB-A7ME TCGA-UB-A7MF TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WX-AA44 
       15.98         7.04        10.75        10.32        11.34        20.22 
TCGA-WX-AA46 TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9D0 TCGA-ZP-A9D2 
       24.85        13.55        35.77        25.71        35.87        25.15 
TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CF TCGA-ZS-A9CG 
       12.99        45.57        79.30        11.21 

  AMP PEAK  9(5Q35.3) MUTATED AMP PEAK  9(5Q35.3) WILD-TYPE 
                         0.03                          0.20 
  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 
                        18.41                         20.17 
[1] "0.0 - 114.3 (18.4)" "0.2 - 120.8 (20.2)"
[1] "hr=" "1.2"
D9V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IIIA
  AMP PEAK  9(5Q35.3) MUTATED        62       34         2         22
  AMP PEAK  9(5Q35.3) WILD-TYPE     109       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                             62                           109
  STAGE II                            34                            51
  STAGE III                            2                             1
  STAGE IIIA                          22                            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      64  37  30   3
  AMP PEAK  9(5Q35.3) WILD-TYPE   118  55  44   9
D9V4, multiclass
       clus
vv      AMP PEAK  9(5Q35.3) MUTATED AMP PEAK  9(5Q35.3) WILD-TYPE
  T0+T1                          64                           118
  T2                             37                            55
  T3                             30                            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    92   0
  AMP PEAK  9(5Q35.3) WILD-TYPE 158   3
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  9(5Q35.3) MUTATED     92    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                          92                           158
  1                           0                             3
[1] 2 2
[1] FALSE
D9V6, binary
                               cls
clus                              0   1
  AMP PEAK  9(5Q35.3) MUTATED    99   2
  AMP PEAK  9(5Q35.3) WILD-TYPE 162   2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  9(5Q35.3) MUTATED     99    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                          99                           162
  1                           2                             2
[1] 2 2
[1] FALSE
D9V7, binary
                               cls
clus                              0   1
  AMP PEAK  9(5Q35.3) MUTATED    38  96
  AMP PEAK  9(5Q35.3) WILD-TYPE  77 151
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  9(5Q35.3) MUTATED     38   96
  AMP PEAK  9(5Q35.3) WILD-TYPE   77  151
        clus
vv       AMP PEAK  9(5Q35.3) MUTATED AMP PEAK  9(5Q35.3) WILD-TYPE
  FEMALE                          38                            77
  MALE                            96                           151
[1] 2 2
[1] FALSE
D9V8, binary
                               cls
clus                              0   1
  AMP PEAK  9(5Q35.3) MUTATED   123   4
  AMP PEAK  9(5Q35.3) WILD-TYPE 213   3
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  9(5Q35.3) MUTATED    123    4
  AMP PEAK  9(5Q35.3) WILD-TYPE  213    3
     clus
vv    AMP PEAK  9(5Q35.3) MUTATED AMP PEAK  9(5Q35.3) WILD-TYPE
  NO                          123                           213
  YES                           4                             3
[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                        129
  AMP PEAK  9(5Q35.3) WILD-TYPE                      224
                               vv
clus                            HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK  9(5Q35.3) MUTATED                                  5
  AMP PEAK  9(5Q35.3) WILD-TYPE                                2
D9V9, multiclass
                                  clus
vv                                 AMP PEAK  9(5Q35.3) MUTATED
  FIBROLAMELLAR CARCINOMA                                    0
  HEPATOCELLULAR CARCINOMA                                 129
  HEPATOCHOLANGIOCARCINOMA (MIXED)                           5
                                  clus
vv                                 AMP PEAK  9(5Q35.3) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                      2
  HEPATOCELLULAR CARCINOMA                                   224
  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   119   8   1   4
  AMP PEAK  9(5Q35.3) WILD-TYPE 199   7   0  17
D9V10, multiclass
    clus
vv   AMP PEAK  9(5Q35.3) MUTATED AMP PEAK  9(5Q35.3) WILD-TYPE
  R0                         119                           199
  R1                           8                             7
  R2                           1                             0
  RX                           4                            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  9(5Q35.3) MUTATED                                  0    62
  AMP PEAK  9(5Q35.3) WILD-TYPE                                1    95
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  9(5Q35.3) MUTATED                           6    61
  AMP PEAK  9(5Q35.3) WILD-TYPE                        11   116
D9V11, multiclass
                                  clus
vv                                 AMP PEAK  9(5Q35.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                     62
  BLACK OR AFRICAN AMERICAN                                  6
  WHITE                                                     61
                                  clus
vv                                 AMP PEAK  9(5Q35.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                       95
  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"
D9V12, binary
                               cls
clus                              0   1
  AMP PEAK  9(5Q35.3) MUTATED     6 121
  AMP PEAK  9(5Q35.3) WILD-TYPE   7 211
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  9(5Q35.3) MUTATED      6  121
  AMP PEAK  9(5Q35.3) WILD-TYPE    7  211
                        clus
vv                       AMP PEAK  9(5Q35.3) MUTATED
  HISPANIC OR LATINO                               6
  NOT HISPANIC OR LATINO                         121
                        clus
vv                       AMP PEAK  9(5Q35.3) WILD-TYPE
  HISPANIC OR LATINO                                 7
  NOT HISPANIC OR LATINO                           211
[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    89  61
  AMP PEAK 10(6P25.2) WILD-TYPE 140  68
  AMP PEAK 10(6P25.2) MUTATED AMP PEAK 10(6P25.2) WILD-TYPE 
                          150                           208 
  AMP PEAK 10(6P25.2) MUTATED AMP PEAK 10(6P25.2) WILD-TYPE 
                           61                            68 
$`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        49.84 
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        17.10        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        45.93        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-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IG 
        4.24        10.36        11.93         8.94         7.13         9.83 
TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IK TCGA-CC-A7IL TCGA-CC-A8HU TCGA-DD-A114 
       12.00        13.12         8.61         9.14        11.31        37.78 
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-A1EG TCGA-DD-A1EH TCGA-DD-A1EJ TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z 
       45.11        49.15        33.04        55.69         5.62        19.76 
TCGA-DD-A3A5 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NH TCGA-DD-A4NJ 
      102.74        13.78         0.36        30.61        30.15        30.51 
TCGA-DD-A4NK TCGA-DD-A4NN TCGA-DD-A4NS TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-AAC8 
       39.78        29.56        80.75        22.78         1.45         0.53 
TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACH 
       75.65        76.41        12.53        63.48        12.00         6.41 
TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACN TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACT 
       53.19        69.11        42.81        13.64        14.20        51.35 
TCGA-DD-AAD3 TCGA-DD-AADA TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADL TCGA-DD-AADM 
       42.58        40.54         3.78        37.64        20.91         0.39 
TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADV TCGA-DD-AADW 
       29.52        14.89        15.06        14.33        18.87        19.30 
TCGA-DD-AAE0 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE9 TCGA-DD-AAEG TCGA-DD-AAEH 
       18.25        20.98        18.61        23.74        23.64        25.78 
TCGA-DD-AAEK TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVV TCGA-DD-AAVW TCGA-DD-AAVY 
       35.08        82.62        59.93        80.71        76.18        64.77 
TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A66X TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A82E 
       49.48        53.69        13.35        12.82         0.20        13.41 
TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-ES-A2HS 
       13.35         1.84        20.61        19.59         0.62        22.85 
TCGA-FV-A3I0 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25U 
       27.88         6.38        12.03         0.39        13.68        53.79 
TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A3CG TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SL 
       58.49        14.86        22.13        19.23        25.25        20.42 
TCGA-G3-A6UC TCGA-G3-AAV1 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV6 TCGA-KR-A7K2 
       22.06        11.80        13.55         0.89         2.14        21.60 
TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-NI-A8LF 
       29.79        12.72        22.95        24.56        20.71        26.27 
TCGA-O8-A75V TCGA-PD-A5DF TCGA-RC-A7S9 TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA 
       17.69        21.01        21.04        15.52        36.10        17.59 
TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7ME TCGA-UB-A7MF TCGA-UB-AA0U TCGA-WJ-A86L 
       19.76        16.44        15.98         7.04        10.75        11.34 
TCGA-WQ-A9G7 TCGA-WX-AA44 TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZS-A9CD TCGA-ZS-A9CF 
        0.99        20.22        22.78        13.55        45.57        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        38.40        22.92         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        14.76         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        23.38 
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-5264 TCGA-CC-A1HT TCGA-CC-A3M9 
        4.24         2.86         3.39         3.35         3.32         9.86 
TCGA-CC-A3MA TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A7IF TCGA-CC-A7IJ TCGA-CC-A8HT 
        9.96        11.41         9.99        21.34        12.56         4.60 
TCGA-CC-A8HV TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A115 TCGA-DD-A116 
        9.17         6.94         8.15        79.73        83.57        53.33 
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-A1EI TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W 
       75.65         6.02        18.35        13.64        21.14        27.19 
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-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NI TCGA-DD-A4NL 
       33.14        32.52        90.28        30.97        26.83        56.25 
TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NV TCGA-DD-A73A 
       73.81       108.76        12.26         0.30        78.84        23.93 
TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC9 
        9.30        23.05        35.67       114.35        13.48        11.41 
TCGA-DD-AACC TCGA-DD-AACG TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACO 
       55.40        15.42         0.30         3.52        58.16        61.68 
TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY 
       59.31        51.52        50.33        46.82         5.59        47.67 
TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD5 TCGA-DD-AAD6 
        5.62         4.50        18.54        21.63        44.22        22.09 
TCGA-DD-AAD8 TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADI 
       40.08        40.83        13.97        40.47        39.52        35.67 
TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADY 
       35.05        34.49        66.67        15.58        18.21        18.25 
TCGA-DD-AAE1 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEA 
       18.15        19.99         4.64        21.17        21.83        18.90 
TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEI TCGA-DD-AAVP TCGA-DD-AAVQ 
       15.72        25.08        26.63        50.33        79.07        89.69 
TCGA-DD-AAVU TCGA-DD-AAVX TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-ED-A459 
       72.39        56.48        62.47        66.25        65.39        29.92 
TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7XO 
       26.93        28.08        13.91         9.73         0.20        14.04 
TCGA-ED-A7XP TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A3JL TCGA-EP-A3RK 
       13.15         0.20        18.74        19.99         9.96        11.93 
TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I1 TCGA-FV-A495 
       14.40        60.89        23.97        19.10         8.12         0.03 
TCGA-FV-A496 TCGA-FV-A4ZP TCGA-G3-A25T TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Z 
        0.33        81.73        51.06        28.27        30.74        21.53 
TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A5SJ TCGA-G3-A5SM TCGA-G3-A7M5 
       25.64         5.92        19.53        22.95        17.10        14.70 
TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV0 
       20.78        11.87        14.14         1.84        15.78        15.65 
TCGA-G3-AAV2 TCGA-G3-AAV5 TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB 
       12.23         8.75        11.87        22.92         1.02         2.20 
TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 
        2.99        37.71        20.75        17.06        16.83        11.80 
TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E 
        2.14        31.27        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 
        7.53        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-WX-AA47 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 
       18.28        35.77        25.71        23.21        35.87         0.69 
TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CE TCGA-ZS-A9CG 
       25.15        12.99        40.80        11.21 

  AMP PEAK 10(6P25.2) MUTATED AMP PEAK 10(6P25.2) WILD-TYPE 
                         0.20                          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 
                        19.76                         19.66 
[1] "0.2 - 113.0 (19.8)" "0.0 - 120.8 (19.7)"
[1] "hr=" "1.3"
D10V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IIIA
  AMP PEAK 10(6P25.2) MUTATED        65       40         2         27
  AMP PEAK 10(6P25.2) WILD-TYPE     106       45         1         33
                               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                             65                           106
  STAGE II                            40                            45
  STAGE III                            2                             1
  STAGE IIIA                          27                            33
  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      67  44  37   4
  AMP PEAK 10(6P25.2) WILD-TYPE   115  48  37   8
D10V4, multiclass
       clus
vv      AMP PEAK 10(6P25.2) MUTATED AMP PEAK 10(6P25.2) WILD-TYPE
  T0+T1                          67                           115
  T2                             44                            48
  T3                             37                            37
  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   103   1
  AMP PEAK 10(6P25.2) WILD-TYPE 147   2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(6P25.2) MUTATED    103    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                         103                           147
  1                           1                             2
[1] 2 2
[1] FALSE
D10V6, binary
                               cls
clus                              0   1
  AMP PEAK 10(6P25.2) MUTATED   110   3
  AMP PEAK 10(6P25.2) WILD-TYPE 151   1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(6P25.2) MUTATED    110    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                         110                           151
  1                           3                             1
[1] 2 2
[1] FALSE
D10V7, binary
                               cls
clus                              0   1
  AMP PEAK 10(6P25.2) MUTATED    53 100
  AMP PEAK 10(6P25.2) WILD-TYPE  62 147
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(6P25.2) MUTATED     53  100
  AMP PEAK 10(6P25.2) WILD-TYPE   62  147
        clus
vv       AMP PEAK 10(6P25.2) MUTATED AMP PEAK 10(6P25.2) WILD-TYPE
  FEMALE                          53                            62
  MALE                           100                           147
[1] 2 2
[1] FALSE
D10V8, binary
                               cls
clus                              0   1
  AMP PEAK 10(6P25.2) MUTATED   143   1
  AMP PEAK 10(6P25.2) WILD-TYPE 193   6
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(6P25.2) MUTATED    143    1
  AMP PEAK 10(6P25.2) WILD-TYPE  193    6
     clus
vv    AMP PEAK 10(6P25.2) MUTATED AMP PEAK 10(6P25.2) WILD-TYPE
  NO                          143                           193
  YES                           1                             6
[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                        150
  AMP PEAK 10(6P25.2) WILD-TYPE                      203
                               vv
clus                            HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK 10(6P25.2) MUTATED                                  3
  AMP PEAK 10(6P25.2) WILD-TYPE                                4
D10V9, multiclass
                                  clus
vv                                 AMP PEAK 10(6P25.2) MUTATED
  FIBROLAMELLAR CARCINOMA                                    0
  HEPATOCELLULAR CARCINOMA                                 150
  HEPATOCHOLANGIOCARCINOMA (MIXED)                           3
                                  clus
vv                                 AMP PEAK 10(6P25.2) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                      2
  HEPATOCELLULAR CARCINOMA                                   203
  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   136   7   1   8
  AMP PEAK 10(6P25.2) WILD-TYPE 182   8   0  13
D10V10, multiclass
    clus
vv   AMP PEAK 10(6P25.2) MUTATED AMP PEAK 10(6P25.2) WILD-TYPE
  R0                         136                           182
  R1                           7                             8
  R2                           1                             0
  RX                           8                            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 10(6P25.2) MUTATED                                  0    69
  AMP PEAK 10(6P25.2) WILD-TYPE                                1    88
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 10(6P25.2) MUTATED                           8    72
  AMP PEAK 10(6P25.2) WILD-TYPE                         9   105
D10V11, multiclass
                                  clus
vv                                 AMP PEAK 10(6P25.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                     69
  BLACK OR AFRICAN AMERICAN                                  8
  WHITE                                                     72
                                  clus
vv                                 AMP PEAK 10(6P25.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                       88
  BLACK OR AFRICAN AMERICAN                                    9
  WHITE                                                      105
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V12, binary
                               cls
clus                              0   1
  AMP PEAK 10(6P25.2) MUTATED     7 138
  AMP PEAK 10(6P25.2) WILD-TYPE   6 194
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(6P25.2) MUTATED      7  138
  AMP PEAK 10(6P25.2) WILD-TYPE    6  194
                        clus
vv                       AMP PEAK 10(6P25.2) MUTATED
  HISPANIC OR LATINO                               7
  NOT HISPANIC OR LATINO                         138
                        clus
vv                       AMP PEAK 10(6P25.2) WILD-TYPE
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                           194
[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    90  61
  AMP PEAK 11(6P21.1) WILD-TYPE 139  68
  AMP PEAK 11(6P21.1) MUTATED AMP PEAK 11(6P21.1) WILD-TYPE 
                          151                           207 
  AMP PEAK 11(6P21.1) MUTATED AMP PEAK 11(6P21.1) WILD-TYPE 
                           61                            68 
$`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        49.84 
TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-3K-AAZ8 TCGA-4R-AA8I 
       18.25        20.81        22.92         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        17.10         1.51        27.52        27.52        23.38 
TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A69H 
        1.12        44.42        45.93         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-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IG TCGA-CC-A7IH 
       10.36        11.93         8.94         7.13         9.83        12.00 
TCGA-CC-A7II TCGA-CC-A7IK TCGA-CC-A7IL TCGA-CC-A8HU TCGA-CC-A8HV TCGA-DD-A114 
       13.12         8.61         9.14        11.31         9.17        37.78 
TCGA-DD-A115 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11C TCGA-DD-A11D 
       83.57       113.00         7.33         2.60        21.76        51.29 
TCGA-DD-A1EB TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A39X 
       66.31        11.47        12.95        45.11        49.15        55.69 
TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A5 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NH 
        5.62        19.76       102.74         0.36        30.61        30.15 
TCGA-DD-A4NK TCGA-DD-A4NN TCGA-DD-A4NS TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F 
       39.78        29.56        80.75        22.78         1.45        35.67 
TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACD 
      114.35        13.48         0.53        75.65        76.41        12.53 
TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACN TCGA-DD-AACP 
       63.48        12.00        53.19        69.11        42.81        13.64 
TCGA-DD-AACT TCGA-DD-AACZ TCGA-DD-AAD3 TCGA-DD-AADA TCGA-DD-AADF TCGA-DD-AADG 
       51.35         5.62        42.58        40.54         3.78        37.64 
TCGA-DD-AADL TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADQ TCGA-DD-AADV TCGA-DD-AAE0 
       20.91        29.52        14.89        14.33        18.87        18.25 
TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE7 TCGA-DD-AAE9 TCGA-DD-AAEH TCGA-DD-AAEK 
       18.61        19.99        21.17        23.74        25.78        35.08 
TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVV TCGA-DD-AAVW TCGA-DD-AAVY TCGA-DD-AAW2 
       82.62        59.93        80.71        76.18        64.77        49.48 
TCGA-DD-AAW3 TCGA-ED-A66X TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A82E TCGA-ED-A8O5 
       53.69        13.35         0.20        14.04        13.41        13.35 
TCGA-ED-A8O6 TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-ES-A2HS TCGA-FV-A23B 
        1.84        20.61        19.59         0.62        22.85        60.89 
TCGA-FV-A3I0 TCGA-FV-A3R2 TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25X 
       27.88         6.38         0.39        13.68        53.79        58.49 
TCGA-G3-A3CG TCGA-G3-A3CK TCGA-G3-A5SL TCGA-G3-A6UC TCGA-G3-AAV1 TCGA-G3-AAV3 
       22.13        19.23        20.42        22.06        11.80        13.55 
TCGA-G3-AAV4 TCGA-HP-A5N0 TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-MI-A75G 
        0.89        37.71        21.60        29.79        12.72        22.95 
TCGA-MI-A75H TCGA-MI-A75I TCGA-NI-A8LF TCGA-O8-A75V TCGA-RC-A7S9 TCGA-RC-A7SK 
       24.56        20.71        26.27        17.69        21.04        15.52 
TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7ME TCGA-UB-A7MF 
       36.10        17.59        19.76        16.44        15.98         7.04 
TCGA-UB-AA0U TCGA-WQ-A9G7 TCGA-WX-AA44 TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZS-A9CD 
       10.75         0.99        20.22        22.78        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        38.40         8.55        10.59         0.66 
TCGA-5R-AA1D TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S 
       14.76        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-5264 TCGA-CC-A1HT 
       36.66         4.24         2.86         3.39         3.35         3.32 
TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A7IF TCGA-CC-A7IJ 
        9.86         9.96        11.41         9.99        21.34        12.56 
TCGA-CC-A8HT TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A116 TCGA-DD-A11B 
        4.60         6.94         8.15        79.73        53.33         0.46 
TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EI TCGA-DD-A1EJ 
       90.71        79.40        19.79        75.65         6.02        33.04 
TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A3A0 TCGA-DD-A3A1 
       18.35        13.64        21.14        27.19        25.81         7.66 
TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A4NA 
       70.06        17.59        20.12       107.11        13.78        33.14 
TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NL 
       32.52        90.28        30.97        26.83        30.51        56.25 
TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NV TCGA-DD-A73A 
       73.81       108.76        12.26         0.30        78.84        23.93 
TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-AAC9 TCGA-DD-AACC TCGA-DD-AACG TCGA-DD-AACH 
        9.30        23.05        11.41        55.40        15.42         6.41 
TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACO TCGA-DD-AACQ TCGA-DD-AACS 
        0.30         3.52        58.16        61.68        14.20        59.31 
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-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADB 
       18.54        21.63        44.22        22.09        40.08        40.83 
TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK 
       13.97        40.47        39.52        35.67        35.05        34.49 
TCGA-DD-AADM TCGA-DD-AADP TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW 
        0.39        15.06        66.67        15.58        18.21        19.30 
TCGA-DD-AADY TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE6 TCGA-DD-AAE8 TCGA-DD-AAEA 
       18.25        18.15        20.98         4.64        21.83        18.90 
TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEI TCGA-DD-AAVP 
       15.72        25.08        26.63        23.64        50.33        79.07 
TCGA-DD-AAVQ TCGA-DD-AAVU TCGA-DD-AAVX TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 
       89.69        72.39        56.48        62.47        66.25        65.39 
TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66Y TCGA-ED-A7PX 
       29.92        26.93        28.08        13.91         9.73         0.20 
TCGA-ED-A7PY TCGA-ED-A7XP TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A3JL 
       12.82        13.15         0.20        18.74        19.99         9.96 
TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I1 TCGA-FV-A3R3 
       11.93        14.40        23.97        19.10         8.12        12.03 
TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-G3-A25T TCGA-G3-A25V TCGA-G3-A25W 
        0.03         0.33        81.73        51.06        28.27        30.74 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A5SI 
       14.86        21.53        25.64         5.92        19.53        25.25 
TCGA-G3-A5SJ TCGA-G3-A5SM TCGA-G3-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 
       22.95        17.10        14.70        20.78        11.87        14.14 
TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV5 TCGA-G3-AAV6 
        1.84        15.78        15.65        12.23         8.75         2.14 
TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-K7-A5RF 
       11.87        22.92         1.02         2.20         2.99        20.75 
TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A9QC 
       17.06        16.83        11.80         2.14        31.27        13.97 
TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 
       12.03         9.57        16.67         7.53        10.85        58.88 
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-A7MD TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-AB4B TCGA-WX-AA46 TCGA-WX-AA47 
        1.71        10.32        11.34        12.99        24.85        18.28 
TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D2 
       35.77        25.71        23.21        35.87         0.69        25.15 
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 
                         0.20                          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 
                        20.61                         19.04 
[1] "0.2 - 114.3 (20.6)" "0.0 - 120.8 (19.0)"
[1] "hr=" "1.2"
D11V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IIIA
  AMP PEAK 11(6P21.1) MUTATED        69       39         2         27
  AMP PEAK 11(6P21.1) WILD-TYPE     102       46         1         33
                               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                             69                           102
  STAGE II                            39                            46
  STAGE III                            2                             1
  STAGE IIIA                          27                            33
  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      70  43  34   5
  AMP PEAK 11(6P21.1) WILD-TYPE   112  49  40   7
D11V4, multiclass
       clus
vv      AMP PEAK 11(6P21.1) MUTATED AMP PEAK 11(6P21.1) WILD-TYPE
  T0+T1                          70                           112
  T2                             43                            49
  T3                             34                            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"
D11V5, binary
                               cls
clus                              0   1
  AMP PEAK 11(6P21.1) MUTATED   105   0
  AMP PEAK 11(6P21.1) WILD-TYPE 145   3
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 11(6P21.1) MUTATED    105    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                         105                           145
  1                           0                             3
[1] 2 2
[1] FALSE
D11V6, binary
                               cls
clus                              0   1
  AMP PEAK 11(6P21.1) MUTATED   110   3
  AMP PEAK 11(6P21.1) WILD-TYPE 151   1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 11(6P21.1) MUTATED    110    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                         110                           151
  1                           3                             1
[1] 2 2
[1] FALSE
D11V7, binary
                               cls
clus                              0   1
  AMP PEAK 11(6P21.1) MUTATED    56  98
  AMP PEAK 11(6P21.1) WILD-TYPE  59 149
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 11(6P21.1) MUTATED     56   98
  AMP PEAK 11(6P21.1) WILD-TYPE   59  149
        clus
vv       AMP PEAK 11(6P21.1) MUTATED AMP PEAK 11(6P21.1) WILD-TYPE
  FEMALE                          56                            59
  MALE                            98                           149
[1] 2 2
[1] FALSE
D11V8, binary
                               cls
clus                              0   1
  AMP PEAK 11(6P21.1) MUTATED   143   1
  AMP PEAK 11(6P21.1) WILD-TYPE 193   6
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 11(6P21.1) MUTATED    143    1
  AMP PEAK 11(6P21.1) WILD-TYPE  193    6
     clus
vv    AMP PEAK 11(6P21.1) MUTATED AMP PEAK 11(6P21.1) WILD-TYPE
  NO                          143                           193
  YES                           1                             6
[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                        150
  AMP PEAK 11(6P21.1) WILD-TYPE                      203
                               vv
clus                            HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK 11(6P21.1) MUTATED                                  4
  AMP PEAK 11(6P21.1) WILD-TYPE                                3
D11V9, multiclass
                                  clus
vv                                 AMP PEAK 11(6P21.1) MUTATED
  FIBROLAMELLAR CARCINOMA                                    0
  HEPATOCELLULAR CARCINOMA                                 150
  HEPATOCHOLANGIOCARCINOMA (MIXED)                           4
                                  clus
vv                                 AMP PEAK 11(6P21.1) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                      2
  HEPATOCELLULAR CARCINOMA                                   203
  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   138   7   1   8
  AMP PEAK 11(6P21.1) WILD-TYPE 180   8   0  13
D11V10, multiclass
    clus
vv   AMP PEAK 11(6P21.1) MUTATED AMP PEAK 11(6P21.1) WILD-TYPE
  R0                         138                           180
  R1                           7                             8
  R2                           1                             0
  RX                           8                            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 11(6P21.1) MUTATED                                  0    64
  AMP PEAK 11(6P21.1) WILD-TYPE                                1    93
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 11(6P21.1) MUTATED                           8    77
  AMP PEAK 11(6P21.1) WILD-TYPE                         9   100
D11V11, multiclass
                                  clus
vv                                 AMP PEAK 11(6P21.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                     64
  BLACK OR AFRICAN AMERICAN                                  8
  WHITE                                                     77
                                  clus
vv                                 AMP PEAK 11(6P21.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                       93
  BLACK OR AFRICAN AMERICAN                                    9
  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"
D11V12, binary
                               cls
clus                              0   1
  AMP PEAK 11(6P21.1) MUTATED     7 136
  AMP PEAK 11(6P21.1) WILD-TYPE   6 196
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 11(6P21.1) MUTATED      7  136
  AMP PEAK 11(6P21.1) WILD-TYPE    6  196
                        clus
vv                       AMP PEAK 11(6P21.1) MUTATED
  HISPANIC OR LATINO                               7
  NOT HISPANIC OR LATINO                         136
                        clus
vv                       AMP PEAK 11(6P21.1) WILD-TYPE
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                           196
[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    60  42
  AMP PEAK 12(6Q12) WILD-TYPE 169  87
  AMP PEAK 12(6Q12) MUTATED AMP PEAK 12(6Q12) WILD-TYPE 
                        102                         256 
  AMP PEAK 12(6Q12) MUTATED AMP PEAK 12(6Q12) WILD-TYPE 
                         42                          87 
$`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        49.84        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        45.93 
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-CC-A5UE TCGA-CC-A7IE 
        0.66         4.24        10.36        11.93         8.94         7.13 
TCGA-CC-A7IG TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A8HU TCGA-DD-A114 
        9.83        13.12        12.56         8.61        11.31        37.78 
TCGA-DD-A115 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11C TCGA-DD-A1EE 
       83.57       113.00         7.33         2.60        21.76        11.47 
TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EJ TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A5 
       12.95        49.15        33.04         5.62        19.76       102.74 
TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NH TCGA-DD-A4NK 
       13.78         0.36        30.61        33.14        30.15        39.78 
TCGA-DD-A4NN TCGA-DD-A4NS TCGA-DD-A73E TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AACB 
       29.56        80.75         1.45       114.35        13.48        76.41 
TCGA-DD-AACD TCGA-DD-AACJ TCGA-DD-AACN TCGA-DD-AACT TCGA-DD-AAD3 TCGA-DD-AADF 
       12.53        69.11        42.81        51.35        42.58         3.78 
TCGA-DD-AADL TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADQ TCGA-DD-AADV TCGA-DD-AAE0 
       20.91        29.52        14.89        14.33        18.87        18.25 
TCGA-DD-AAE3 TCGA-DD-AAEG TCGA-DD-AAEK TCGA-DD-AAVS TCGA-DD-AAVV TCGA-DD-AAVW 
       18.61        23.64        35.08        59.93        80.71        76.18 
TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A66X TCGA-ED-A7PZ TCGA-ED-A8O5 TCGA-EP-A2KB 
       49.48        53.69        13.35         0.20        13.35        19.59 
TCGA-EP-A2KC TCGA-ES-A2HS TCGA-FV-A3I0 TCGA-G3-A25U TCGA-G3-A3CG TCGA-G3-A3CK 
        0.62        22.85        27.88        53.79        22.13        19.23 
TCGA-G3-A6UC TCGA-G3-AAV1 TCGA-KR-A7K2 TCGA-LG-A6GG TCGA-O8-A75V TCGA-RC-A7SK 
       22.06        11.80        21.60        12.72        17.69        15.52 
TCGA-RG-A7D4 TCGA-T1-A6J8 TCGA-UB-A7MA TCGA-UB-A7MC TCGA-UB-A7ME TCGA-UB-A7MF 
       36.10         0.76        17.59        16.44        15.98         7.04 
TCGA-UB-AA0U TCGA-WQ-A9G7 TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZS-A9CD TCGA-ZS-A9CF 
       10.75         0.99        22.78        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        38.40        22.92 
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        17.10        14.76 
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        23.38         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         4.24         2.86 
TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5264 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA 
        3.19         3.39         3.35         3.32         9.86         9.96 
TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A7IF TCGA-CC-A7IH TCGA-CC-A7IL TCGA-CC-A8HT 
       11.41         9.99        21.34        12.00         9.14         4.60 
TCGA-CC-A8HV TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A116 TCGA-DD-A11B 
        9.17         6.94         8.15        79.73        53.33         0.46 
TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED 
       51.29        90.71        79.40        66.31        19.79        75.65 
TCGA-DD-A1EG TCGA-DD-A1EI TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W 
       45.11         6.02        18.35        13.64        21.14        27.19 
TCGA-DD-A39X TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 
       55.69        25.81         7.66        70.06        17.59        20.12 
TCGA-DD-A3A6 TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NI TCGA-DD-A4NJ 
      107.11        32.52        90.28        30.97        26.83        30.51 
TCGA-DD-A4NL TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NV 
       56.25        73.81       108.76        12.26         0.30        78.84 
TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73F TCGA-DD-AAC8 
       23.93         9.30        23.05        22.78        35.67         0.53 
TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACC TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG 
       11.41        75.65        55.40        63.48        12.00        15.42 
TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACO 
        6.41        53.19         0.30         3.52        58.16        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-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-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-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-AADM TCGA-DD-AADP TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW 
        0.39        15.06        66.67        15.58        18.21        19.30 
TCGA-DD-AADY 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        26.63 
TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVU 
       25.78        50.33        79.07        89.69        82.62        72.39 
TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-ED-A459 
       56.48        64.77        62.47        66.25        65.39        29.92 
TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY 
       26.93        28.08        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-A12J 
       14.04        13.15        13.41         1.84         0.20        18.74 
TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B 
       19.99        20.61         9.96        11.93        14.40        60.89 
TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 
       23.97        19.10         8.12         6.38        12.03         0.03 
TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25V 
        0.33        81.73         0.39        13.68        51.06        28.27 
TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI 
       30.74        58.49        14.86        21.53        25.64         5.92 
TCGA-G3-A3CJ TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A7M5 
       19.53        25.25        22.95        20.42        17.10        14.70 
TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV0 
       20.78        11.87        14.14         1.84        15.78        15.65 
TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 
       12.23        13.55         0.89         8.75         2.14        11.87 
TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF 
       22.92         1.02         2.20         2.99        37.71        20.75 
TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-KR-A7K8 
       17.06        16.83        11.80         2.14        31.27        29.79 
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        22.95        24.56 
TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-PD-A5DF 
       20.71         7.53        10.85        58.88        26.27        21.01 
TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH TCGA-UB-A7MB 
        3.09        21.04        19.33        19.04        15.39        19.76 
TCGA-UB-A7MD TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-WX-AA46 
        1.71        10.32        11.34        12.99        20.22        24.85 
TCGA-WX-AA47 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 
       18.28        35.77        25.71        23.21        35.87         0.69 
TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CE TCGA-ZS-A9CG 
       25.15        12.99        40.80        11.21 

  AMP PEAK 12(6Q12) MUTATED AMP PEAK 12(6Q12) WILD-TYPE 
                       0.20                        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 
                      19.05                       19.99 
[1] "0.2 - 114.3 (19.1)" "0.0 - 120.8 (20.0)"
[1] "hr=" "1.2"
D12V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 12(6Q12) MUTATED        40       27         2         18          5
  AMP PEAK 12(6Q12) WILD-TYPE     131       58         1         42          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                           40                         131
  STAGE II                          27                          58
  STAGE III                          2                           1
  STAGE IIIA                        18                          42
  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      43  30  26   5
  AMP PEAK 12(6Q12) WILD-TYPE   139  62  48   7
D12V4, multiclass
       clus
vv      AMP PEAK 12(6Q12) MUTATED AMP PEAK 12(6Q12) WILD-TYPE
  T0+T1                        43                         139
  T2                           30                          62
  T3                           26                          48
  T4                            5                           7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V5, binary
                             cls
clus                            0   1
  AMP PEAK 12(6Q12) MUTATED    68   2
  AMP PEAK 12(6Q12) WILD-TYPE 182   1
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 12(6Q12) MUTATED     68    2
  AMP PEAK 12(6Q12) WILD-TYPE  182    1
   clus
vv  AMP PEAK 12(6Q12) MUTATED AMP PEAK 12(6Q12) WILD-TYPE
  0                        68                         182
  1                         2                           1
[1] 2 2
[1] FALSE
D12V6, binary
                             cls
clus                            0   1
  AMP PEAK 12(6Q12) MUTATED    75   2
  AMP PEAK 12(6Q12) WILD-TYPE 186   2
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 12(6Q12) MUTATED     75    2
  AMP PEAK 12(6Q12) WILD-TYPE  186    2
   clus
vv  AMP PEAK 12(6Q12) MUTATED AMP PEAK 12(6Q12) WILD-TYPE
  0                        75                         186
  1                         2                           2
[1] 2 2
[1] FALSE
D12V7, binary
                             cls
clus                            0   1
  AMP PEAK 12(6Q12) MUTATED    37  67
  AMP PEAK 12(6Q12) WILD-TYPE  78 180
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 12(6Q12) MUTATED     37   67
  AMP PEAK 12(6Q12) WILD-TYPE   78  180
        clus
vv       AMP PEAK 12(6Q12) MUTATED AMP PEAK 12(6Q12) WILD-TYPE
  FEMALE                        37                          78
  MALE                          67                         180
[1] 2 2
[1] FALSE
D12V8, binary
                             cls
clus                            0   1
  AMP PEAK 12(6Q12) MUTATED    94   0
  AMP PEAK 12(6Q12) WILD-TYPE 242   7
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 12(6Q12) MUTATED     94    0
  AMP PEAK 12(6Q12) WILD-TYPE  242    7
     clus
vv    AMP PEAK 12(6Q12) MUTATED AMP PEAK 12(6Q12) WILD-TYPE
  NO                         94                         242
  YES                         0                           7
[1] 2 2
[1] FALSE
                             vv
clus                          FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  AMP PEAK 12(6Q12) MUTATED                         0                      100
  AMP PEAK 12(6Q12) WILD-TYPE                       2                      253
                             vv
clus                          HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK 12(6Q12) MUTATED                                  4
  AMP PEAK 12(6Q12) WILD-TYPE                                3
D12V9, multiclass
                                  clus
vv                                 AMP PEAK 12(6Q12) MUTATED
  FIBROLAMELLAR CARCINOMA                                  0
  HEPATOCELLULAR CARCINOMA                               100
  HEPATOCHOLANGIOCARCINOMA (MIXED)                         4
                                  clus
vv                                 AMP PEAK 12(6Q12) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                    2
  HEPATOCELLULAR CARCINOMA                                 253
  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    91   6   1   6
  AMP PEAK 12(6Q12) WILD-TYPE 227   9   0  15
D12V10, multiclass
    clus
vv   AMP PEAK 12(6Q12) MUTATED AMP PEAK 12(6Q12) WILD-TYPE
  R0                        91                         227
  R1                         6                           9
  R2                         1                           0
  RX                         6                          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 12(6Q12) MUTATED                                  0    42
  AMP PEAK 12(6Q12) WILD-TYPE                                1   115
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 12(6Q12) MUTATED                           7    52
  AMP PEAK 12(6Q12) WILD-TYPE                        10   125
D12V11, multiclass
                                  clus
vv                                 AMP PEAK 12(6Q12) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         0
  ASIAN                                                   42
  BLACK OR AFRICAN AMERICAN                                7
  WHITE                                                   52
                                  clus
vv                                 AMP PEAK 12(6Q12) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                    115
  BLACK OR AFRICAN AMERICAN                                 10
  WHITE                                                    125
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V12, binary
                             cls
clus                            0   1
  AMP PEAK 12(6Q12) MUTATED     5  92
  AMP PEAK 12(6Q12) WILD-TYPE   8 240
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 12(6Q12) MUTATED      5   92
  AMP PEAK 12(6Q12) WILD-TYPE    8  240
                        clus
vv                       AMP PEAK 12(6Q12) MUTATED AMP PEAK 12(6Q12) WILD-TYPE
  HISPANIC OR LATINO                             5                           8
  NOT HISPANIC OR LATINO                        92                         240
[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  32
  AMP PEAK 13(6Q12) WILD-TYPE 183  97
  AMP PEAK 13(6Q12) MUTATED AMP PEAK 13(6Q12) WILD-TYPE 
                         78                         280 
  AMP PEAK 13(6Q12) MUTATED AMP PEAK 13(6Q12) WILD-TYPE 
                         32                          97 
$`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        49.84        18.25        38.40        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        45.93         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        10.36 
TCGA-CC-A3MC TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IG TCGA-CC-A7II TCGA-CC-A7IK 
       11.93         8.94         7.13         9.83        13.12         8.61 
TCGA-CC-A8HU TCGA-CC-A8HV TCGA-DD-A115 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A 
       11.31         9.17        83.57       113.00         7.33         2.60 
TCGA-DD-A11D TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A39Y TCGA-DD-A3A8 TCGA-DD-A3A9 
       51.29        12.95        49.15         5.62         0.36        30.61 
TCGA-DD-A73G TCGA-DD-AACJ TCGA-DD-AACN TCGA-DD-AACT TCGA-DD-AADF TCGA-DD-AADN 
      114.35        69.11        42.81        51.35         3.78        29.52 
TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AAE0 TCGA-DD-AAE3 TCGA-DD-AAE9 TCGA-DD-AAEG 
       14.89        15.06        18.25        18.61        23.74        23.64 
TCGA-DD-AAEK TCGA-DD-AAVV TCGA-DD-AAVW TCGA-DD-AAW2 TCGA-ED-A66X TCGA-ED-A7PZ 
       35.08        80.71        76.18        49.48        13.35         0.20 
TCGA-ED-A8O5 TCGA-EP-A12J TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-ES-A2HS 
       13.35        18.74        20.61        19.59         0.62        22.85 
TCGA-FV-A3I0 TCGA-G3-A25U TCGA-G3-A3CK TCGA-G3-AAV1 TCGA-KR-A7K2 TCGA-LG-A6GG 
       27.88        53.79        19.23        11.80        21.60        12.72 
TCGA-O8-A75V TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MC TCGA-UB-A7ME 
       17.69        15.52        36.10        17.59        16.44        15.98 
TCGA-UB-A7MF TCGA-UB-AA0U TCGA-WQ-A9G7 TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZS-A9CD 
        7.04        10.75         0.99        22.78        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        22.92 
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        17.10        14.76 
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        23.38         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-5264 
       36.66         0.66         4.24         3.19         3.39         3.35 
TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A7IF 
        3.32         9.86         9.96        11.41         9.99        21.34 
TCGA-CC-A7IH TCGA-CC-A7IJ TCGA-CC-A7IL TCGA-CC-A8HT TCGA-CC-A9FS TCGA-CC-A9FW 
       12.00        12.56         9.14         4.60         6.94         8.15 
TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A116 TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A1E9 
       79.73        37.78        53.33         0.46        21.76        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-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-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 
       55.69        19.76        25.81         7.66        70.06        17.59 
TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A4NA TCGA-DD-A4NB 
       20.12       102.74       107.11        13.78        33.14        32.52 
TCGA-DD-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-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-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACO 
        6.41        53.19         0.30         3.52        58.16        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-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-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-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-AADQ TCGA-DD-AADR TCGA-DD-AADS 
       34.49        20.91         0.39        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-AAE6 TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEB 
       19.99         4.64        21.17        21.83        18.90        15.72 
TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAVP TCGA-DD-AAVQ 
       25.08        26.63        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-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG 
       66.25        65.39        53.69        29.92        26.93        28.08 
TCGA-ED-A627 TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7XO TCGA-ED-A7XP 
       13.91         9.73         0.20        12.82        14.04        13.15 
TCGA-ED-A82E TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A26S TCGA-EP-A3JL TCGA-EP-A3RK 
       13.41         1.84         0.20        19.99         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-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A5SI TCGA-G3-A5SJ 
       22.13        25.64         5.92        19.53        25.25        22.95 
TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M7 
       20.42        17.10        22.06        14.70        20.78        11.87 
TCGA-G3-A7M8 TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV3 
       14.14         1.84        15.78        15.65        12.23        13.55 
TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 
        0.89         8.75         2.14        11.87        22.92         1.02 
TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 
        2.20         2.99        37.71        20.75        17.06        16.83 
TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD 
       11.80         2.14        31.27        29.79        13.97        12.03 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A520 
        9.57        16.67        22.95        24.56        20.71         7.53 
TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 
       10.85        58.88        26.27        21.01         3.09        21.04 
TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH TCGA-T1-A6J8 TCGA-UB-A7MB TCGA-UB-A7MD 
       19.33        19.04        15.39         0.76        19.76         1.71 
TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 
       10.32        11.34        12.99        20.22        24.85        18.28 
TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D2 
       35.77        25.71        23.21        35.87         0.69        25.15 
TCGA-ZP-A9D4 TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       12.99        40.80        79.30        11.21 

  AMP PEAK 13(6Q12) MUTATED AMP PEAK 13(6Q12) WILD-TYPE 
                       0.20                        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 
                     17.640                      20.565 
[1] "0.2 - 114.3 (17.6)" "0.0 - 120.8 (20.6)"
[1] "hr=" "1.3"
D13V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 13(6Q12) MUTATED        32       22         1         16          2
  AMP PEAK 13(6Q12) WILD-TYPE     139       63         2         44          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                           32                         139
  STAGE II                          22                          63
  STAGE III                          1                           2
  STAGE IIIA                        16                          44
  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      33  23  20   4
  AMP PEAK 13(6Q12) WILD-TYPE   149  69  54   8
D13V4, multiclass
       clus
vv      AMP PEAK 13(6Q12) MUTATED AMP PEAK 13(6Q12) WILD-TYPE
  T0+T1                        33                         149
  T2                           23                          69
  T3                           20                          54
  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    52   0
  AMP PEAK 13(6Q12) WILD-TYPE 198   3
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 13(6Q12) MUTATED     52    0
  AMP PEAK 13(6Q12) WILD-TYPE  198    3
   clus
vv  AMP PEAK 13(6Q12) MUTATED AMP PEAK 13(6Q12) WILD-TYPE
  0                        52                         198
  1                         0                           3
[1] 2 2
[1] FALSE
D13V6, binary
                             cls
clus                            0   1
  AMP PEAK 13(6Q12) MUTATED    54   2
  AMP PEAK 13(6Q12) WILD-TYPE 207   2
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 13(6Q12) MUTATED     54    2
  AMP PEAK 13(6Q12) WILD-TYPE  207    2
   clus
vv  AMP PEAK 13(6Q12) MUTATED AMP PEAK 13(6Q12) WILD-TYPE
  0                        54                         207
  1                         2                           2
[1] 2 2
[1] FALSE
D13V7, binary
                             cls
clus                            0   1
  AMP PEAK 13(6Q12) MUTATED    29  51
  AMP PEAK 13(6Q12) WILD-TYPE  86 196
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 13(6Q12) MUTATED     29   51
  AMP PEAK 13(6Q12) WILD-TYPE   86  196
        clus
vv       AMP PEAK 13(6Q12) MUTATED AMP PEAK 13(6Q12) WILD-TYPE
  FEMALE                        29                          86
  MALE                          51                         196
[1] 2 2
[1] FALSE
D13V8, binary
                             cls
clus                            0   1
  AMP PEAK 13(6Q12) MUTATED    72   0
  AMP PEAK 13(6Q12) WILD-TYPE 264   7
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 13(6Q12) MUTATED     72    0
  AMP PEAK 13(6Q12) WILD-TYPE  264    7
     clus
vv    AMP PEAK 13(6Q12) MUTATED AMP PEAK 13(6Q12) WILD-TYPE
  NO                         72                         264
  YES                         0                           7
[1] 2 2
[1] FALSE
                             vv
clus                          FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  AMP PEAK 13(6Q12) MUTATED                         0                       77
  AMP PEAK 13(6Q12) WILD-TYPE                       2                      276
                             vv
clus                          HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK 13(6Q12) MUTATED                                  3
  AMP PEAK 13(6Q12) WILD-TYPE                                4
D13V9, multiclass
                                  clus
vv                                 AMP PEAK 13(6Q12) MUTATED
  FIBROLAMELLAR CARCINOMA                                  0
  HEPATOCELLULAR CARCINOMA                                77
  HEPATOCHOLANGIOCARCINOMA (MIXED)                         3
                                  clus
vv                                 AMP PEAK 13(6Q12) 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 13(6Q12) MUTATED    72   3   1   4
  AMP PEAK 13(6Q12) WILD-TYPE 246  12   0  17
D13V10, multiclass
    clus
vv   AMP PEAK 13(6Q12) MUTATED AMP PEAK 13(6Q12) WILD-TYPE
  R0                        72                         246
  R1                         3                          12
  R2                         1                           0
  RX                         4                          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 13(6Q12) MUTATED                                  0    37
  AMP PEAK 13(6Q12) WILD-TYPE                                1   120
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 13(6Q12) MUTATED                           6    36
  AMP PEAK 13(6Q12) WILD-TYPE                        11   141
D13V11, multiclass
                                  clus
vv                                 AMP PEAK 13(6Q12) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         0
  ASIAN                                                   37
  BLACK OR AFRICAN AMERICAN                                6
  WHITE                                                   36
                                  clus
vv                                 AMP PEAK 13(6Q12) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                    120
  BLACK OR AFRICAN AMERICAN                                 11
  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"
D13V12, binary
                             cls
clus                            0   1
  AMP PEAK 13(6Q12) MUTATED     5  70
  AMP PEAK 13(6Q12) WILD-TYPE   8 262
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 13(6Q12) MUTATED      5   70
  AMP PEAK 13(6Q12) WILD-TYPE    8  262
                        clus
vv                       AMP PEAK 13(6Q12) MUTATED AMP PEAK 13(6Q12) WILD-TYPE
  HISPANIC OR LATINO                             5                           8
  NOT HISPANIC OR LATINO                        70                         262
[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    73  41
  AMP PEAK 14(7Q31.2) WILD-TYPE 156  88
  AMP PEAK 14(7Q31.2) MUTATED AMP PEAK 14(7Q31.2) WILD-TYPE 
                          114                           244 
  AMP PEAK 14(7Q31.2) MUTATED AMP PEAK 14(7Q31.2) WILD-TYPE 
                           41                            88 
$`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 
       49.84        22.92        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-5264 TCGA-CC-A3M9 TCGA-CC-A3MB 
       36.66         0.66         2.86         3.35         9.86        10.36 
TCGA-CC-A5UE TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A8HU TCGA-CC-A9FW TCGA-DD-A118 
        8.94        13.12        12.56        11.31         8.15       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-AAVV TCGA-DD-AAVX 
       23.74        18.90        15.72        50.33        80.71        56.48 
TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A66Y TCGA-ED-A7PY TCGA-EP-A26S 
       49.48        53.69        29.92         9.73        12.82        19.99 
TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3JL TCGA-ES-A2HS TCGA-FV-A3I1 TCGA-FV-A3R2 
       20.61         0.62         9.96        22.85         8.12         6.38 
TCGA-FV-A4ZP TCGA-G3-A25T TCGA-G3-A25V TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A3CG 
       81.73        51.06        28.27        58.49        14.86        22.13 
TCGA-G3-A3CJ TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M5 TCGA-G3-AAV1 
       19.53        20.42        17.10        22.06        14.70        11.80 
TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-MI-A75E 
        8.75         2.14        21.60        29.79        12.72        16.67 
TCGA-MI-A75G TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-RC-A7S9 TCGA-UB-A7MD TCGA-UB-AA0U 
       22.95        58.88        26.27        21.04         1.71        10.75 
TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA46 TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9D1 
        0.99        12.99        24.85        22.78        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        38.40        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        17.10        14.76         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        23.38 
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        45.93        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         4.24         3.19         3.39 
TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3MA TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A5UD 
        4.24         3.32         9.96        11.93        11.41         9.99 
TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7IK TCGA-CC-A7IL 
        7.13        21.34         9.83        12.00         8.61         9.14 
TCGA-CC-A8HT TCGA-CC-A8HV TCGA-CC-A9FS TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 
        4.60         9.17         6.94        79.73        37.78        83.57 
TCGA-DD-A116 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A1EA 
       53.33         7.33         2.60         0.46        21.76        79.40 
TCGA-DD-A1EB TCGA-DD-A1ED TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI 
       66.31        75.65        12.95        45.11        49.15         6.02 
TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A3A0 TCGA-DD-A3A1 
       18.35        13.64        27.19        55.69        25.81         7.66 
TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 
       17.59        20.12       102.74       107.11        13.78         0.36 
TCGA-DD-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-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NR TCGA-DD-A4NS 
       56.25        29.56        73.81       108.76         0.30        80.75 
TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73D TCGA-DD-A73F TCGA-DD-AA3A TCGA-DD-AAC8 
       23.93         9.30        22.78        35.67        13.48         0.53 
TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACJ TCGA-DD-AACK 
       76.41        55.40        15.42         6.41        69.11         0.30 
TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACQ TCGA-DD-AACU 
        3.52        58.16        42.81        61.68        14.20        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-AADE TCGA-DD-AADF TCGA-DD-AADI 
       40.54        40.83        13.97        39.52         3.78        35.67 
TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ 
       35.05        34.49        29.52        14.89        15.06        14.33 
TCGA-DD-AADR TCGA-DD-AADU TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE4 
       66.67        18.21        18.25        18.25        18.15        19.99 
TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEH 
       21.17        21.83        25.08        26.63        23.64        25.78 
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-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-ED-A4XI 
       76.18        64.77        62.47        66.25        65.39        26.93 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A7PX TCGA-ED-A7PZ TCGA-ED-A7XO 
       28.08        13.91        13.35         0.20         0.20        14.04 
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-A2KB TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR 
       19.59        11.93        14.40        60.89        23.97        19.10 
TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25S 
       27.88        12.03         0.03         0.33         0.39        13.68 
TCGA-G3-A25U TCGA-G3-A25W TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CK 
       53.79        30.74        21.53        25.64         5.92        19.23 
TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-A7M9 
       25.25        22.95        20.78        11.87        14.14         1.84 
TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV7 
       15.78        15.65        12.23        13.55         0.89        11.87 
TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF 
       22.92         1.02         2.20         2.99        37.71        20.75 
TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A9QC 
       17.06        16.83        11.80         2.14        31.27        13.97 
TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO 
       12.03         9.57        24.56        20.71         7.53        10.85 
TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH 
       17.69        21.01         3.09        19.33        19.04        15.39 
TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-T1-A6J8 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC 
       15.52        36.10         0.76        17.59        19.76        16.44 
TCGA-UB-A7ME TCGA-UB-A7MF TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WX-AA44 TCGA-WX-AA47 
       15.98         7.04        10.32        11.34        20.22        18.28 
TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 
       35.77        25.71        23.21        35.87        25.15        12.99 
TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       45.57        40.80        79.30        11.21 

  AMP PEAK 14(7Q31.2) MUTATED AMP PEAK 14(7Q31.2) WILD-TYPE 
                         0.26                          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 
                        19.89                         19.46 
[1] "0.3 - 114.3 (19.9)" "0.0 - 120.8 (19.5)"
[1] "hr=" "1"  
D14V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IIIA
  AMP PEAK 14(7Q31.2) MUTATED        52       29         0         21
  AMP PEAK 14(7Q31.2) WILD-TYPE     119       56         3         39
                               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                             52                           119
  STAGE II                            29                            56
  STAGE III                            0                             3
  STAGE IIIA                          21                            39
  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      54  34  25   4
  AMP PEAK 14(7Q31.2) WILD-TYPE   128  58  49   8
D14V4, multiclass
       clus
vv      AMP PEAK 14(7Q31.2) MUTATED AMP PEAK 14(7Q31.2) WILD-TYPE
  T0+T1                          54                           128
  T2                             34                            58
  T3                             25                            49
  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    77   2
  AMP PEAK 14(7Q31.2) WILD-TYPE 173   1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 14(7Q31.2) MUTATED     77    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                          77                           173
  1                           2                             1
[1] 2 2
[1] FALSE
D14V6, binary
                               cls
clus                              0   1
  AMP PEAK 14(7Q31.2) MUTATED    85   1
  AMP PEAK 14(7Q31.2) WILD-TYPE 176   3
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 14(7Q31.2) MUTATED     85    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                          85                           176
  1                           1                             3
[1] 2 2
[1] FALSE
D14V7, binary
                               cls
clus                              0   1
  AMP PEAK 14(7Q31.2) MUTATED    35  82
  AMP PEAK 14(7Q31.2) WILD-TYPE  80 165
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 14(7Q31.2) MUTATED     35   82
  AMP PEAK 14(7Q31.2) WILD-TYPE   80  165
        clus
vv       AMP PEAK 14(7Q31.2) MUTATED AMP PEAK 14(7Q31.2) WILD-TYPE
  FEMALE                          35                            80
  MALE                            82                           165
[1] 2 2
[1] FALSE
D14V8, binary
                               cls
clus                              0   1
  AMP PEAK 14(7Q31.2) MUTATED   109   3
  AMP PEAK 14(7Q31.2) WILD-TYPE 227   4
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 14(7Q31.2) MUTATED    109    3
  AMP PEAK 14(7Q31.2) WILD-TYPE  227    4
     clus
vv    AMP PEAK 14(7Q31.2) MUTATED AMP PEAK 14(7Q31.2) WILD-TYPE
  NO                          109                           227
  YES                           3                             4
[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                        116
  AMP PEAK 14(7Q31.2) WILD-TYPE                      237
                               vv
clus                            HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK 14(7Q31.2) MUTATED                                  1
  AMP PEAK 14(7Q31.2) WILD-TYPE                                6
D14V9, multiclass
                                  clus
vv                                 AMP PEAK 14(7Q31.2) MUTATED
  FIBROLAMELLAR CARCINOMA                                    0
  HEPATOCELLULAR CARCINOMA                                 116
  HEPATOCHOLANGIOCARCINOMA (MIXED)                           1
                                  clus
vv                                 AMP PEAK 14(7Q31.2) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                      2
  HEPATOCELLULAR CARCINOMA                                   237
  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   103   6   0   6
  AMP PEAK 14(7Q31.2) WILD-TYPE 215   9   1  15
D14V10, multiclass
    clus
vv   AMP PEAK 14(7Q31.2) MUTATED AMP PEAK 14(7Q31.2) WILD-TYPE
  R0                         103                           215
  R1                           6                             9
  R2                           0                             1
  RX                           6                            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 14(7Q31.2) MUTATED                                  1    46
  AMP PEAK 14(7Q31.2) WILD-TYPE                                0   111
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 14(7Q31.2) MUTATED                           5    63
  AMP PEAK 14(7Q31.2) WILD-TYPE                        12   114
D14V11, multiclass
                                  clus
vv                                 AMP PEAK 14(7Q31.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                     46
  BLACK OR AFRICAN AMERICAN                                  5
  WHITE                                                     63
                                  clus
vv                                 AMP PEAK 14(7Q31.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                      111
  BLACK OR AFRICAN AMERICAN                                   12
  WHITE                                                      114
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V12, binary
                               cls
clus                              0   1
  AMP PEAK 14(7Q31.2) MUTATED     6 107
  AMP PEAK 14(7Q31.2) WILD-TYPE   7 225
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 14(7Q31.2) MUTATED      6  107
  AMP PEAK 14(7Q31.2) WILD-TYPE    7  225
                        clus
vv                       AMP PEAK 14(7Q31.2) MUTATED
  HISPANIC OR LATINO                               6
  NOT HISPANIC OR LATINO                         107
                        clus
vv                       AMP PEAK 14(7Q31.2) WILD-TYPE
  HISPANIC OR LATINO                                 7
  NOT HISPANIC OR LATINO                           225
[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   131  69
  AMP PEAK 15(8Q13.3) WILD-TYPE  98  60
  AMP PEAK 15(8Q13.3) MUTATED AMP PEAK 15(8Q13.3) WILD-TYPE 
                          200                           158 
  AMP PEAK 15(8Q13.3) MUTATED AMP PEAK 15(8Q13.3) WILD-TYPE 
                           69                            60 
$`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 
       22.92         1.18        13.02        10.78        10.59        17.10 
TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-A10S TCGA-BC-A10U TCGA-BC-A10W 
       14.76         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         4.24 
TCGA-CC-5264 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UC 
        3.35         3.32         9.86        10.36        11.93        11.41 
TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7II 
        8.94         7.13        21.34         9.83        12.00        13.12 
TCGA-CC-A7IK TCGA-CC-A8HT TCGA-CC-A8HV TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A113 
        8.61         4.60         9.17         6.94         8.15        79.73 
TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11C TCGA-DD-A1E9 
       53.33       113.00         7.33         2.60        21.76        90.71 
TCGA-DD-A1EC TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EI TCGA-DD-A1EL 
       19.79        11.47        12.95        45.11         6.02        13.64 
TCGA-DD-A39V TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A1 TCGA-DD-A3A3 TCGA-DD-A3A8 
       21.14         5.62        19.76         7.66        17.59         0.36 
TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NN 
       90.28        30.97        26.83        30.51        39.78        29.56 
TCGA-DD-A4NO TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A73D TCGA-DD-A73G 
       73.81        12.26         0.30        80.75        22.78       114.35 
TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACD TCGA-DD-AACF 
        0.53        11.41        75.65        76.41        12.53        12.00 
TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACM TCGA-DD-AACN 
       15.42         6.41        53.19        69.11        58.16        42.81 
TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACT TCGA-DD-AACY TCGA-DD-AACZ 
       61.68        13.64        14.20        51.35        47.67         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-AADL 
       13.97        40.47        39.52        35.67        34.49        20.91 
TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR 
        0.39        29.52        14.89        15.06        14.33        66.67 
TCGA-DD-AADU TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE3 TCGA-DD-AAE6 TCGA-DD-AAE8 
       18.21        18.25        18.15        18.61         4.64        21.83 
TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEG TCGA-DD-AAEI TCGA-DD-AAEK 
       23.74        15.72        25.08        23.64        50.33        35.08 
TCGA-DD-AAVQ TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVV TCGA-DD-AAVW TCGA-DD-AAVX 
       89.69        59.93        72.39        80.71        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-A66X TCGA-ED-A66Y TCGA-ED-A7PZ TCGA-ED-A8O6 TCGA-EP-A12J 
       29.92        13.35         9.73         0.20         1.84        18.74 
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-A2QQ TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-FV-A4ZQ 
       14.40        23.97         8.12         6.38        81.73         0.39 
TCGA-G3-A25T TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Z TCGA-G3-A3CG 
       51.06        28.27        30.74        58.49        21.53        22.13 
TCGA-G3-A3CH TCGA-G3-A3CJ TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A7M6 
       25.64        19.53        25.25        22.95        20.42        20.78 
TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 
       11.87         1.84        15.78        11.80        12.23        13.55 
TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-GJ-A3OU TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-K7-AAU7 
        8.75         2.14        22.92         2.99        16.83        11.80 
TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E 
       21.60        31.27        29.79        12.03         9.57        16.67 
TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A8JO TCGA-NI-A8LF TCGA-O8-A75V TCGA-RC-A7SF 
       24.56        20.71        10.85        26.27        17.69        19.04 
TCGA-RC-A7SH TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0U 
       15.39        36.10        17.59         1.71        15.98        10.75 
TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9D4 
        0.99        12.99        20.22        13.55        35.77        12.99 
TCGA-ZS-A9CD TCGA-ZS-A9CG 
       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 
       49.84        47.74        11.74        38.40        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        23.38         1.12        69.57         5.03        45.93 
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-CC-A5UD 
        2.86         3.19         3.39         4.24         9.96         9.99 
TCGA-CC-A7IJ TCGA-CC-A7IL TCGA-CC-A8HU TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A11B 
       12.56         9.14        11.31        37.78        83.57         0.46 
TCGA-DD-A11D TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1ED TCGA-DD-A1EH TCGA-DD-A1EJ 
       51.29        79.40        66.31        75.65        49.15        33.04 
TCGA-DD-A1EK TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A3A0 TCGA-DD-A3A2 TCGA-DD-A3A4 
       18.35        27.19        55.69        25.81        70.06        20.12 
TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB 
      102.74       107.11        13.78        30.61        33.14        32.52 
TCGA-DD-A4NH TCGA-DD-A4NL TCGA-DD-A4NP TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B 
       30.15        56.25       108.76        78.84        23.93         9.30 
TCGA-DD-A73C TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-AA3A TCGA-DD-AACC TCGA-DD-AACE 
       23.05         1.45        35.67        13.48        55.40        63.48 
TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW 
        0.30         3.52        59.31        51.52        50.33        46.82 
TCGA-DD-AACX TCGA-DD-AAD0 TCGA-DD-AAD3 TCGA-DD-AAD8 TCGA-DD-AADF TCGA-DD-AADG 
        5.59         4.50        42.58        40.08         3.78        37.64 
TCGA-DD-AADJ TCGA-DD-AADS TCGA-DD-AADV TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE2 
       35.05        15.58        18.87        19.30        18.25        20.98 
TCGA-DD-AAE4 TCGA-DD-AAE7 TCGA-DD-AAEA TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAVP 
       19.99        21.17        18.90        26.63        25.78        79.07 
TCGA-DD-AAVR TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A7PX TCGA-ED-A7PY 
       82.62        26.93        28.08        13.91         0.20        12.82 
TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A97K TCGA-EP-A26S 
       14.04        13.15        13.41        13.35         0.20        19.99 
TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 
       60.89        19.10        27.88        12.03         0.03         0.33 
TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25Y TCGA-G3-A3CI TCGA-G3-A3CK TCGA-G3-A5SM 
       13.68        53.79        14.86         5.92        19.23        17.10 
TCGA-G3-A6UC TCGA-G3-A7M5 TCGA-G3-A7M8 TCGA-G3-AAV0 TCGA-G3-AAV4 TCGA-G3-AAV7 
       22.06        14.70        14.14        15.65         0.89        11.87 
TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-KR-A7K0 
        1.02         2.20        37.71        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        22.95         7.53        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-WX-AA47 
       16.44         7.04        10.32        11.34        24.85        18.28 
TCGA-XR-A8TF TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D2 
       22.78        25.71        23.21        35.87         0.69        25.15 
TCGA-ZS-A9CE TCGA-ZS-A9CF 
       40.80        79.30 

  AMP PEAK 15(8Q13.3) MUTATED AMP PEAK 15(8Q13.3) WILD-TYPE 
                         0.20                          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 
                       18.890                        20.435 
[1] "0.2 - 114.3 (18.9)" "0.0 - 120.8 (20.4)"
[1] "hr=" "1"  
D15V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IIIA
  AMP PEAK 15(8Q13.3) MUTATED        96       53         0         37
  AMP PEAK 15(8Q13.3) WILD-TYPE      75       32         3         23
                               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                             96                            75
  STAGE II                            53                            32
  STAGE III                            0                             3
  STAGE IIIA                          37                            23
  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      99 56 43  4
  AMP PEAK 15(8Q13.3) WILD-TYPE    83 36 31  8
D15V4, multiclass
       clus
vv      AMP PEAK 15(8Q13.3) MUTATED AMP PEAK 15(8Q13.3) WILD-TYPE
  T0+T1                          99                            83
  T2                             56                            36
  T3                             43                            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"
D15V5, binary
                               cls
clus                              0   1
  AMP PEAK 15(8Q13.3) MUTATED   149   1
  AMP PEAK 15(8Q13.3) WILD-TYPE 101   2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 15(8Q13.3) MUTATED    149    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                         149                           101
  1                           1                             2
[1] 2 2
[1] FALSE
D15V6, binary
                               cls
clus                              0   1
  AMP PEAK 15(8Q13.3) MUTATED   153   2
  AMP PEAK 15(8Q13.3) WILD-TYPE 108   2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 15(8Q13.3) MUTATED    153    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                         153                           108
  1                           2                             2
[1] 2 2
[1] FALSE
D15V7, binary
                               cls
clus                              0   1
  AMP PEAK 15(8Q13.3) MUTATED    49 154
  AMP PEAK 15(8Q13.3) WILD-TYPE  66  93
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 15(8Q13.3) MUTATED     49  154
  AMP PEAK 15(8Q13.3) WILD-TYPE   66   93
        clus
vv       AMP PEAK 15(8Q13.3) MUTATED AMP PEAK 15(8Q13.3) WILD-TYPE
  FEMALE                          49                            66
  MALE                           154                            93
[1] 2 2
[1] FALSE
D15V8, binary
                               cls
clus                              0   1
  AMP PEAK 15(8Q13.3) MUTATED   185   6
  AMP PEAK 15(8Q13.3) WILD-TYPE 151   1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 15(8Q13.3) MUTATED    185    6
  AMP PEAK 15(8Q13.3) WILD-TYPE  151    1
     clus
vv    AMP PEAK 15(8Q13.3) MUTATED AMP PEAK 15(8Q13.3) WILD-TYPE
  NO                          185                           151
  YES                           6                             1
[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                        199
  AMP PEAK 15(8Q13.3) WILD-TYPE                      154
                               vv
clus                            HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK 15(8Q13.3) MUTATED                                  3
  AMP PEAK 15(8Q13.3) WILD-TYPE                                4
D15V9, multiclass
                                  clus
vv                                 AMP PEAK 15(8Q13.3) MUTATED
  FIBROLAMELLAR CARCINOMA                                    1
  HEPATOCELLULAR CARCINOMA                                 199
  HEPATOCHOLANGIOCARCINOMA (MIXED)                           3
                                  clus
vv                                 AMP PEAK 15(8Q13.3) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                      1
  HEPATOCELLULAR CARCINOMA                                   154
  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   177  10   1  12
  AMP PEAK 15(8Q13.3) WILD-TYPE 141   5   0   9
D15V10, multiclass
    clus
vv   AMP PEAK 15(8Q13.3) MUTATED AMP PEAK 15(8Q13.3) WILD-TYPE
  R0                         177                           141
  R1                          10                             5
  R2                           1                             0
  RX                          12                             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    98
  AMP PEAK 15(8Q13.3) WILD-TYPE                                0    59
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 15(8Q13.3) MUTATED                          10    88
  AMP PEAK 15(8Q13.3) WILD-TYPE                         7    89
D15V11, multiclass
                                  clus
vv                                 AMP PEAK 15(8Q13.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                     98
  BLACK OR AFRICAN AMERICAN                                 10
  WHITE                                                     88
                                  clus
vv                                 AMP PEAK 15(8Q13.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                       59
  BLACK OR AFRICAN AMERICAN                                    7
  WHITE                                                       89
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V12, binary
                               cls
clus                              0   1
  AMP PEAK 15(8Q13.3) MUTATED     7 187
  AMP PEAK 15(8Q13.3) WILD-TYPE   6 145
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 15(8Q13.3) MUTATED      7  187
  AMP PEAK 15(8Q13.3) WILD-TYPE    6  145
                        clus
vv                       AMP PEAK 15(8Q13.3) MUTATED
  HISPANIC OR LATINO                               7
  NOT HISPANIC OR LATINO                         187
                        clus
vv                       AMP PEAK 15(8Q13.3) WILD-TYPE
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                           145
[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   149  75
  AMP PEAK 16(8Q24.21) WILD-TYPE  80  54
  AMP PEAK 16(8Q24.21) MUTATED AMP PEAK 16(8Q24.21) WILD-TYPE 
                           224                            134 
  AMP PEAK 16(8Q24.21) MUTATED AMP PEAK 16(8Q24.21) WILD-TYPE 
                            75                             54 
$`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        17.10 
TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
       14.76         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         4.24 
TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5264 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA 
        3.19         3.39         3.35         3.32         9.86         9.96 
TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IE 
       10.36        11.93        11.41         9.99         8.94         7.13 
TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IK 
       21.34         9.83        12.00        13.12        12.56         8.61 
TCGA-CC-A7IL TCGA-CC-A8HT TCGA-CC-A8HV TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A113 
        9.14         4.60         9.17         6.94         8.15        79.73 
TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11C TCGA-DD-A1E9 
       53.33       113.00         7.33         2.60        21.76        90.71 
TCGA-DD-A1EC TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EI TCGA-DD-A1EL 
       19.79        11.47        12.95        45.11         6.02        13.64 
TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A1 TCGA-DD-A3A3 
       21.14        55.69         5.62        19.76         7.66        17.59 
TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NI TCGA-DD-A4NJ 
       13.78         0.36        90.28        30.97        26.83        30.51 
TCGA-DD-A4NK TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS 
       39.78        29.56        73.81        12.26         0.30        80.75 
TCGA-DD-A73A TCGA-DD-A73D TCGA-DD-A73G TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA 
       23.93        22.78       114.35         0.53        11.41        75.65 
TCGA-DD-AACB TCGA-DD-AACD TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI 
       76.41        12.53        12.00        15.42         6.41        53.19 
TCGA-DD-AACJ TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACS 
       69.11        58.16        42.81        61.68        13.64        59.31 
TCGA-DD-AACT TCGA-DD-AACW TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 
       51.35        46.82        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-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-AADV TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE3 TCGA-DD-AAE6 TCGA-DD-AAE7 
       18.87        18.25        18.15        18.61         4.64        21.17 
TCGA-DD-AAE8 TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEG 
       21.83        23.74        15.72        25.08        26.63        23.64 
TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS 
       25.78        50.33        35.08        89.69        82.62        59.93 
TCGA-DD-AAVU TCGA-DD-AAVV TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ 
       72.39        80.71        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        29.92        13.35 
TCGA-ED-A66Y TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O6 
        9.73        12.82         0.20        13.15        13.41         1.84 
TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL 
        0.20        18.74        20.61        19.59         0.62         9.96 
TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A2QQ TCGA-FV-A3I0 TCGA-FV-A3I1 
       11.93        22.85        14.40        23.97        27.88         8.12 
TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V 
        6.38        81.73         0.39        51.06        53.79        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-AAUZ 
       25.25        22.95        20.42        20.78        11.87        15.78 
TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 
       11.80        12.23        13.55         8.75         2.14        11.87 
TCGA-GJ-A3OU TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-KR-A7K7 
       22.92         2.99        16.83        11.80        21.60        31.27 
TCGA-KR-A7K8 TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75H TCGA-MI-A75I 
       29.79        12.03         9.57        16.67        24.56        20.71 
TCGA-MR-A8JO TCGA-NI-A8LF TCGA-O8-A75V TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK 
       10.85        26.27        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 
       36.10        17.59        16.44         1.71        15.98        10.75 
TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9D4 
        0.99        12.99        20.22        13.55        35.77        12.99 
TCGA-ZS-A9CD TCGA-ZS-A9CG 
       45.57        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 
       49.84        11.74        38.40        20.81        22.92         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 
       23.38         1.12        69.57         5.03        44.42        45.93 
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-CC-A8HU TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A11B 
        2.86         4.24        11.31        37.78        83.57         0.46 
TCGA-DD-A11D TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1ED TCGA-DD-A1EH TCGA-DD-A1EJ 
       51.29        79.40        66.31        75.65        49.15        33.04 
TCGA-DD-A1EK TCGA-DD-A39W TCGA-DD-A3A0 TCGA-DD-A3A2 TCGA-DD-A3A4 TCGA-DD-A3A5 
       18.35        27.19        25.81        70.06        20.12       102.74 
TCGA-DD-A3A6 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NH TCGA-DD-A4NL 
      107.11        30.61        33.14        32.52        30.15        56.25 
TCGA-DD-A4NP TCGA-DD-A4NV TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73E TCGA-DD-A73F 
      108.76        78.84         9.30        23.05         1.45        35.67 
TCGA-DD-AA3A TCGA-DD-AACC TCGA-DD-AACE TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACQ 
       13.48        55.40        63.48         0.30         3.52        14.20 
TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACX TCGA-DD-AAD3 TCGA-DD-AAD8 TCGA-DD-AADF 
       51.52        50.33         5.59        42.58        40.08         3.78 
TCGA-DD-AADG TCGA-DD-AADJ TCGA-DD-AADS TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE2 
       37.64        35.05        15.58        19.30        18.25        20.98 
TCGA-DD-AAE4 TCGA-DD-AAEA TCGA-DD-AAVP TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 
       19.99        18.90        79.07        26.93        28.08        13.91 
TCGA-ED-A7PX TCGA-ED-A7XO TCGA-ED-A8O5 TCGA-EP-A26S TCGA-FV-A23B TCGA-FV-A2QR 
        0.20        14.04        13.35        19.99        60.89        19.10 
TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-G3-A25S TCGA-G3-A25Y TCGA-G3-A3CI 
       12.03         0.03         0.33        13.68        14.86         5.92 
TCGA-G3-A3CK TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M5 TCGA-G3-A7M8 TCGA-G3-A7M9 
       19.23        17.10        22.06        14.70        14.14         1.84 
TCGA-G3-AAV0 TCGA-G3-AAV4 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5N0 TCGA-K7-A5RF 
       15.65         0.89         1.02         2.20        37.71        20.75 
TCGA-K7-A5RG TCGA-KR-A7K0 TCGA-LG-A6GG TCGA-LG-A9QC TCGA-MI-A75G TCGA-MR-A520 
       17.06         2.14        12.72        13.97        22.95         7.53 
TCGA-NI-A4U2 TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-T1-A6J8 
       58.88        21.01         3.09        21.04        19.33         0.76 
TCGA-UB-A7MB TCGA-UB-A7MF TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WX-AA46 TCGA-WX-AA47 
       19.76         7.04        10.32        11.34        24.85        18.28 
TCGA-XR-A8TF TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D2 
       22.78        25.71        23.21        35.87         0.69        25.15 
TCGA-ZS-A9CE TCGA-ZS-A9CF 
       40.80        79.30 

  AMP PEAK 16(8Q24.21) MUTATED AMP PEAK 16(8Q24.21) WILD-TYPE 
                          0.20                           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 
                        18.675                         20.895 
[1] "0.2 - 114.3 (18.7)" "0.0 - 120.8 (20.9)"
[1] "hr=" "1.1"
D16V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IIIA
  AMP PEAK 16(8Q24.21) MUTATED       109       58         0         41
  AMP PEAK 16(8Q24.21) WILD-TYPE      62       27         3         19
                                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                             109                             62
  STAGE II                             58                             27
  STAGE III                             0                              3
  STAGE IIIA                           41                             19
  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     112  61  47   6
  AMP PEAK 16(8Q24.21) WILD-TYPE    70  31  27   6
D16V4, multiclass
       clus
vv      AMP PEAK 16(8Q24.21) MUTATED AMP PEAK 16(8Q24.21) WILD-TYPE
  T0+T1                          112                             70
  T2                              61                             31
  T3                              47                             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"
D16V5, binary
                                cls
clus                               0   1
  AMP PEAK 16(8Q24.21) MUTATED   172   1
  AMP PEAK 16(8Q24.21) WILD-TYPE  78   2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(8Q24.21) MUTATED    172    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                          172                             78
  1                            1                              2
[1] 2 2
[1] FALSE
D16V6, binary
                                cls
clus                               0   1
  AMP PEAK 16(8Q24.21) MUTATED   177   2
  AMP PEAK 16(8Q24.21) WILD-TYPE  84   2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(8Q24.21) MUTATED    177    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                          177                             84
  1                            2                              2
[1] 2 2
[1] FALSE
D16V7, binary
                                cls
clus                               0   1
  AMP PEAK 16(8Q24.21) MUTATED    56 171
  AMP PEAK 16(8Q24.21) WILD-TYPE  59  76
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(8Q24.21) MUTATED     56  171
  AMP PEAK 16(8Q24.21) WILD-TYPE   59   76
        clus
vv       AMP PEAK 16(8Q24.21) MUTATED AMP PEAK 16(8Q24.21) WILD-TYPE
  FEMALE                           56                             59
  MALE                            171                             76
[1] 2 2
[1] FALSE
D16V8, binary
                                cls
clus                               0   1
  AMP PEAK 16(8Q24.21) MUTATED   209   6
  AMP PEAK 16(8Q24.21) WILD-TYPE 127   1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(8Q24.21) MUTATED    209    6
  AMP PEAK 16(8Q24.21) WILD-TYPE  127    1
     clus
vv    AMP PEAK 16(8Q24.21) MUTATED AMP PEAK 16(8Q24.21) WILD-TYPE
  NO                           209                            127
  YES                            6                              1
[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                        221
  AMP PEAK 16(8Q24.21) WILD-TYPE                      132
                                vv
clus                             HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK 16(8Q24.21) MUTATED                                  5
  AMP PEAK 16(8Q24.21) WILD-TYPE                                2
D16V9, multiclass
                                  clus
vv                                 AMP PEAK 16(8Q24.21) MUTATED
  FIBROLAMELLAR CARCINOMA                                     1
  HEPATOCELLULAR CARCINOMA                                  221
  HEPATOCHOLANGIOCARCINOMA (MIXED)                            5
                                  clus
vv                                 AMP PEAK 16(8Q24.21) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                       1
  HEPATOCELLULAR CARCINOMA                                    132
  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   199  11   1  12
  AMP PEAK 16(8Q24.21) WILD-TYPE 119   4   0   9
D16V10, multiclass
    clus
vv   AMP PEAK 16(8Q24.21) MUTATED AMP PEAK 16(8Q24.21) WILD-TYPE
  R0                          199                            119
  R1                           11                              4
  R2                            1                              0
  RX                           12                              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   118
  AMP PEAK 16(8Q24.21) WILD-TYPE                                0    39
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 16(8Q24.21) MUTATED                          11    90
  AMP PEAK 16(8Q24.21) WILD-TYPE                         6    87
D16V11, multiclass
                                  clus
vv                                 AMP PEAK 16(8Q24.21) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                     118
  BLACK OR AFRICAN AMERICAN                                  11
  WHITE                                                      90
                                  clus
vv                                 AMP PEAK 16(8Q24.21) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                        39
  BLACK OR AFRICAN AMERICAN                                     6
  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"
D16V12, binary
                                cls
clus                               0   1
  AMP PEAK 16(8Q24.21) MUTATED     7 211
  AMP PEAK 16(8Q24.21) WILD-TYPE   6 121
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(8Q24.21) MUTATED      7  211
  AMP PEAK 16(8Q24.21) WILD-TYPE    6  121
                        clus
vv                       AMP PEAK 16(8Q24.21) MUTATED
  HISPANIC OR LATINO                                7
  NOT HISPANIC OR LATINO                          211
                        clus
vv                       AMP PEAK 16(8Q24.21) WILD-TYPE
  HISPANIC OR LATINO                                  6
  NOT HISPANIC OR LATINO                            121
[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    25  18
  AMP PEAK 17(9Q34.2) WILD-TYPE 204 111
  AMP PEAK 17(9Q34.2) MUTATED AMP PEAK 17(9Q34.2) WILD-TYPE 
                           43                           315 
  AMP PEAK 17(9Q34.2) MUTATED AMP PEAK 17(9Q34.2) WILD-TYPE 
                           18                           111 
$`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        22.92        17.10        27.52 
TCGA-BC-A10Y TCGA-BC-A8YO TCGA-BW-A5NO TCGA-CC-5261 TCGA-CC-5263 TCGA-CC-5264 
       23.38        18.48         0.66         3.19         4.24         3.35 
TCGA-CC-A7IG TCGA-CC-A7II TCGA-CC-A7IK TCGA-DD-A1EG TCGA-DD-A3A0 TCGA-DD-A3A5 
        9.83        13.12         8.61        45.11        25.81       102.74 
TCGA-DD-A3A6 TCGA-DD-A4NV TCGA-DD-A73G TCGA-DD-AACY TCGA-DD-AAD6 TCGA-DD-AADJ 
      107.11        78.84       114.35        47.67        22.09        35.05 
TCGA-DD-AADO TCGA-DD-AAE0 TCGA-DD-AAE2 TCGA-DD-AAVV TCGA-DD-AAVZ TCGA-ED-A66Y 
       14.89        18.25        20.98        80.71        62.47         9.73 
TCGA-ED-A82E TCGA-EP-A2KB TCGA-ES-A2HS TCGA-FV-A2QQ TCGA-FV-A495 TCGA-FV-A4ZP 
       13.41        19.59        22.85        23.97         0.03        81.73 
TCGA-G3-A25U TCGA-G3-A3CG TCGA-G3-A7M9 TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-WQ-A9G7 
       53.79        22.13         1.84        21.60        29.79         0.99 
TCGA-ZS-A9CF 
       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        49.84        47.74        18.25        11.74 
TCGA-2Y-A9H7 TCGA-2Y-A9H8 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-4R-AA8I 
       38.40        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        14.76         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        45.93 
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         4.24         2.86         3.39         3.32 
TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A5UD 
        9.86         9.96        10.36        11.93        11.41         9.99 
TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IH TCGA-CC-A7IJ TCGA-CC-A7IL 
        8.94         7.13        21.34        12.00        12.56         9.14 
TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A113 
        4.60        11.31         9.17         6.94         8.15        79.73 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A 
       37.78        83.57        53.33       113.00         7.33         2.60 
TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB 
        0.46        21.76        51.29        90.71        79.40        66.31 
TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EI 
       19.79        75.65        11.47        12.95        49.15         6.02 
TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39X 
       33.04        18.35        13.64        21.14        27.19        55.69 
TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 
        5.62        19.76         7.66        70.06        17.59        20.12 
TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND 
       13.78         0.36        30.61        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-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-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-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-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-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-AAD5 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC 
       42.58        44.22        40.08        40.54        40.83        13.97 
TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADK 
       40.47        39.52         3.78        37.64        35.67        34.49 
TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR 
       20.91         0.39        29.52        15.06        14.33        66.67 
TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADV TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE1 
       15.58        18.21        18.87        19.30        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        26.63        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-AAW0 TCGA-DD-AAW1 
       72.39        76.18        56.48        64.77        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        29.92        26.93        28.08        13.91 
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-A8O6 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
       13.35         1.84         0.20        18.74        19.99        20.61 
TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR 
        0.62         9.96        11.93        14.40        60.89        19.10 
TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A496 TCGA-FV-A4ZQ 
       27.88         8.12         6.38        12.03         0.33         0.39 
TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y 
       13.68        51.06        28.27        30.74        58.49        14.86 
TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI 
       21.53        25.64         5.92        19.53        19.23        25.25 
TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M5 TCGA-G3-A7M6 
       22.95        20.42        17.10        22.06        14.70        20.78 
TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 
       11.87        14.14        15.78        15.65        11.80        12.23 
TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A3OU 
       13.55         0.89         8.75         2.14        11.87        22.92 
TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG 
        1.02         2.20         2.99        37.71        20.75        17.06 
TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-LG-A9QC 
       16.83        11.80         2.14        31.27        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        22.95        24.56        20.71 
TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF 
        7.53        10.85        58.88        26.27        17.69        21.01 
TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK 
        3.09        21.04        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-A7MD 
       36.10         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-AA44 TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CV 
       20.22        24.85        18.28        22.78        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        35.87         0.69        25.15        12.99 
TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CG 
       45.57        40.80        11.21 

  AMP PEAK 17(9Q34.2) MUTATED AMP PEAK 17(9Q34.2) WILD-TYPE 
                         0.03                          0.20 
  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 
                        22.85                         19.23 
[1] "0.0 - 120.8 (22.9)" "0.2 - 113.0 (19.2)"
[1] "hr=" "1.1"
D17V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IIIA
  AMP PEAK 17(9Q34.2) MUTATED        15        9         1         13
  AMP PEAK 17(9Q34.2) WILD-TYPE     156       76         2         47
                               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                           156
  STAGE II                             9                            76
  STAGE III                            1                             2
  STAGE IIIA                          13                            47
  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  10  16   3
  AMP PEAK 17(9Q34.2) WILD-TYPE   166  82  58   9
D17V4, multiclass
       clus
vv      AMP PEAK 17(9Q34.2) MUTATED AMP PEAK 17(9Q34.2) WILD-TYPE
  T0+T1                          16                           166
  T2                             10                            82
  T3                             16                            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"
D17V5, binary
                               cls
clus                              0   1
  AMP PEAK 17(9Q34.2) MUTATED    31   1
  AMP PEAK 17(9Q34.2) WILD-TYPE 219   2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 17(9Q34.2) MUTATED     31    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                          31                           219
  1                           1                             2
[1] 2 2
[1] FALSE
D17V6, binary
                               cls
clus                              0   1
  AMP PEAK 17(9Q34.2) MUTATED    33   1
  AMP PEAK 17(9Q34.2) WILD-TYPE 228   3
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 17(9Q34.2) MUTATED     33    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                          33                           228
  1                           1                             3
[1] 2 2
[1] FALSE
D17V7, binary
                               cls
clus                              0   1
  AMP PEAK 17(9Q34.2) MUTATED    16  29
  AMP PEAK 17(9Q34.2) WILD-TYPE  99 218
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 17(9Q34.2) MUTATED     16   29
  AMP PEAK 17(9Q34.2) WILD-TYPE   99  218
        clus
vv       AMP PEAK 17(9Q34.2) MUTATED AMP PEAK 17(9Q34.2) WILD-TYPE
  FEMALE                          16                            99
  MALE                            29                           218
[1] 2 2
[1] FALSE
D17V8, binary
                               cls
clus                              0   1
  AMP PEAK 17(9Q34.2) MUTATED    42   0
  AMP PEAK 17(9Q34.2) WILD-TYPE 294   7
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 17(9Q34.2) MUTATED     42    0
  AMP PEAK 17(9Q34.2) WILD-TYPE  294    7
     clus
vv    AMP PEAK 17(9Q34.2) MUTATED AMP PEAK 17(9Q34.2) WILD-TYPE
  NO                           42                           294
  YES                           0                             7
[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                         44
  AMP PEAK 17(9Q34.2) WILD-TYPE                      309
                               vv
clus                            HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK 17(9Q34.2) MUTATED                                  1
  AMP PEAK 17(9Q34.2) WILD-TYPE                                6
D17V9, multiclass
                                  clus
vv                                 AMP PEAK 17(9Q34.2) MUTATED
  FIBROLAMELLAR CARCINOMA                                    0
  HEPATOCELLULAR CARCINOMA                                  44
  HEPATOCHOLANGIOCARCINOMA (MIXED)                           1
                                  clus
vv                                 AMP PEAK 17(9Q34.2) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                      2
  HEPATOCELLULAR CARCINOMA                                   309
  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    37   3   0   5
  AMP PEAK 17(9Q34.2) WILD-TYPE 281  12   1  16
D17V10, multiclass
    clus
vv   AMP PEAK 17(9Q34.2) MUTATED AMP PEAK 17(9Q34.2) WILD-TYPE
  R0                          37                           281
  R1                           3                            12
  R2                           0                             1
  RX                           5                            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 17(9Q34.2) MUTATED                                  0    18
  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   152
D17V11, multiclass
                                  clus
vv                                 AMP PEAK 17(9Q34.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                     18
  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                                                      152
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V12, binary
                               cls
clus                              0   1
  AMP PEAK 17(9Q34.2) MUTATED     2  41
  AMP PEAK 17(9Q34.2) WILD-TYPE  11 291
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 17(9Q34.2) MUTATED      2   41
  AMP PEAK 17(9Q34.2) WILD-TYPE   11  291
                        clus
vv                       AMP PEAK 17(9Q34.2) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          41
                        clus
vv                       AMP PEAK 17(9Q34.2) WILD-TYPE
  HISPANIC OR LATINO                                11
  NOT HISPANIC OR LATINO                           291
[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  17
  AMP PEAK 18(11Q13.3) WILD-TYPE 191 112
  AMP PEAK 18(11Q13.3) MUTATED AMP PEAK 18(11Q13.3) WILD-TYPE 
                            55                            303 
  AMP PEAK 18(11Q13.3) MUTATED AMP PEAK 18(11Q13.3) WILD-TYPE 
                            17                            112 
$`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        22.92        27.91        27.52 
TCGA-BC-A3KG TCGA-BC-A69I TCGA-BD-A3EP TCGA-BD-A3ER TCGA-CC-5264 TCGA-CC-A3M9 
       22.36        12.72        13.45        36.66         3.35         9.86 
TCGA-CC-A3MB TCGA-CC-A7IE TCGA-CC-A7II TCGA-CC-A7IJ TCGA-DD-A115 TCGA-DD-A119 
       10.36         7.13        13.12        12.56        83.57         7.33 
TCGA-DD-A11A TCGA-DD-A1EB TCGA-DD-A39Y TCGA-DD-A3A0 TCGA-DD-A4ND TCGA-DD-A4NN 
        2.60        66.31         5.62        25.81        90.28        29.56 
TCGA-DD-A4NV TCGA-DD-A73E TCGA-DD-A73G TCGA-DD-AACB TCGA-DD-AAD1 TCGA-DD-AAD8 
       78.84         1.45       114.35        76.41        18.54        40.08 
TCGA-DD-AADL TCGA-DD-AADP TCGA-DD-AADV TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE6 
       20.91        15.06        18.87        18.25        18.25         4.64 
TCGA-DD-AAED TCGA-ED-A66Y TCGA-ED-A82E TCGA-EP-A2KA TCGA-FV-A496 TCGA-FV-A4ZQ 
       25.08         9.73        13.41        20.61         0.33         0.39 
TCGA-G3-A25S TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A5SJ TCGA-G3-AAV0 TCGA-GJ-A9DB 
       13.68        30.74        22.13        22.95        15.65         2.20 
TCGA-K7-A5RG TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-RC-A7SB TCGA-RC-A7SF TCGA-UB-A7ME 
       17.06        29.79        12.72        19.33        19.04        15.98 
TCGA-WQ-A9G7 
        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        49.84        47.74        18.25        11.74 
TCGA-2Y-A9H7 TCGA-2Y-A9H8 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-4R-AA8I 
       38.40        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        17.10        14.76         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        23.38         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 
       45.93         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         4.24         2.86         3.19         3.39         4.24 
TCGA-CC-A1HT TCGA-CC-A3MA TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A5UE 
        3.32         9.96        11.93        11.41         9.99         8.94 
TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7IK TCGA-CC-A7IL TCGA-CC-A8HT 
       21.34         9.83        12.00         8.61         9.14         4.60 
TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A114 
       11.31         9.17         6.94         8.15        79.73        37.78 
TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 
       53.33       113.00         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-A39X TCGA-DD-A39Z TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 
       27.19        55.69        19.76         7.66        70.06        17.59 
TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 
       20.12       102.74       107.11        13.78         0.36        30.61 
TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ 
       33.14        32.52        30.97        30.15        26.83        30.51 
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-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73F 
       80.75        23.93         9.30        23.05        22.78        35.67 
TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACC TCGA-DD-AACD 
       13.48         0.53        11.41        75.65        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-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-AADC TCGA-DD-AADD 
       44.22        22.09        40.54        40.83        13.97        40.47 
TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK 
       39.52         3.78        37.64        35.67        35.05        34.49 
TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS 
        0.39        29.52        14.89        14.33        66.67        15.58 
TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 
       18.21        19.30        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-AAEE 
       21.17        21.83        23.74        18.90        15.72        26.63 
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-AAVV TCGA-DD-AAVW TCGA-DD-AAVX 
       82.62        59.93        72.39        80.71        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-A66X TCGA-ED-A7PX 
       29.92        26.93        28.08        13.91        13.35         0.20 
TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A8O5 TCGA-ED-A8O6 
       12.82         0.20        14.04        13.15        13.35         1.84 
TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL 
        0.20        18.74        19.99        19.59         0.62         9.96 
TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR 
       11.93        22.85        14.40        60.89        23.97        19.10 
TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A4ZP 
       27.88         8.12         6.38        12.03         0.03        81.73 
TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z 
       51.06        53.79        28.27        58.49        14.86        21.53 
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-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 
       17.10        22.06        14.70        20.78        11.87        14.14 
TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 
        1.84        15.78        11.80        12.23        13.55         0.89 
TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-HP-A5MZ 
        8.75         2.14        11.87        22.92         1.02         2.99 
TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K2 
       37.71        20.75        16.83        11.80         2.14        21.60 
TCGA-KR-A7K7 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G 
       31.27        13.97        12.03         9.57        16.67        22.95 
TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF 
       24.56        20.71         7.53        10.85        58.88        26.27 
TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SH TCGA-RC-A7SK 
       17.69        21.01         3.09        21.04        15.39        15.52 
TCGA-RG-A7D4 TCGA-T1-A6J8 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD 
       36.10         0.76        17.59        19.76        16.44         1.71 
TCGA-UB-A7MF TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-AB4B TCGA-WX-AA44 
        7.04        10.75        10.32        11.34        12.99        20.22 
TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY 
       24.85        18.28        22.78        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        35.87         0.69        25.15        12.99        45.57 
TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       40.80        79.30        11.21 

  AMP PEAK 18(11Q13.3) MUTATED AMP PEAK 18(11Q13.3) WILD-TYPE 
                          0.33                           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 
                         18.54                          19.99 
[1] "0.3 - 114.3 (18.5)" "0.0 - 120.8 (20.0)"
[1] "hr=" "1.1"
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     138       79         3         48
                                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                            138
  STAGE II                              6                             79
  STAGE III                             0                              3
  STAGE IIIA                           12                             48
  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   149  85  59  11
D18V4, multiclass
       clus
vv      AMP PEAK 18(11Q13.3) MUTATED AMP PEAK 18(11Q13.3) WILD-TYPE
  T0+T1                           33                            149
  T2                               7                             85
  T3                              15                             59
  T4                               1                             11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V5, binary
                                cls
clus                               0   1
  AMP PEAK 18(11Q13.3) MUTATED    40   0
  AMP PEAK 18(11Q13.3) WILD-TYPE 210   3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 18(11Q13.3) MUTATED     40    0
  AMP PEAK 18(11Q13.3) WILD-TYPE  210    3
   clus
vv  AMP PEAK 18(11Q13.3) MUTATED AMP PEAK 18(11Q13.3) WILD-TYPE
  0                           40                            210
  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 218   3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 18(11Q13.3) MUTATED     43    1
  AMP PEAK 18(11Q13.3) WILD-TYPE  218    3
   clus
vv  AMP PEAK 18(11Q13.3) MUTATED AMP PEAK 18(11Q13.3) WILD-TYPE
  0                           43                            218
  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  95 211
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 18(11Q13.3) MUTATED     20   36
  AMP PEAK 18(11Q13.3) WILD-TYPE   95  211
        clus
vv       AMP PEAK 18(11Q13.3) MUTATED AMP PEAK 18(11Q13.3) WILD-TYPE
  FEMALE                           20                             95
  MALE                             36                            211
[1] 2 2
[1] FALSE
D18V8, binary
                                cls
clus                               0   1
  AMP PEAK 18(11Q13.3) MUTATED    51   0
  AMP PEAK 18(11Q13.3) WILD-TYPE 285   7
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 18(11Q13.3) MUTATED     51    0
  AMP PEAK 18(11Q13.3) WILD-TYPE  285    7
     clus
vv    AMP PEAK 18(11Q13.3) MUTATED AMP PEAK 18(11Q13.3) WILD-TYPE
  NO                            51                            285
  YES                            0                              7
[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                      297
                                vv
clus                             HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK 18(11Q13.3) MUTATED                                  0
  AMP PEAK 18(11Q13.3) WILD-TYPE                                7
D18V9, 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                                    297
  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 270  10   0  19
D18V10, multiclass
    clus
vv   AMP PEAK 18(11Q13.3) MUTATED AMP PEAK 18(11Q13.3) WILD-TYPE
  R0                           48                            270
  R1                            5                             10
  R2                            1                              0
  RX                            2                             19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 18(11Q13.3) MUTATED                                  0    24
  AMP PEAK 18(11Q13.3) WILD-TYPE                                1   133
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 18(11Q13.3) MUTATED                           3    27
  AMP PEAK 18(11Q13.3) WILD-TYPE                        14   150
D18V11, 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                                                       133
  BLACK OR AFRICAN AMERICAN                                    14
  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"
D18V12, binary
                                cls
clus                               0   1
  AMP PEAK 18(11Q13.3) MUTATED     1  51
  AMP PEAK 18(11Q13.3) WILD-TYPE  12 281
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 18(11Q13.3) MUTATED      1   51
  AMP PEAK 18(11Q13.3) WILD-TYPE   12  281
                        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                                 12
  NOT HISPANIC OR LATINO                            281
[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    36  27
  AMP PEAK 19(13Q32.3) WILD-TYPE 193 102
  AMP PEAK 19(13Q32.3) MUTATED AMP PEAK 19(13Q32.3) WILD-TYPE 
                            63                            295 
  AMP PEAK 19(13Q32.3) MUTATED AMP PEAK 19(13Q32.3) WILD-TYPE 
                            27                            102 
$`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         4.24         3.19         4.24 
TCGA-CC-A3MA TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A8HU TCGA-DD-A113 
        9.96         7.13        21.34         9.83        11.31        79.73 
TCGA-DD-A11A TCGA-DD-A11C TCGA-DD-A1EG TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39X 
        2.60        21.76        45.11        33.04        13.64        55.69 
TCGA-DD-A39Y TCGA-DD-A3A7 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACE TCGA-DD-AACO 
        5.62        13.78        75.65        76.41        63.48        61.68 
TCGA-DD-AAD5 TCGA-DD-AADD TCGA-DD-AADF TCGA-DD-AADV TCGA-DD-AADW TCGA-DD-AAE0 
       44.22        40.47         3.78        18.87        19.30        18.25 
TCGA-DD-AAE3 TCGA-DD-AAE6 TCGA-DD-AAE8 TCGA-DD-AAEK TCGA-DD-AAVW TCGA-ED-A7PY 
       18.61         4.64        21.83        35.08        76.18        12.82 
TCGA-EP-A2KA TCGA-EP-A3JL TCGA-FV-A23B TCGA-FV-A3I0 TCGA-FV-A496 TCGA-G3-A7M6 
       20.61         9.96        60.89        27.88         0.33        20.78 
TCGA-G3-AAV1 TCGA-G3-AAV6 TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-NI-A8LF TCGA-PD-A5DF 
       11.80         2.14        21.60        29.79        26.27        21.01 
TCGA-RC-A7S9 TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MC TCGA-UB-A7MF TCGA-UB-AA0U 
       21.04        36.10        17.59        16.44         7.04        10.75 
TCGA-WX-AA44 TCGA-WX-AA47 TCGA-ZP-A9CZ 
       20.22        18.28        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        49.84        47.74        18.25 
TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 
       11.74        38.40        22.92         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        17.10        14.76 
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        23.38        69.57         5.03 
TCGA-BC-A217 TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I TCGA-BD-A2L6 
       45.93        22.36        17.98        14.60        12.72        44.81 
TCGA-BD-A3ER TCGA-BW-A5NO TCGA-CC-5260 TCGA-CC-5262 TCGA-CC-5264 TCGA-CC-A1HT 
       36.66         0.66         2.86         3.39         3.35         3.32 
TCGA-CC-A3M9 TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A5UE 
        9.86        10.36        11.93        11.41         9.99         8.94 
TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A7IL TCGA-CC-A8HT 
       12.00        13.12        12.56         8.61         9.14         4.60 
TCGA-CC-A8HV TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 
        9.17         6.94         8.15        37.78        83.57        53.33 
TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA 
      113.00         7.33         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-A1EH 
       66.31        19.79        75.65        11.47        12.95        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-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 
        7.66        70.06        17.59        20.12       102.74       107.11 
TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NF 
        0.36        30.61        33.14        32.52        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-A4NV 
       73.81       108.76        12.26         0.30        80.75        78.84 
TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F 
       23.93         9.30        23.05        22.78         1.45        35.67 
TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACC TCGA-DD-AACD 
      114.35        13.48         0.53        11.41        55.40        12.53 
TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK 
       12.00        15.42         6.41        53.19        69.11         0.30 
TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS 
        3.52        58.16        42.81        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-AAD6 
        5.62         4.50        18.54        21.63        42.58        22.09 
TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADE TCGA-DD-AADG 
       40.08        40.54        40.83        13.97        39.52        37.64 
TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN 
       35.67        35.05        34.49        20.91         0.39        29.52 
TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU 
       14.89        15.06        14.33        66.67        15.58        18.21 
TCGA-DD-AADY TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE4 TCGA-DD-AAE7 TCGA-DD-AAE9 
       18.25        18.15        20.98        19.99        21.17        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        26.63        23.64        25.78 
TCGA-DD-AAEI TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU 
       50.33        79.07        89.69        82.62        59.93        72.39 
TCGA-DD-AAVV TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 
       80.71        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        29.92        26.93        28.08        13.91 
TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP 
       13.35         9.73         0.20         0.20        14.04        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-A2KB TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A2QQ 
       19.59         0.62        11.93        22.85        14.40        23.97 
TCGA-FV-A2QR TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A4ZP 
       19.10         8.12         6.38        12.03         0.03        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-A7M5 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-A7M9 TCGA-G3-AAUZ 
       22.06        14.70        11.87        14.14         1.84        15.78 
TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV7 
       15.65        12.23        13.55         0.89         8.75        11.87 
TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF 
       22.92         1.02         2.20         2.99        37.71        20.75 
TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG 
       17.06        16.83        11.80         2.14        31.27        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        22.95        24.56 
TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-O8-A75V TCGA-QA-A7B7 
       20.71         7.53        10.85        58.88        17.69         3.09 
TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-T1-A6J8 TCGA-UB-A7MB 
       19.33        19.04        15.39        15.52         0.76        19.76 
TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B 
        1.71        15.98        10.32        11.34         0.99        12.99 
TCGA-WX-AA46 TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9D0 
       24.85        22.78        13.55        35.77        25.71        35.87 
TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CF 
        0.69        25.15        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 
                          0.26                           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 
                         19.30                          19.76 
[1] "0.3 - 79.7 (19.3)"  "0.0 - 120.8 (19.8)"
[1] "hr=" "1.4"
D19V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IIIA
  AMP PEAK 19(13Q32.3) MUTATED        30       14         0         13
  AMP PEAK 19(13Q32.3) WILD-TYPE     141       71         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                              30                            141
  STAGE II                             14                             71
  STAGE III                             0                              3
  STAGE IIIA                           13                             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      33  14  14   4
  AMP PEAK 19(13Q32.3) WILD-TYPE   149  78  60   8
D19V4, multiclass
       clus
vv      AMP PEAK 19(13Q32.3) MUTATED AMP PEAK 19(13Q32.3) WILD-TYPE
  T0+T1                           33                            149
  T2                              14                             78
  T3                              14                             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 205   2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 19(13Q32.3) MUTATED     45    1
  AMP PEAK 19(13Q32.3) WILD-TYPE  205    2
   clus
vv  AMP PEAK 19(13Q32.3) MUTATED AMP PEAK 19(13Q32.3) WILD-TYPE
  0                           45                            205
  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 212   3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 19(13Q32.3) MUTATED     49    1
  AMP PEAK 19(13Q32.3) WILD-TYPE  212    3
   clus
vv  AMP PEAK 19(13Q32.3) MUTATED AMP PEAK 19(13Q32.3) WILD-TYPE
  0                           49                            212
  1                            1                              3
[1] 2 2
[1] FALSE
D19V7, binary
                                cls
clus                               0   1
  AMP PEAK 19(13Q32.3) MUTATED    29  36
  AMP PEAK 19(13Q32.3) WILD-TYPE  86 211
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 19(13Q32.3) MUTATED     29   36
  AMP PEAK 19(13Q32.3) WILD-TYPE   86  211
        clus
vv       AMP PEAK 19(13Q32.3) MUTATED AMP PEAK 19(13Q32.3) WILD-TYPE
  FEMALE                           29                             86
  MALE                             36                            211
[1] 2 2
[1] FALSE
D19V8, binary
                                cls
clus                               0   1
  AMP PEAK 19(13Q32.3) MUTATED    59   2
  AMP PEAK 19(13Q32.3) WILD-TYPE 277   5
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 19(13Q32.3) MUTATED     59    2
  AMP PEAK 19(13Q32.3) WILD-TYPE  277    5
     clus
vv    AMP PEAK 19(13Q32.3) MUTATED AMP PEAK 19(13Q32.3) WILD-TYPE
  NO                            59                            277
  YES                            2                              5
[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                         62
  AMP PEAK 19(13Q32.3) WILD-TYPE                      291
                                vv
clus                             HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK 19(13Q32.3) MUTATED                                  3
  AMP PEAK 19(13Q32.3) WILD-TYPE                                4
D19V9, multiclass
                                  clus
vv                                 AMP PEAK 19(13Q32.3) MUTATED
  FIBROLAMELLAR CARCINOMA                                     0
  HEPATOCELLULAR CARCINOMA                                   62
  HEPATOCHOLANGIOCARCINOMA (MIXED)                            3
                                  clus
vv                                 AMP PEAK 19(13Q32.3) 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
  AMP PEAK 19(13Q32.3) MUTATED    54   3   0   6
  AMP PEAK 19(13Q32.3) WILD-TYPE 264  12   1  15
D19V10, multiclass
    clus
vv   AMP PEAK 19(13Q32.3) MUTATED AMP PEAK 19(13Q32.3) WILD-TYPE
  R0                           54                            264
  R1                            3                             12
  R2                            0                              1
  RX                            6                             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 19(13Q32.3) MUTATED                                  0    30
  AMP PEAK 19(13Q32.3) WILD-TYPE                                1   127
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 19(13Q32.3) MUTATED                           4    29
  AMP PEAK 19(13Q32.3) WILD-TYPE                        13   148
D19V11, multiclass
                                  clus
vv                                 AMP PEAK 19(13Q32.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                      30
  BLACK OR AFRICAN AMERICAN                                   4
  WHITE                                                      29
                                  clus
vv                                 AMP PEAK 19(13Q32.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                       127
  BLACK OR AFRICAN AMERICAN                                    13
  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"
D19V12, binary
                                cls
clus                               0   1
  AMP PEAK 19(13Q32.3) MUTATED     2  58
  AMP PEAK 19(13Q32.3) WILD-TYPE  11 274
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 19(13Q32.3) MUTATED      2   58
  AMP PEAK 19(13Q32.3) WILD-TYPE   11  274
                        clus
vv                       AMP PEAK 19(13Q32.3) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           58
                        clus
vv                       AMP PEAK 19(13Q32.3) WILD-TYPE
  HISPANIC OR LATINO                                 11
  NOT HISPANIC OR LATINO                            274
[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    37  27
  AMP PEAK 20(13Q33.3) WILD-TYPE 192 102
  AMP PEAK 20(13Q33.3) MUTATED AMP PEAK 20(13Q33.3) WILD-TYPE 
                            64                            294 
  AMP PEAK 20(13Q33.3) MUTATED AMP PEAK 20(13Q33.3) WILD-TYPE 
                            27                            102 
$`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        45.93         0.26 
TCGA-BD-A3EP TCGA-CC-5258 TCGA-CC-5261 TCGA-CC-5263 TCGA-CC-A3MA TCGA-CC-A7IE 
       13.45         4.24         3.19         4.24         9.96         7.13 
TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A8HU TCGA-DD-A113 TCGA-DD-A11A TCGA-DD-A1EG 
       21.34         9.83        11.31        79.73         2.60        45.11 
TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A3A7 TCGA-DD-AACA 
       33.04        13.64        55.69         5.62        13.78        75.65 
TCGA-DD-AACB TCGA-DD-AACE TCGA-DD-AACO TCGA-DD-AAD5 TCGA-DD-AADD TCGA-DD-AADF 
       76.41        63.48        61.68        44.22        40.47         3.78 
TCGA-DD-AADQ TCGA-DD-AADW TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE3 TCGA-DD-AAE6 
       14.33        19.30        18.25        18.15        18.61         4.64 
TCGA-DD-AAE8 TCGA-DD-AAEK TCGA-DD-AAVW TCGA-ED-A66Y TCGA-ED-A7PY TCGA-EP-A26S 
       21.83        35.08        76.18         9.73        12.82        19.99 
TCGA-EP-A2KC TCGA-EP-A3JL TCGA-FV-A23B TCGA-FV-A3I0 TCGA-FV-A496 TCGA-G3-A7M6 
        0.62         9.96        60.89        27.88         0.33        20.78 
TCGA-G3-AAV1 TCGA-G3-AAV6 TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-NI-A8LF TCGA-RC-A7S9 
       11.80         2.14        21.60        29.79        26.27        21.04 
TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MC TCGA-UB-A7MF TCGA-UB-AA0U 
       15.52        36.10        17.59        16.44         7.04        10.75 
TCGA-WJ-A86L TCGA-WX-AA44 TCGA-WX-AA47 TCGA-ZP-A9CZ 
       11.34        20.22        18.28        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        49.84        47.74        18.25 
TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 
       11.74        38.40        22.92         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        17.10        14.76 
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        23.38         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-5264 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UC 
        3.35         3.32         9.86        10.36        11.93        11.41 
TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IK 
        9.99         8.94        12.00        13.12        12.56         8.61 
TCGA-CC-A7IL TCGA-CC-A8HT TCGA-CC-A8HV TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A114 
        9.14         4.60         9.17         6.94         8.15        37.78 
TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11C 
       83.57        53.33       113.00         7.33         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-A1EH TCGA-DD-A1EI TCGA-DD-A1EK TCGA-DD-A39V 
       11.47        12.95        49.15         6.02        18.35        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-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA 
       20.12       102.74       107.11         0.36        30.61        33.14 
TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ 
       32.52        90.28        30.97        30.15        26.83        30.51 
TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ 
       39.78        56.25        29.56        73.81       108.76        12.26 
TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C 
        0.30        80.75        78.84        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-AACC TCGA-DD-AACD TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH 
       11.41        55.40        12.53        12.00        15.42         6.41 
TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN 
       53.19        69.11         0.30         3.52        58.16        42.81 
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-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB 
       21.63        42.58        22.09        40.08        40.54        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-AADN TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADR 
       20.91         0.39        29.52        14.89        15.06        66.67 
TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADV TCGA-DD-AADY TCGA-DD-AAE2 TCGA-DD-AAE4 
       15.58        18.21        18.87        18.25        20.98        19.99 
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        26.63 
TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR 
       23.64        25.78        50.33        79.07        89.69        82.62 
TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVV TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ 
       59.93        72.39        80.71        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        29.92        26.93 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A7PX TCGA-ED-A7PZ TCGA-ED-A7XO 
       28.08        13.91        13.35         0.20         0.20        14.04 
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-A2KA TCGA-EP-A2KB TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A2QQ 
       20.61        19.59        11.93        22.85        14.40        23.97 
TCGA-FV-A2QR TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A4ZP 
       19.10         8.12         6.38        12.03         0.03        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-A7M5 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-A7M9 TCGA-G3-AAUZ 
       22.06        14.70        11.87        14.14         1.84        15.78 
TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV7 
       15.65        12.23        13.55         0.89         8.75        11.87 
TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF 
       22.92         1.02         2.20         2.99        37.71        20.75 
TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG 
       17.06        16.83        11.80         2.14        31.27        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        22.95        24.56 
TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-O8-A75V TCGA-PD-A5DF 
       20.71         7.53        10.85        58.88        17.69        21.01 
TCGA-QA-A7B7 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH TCGA-T1-A6J8 TCGA-UB-A7MB 
        3.09        19.33        19.04        15.39         0.76        19.76 
TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0V TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA46 
        1.71        15.98        10.32         0.99        12.99        24.85 
TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9D0 TCGA-ZP-A9D1 
       22.78        13.55        35.77        25.71        35.87         0.69 
TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       25.15        12.99        45.57        40.80        79.30        11.21 

  AMP PEAK 20(13Q33.3) MUTATED AMP PEAK 20(13Q33.3) WILD-TYPE 
                          0.26                           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 
                        18.265                         20.055 
[1] "0.3 - 79.7 (18.3)"  "0.0 - 120.8 (20.1)"
[1] "hr=" "1.5"
D20V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IIIA
  AMP PEAK 20(13Q33.3) MUTATED        32       16         0         12
  AMP PEAK 20(13Q33.3) WILD-TYPE     139       69         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                              32                            139
  STAGE II                             16                             69
  STAGE III                             0                              3
  STAGE IIIA                           12                             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      35  16  13   2
  AMP PEAK 20(13Q33.3) WILD-TYPE   147  76  61  10
D20V4, multiclass
       clus
vv      AMP PEAK 20(13Q33.3) MUTATED AMP PEAK 20(13Q33.3) WILD-TYPE
  T0+T1                           35                            147
  T2                              16                             76
  T3                              13                             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 205   2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(13Q33.3) MUTATED     45    1
  AMP PEAK 20(13Q33.3) WILD-TYPE  205    2
   clus
vv  AMP PEAK 20(13Q33.3) MUTATED AMP PEAK 20(13Q33.3) WILD-TYPE
  0                           45                            205
  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 212   3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(13Q33.3) MUTATED     49    1
  AMP PEAK 20(13Q33.3) WILD-TYPE  212    3
   clus
vv  AMP PEAK 20(13Q33.3) MUTATED AMP PEAK 20(13Q33.3) WILD-TYPE
  0                           49                            212
  1                            1                              3
[1] 2 2
[1] FALSE
D20V7, binary
                                cls
clus                               0   1
  AMP PEAK 20(13Q33.3) MUTATED    27  39
  AMP PEAK 20(13Q33.3) WILD-TYPE  88 208
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(13Q33.3) MUTATED     27   39
  AMP PEAK 20(13Q33.3) WILD-TYPE   88  208
        clus
vv       AMP PEAK 20(13Q33.3) MUTATED AMP PEAK 20(13Q33.3) WILD-TYPE
  FEMALE                           27                             88
  MALE                             39                            208
[1] 2 2
[1] FALSE
D20V8, binary
                                cls
clus                               0   1
  AMP PEAK 20(13Q33.3) MUTATED    60   2
  AMP PEAK 20(13Q33.3) WILD-TYPE 276   5
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(13Q33.3) MUTATED     60    2
  AMP PEAK 20(13Q33.3) WILD-TYPE  276    5
     clus
vv    AMP PEAK 20(13Q33.3) MUTATED AMP PEAK 20(13Q33.3) WILD-TYPE
  NO                            60                            276
  YES                            2                              5
[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                         63
  AMP PEAK 20(13Q33.3) WILD-TYPE                      290
                                vv
clus                             HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK 20(13Q33.3) MUTATED                                  3
  AMP PEAK 20(13Q33.3) WILD-TYPE                                4
D20V9, multiclass
                                  clus
vv                                 AMP PEAK 20(13Q33.3) MUTATED
  FIBROLAMELLAR CARCINOMA                                     0
  HEPATOCELLULAR CARCINOMA                                   63
  HEPATOCHOLANGIOCARCINOMA (MIXED)                            3
                                  clus
vv                                 AMP PEAK 20(13Q33.3) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                       2
  HEPATOCELLULAR CARCINOMA                                    290
  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    56   3   0   5
  AMP PEAK 20(13Q33.3) WILD-TYPE 262  12   1  16
D20V10, multiclass
    clus
vv   AMP PEAK 20(13Q33.3) MUTATED AMP PEAK 20(13Q33.3) WILD-TYPE
  R0                           56                            262
  R1                            3                             12
  R2                            0                              1
  RX                            5                             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 20(13Q33.3) MUTATED                                  0    33
  AMP PEAK 20(13Q33.3) WILD-TYPE                                1   124
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 20(13Q33.3) MUTATED                           5    26
  AMP PEAK 20(13Q33.3) WILD-TYPE                        12   151
D20V11, multiclass
                                  clus
vv                                 AMP PEAK 20(13Q33.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                      33
  BLACK OR AFRICAN AMERICAN                                   5
  WHITE                                                      26
                                  clus
vv                                 AMP PEAK 20(13Q33.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                       124
  BLACK OR AFRICAN AMERICAN                                    12
  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"
D20V12, binary
                                cls
clus                               0   1
  AMP PEAK 20(13Q33.3) MUTATED     2  59
  AMP PEAK 20(13Q33.3) WILD-TYPE  11 273
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(13Q33.3) MUTATED      2   59
  AMP PEAK 20(13Q33.3) WILD-TYPE   11  273
                        clus
vv                       AMP PEAK 20(13Q33.3) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           59
                        clus
vv                       AMP PEAK 20(13Q33.3) WILD-TYPE
  HISPANIC OR LATINO                                 11
  NOT HISPANIC OR LATINO                            273
[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    36  17
  AMP PEAK 21(15Q26.3) WILD-TYPE 193 112
  AMP PEAK 21(15Q26.3) MUTATED AMP PEAK 21(15Q26.3) WILD-TYPE 
                            53                            305 
  AMP PEAK 21(15Q26.3) MUTATED AMP PEAK 21(15Q26.3) WILD-TYPE 
                            17                            112 
$`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        49.84         8.55        10.78        37.32 
TCGA-BC-A10Y TCGA-BC-A217 TCGA-BC-A3KF TCGA-BW-A5NO TCGA-CC-5262 TCGA-CC-5263 
       23.38        45.93         0.26         0.66         3.39         4.24 
TCGA-CC-A3M9 TCGA-CC-A5UE TCGA-CC-A7IF TCGA-CC-A9FW TCGA-DD-A11A TCGA-DD-A39Z 
        9.86         8.94        21.34         8.15         2.60        19.76 
TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NV TCGA-DD-A73G TCGA-DD-AACB TCGA-DD-AACP 
       26.83        30.51        78.84       114.35        76.41        13.64 
TCGA-DD-AACV TCGA-DD-AACZ TCGA-DD-AADO TCGA-DD-AADU TCGA-DD-AADV TCGA-DD-AAE0 
       50.33         5.62        14.89        18.21        18.87        18.25 
TCGA-DD-AAE3 TCGA-DD-AAE6 TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-ED-A5KG TCGA-ED-A66X 
       18.61         4.64        21.83        18.90        28.08        13.35 
TCGA-ED-A7PZ TCGA-ED-A8O6 TCGA-EP-A2KA TCGA-ES-A2HS TCGA-FV-A23B TCGA-FV-A4ZQ 
        0.20         1.84        20.61        22.85        60.89         0.39 
TCGA-G3-A25T TCGA-G3-A25Y TCGA-G3-A3CH TCGA-G3-A6UC TCGA-MI-A75G TCGA-MR-A8JO 
       51.06        14.86        25.64        22.06        22.95        10.85 
TCGA-O8-A75V TCGA-RC-A7SK TCGA-UB-A7MA TCGA-WQ-AB4B TCGA-WX-AA47 
       17.69        15.52        17.59        12.99        18.28 

$`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 
       38.40        20.81        22.92         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        17.10        14.76         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-5264 TCGA-CC-A1HT 
       36.66         4.24         2.86         3.19         3.35         3.32 
TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A7IE 
        9.96        10.36        11.93        11.41         9.99         7.13 
TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A7IL 
        9.83        12.00        13.12        12.56         8.61         9.14 
TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FS TCGA-DD-A113 TCGA-DD-A114 
        4.60        11.31         9.17         6.94        79.73        37.78 
TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11C 
       83.57        53.33       113.00         7.33         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-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 
       25.81         7.66        70.06        17.59        20.12       102.74 
TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB 
      107.11        13.78         0.36        30.61        33.14        32.52 
TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN 
       90.28        30.97        30.15        39.78        56.25        29.56 
TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A73A 
       73.81       108.76        12.26         0.30        80.75        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-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-AACQ TCGA-DD-AACS 
        3.52        58.16        42.81        61.68        14.20        59.31 
TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AAD0 
       51.35        51.52        46.82         5.59        47.67         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-AADF 
       40.54        40.83        13.97        40.47        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-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADW 
       29.52        15.06        14.33        66.67        15.58        19.30 
TCGA-DD-AADY TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE4 TCGA-DD-AAE7 TCGA-DD-AAE9 
       18.25        18.15        20.98        19.99        21.17        23.74 
TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAEI 
       15.72        25.08        26.63        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-AAVV TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 
       80.71        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-A627 
       65.39        49.48        53.69        29.92        26.93        13.91 
TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E 
        9.73         0.20        12.82        14.04        13.15        13.41 
TCGA-ED-A8O5 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KB TCGA-EP-A2KC 
       13.35         0.20        18.74        19.99        19.59         0.62 
TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 
        9.96        11.93        14.40        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-G3-A25S TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Z 
       13.68        53.79        28.27        30.74        58.49        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-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 
       20.42        17.10        14.70        20.78        11.87        14.14 
TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 
        1.84        15.78        15.65        11.80        12.23        13.55 
TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 
        0.89         8.75         2.14        11.87        22.92         1.02 
TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 
        2.20         2.99        37.71        20.75        17.06        16.83 
TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG 
       11.80         2.14        21.60        31.27        29.79        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        24.56        20.71 
TCGA-MR-A520 TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 
        7.53        58.88        26.27        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        36.10         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-AA44 TCGA-WX-AA46 TCGA-XR-A8TF TCGA-YA-A8S7 
       11.34         0.99        20.22        24.85        22.78        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        35.87         0.69        25.15 
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 21(15Q26.3) MUTATED AMP PEAK 21(15Q26.3) WILD-TYPE 
                          0.20                           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 
                         18.28                          20.12 
[1] "0.2 - 114.3 (18.3)" "0.0 - 120.8 (20.1)"
[1] "hr=" "1"  
D21V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IIIA
  AMP PEAK 21(15Q26.3) MUTATED        21       13         0         13
  AMP PEAK 21(15Q26.3) WILD-TYPE     150       72         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                            150
  STAGE II                             13                             72
  STAGE III                             0                              3
  STAGE IIIA                           13                             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  14   3
  AMP PEAK 21(15Q26.3) WILD-TYPE   161  76  60   9
D21V4, multiclass
       clus
vv      AMP PEAK 21(15Q26.3) MUTATED AMP PEAK 21(15Q26.3) WILD-TYPE
  T0+T1                           21                            161
  T2                              16                             76
  T3                              14                             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 213   3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 21(15Q26.3) MUTATED     37    0
  AMP PEAK 21(15Q26.3) WILD-TYPE  213    3
   clus
vv  AMP PEAK 21(15Q26.3) MUTATED AMP PEAK 21(15Q26.3) WILD-TYPE
  0                           37                            213
  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 220   3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 21(15Q26.3) MUTATED     41    1
  AMP PEAK 21(15Q26.3) WILD-TYPE  220    3
   clus
vv  AMP PEAK 21(15Q26.3) MUTATED AMP PEAK 21(15Q26.3) WILD-TYPE
  0                           41                            220
  1                            1                              3
[1] 2 2
[1] FALSE
D21V7, binary
                                cls
clus                               0   1
  AMP PEAK 21(15Q26.3) MUTATED    20  34
  AMP PEAK 21(15Q26.3) WILD-TYPE  95 213
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 21(15Q26.3) MUTATED     20   34
  AMP PEAK 21(15Q26.3) WILD-TYPE   95  213
        clus
vv       AMP PEAK 21(15Q26.3) MUTATED AMP PEAK 21(15Q26.3) WILD-TYPE
  FEMALE                           20                             95
  MALE                             34                            213
[1] 2 2
[1] FALSE
D21V8, binary
                                cls
clus                               0   1
  AMP PEAK 21(15Q26.3) MUTATED    48   1
  AMP PEAK 21(15Q26.3) WILD-TYPE 288   6
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 21(15Q26.3) MUTATED     48    1
  AMP PEAK 21(15Q26.3) WILD-TYPE  288    6
     clus
vv    AMP PEAK 21(15Q26.3) MUTATED AMP PEAK 21(15Q26.3) WILD-TYPE
  NO                            48                            288
  YES                            1                              6
[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                         52
  AMP PEAK 21(15Q26.3) WILD-TYPE                      301
                                vv
clus                             HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK 21(15Q26.3) MUTATED                                  1
  AMP PEAK 21(15Q26.3) WILD-TYPE                                6
D21V9, multiclass
                                  clus
vv                                 AMP PEAK 21(15Q26.3) MUTATED
  FIBROLAMELLAR CARCINOMA                                     1
  HEPATOCELLULAR CARCINOMA                                   52
  HEPATOCHOLANGIOCARCINOMA (MIXED)                            1
                                  clus
vv                                 AMP PEAK 21(15Q26.3) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                       1
  HEPATOCELLULAR CARCINOMA                                    301
  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    46   3   0   4
  AMP PEAK 21(15Q26.3) WILD-TYPE 272  12   1  17
D21V10, multiclass
    clus
vv   AMP PEAK 21(15Q26.3) MUTATED AMP PEAK 21(15Q26.3) WILD-TYPE
  R0                           46                            272
  R1                            3                             12
  R2                            0                              1
  RX                            4                             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 21(15Q26.3) MUTATED                                  0    25
  AMP PEAK 21(15Q26.3) WILD-TYPE                                1   132
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 21(15Q26.3) MUTATED                           2    24
  AMP PEAK 21(15Q26.3) WILD-TYPE                        15   153
D21V11, multiclass
                                  clus
vv                                 AMP PEAK 21(15Q26.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                      25
  BLACK OR AFRICAN AMERICAN                                   2
  WHITE                                                      24
                                  clus
vv                                 AMP PEAK 21(15Q26.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                       132
  BLACK OR AFRICAN AMERICAN                                    15
  WHITE                                                       153
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V12, binary
                                cls
clus                               0   1
  AMP PEAK 21(15Q26.3) MUTATED     5  45
  AMP PEAK 21(15Q26.3) WILD-TYPE   8 287
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 21(15Q26.3) MUTATED      5   45
  AMP PEAK 21(15Q26.3) WILD-TYPE    8  287
                        clus
vv                       AMP PEAK 21(15Q26.3) MUTATED
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                           45
                        clus
vv                       AMP PEAK 21(15Q26.3) WILD-TYPE
  HISPANIC OR LATINO                                  8
  NOT HISPANIC OR LATINO                            287
[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    25  21
  AMP PEAK 22(17P11.2) WILD-TYPE 204 108
  AMP PEAK 22(17P11.2) MUTATED AMP PEAK 22(17P11.2) WILD-TYPE 
                            46                            312 
  AMP PEAK 22(17P11.2) MUTATED AMP PEAK 22(17P11.2) WILD-TYPE 
                            21                            108 
$`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        45.93 
TCGA-BC-A3KF TCGA-CC-5260 TCGA-CC-5264 TCGA-CC-A3M9 TCGA-CC-A5UE TCGA-CC-A7IE 
        0.26         2.86         3.35         9.86         8.94         7.13 
TCGA-CC-A7IK TCGA-CC-A9FW TCGA-DD-A115 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A3A3 
        8.61         8.15        83.57         7.33         2.60        17.59 
TCGA-DD-A3A5 TCGA-DD-A3A7 TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A73E TCGA-DD-AACB 
      102.74        13.78        73.81       108.76         1.45        76.41 
TCGA-DD-AACI TCGA-DD-AAD0 TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADO TCGA-DD-AADR 
       53.19         4.50        40.47        39.52        14.89        66.67 
TCGA-DD-AAVR TCGA-DD-AAW1 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PZ TCGA-ED-A8O6 
       82.62        65.39        13.35         9.73         0.20         1.84 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-ES-A2HS TCGA-FV-A4ZP TCGA-G3-AAUZ TCGA-G3-AAV6 
       20.61        19.59        22.85        81.73        15.78         2.14 
TCGA-MI-A75G TCGA-O8-A75V TCGA-UB-A7MA TCGA-UB-A7MB 
       22.95        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        49.84        47.74        18.25 
TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB 
       11.74        38.40        20.81        22.92         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        17.10        14.76 
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        23.38         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         4.24         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         9.96        10.36        11.93 
TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7II 
       11.41         9.99        21.34         9.83        12.00        13.12 
TCGA-CC-A7IJ TCGA-CC-A7IL TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FS 
       12.56         9.14         4.60        11.31         9.17         6.94 
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 
       26.63        23.64        25.78        50.33        35.08        79.07 
TCGA-DD-AAVQ TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVV TCGA-DD-AAVW TCGA-DD-AAVX 
       89.69        59.93        72.39        80.71        76.18        56.48 
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        29.92 
TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7XO 
       26.93        28.08        13.91         0.20        12.82        14.04 
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-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-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V 
        0.33         0.39        13.68        51.06        53.79        28.27 
TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH 
       30.74        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-A5SM TCGA-G3-A6UC TCGA-G3-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 
       17.10        22.06        14.70        20.78        11.87        14.14 
TCGA-G3-A7M9 TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 
        1.84        15.65        11.80        12.23        13.55         0.89 
TCGA-G3-AAV5 TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ 
        8.75        11.87        22.92         1.02         2.20         2.99 
TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 
       37.71        20.75        17.06        16.83        11.80         2.14 
TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD 
       21.60        31.27        29.79        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        24.56        20.71         7.53        10.85 
TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SB 
       58.88        26.27        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        36.10         0.76        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-AA44 TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TF 
        0.99        12.99        20.22        24.85        18.28        22.78 
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        35.87         0.69 
TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       25.15        12.99        45.57        40.80        79.30        11.21 

  AMP PEAK 22(17P11.2) MUTATED AMP PEAK 22(17P11.2) WILD-TYPE 
                          0.20                           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 
                         17.64                          19.99 
[1] "0.2 - 120.8 (17.6)" "0.0 - 114.3 (20.0)"
[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     154       78         2         45
                                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                            154
  STAGE II                              7                             78
  STAGE III                             1                              2
  STAGE IIIA                           15                             45
  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   165  84  55  10
D22V4, multiclass
       clus
vv      AMP PEAK 22(17P11.2) MUTATED AMP PEAK 22(17P11.2) WILD-TYPE
  T0+T1                           17                            165
  T2                               8                             84
  T3                              19                             55
  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 216   3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 22(17P11.2) MUTATED     34    0
  AMP PEAK 22(17P11.2) WILD-TYPE  216    3
   clus
vv  AMP PEAK 22(17P11.2) MUTATED AMP PEAK 22(17P11.2) WILD-TYPE
  0                           34                            216
  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 225   3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 22(17P11.2) MUTATED     36    1
  AMP PEAK 22(17P11.2) WILD-TYPE  225    3
   clus
vv  AMP PEAK 22(17P11.2) MUTATED AMP PEAK 22(17P11.2) WILD-TYPE
  0                           36                            225
  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 101 215
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 22(17P11.2) MUTATED     14   32
  AMP PEAK 22(17P11.2) WILD-TYPE  101  215
        clus
vv       AMP PEAK 22(17P11.2) MUTATED AMP PEAK 22(17P11.2) WILD-TYPE
  FEMALE                           14                            101
  MALE                             32                            215
[1] 2 2
[1] FALSE
D22V8, binary
                                cls
clus                               0   1
  AMP PEAK 22(17P11.2) MUTATED    41   0
  AMP PEAK 22(17P11.2) WILD-TYPE 295   7
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 22(17P11.2) MUTATED     41    0
  AMP PEAK 22(17P11.2) WILD-TYPE  295    7
     clus
vv    AMP PEAK 22(17P11.2) MUTATED AMP PEAK 22(17P11.2) WILD-TYPE
  NO                            41                            295
  YES                            0                              7
[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                      308
                                vv
clus                             HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK 22(17P11.2) MUTATED                                  1
  AMP PEAK 22(17P11.2) WILD-TYPE                                6
D22V9, 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                                    308
  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 281  10   0  18
D22V10, multiclass
    clus
vv   AMP PEAK 22(17P11.2) MUTATED AMP PEAK 22(17P11.2) WILD-TYPE
  R0                           37                            281
  R1                            5                             10
  R2                            1                              0
  RX                            3                             18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 22(17P11.2) MUTATED                                  0    22
  AMP PEAK 22(17P11.2) WILD-TYPE                                1   135
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 22(17P11.2) MUTATED                           2    19
  AMP PEAK 22(17P11.2) WILD-TYPE                        15   158
D22V11, 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                                                       135
  BLACK OR AFRICAN AMERICAN                                    15
  WHITE                                                       158
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V12, binary
                                cls
clus                               0   1
  AMP PEAK 22(17P11.2) MUTATED     3  39
  AMP PEAK 22(17P11.2) WILD-TYPE  10 293
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 22(17P11.2) MUTATED      3   39
  AMP PEAK 22(17P11.2) WILD-TYPE   10  293
                        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                                 10
  NOT HISPANIC OR LATINO                            293
[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  56
  AMP PEAK 23(17Q25.3) WILD-TYPE 145  73
  AMP PEAK 23(17Q25.3) MUTATED AMP PEAK 23(17Q25.3) WILD-TYPE 
                           140                            218 
  AMP PEAK 23(17Q25.3) MUTATED AMP PEAK 23(17Q25.3) WILD-TYPE 
                            56                             73 
$`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        22.92 
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        23.38         1.12         5.03        44.42        45.93 
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-5264 TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A5UE 
        4.24         3.35        10.36        11.93        11.41         8.94 
TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A7IL 
        7.13        21.34         9.83        12.56         8.61         9.14 
TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A9FW TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 
        4.60        11.31         8.15        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-AAVV TCGA-DD-AAW1 TCGA-ED-A66X 
       26.63        35.08        82.62        80.71        65.39        13.35 
TCGA-ED-A66Y TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-ED-A8O6 TCGA-EP-A2KB TCGA-EP-A2KC 
        9.73         0.20        13.15         1.84        19.59         0.62 
TCGA-ES-A2HS TCGA-FV-A2QR TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-G3-A25S 
       22.85        19.10         0.03         0.33        81.73        13.68 
TCGA-G3-A25U TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Z TCGA-G3-A3CJ TCGA-G3-A3CK 
       53.79        30.74        58.49        21.53        19.53        19.23 
TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A7M6 TCGA-G3-AAUZ TCGA-G3-AAV1 
       25.25        22.95        20.42        20.78        15.78        11.80 
TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-K7-AAU7 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC 
        8.75         2.14        11.80        29.79        12.72        13.97 
TCGA-MI-A75G TCGA-MI-A75I TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF 
       22.95        20.71        58.88        26.27        17.69        21.01 
TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MC TCGA-UB-AA0U TCGA-ZP-A9CZ TCGA-ZP-A9D2 
       36.10        17.59        16.44        10.75        23.21        25.15 
TCGA-ZP-A9D4 TCGA-ZS-A9CF 
       12.99        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 
       49.84        47.74        18.25        11.74        38.40        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 
       17.10        14.76        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         4.24         3.39         3.32         9.86         9.96 
TCGA-CC-A5UD TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A8HV TCGA-CC-A9FS TCGA-DD-A113 
        9.99        12.00        13.12         9.17         6.94        79.73 
TCGA-DD-A118 TCGA-DD-A11B TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EC TCGA-DD-A1ED 
      113.00         0.46        51.29        90.71        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-A39X TCGA-DD-A39Z TCGA-DD-A3A2 TCGA-DD-A3A5 
       21.14        27.19        55.69        19.76        70.06       102.74 
TCGA-DD-A3A6 TCGA-DD-A3A8 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NF 
      107.11         0.36        33.14        32.52        90.28        30.97 
TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS 
       39.78        56.25        29.56        12.26         0.30        80.75 
TCGA-DD-A4NV TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AACC 
       78.84         9.30        23.05       114.35        13.48        55.40 
TCGA-DD-AACD TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACK TCGA-DD-AACL 
       12.53        12.00        15.42         6.41         0.30         3.52 
TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACT 
       58.16        42.81        61.68        13.64        14.20        51.35 
TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD0 
       51.52        50.33        46.82        47.67         5.62         4.50 
TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB 
       18.54        21.63        42.58        40.08        40.54        40.83 
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-AADS TCGA-DD-AADV TCGA-DD-AADY TCGA-DD-AAE1 TCGA-DD-AAE4 
       14.33        15.58        18.87        18.25        18.15        19.99 
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-AAEG TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVS 
       23.64        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-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 
       49.48        53.69        29.92        26.93        28.08        13.91 
TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7XO TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A97K 
        0.20        12.82        14.04        13.41        13.35         0.20 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HT 
       18.74        19.99        20.61         9.96        11.93        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-A4ZQ TCGA-G3-A25T TCGA-G3-A25V TCGA-G3-A25Y TCGA-G3-A3CG TCGA-G3-A3CH 
        0.39        51.06        28.27        14.86        22.13        25.64 
TCGA-G3-A3CI TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M5 TCGA-G3-A7M7 TCGA-G3-A7M8 
        5.92        17.10        22.06        14.70        11.87        14.14 
TCGA-G3-A7M9 TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV7 
        1.84        15.65        12.23        13.55         0.89        11.87 
TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF 
       22.92         1.02         2.20         2.99        37.71        20.75 
TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-LG-A9QD 
       17.06        16.83         2.14        21.60        31.27        12.03 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75H TCGA-MR-A520 TCGA-MR-A8JO TCGA-QA-A7B7 
        9.57        16.67        24.56         7.53        10.85         3.09 
TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-T1-A6J8 
       21.04        19.33        19.04        15.39        15.52         0.76 
TCGA-UB-A7MB TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-A7MF TCGA-UB-AA0V TCGA-WJ-A86L 
       19.76         1.71        15.98         7.04        10.32        11.34 
TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TF 
        0.99        12.99        20.22        24.85        18.28        22.78 
TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZS-A9CD 
       13.55        35.77        25.71        35.87         0.69        45.57 
TCGA-ZS-A9CE TCGA-ZS-A9CG 
       40.80        11.21 

  AMP PEAK 23(17Q25.3) MUTATED AMP PEAK 23(17Q25.3) WILD-TYPE 
                          0.03                           0.20 
  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 
                        20.565                         19.185 
[1] "0.0 - 120.8 (20.6)" "0.2 - 114.3 (19.2)"
[1] "hr=" "1.2"
D23V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IIIA
  AMP PEAK 23(17Q25.3) MUTATED        54       35         0         32
  AMP PEAK 23(17Q25.3) WILD-TYPE     117       50         3         28
                                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                            117
  STAGE II                             35                             50
  STAGE III                             0                              3
  STAGE IIIA                           32                             28
  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  39  38   8
  AMP PEAK 23(17Q25.3) WILD-TYPE   125  53  36   4
D23V4, multiclass
       clus
vv      AMP PEAK 23(17Q25.3) MUTATED AMP PEAK 23(17Q25.3) WILD-TYPE
  T0+T1                           57                            125
  T2                              39                             53
  T3                              38                             36
  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    98   1
  AMP PEAK 23(17Q25.3) WILD-TYPE 152   2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 23(17Q25.3) MUTATED     98    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                           98                            152
  1                            1                              2
[1] 2 2
[1] FALSE
D23V6, binary
                                cls
clus                               0   1
  AMP PEAK 23(17Q25.3) MUTATED   108   2
  AMP PEAK 23(17Q25.3) WILD-TYPE 153   2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 23(17Q25.3) MUTATED    108    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                          108                            153
  1                            2                              2
[1] 2 2
[1] FALSE
D23V7, binary
                                cls
clus                               0   1
  AMP PEAK 23(17Q25.3) MUTATED    38 104
  AMP PEAK 23(17Q25.3) WILD-TYPE  77 143
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 23(17Q25.3) MUTATED     38  104
  AMP PEAK 23(17Q25.3) WILD-TYPE   77  143
        clus
vv       AMP PEAK 23(17Q25.3) MUTATED AMP PEAK 23(17Q25.3) WILD-TYPE
  FEMALE                           38                             77
  MALE                            104                            143
[1] 2 2
[1] FALSE
D23V8, binary
                                cls
clus                               0   1
  AMP PEAK 23(17Q25.3) MUTATED   130   2
  AMP PEAK 23(17Q25.3) WILD-TYPE 206   5
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 23(17Q25.3) MUTATED    130    2
  AMP PEAK 23(17Q25.3) WILD-TYPE  206    5
     clus
vv    AMP PEAK 23(17Q25.3) MUTATED AMP PEAK 23(17Q25.3) WILD-TYPE
  NO                           130                            206
  YES                            2                              5
[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                        140
  AMP PEAK 23(17Q25.3) WILD-TYPE                      213
                                vv
clus                             HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK 23(17Q25.3) MUTATED                                  2
  AMP PEAK 23(17Q25.3) WILD-TYPE                                5
D23V9, multiclass
                                  clus
vv                                 AMP PEAK 23(17Q25.3) MUTATED
  FIBROLAMELLAR CARCINOMA                                     0
  HEPATOCELLULAR CARCINOMA                                  140
  HEPATOCHOLANGIOCARCINOMA (MIXED)                            2
                                  clus
vv                                 AMP PEAK 23(17Q25.3) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                       2
  HEPATOCELLULAR CARCINOMA                                    213
  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   120  10   1  10
  AMP PEAK 23(17Q25.3) WILD-TYPE 198   5   0  11
D23V10, multiclass
    clus
vv   AMP PEAK 23(17Q25.3) MUTATED AMP PEAK 23(17Q25.3) WILD-TYPE
  R0                          120                            198
  R1                           10                              5
  R2                            1                              0
  RX                           10                             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 23(17Q25.3) MUTATED                                  1    67
  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   117
D23V11, multiclass
                                  clus
vv                                 AMP PEAK 23(17Q25.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                      67
  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                                                       117
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V12, binary
                                cls
clus                               0   1
  AMP PEAK 23(17Q25.3) MUTATED     3 132
  AMP PEAK 23(17Q25.3) WILD-TYPE  10 200
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 23(17Q25.3) MUTATED      3  132
  AMP PEAK 23(17Q25.3) WILD-TYPE   10  200
                        clus
vv                       AMP PEAK 23(17Q25.3) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                          132
                        clus
vv                       AMP PEAK 23(17Q25.3) WILD-TYPE
  HISPANIC OR LATINO                                 10
  NOT HISPANIC OR LATINO                            200
[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    43  23
  AMP PEAK 24(19P13.12) WILD-TYPE 186 106
  AMP PEAK 24(19P13.12) MUTATED AMP PEAK 24(19P13.12) WILD-TYPE 
                             66                             292 
  AMP PEAK 24(19P13.12) MUTATED AMP PEAK 24(19P13.12) WILD-TYPE 
                             23                             106 
$`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        49.84        11.74        13.02        37.32 
TCGA-BC-A10R TCGA-BC-A112 TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5261 TCGA-CC-A7II 
       10.13         5.03        13.45         0.66         3.19        13.12 
TCGA-CC-A9FS TCGA-DD-A113 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A1E9 TCGA-DD-A1EC 
        6.94        79.73       113.00         7.33        90.71        19.79 
TCGA-DD-A1EF TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4ND 
       12.95        21.14        55.69        13.78        30.61        90.28 
TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NV TCGA-DD-A73G TCGA-DD-AACL TCGA-DD-AACT 
       29.56        73.81        78.84       114.35         3.52        51.35 
TCGA-DD-AACY TCGA-DD-AAD5 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADF TCGA-DD-AAE0 
       47.67        44.22        40.54        40.83         3.78        18.25 
TCGA-DD-AAE3 TCGA-DD-AAE6 TCGA-DD-AAE9 TCGA-DD-AAEG TCGA-DD-AAEK TCGA-DD-AAVR 
       18.61         4.64        23.74        23.64        35.08        82.62 
TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A82E TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC 
       13.35         9.73        13.41        20.61        19.59         0.62 
TCGA-ES-A2HS TCGA-FV-A2QQ TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A4ZP TCGA-G3-A25T 
       22.85        23.97        27.88         8.12        81.73        51.06 
TCGA-G3-A25X TCGA-G3-A5SM TCGA-G3-A7M7 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV7 
       58.49        17.10        11.87        15.78        15.65        11.87 
TCGA-GJ-A3OU TCGA-KR-A7K2 TCGA-RC-A7S9 TCGA-UB-A7MA TCGA-YA-A8S7 TCGA-ZP-A9D1 
       22.92        21.60        21.04        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        38.40 
TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-4R-AA8I TCGA-5C-A9VG 
       20.81        22.92         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        17.10        14.76         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 
       23.38         1.12        69.57        44.42        45.93         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-5264 
       36.66         4.24         2.86         3.39         4.24         3.35 
TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UC 
        3.32         9.86         9.96        10.36        11.93        11.41 
TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7IH 
        9.99         8.94         7.13        21.34         9.83        12.00 
TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A7IL TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV 
       12.56         8.61         9.14         4.60        11.31         9.17 
TCGA-CC-A9FW TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A11A TCGA-DD-A11B 
        8.15        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-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-A39W TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 
       27.19         5.62        19.76        25.81         7.66        70.06 
TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A8 TCGA-DD-A4NA 
       17.59        20.12       102.74       107.11         0.36        33.14 
TCGA-DD-A4NB TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK 
       32.52        30.97        30.15        26.83        30.51        39.78 
TCGA-DD-A4NL TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A73A 
       56.25       108.76        12.26         0.30        80.75        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-AACM TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ 
        0.30        58.16        42.81        61.68        13.64        14.20 
TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACZ 
       59.31        51.52        50.33        46.82         5.59         5.62 
TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD6 TCGA-DD-AAD8 
        4.50        18.54        21.63        42.58        22.09        40.08 
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-AADN TCGA-DD-AADO TCGA-DD-AADP 
       34.49        20.91         0.39        29.52        14.89        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-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-AAEA TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAEI 
       18.90        15.72        25.08        26.63        25.78        50.33 
TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVV TCGA-DD-AAVW 
       79.07        89.69        59.93        72.39        80.71        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-A7PX 
       53.69        29.92        26.93        28.08        13.91         0.20 
TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A8O5 TCGA-ED-A8O6 
       12.82         0.20        14.04        13.15        13.35         1.84 
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-A23B TCGA-FV-A2QR TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 
       60.89        19.10         6.38        12.03         0.03         0.33 
TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y 
        0.39        13.68        53.79        28.27        30.74        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-A6UC TCGA-G3-A7M5 TCGA-G3-A7M6 
       25.25        22.95        20.42        22.06        14.70        20.78 
TCGA-G3-A7M8 TCGA-G3-A7M9 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 
       14.14         1.84        11.80        12.23        13.55         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        37.71 
TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K7 
       20.75        17.06        16.83        11.80         2.14        31.27 
TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E 
       29.79        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 
       22.95        24.56        20.71         7.53        10.85        58.88 
TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7SB TCGA-RC-A7SF 
       26.27        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        36.10         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-AA44 TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TF 
        0.99        12.99        20.22        24.85        18.28        22.78 
TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 
       35.77        25.71        23.21        35.87        25.15        12.99 
TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       45.57        40.80        79.30        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 
                         20.825                          19.430 
[1] "0.6 - 114.3 (20.8)" "0.0 - 120.8 (19.4)"
[1] "hr=" "1.2"
D24V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE III STAGE IIIA
  AMP PEAK 24(19P13.12) MUTATED        33       13         0         11
  AMP PEAK 24(19P13.12) WILD-TYPE     138       72         3         49
                                 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                               33                             138
  STAGE II                              13                              72
  STAGE III                              0                               3
  STAGE IIIA                            11                              49
  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      35  15  16   1
  AMP PEAK 24(19P13.12) WILD-TYPE   147  77  58  11
D24V4, multiclass
       clus
vv      AMP PEAK 24(19P13.12) MUTATED AMP PEAK 24(19P13.12) WILD-TYPE
  T0+T1                            35                             147
  T2                               15                              77
  T3                               16                              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"
D24V5, binary
                                 cls
clus                                0   1
  AMP PEAK 24(19P13.12) MUTATED    46   1
  AMP PEAK 24(19P13.12) WILD-TYPE 204   2
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 24(19P13.12) MUTATED     46    1
  AMP PEAK 24(19P13.12) WILD-TYPE  204    2
   clus
vv  AMP PEAK 24(19P13.12) MUTATED AMP PEAK 24(19P13.12) WILD-TYPE
  0                            46                             204
  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 216   1
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 24(19P13.12) MUTATED     45    3
  AMP PEAK 24(19P13.12) WILD-TYPE  216    1
   clus
vv  AMP PEAK 24(19P13.12) MUTATED AMP PEAK 24(19P13.12) WILD-TYPE
  0                            45                             216
  1                             3                               1
[1] 2 2
[1] FALSE
D24V7, binary
                                 cls
clus                                0   1
  AMP PEAK 24(19P13.12) MUTATED    32  35
  AMP PEAK 24(19P13.12) WILD-TYPE  83 212
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 24(19P13.12) MUTATED     32   35
  AMP PEAK 24(19P13.12) WILD-TYPE   83  212
        clus
vv       AMP PEAK 24(19P13.12) MUTATED AMP PEAK 24(19P13.12) WILD-TYPE
  FEMALE                            32                              83
  MALE                              35                             212
[1] 2 2
[1] FALSE
D24V8, binary
                                 cls
clus                                0   1
  AMP PEAK 24(19P13.12) MUTATED    62   1
  AMP PEAK 24(19P13.12) WILD-TYPE 274   6
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 24(19P13.12) MUTATED     62    1
  AMP PEAK 24(19P13.12) WILD-TYPE  274    6
     clus
vv    AMP PEAK 24(19P13.12) MUTATED AMP PEAK 24(19P13.12) WILD-TYPE
  NO                             62                             274
  YES                             1                               6
[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                         64
  AMP PEAK 24(19P13.12) WILD-TYPE                      289
                                 vv
clus                              HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK 24(19P13.12) MUTATED                                  3
  AMP PEAK 24(19P13.12) WILD-TYPE                                4
D24V9, multiclass
                                  clus
vv                                 AMP PEAK 24(19P13.12) MUTATED
  FIBROLAMELLAR CARCINOMA                                      0
  HEPATOCELLULAR CARCINOMA                                    64
  HEPATOCHOLANGIOCARCINOMA (MIXED)                             3
                                  clus
vv                                 AMP PEAK 24(19P13.12) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                        2
  HEPATOCELLULAR CARCINOMA                                     289
  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   5
  AMP PEAK 24(19P13.12) WILD-TYPE 260  12   0  16
D24V10, multiclass
    clus
vv   AMP PEAK 24(19P13.12) MUTATED AMP PEAK 24(19P13.12) WILD-TYPE
  R0                            58                             260
  R1                             3                              12
  R2                             1                               0
  RX                             5                              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 24(19P13.12) MUTATED                                  0    25
  AMP PEAK 24(19P13.12) WILD-TYPE                                1   132
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 24(19P13.12) MUTATED                           4    36
  AMP PEAK 24(19P13.12) WILD-TYPE                        13   141
D24V11, multiclass
                                  clus
vv                                 AMP PEAK 24(19P13.12) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                       25
  BLACK OR AFRICAN AMERICAN                                    4
  WHITE                                                       36
                                  clus
vv                                 AMP PEAK 24(19P13.12) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               1
  ASIAN                                                        132
  BLACK OR AFRICAN AMERICAN                                     13
  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"
D24V12, binary
                                 cls
clus                                0   1
  AMP PEAK 24(19P13.12) MUTATED     4  61
  AMP PEAK 24(19P13.12) WILD-TYPE   9 271
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 24(19P13.12) MUTATED      4   61
  AMP PEAK 24(19P13.12) WILD-TYPE    9  271
                        clus
vv                       AMP PEAK 24(19P13.12) MUTATED
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                            61
                        clus
vv                       AMP PEAK 24(19P13.12) WILD-TYPE
  HISPANIC OR LATINO                                   9
  NOT HISPANIC OR LATINO                             271
[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    51  25
  AMP PEAK 25(19Q12) WILD-TYPE 178 104
  AMP PEAK 25(19Q12) MUTATED AMP PEAK 25(19Q12) WILD-TYPE 
                          76                          282 
  AMP PEAK 25(19Q12) MUTATED AMP PEAK 25(19Q12) WILD-TYPE 
                          25                          104 
$`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        49.84        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-CC-A7II TCGA-DD-A113 TCGA-DD-A118 TCGA-DD-A119 
        2.86         3.19        13.12        79.73       113.00         7.33 
TCGA-DD-A1E9 TCGA-DD-A1EC TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EI TCGA-DD-A39V 
       90.71        19.79        12.95        45.11         6.02        21.14 
TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4ND TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NQ 
       13.78        30.61        90.28        29.56        73.81        12.26 
TCGA-DD-A4NV TCGA-DD-A73G TCGA-DD-AACG TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACT 
       78.84       114.35        15.42        61.68        13.64        51.35 
TCGA-DD-AACV TCGA-DD-AADB TCGA-DD-AADF TCGA-DD-AADM TCGA-DD-AADV TCGA-DD-AAE0 
       50.33        40.83         3.78         0.39        18.87        18.25 
TCGA-DD-AAE4 TCGA-DD-AAE7 TCGA-DD-AAEK TCGA-DD-AAVV TCGA-DD-AAVW TCGA-ED-A66X 
       19.99        21.17        35.08        80.71        76.18        13.35 
TCGA-ED-A66Y TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A82E TCGA-EP-A2KB TCGA-EP-A2KC 
        9.73         0.20        14.04        13.41        19.59         0.62 
TCGA-ES-A2HS TCGA-FV-A2QQ TCGA-FV-A3I0 TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25X 
       22.85        23.97        27.88         0.39        51.06        58.49 
TCGA-G3-A5SM TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-AAV0 TCGA-GJ-A3OU TCGA-KR-A7K2 
       17.10        20.78        11.87        15.65        22.92        21.60 
TCGA-MI-A75G TCGA-NI-A8LF TCGA-RC-A7S9 TCGA-RC-A7SH TCGA-UB-A7MA TCGA-UB-A7ME 
       22.95        26.27        21.04        15.39        17.59        15.98 
TCGA-WJ-A86L TCGA-WQ-AB4B TCGA-YA-A8S7 TCGA-ZP-A9D1 
       11.34        12.99        13.55         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        38.40        20.81 
TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-A9VH 
       22.92         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        17.10        14.76         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        23.38         1.12 
TCGA-BC-A110 TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 
       69.57        44.42        45.93         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         4.24 
TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-5264 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA 
        3.39         4.24         3.35         3.32         9.86         9.96 
TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IE 
       10.36        11.93        11.41         9.99         8.94         7.13 
TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A7IL 
       21.34         9.83        12.00        12.56         8.61         9.14 
TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A114 
        4.60        11.31         9.17         6.94         8.15        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-A1EL TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z 
       18.35        13.64        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-A3A8 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NF TCGA-DD-A4NH 
      107.11         0.36        33.14        32.52        30.97        30.15 
TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NP TCGA-DD-A4NR 
       26.83        30.51        39.78        56.25       108.76         0.30 
TCGA-DD-A4NS TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E 
       80.75        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-AACI 
       55.40        12.53        63.48        12.00         6.41        53.19 
TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACQ 
       69.11         0.30         3.52        58.16        42.81        14.20 
TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AACZ 
       59.31        51.52        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-AADC TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADG 
       40.08        40.54        13.97        40.47        39.52        37.64 
TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADN TCGA-DD-AADO 
       35.67        35.05        34.49        20.91        29.52        14.89 
TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW 
       15.06        14.33        66.67        15.58        18.21        19.30 
TCGA-DD-AADY TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE6 TCGA-DD-AAE8 
       18.25        18.15        20.98        18.61         4.64        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        26.63        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        29.92        26.93        28.08        13.91 
TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7XP TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K 
        0.20        12.82        13.15        13.35         1.84         0.20 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HT 
       18.74        19.99        20.61         9.96        11.93        14.40 
TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 
       60.89        19.10         8.12         6.38        12.03         0.03 
TCGA-FV-A496 TCGA-FV-A4ZP TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W 
        0.33        81.73        13.68        53.79        28.27        30.74 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ 
       14.86        21.53        22.13        25.64         5.92        19.53 
TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A6UC TCGA-G3-A7M5 
       19.23        25.25        22.95        20.42        22.06        14.70 
TCGA-G3-A7M8 TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 
       14.14         1.84        15.78        11.80        12.23        13.55 
TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB 
        0.89         8.75         2.14        11.87         1.02         2.20 
TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 
        2.99        37.71        20.75        17.06        16.83        11.80 
TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD 
        2.14        31.27        29.79        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        24.56        20.71         7.53        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        36.10         0.76        19.76        16.44         1.71 
TCGA-UB-A7MF TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WQ-A9G7 TCGA-WX-AA44 TCGA-WX-AA46 
        7.04        10.75        10.32         0.99        20.22        24.85 
TCGA-WX-AA47 TCGA-XR-A8TF TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 
       18.28        22.78        35.77        25.71        23.21        35.87 
TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       25.15        12.99        45.57        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 
                      19.890                       19.645 
[1] "0.2 - 120.8 (19.9)" "0.0 - 108.8 (19.6)"
[1] "hr=" "1.3"
D25V2, continuous
                              vv
clus                           STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 25(19Q12) MUTATED        35       19         0         11          2
  AMP PEAK 25(19Q12) WILD-TYPE     136       66         3         49          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                            35                          136
  STAGE II                           19                           66
  STAGE III                           0                            3
  STAGE IIIA                         11                           49
  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      37  21  16   3
  AMP PEAK 25(19Q12) WILD-TYPE   145  71  58   9
D25V4, multiclass
       clus
vv      AMP PEAK 25(19Q12) MUTATED AMP PEAK 25(19Q12) WILD-TYPE
  T0+T1                         37                          145
  T2                            21                           71
  T3                            16                           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"
D25V5, binary
                              cls
clus                             0   1
  AMP PEAK 25(19Q12) MUTATED    51   1
  AMP PEAK 25(19Q12) WILD-TYPE 199   2
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 25(19Q12) MUTATED     51    1
  AMP PEAK 25(19Q12) WILD-TYPE  199    2
   clus
vv  AMP PEAK 25(19Q12) MUTATED AMP PEAK 25(19Q12) WILD-TYPE
  0                         51                          199
  1                          1                            2
[1] 2 2
[1] FALSE
D25V6, binary
                              cls
clus                             0   1
  AMP PEAK 25(19Q12) MUTATED    52   3
  AMP PEAK 25(19Q12) WILD-TYPE 209   1
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 25(19Q12) MUTATED     52    3
  AMP PEAK 25(19Q12) WILD-TYPE  209    1
   clus
vv  AMP PEAK 25(19Q12) MUTATED AMP PEAK 25(19Q12) WILD-TYPE
  0                         52                          209
  1                          3                            1
[1] 2 2
[1] FALSE
D25V7, binary
                              cls
clus                             0   1
  AMP PEAK 25(19Q12) MUTATED    29  48
  AMP PEAK 25(19Q12) WILD-TYPE  86 199
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 25(19Q12) MUTATED     29   48
  AMP PEAK 25(19Q12) WILD-TYPE   86  199
        clus
vv       AMP PEAK 25(19Q12) MUTATED AMP PEAK 25(19Q12) WILD-TYPE
  FEMALE                         29                           86
  MALE                           48                          199
[1] 2 2
[1] FALSE
D25V8, binary
                              cls
clus                             0   1
  AMP PEAK 25(19Q12) MUTATED    70   1
  AMP PEAK 25(19Q12) WILD-TYPE 266   6
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 25(19Q12) MUTATED     70    1
  AMP PEAK 25(19Q12) WILD-TYPE  266    6
     clus
vv    AMP PEAK 25(19Q12) MUTATED AMP PEAK 25(19Q12) WILD-TYPE
  NO                          70                          266
  YES                          1                            6
[1] 2 2
[1] FALSE
                              vv
clus                           FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  AMP PEAK 25(19Q12) MUTATED                         0                       74
  AMP PEAK 25(19Q12) WILD-TYPE                       2                      279
                              vv
clus                           HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK 25(19Q12) MUTATED                                  3
  AMP PEAK 25(19Q12) WILD-TYPE                                4
D25V9, multiclass
                                  clus
vv                                 AMP PEAK 25(19Q12) MUTATED
  FIBROLAMELLAR CARCINOMA                                   0
  HEPATOCELLULAR CARCINOMA                                 74
  HEPATOCHOLANGIOCARCINOMA (MIXED)                          3
                                  clus
vv                                 AMP PEAK 25(19Q12) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                     2
  HEPATOCELLULAR CARCINOMA                                  279
  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    67   3   1   6
  AMP PEAK 25(19Q12) WILD-TYPE 251  12   0  15
D25V10, multiclass
    clus
vv   AMP PEAK 25(19Q12) MUTATED AMP PEAK 25(19Q12) WILD-TYPE
  R0                         67                          251
  R1                          3                           12
  R2                          1                            0
  RX                          6                           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 25(19Q12) MUTATED                                  0    30
  AMP PEAK 25(19Q12) WILD-TYPE                                1   127
                              vv
clus                           BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 25(19Q12) MUTATED                           4    42
  AMP PEAK 25(19Q12) WILD-TYPE                        13   135
D25V11, multiclass
                                  clus
vv                                 AMP PEAK 25(19Q12) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          0
  ASIAN                                                    30
  BLACK OR AFRICAN AMERICAN                                 4
  WHITE                                                    42
                                  clus
vv                                 AMP PEAK 25(19Q12) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                     127
  BLACK OR AFRICAN AMERICAN                                  13
  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"
D25V12, binary
                              cls
clus                             0   1
  AMP PEAK 25(19Q12) MUTATED     5  70
  AMP PEAK 25(19Q12) WILD-TYPE   8 262
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 25(19Q12) MUTATED      5   70
  AMP PEAK 25(19Q12) WILD-TYPE    8  262
                        clus
vv                       AMP PEAK 25(19Q12) MUTATED
  HISPANIC OR LATINO                              5
  NOT HISPANIC OR LATINO                         70
                        clus
vv                       AMP PEAK 25(19Q12) WILD-TYPE
  HISPANIC OR LATINO                                8
  NOT HISPANIC OR LATINO                          262
[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    52  34
  AMP PEAK 26(19Q13.11) WILD-TYPE 177  95
  AMP PEAK 26(19Q13.11) MUTATED AMP PEAK 26(19Q13.11) WILD-TYPE 
                             86                             272 
  AMP PEAK 26(19Q13.11) MUTATED AMP PEAK 26(19Q13.11) WILD-TYPE 
                             34                              95 
$`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        49.84        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        23.38         5.03        45.93        22.36 
TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5261 TCGA-CC-A3M9 TCGA-CC-A7II TCGA-CC-A8HU 
       13.45         0.66         3.19         9.86        13.12        11.31 
TCGA-DD-A113 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A1E9 TCGA-DD-A1EC TCGA-DD-A1EF 
       79.73       113.00         7.33        90.71        19.79        12.95 
TCGA-DD-A1EG TCGA-DD-A1EI TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A3A7 TCGA-DD-A3A9 
       45.11         6.02        13.64        21.14        13.78        30.61 
TCGA-DD-A4ND TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NQ TCGA-DD-A4NV TCGA-DD-A73F 
       90.28        29.56        73.81        12.26        78.84        35.67 
TCGA-DD-A73G TCGA-DD-AACG TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACT TCGA-DD-AACW 
      114.35        15.42        61.68        13.64        51.35        46.82 
TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADF TCGA-DD-AADM TCGA-DD-AAE0 
       40.83        13.97        40.47         3.78         0.39        18.25 
TCGA-DD-AAE7 TCGA-DD-AAEA TCGA-DD-AAEK TCGA-DD-AAVV TCGA-ED-A66X TCGA-ED-A66Y 
       21.17        18.90        35.08        80.71        13.35         9.73 
TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A82E TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC 
        0.20        14.04        13.41        20.61        19.59         0.62 
TCGA-ES-A2HS TCGA-FV-A2QQ TCGA-FV-A3I0 TCGA-FV-A495 TCGA-FV-A4ZQ TCGA-G3-A25T 
       22.85        23.97        27.88         0.03         0.39        51.06 
TCGA-G3-A25X TCGA-G3-A5SM TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-G3-AAV0 
       58.49        17.10        20.78        11.87         1.84        15.65 
TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-MI-A75G TCGA-NI-A8LF 
       22.92         1.02        11.80        21.60        22.95        26.27 
TCGA-PD-A5DF TCGA-RC-A7S9 TCGA-RC-A7SH TCGA-UB-A7ME TCGA-WQ-AB4B TCGA-YA-A8S7 
       21.01        21.04        15.39        15.98        12.99        13.55 
TCGA-ZP-A9D1 TCGA-ZS-A9CF 
        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        38.40 
TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-4R-AA8I TCGA-5C-A9VG 
       20.81        22.92         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        17.10        14.76         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         4.24         2.86         3.39 
TCGA-CC-5263 TCGA-CC-5264 TCGA-CC-A1HT TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC 
        4.24         3.35         3.32         9.96        10.36        11.93 
TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IG 
       11.41         9.99         8.94         7.13        21.34         9.83 
TCGA-CC-A7IH TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A7IL TCGA-CC-A8HT TCGA-CC-A8HV 
       12.00        12.56         8.61         9.14         4.60         9.17 
TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A11A 
        6.94         8.15        37.78        83.57        53.33         2.60 
TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1ED 
        0.46        21.76        51.29        79.40        66.31        75.65 
TCGA-DD-A1EE TCGA-DD-A1EH TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A39W TCGA-DD-A39X 
       11.47        49.15        33.04        18.35        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-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA 
       22.78         1.45        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-AACN 
       53.19        69.11         0.30         3.52        58.16        42.81 
TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACX TCGA-DD-AACY 
       14.20        59.31        51.52        50.33         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-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADE TCGA-DD-AADG TCGA-DD-AADI 
       22.09        40.08        40.54        39.52        37.64        35.67 
TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP 
       35.05        34.49        20.91        29.52        14.89        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-AADY 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-AAE8 TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEG 
       21.83        23.74        15.72        25.08        26.63        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-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        29.92        26.93        28.08 
TCGA-ED-A627 TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7XP TCGA-ED-A8O5 TCGA-ED-A8O6 
       13.91         0.20        12.82        13.15        13.35         1.84 
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-A23B TCGA-FV-A2QR TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A496 
       60.89        19.10         8.12         6.38        12.03         0.33 
TCGA-FV-A4ZP TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y 
       81.73        13.68        53.79        28.27        30.74        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-A6UC TCGA-G3-A7M5 TCGA-G3-A7M8 
       25.25        22.95        20.42        22.06        14.70        14.14 
TCGA-G3-AAUZ TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 
       15.78        11.80        12.23        13.55         0.89         8.75 
TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF 
        2.14        11.87         2.20         2.99        37.71        20.75 
TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG 
       17.06        16.83         2.14        31.27        29.79        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        24.56        20.71 
TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-O8-A75V TCGA-QA-A7B7 TCGA-RC-A7SB 
        7.53        10.85        58.88        17.69         3.09        19.33 
TCGA-RC-A7SF TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-T1-A6J8 TCGA-UB-A7MA TCGA-UB-A7MB 
       19.04        15.52        36.10         0.76        17.59        19.76 
TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7MF TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WJ-A86L 
       16.44         1.71         7.04        10.75        10.32        11.34 
TCGA-WQ-A9G7 TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TF TCGA-ZP-A9CV 
        0.99        20.22        24.85        18.28        22.78        35.77 
TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD 
       25.71        23.21        35.87        25.15        12.99        45.57 
TCGA-ZS-A9CE TCGA-ZS-A9CG 
       40.80        11.21 

  AMP PEAK 26(19Q13.11) MUTATED AMP PEAK 26(19Q13.11) WILD-TYPE 
                           0.03                            0.20 
  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 
                         20.200                          19.645 
[1] "0.0 - 114.3 (20.2)" "0.2 - 120.8 (19.6)"
[1] "hr=" "1.1"
D26V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE III STAGE IIIA
  AMP PEAK 26(19Q13.11) MUTATED        36       25         0         14
  AMP PEAK 26(19Q13.11) WILD-TYPE     135       60         3         46
                                 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                               36                             135
  STAGE II                              25                              60
  STAGE III                              0                               3
  STAGE IIIA                            14                              46
  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      38  27  20   4
  AMP PEAK 26(19Q13.11) WILD-TYPE   144  65  54   8
D26V4, multiclass
       clus
vv      AMP PEAK 26(19Q13.11) MUTATED AMP PEAK 26(19Q13.11) WILD-TYPE
  T0+T1                            38                             144
  T2                               27                              65
  T3                               20                              54
  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    55   1
  AMP PEAK 26(19Q13.11) WILD-TYPE 195   2
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 26(19Q13.11) MUTATED     55    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                            55                             195
  1                             1                               2
[1] 2 2
[1] FALSE
D26V6, binary
                                 cls
clus                                0   1
  AMP PEAK 26(19Q13.11) MUTATED    58   3
  AMP PEAK 26(19Q13.11) WILD-TYPE 203   1
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 26(19Q13.11) MUTATED     58    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                            58                             203
  1                             3                               1
[1] 2 2
[1] FALSE
D26V7, binary
                                 cls
clus                                0   1
  AMP PEAK 26(19Q13.11) MUTATED    34  55
  AMP PEAK 26(19Q13.11) WILD-TYPE  81 192
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 26(19Q13.11) MUTATED     34   55
  AMP PEAK 26(19Q13.11) WILD-TYPE   81  192
        clus
vv       AMP PEAK 26(19Q13.11) MUTATED AMP PEAK 26(19Q13.11) WILD-TYPE
  FEMALE                            34                              81
  MALE                              55                             192
[1] 2 2
[1] FALSE
D26V8, binary
                                 cls
clus                                0   1
  AMP PEAK 26(19Q13.11) MUTATED    79   1
  AMP PEAK 26(19Q13.11) WILD-TYPE 257   6
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 26(19Q13.11) MUTATED     79    1
  AMP PEAK 26(19Q13.11) WILD-TYPE  257    6
     clus
vv    AMP PEAK 26(19Q13.11) MUTATED AMP PEAK 26(19Q13.11) WILD-TYPE
  NO                             79                             257
  YES                             1                               6
[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                         86
  AMP PEAK 26(19Q13.11) WILD-TYPE                      267
                                 vv
clus                              HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK 26(19Q13.11) MUTATED                                  3
  AMP PEAK 26(19Q13.11) WILD-TYPE                                4
D26V9, multiclass
                                  clus
vv                                 AMP PEAK 26(19Q13.11) MUTATED
  FIBROLAMELLAR CARCINOMA                                      0
  HEPATOCELLULAR CARCINOMA                                    86
  HEPATOCHOLANGIOCARCINOMA (MIXED)                             3
                                  clus
vv                                 AMP PEAK 26(19Q13.11) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                        2
  HEPATOCELLULAR CARCINOMA                                     267
  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    77   2   1   8
  AMP PEAK 26(19Q13.11) WILD-TYPE 241  13   0  13
D26V10, multiclass
    clus
vv   AMP PEAK 26(19Q13.11) MUTATED AMP PEAK 26(19Q13.11) WILD-TYPE
  R0                            77                             241
  R1                             2                              13
  R2                             1                               0
  RX                             8                              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 26(19Q13.11) MUTATED                                  0    32
  AMP PEAK 26(19Q13.11) WILD-TYPE                                1   125
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 26(19Q13.11) MUTATED                           5    51
  AMP PEAK 26(19Q13.11) WILD-TYPE                        12   126
D26V11, multiclass
                                  clus
vv                                 AMP PEAK 26(19Q13.11) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                       32
  BLACK OR AFRICAN AMERICAN                                    5
  WHITE                                                       51
                                  clus
vv                                 AMP PEAK 26(19Q13.11) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               1
  ASIAN                                                        125
  BLACK OR AFRICAN AMERICAN                                     12
  WHITE                                                        126
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V12, binary
                                 cls
clus                                0   1
  AMP PEAK 26(19Q13.11) MUTATED     4  82
  AMP PEAK 26(19Q13.11) WILD-TYPE   9 250
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 26(19Q13.11) MUTATED      4   82
  AMP PEAK 26(19Q13.11) WILD-TYPE    9  250
                        clus
vv                       AMP PEAK 26(19Q13.11) MUTATED
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                            82
                        clus
vv                       AMP PEAK 26(19Q13.11) WILD-TYPE
  HISPANIC OR LATINO                                   9
  NOT HISPANIC OR LATINO                             250
[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  52
  AMP PEAK 27(20Q13.13) WILD-TYPE 162  77
  AMP PEAK 27(20Q13.13) MUTATED AMP PEAK 27(20Q13.13) WILD-TYPE 
                            119                             239 
  AMP PEAK 27(20Q13.13) MUTATED AMP PEAK 27(20Q13.13) WILD-TYPE 
                             52                              77 
$`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 
       22.92         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        23.38        45.93         0.26        14.60 
TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5261 TCGA-CC-5264 TCGA-CC-A1HT 
       44.81        13.45         0.66         3.19         3.35         3.32 
TCGA-CC-A3M9 TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A5UE TCGA-CC-A7IE 
        9.86        10.36        11.93        11.41         8.94         7.13 
TCGA-CC-A7II TCGA-CC-A7IL TCGA-CC-A8HU TCGA-CC-A9FW TCGA-DD-A118 TCGA-DD-A119 
       13.12         9.14        11.31         8.15       113.00         7.33 
TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH 
        2.60         0.46        21.76        12.95        45.11        49.15 
TCGA-DD-A1EJ TCGA-DD-A39V TCGA-DD-A3A5 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4ND 
       33.04        21.14       102.74        13.78        30.61        90.28 
TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NR TCGA-DD-A4NV TCGA-DD-A73G TCGA-DD-AAC8 
       29.56        73.81         0.30        78.84       114.35         0.53 
TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACI TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACS 
       76.41        55.40        53.19        61.68        13.64        59.31 
TCGA-DD-AACT TCGA-DD-AACV TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD6 TCGA-DD-AADA 
       51.35        50.33         5.62         4.50        22.09        40.54 
TCGA-DD-AADD TCGA-DD-AADF TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADS TCGA-DD-AADU 
       40.47         3.78        29.52        14.89        15.58        18.21 
TCGA-DD-AADW TCGA-DD-AAE0 TCGA-DD-AAE3 TCGA-DD-AAE6 TCGA-DD-AAE9 TCGA-DD-AAEA 
       19.30        18.25        18.61         4.64        23.74        18.90 
TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAEK TCGA-DD-AAVV TCGA-ED-A66X TCGA-ED-A66Y 
       23.64        25.78        35.08        80.71        13.35         9.73 
TCGA-ED-A7XO TCGA-ED-A82E TCGA-ED-A8O6 TCGA-EP-A2KB TCGA-EP-A3JL TCGA-ES-A2HS 
       14.04        13.41         1.84        19.59         9.96        22.85 
TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A3R2 TCGA-FV-A495 TCGA-FV-A4ZQ TCGA-G3-A25S 
       60.89        23.97         6.38         0.03         0.39        13.68 
TCGA-G3-A25W TCGA-G3-A5SM TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-G3-AAV1 
       30.74        17.10        20.78        11.87         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        21.60        31.27        12.72        22.95 
TCGA-PD-A5DF TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7ME TCGA-UB-AA0U 
       21.01        36.10        17.59        19.76        15.98        10.75 
TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZS-A9CD 
        0.99        12.99        22.78        13.55        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 
       49.84        47.74        18.25        11.74        38.40         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        17.10        14.76 
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         4.24         2.86         3.39         4.24 
TCGA-CC-A3MA TCGA-CC-A5UD TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7IJ 
        9.96         9.99        21.34         9.83        12.00        12.56 
TCGA-CC-A7IK TCGA-CC-A8HT TCGA-CC-A8HV TCGA-CC-A9FS TCGA-DD-A113 TCGA-DD-A114 
        8.61         4.60         9.17         6.94        79.73        37.78 
TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB 
       83.57        53.33        51.29        90.71        79.40        66.31 
TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EI TCGA-DD-A1EK TCGA-DD-A1EL 
       19.79        75.65        11.47         6.02        18.35        13.64 
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-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A6 TCGA-DD-A3A8 TCGA-DD-A4NA 
       70.06        17.59        20.12       107.11         0.36        33.14 
TCGA-DD-A4NB TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK 
       32.52        30.97        30.15        26.83        30.51        39.78 
TCGA-DD-A4NL TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NS TCGA-DD-A73A TCGA-DD-A73B 
       56.25       108.76        12.26        80.75        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-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH 
       75.65        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-AACU TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AAD1 TCGA-DD-AAD2 
       51.52        46.82         5.59        47.67        18.54        21.63 
TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD8 TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADE 
       42.58        44.22        40.08        40.83        13.97        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-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADV TCGA-DD-AADY TCGA-DD-AAE1 
       15.06        14.33        66.67        18.87        18.25        18.15 
TCGA-DD-AAE2 TCGA-DD-AAE4 TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEB TCGA-DD-AAED 
       20.98        19.99        21.17        21.83        15.72        25.08 
TCGA-DD-AAEE TCGA-DD-AAEI TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS 
       26.63        50.33        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        29.92        26.93        28.08 
TCGA-ED-A627 TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-ED-A8O5 
       13.91         0.20        12.82         0.20        13.15        13.35 
TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3RK 
        0.20        18.74        19.99        20.61         0.62        11.93 
TCGA-ES-A2HT TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R3 TCGA-FV-A496 
       14.40        19.10        27.88         8.12        12.03         0.33 
TCGA-FV-A4ZP TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25X TCGA-G3-A25Y 
       81.73        51.06        53.79        28.27        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-A6UC TCGA-G3-A7M5 TCGA-G3-A7M8 
       25.25        22.95        20.42        22.06        14.70        14.14 
TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 
       15.78        15.65        12.23        13.55         0.89         8.75 
TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5N0 TCGA-K7-A5RF 
       11.87        22.92         1.02         2.20        37.71        20.75 
TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K8 TCGA-LG-A9QC 
       17.06        16.83        11.80         2.14        29.79        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        24.56        20.71         7.53 
TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-QA-A7B7 TCGA-RC-A7S9 
       10.85        58.88        26.27        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-AA44 TCGA-WX-AA46 
        1.71         7.04        10.32        11.34        20.22        24.85 
TCGA-WX-AA47 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 
       18.28        35.77        25.71        23.21        35.87         0.69 
TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       25.15        12.99        40.80        79.30        11.21 

  AMP PEAK 27(20Q13.13) MUTATED AMP PEAK 27(20Q13.13) WILD-TYPE 
                           0.03                            0.20 
  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 
                          18.25                           20.22 
[1] "0.0 - 120.8 (18.2)" "0.2 - 108.8 (20.2)"
[1] "hr=" "1.4"
D27V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE III STAGE IIIA
  AMP PEAK 27(20Q13.13) MUTATED        50       26         2         25
  AMP PEAK 27(20Q13.13) WILD-TYPE     121       59         1         35
                                 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                               50                             121
  STAGE II                              26                              59
  STAGE III                              2                               1
  STAGE IIIA                            25                              35
  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      53  28  33   6
  AMP PEAK 27(20Q13.13) WILD-TYPE   129  64  41   6
D27V4, multiclass
       clus
vv      AMP PEAK 27(20Q13.13) MUTATED AMP PEAK 27(20Q13.13) WILD-TYPE
  T0+T1                            53                             129
  T2                               28                              64
  T3                               33                              41
  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    82   2
  AMP PEAK 27(20Q13.13) WILD-TYPE 168   1
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 27(20Q13.13) MUTATED     82    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                            82                             168
  1                             2                               1
[1] 2 2
[1] FALSE
D27V6, binary
                                 cls
clus                                0   1
  AMP PEAK 27(20Q13.13) MUTATED    90   2
  AMP PEAK 27(20Q13.13) WILD-TYPE 171   2
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 27(20Q13.13) MUTATED     90    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                            90                             171
  1                             2                               2
[1] 2 2
[1] FALSE
D27V7, binary
                                 cls
clus                                0   1
  AMP PEAK 27(20Q13.13) MUTATED    44  76
  AMP PEAK 27(20Q13.13) WILD-TYPE  71 171
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 27(20Q13.13) MUTATED     44   76
  AMP PEAK 27(20Q13.13) WILD-TYPE   71  171
        clus
vv       AMP PEAK 27(20Q13.13) MUTATED AMP PEAK 27(20Q13.13) WILD-TYPE
  FEMALE                            44                              71
  MALE                              76                             171
[1] 2 2
[1] FALSE
D27V8, binary
                                 cls
clus                                0   1
  AMP PEAK 27(20Q13.13) MUTATED   110   1
  AMP PEAK 27(20Q13.13) WILD-TYPE 226   6
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 27(20Q13.13) MUTATED    110    1
  AMP PEAK 27(20Q13.13) WILD-TYPE  226    6
     clus
vv    AMP PEAK 27(20Q13.13) MUTATED AMP PEAK 27(20Q13.13) WILD-TYPE
  NO                            110                             226
  YES                             1                               6
[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                        118
  AMP PEAK 27(20Q13.13) WILD-TYPE                      235
                                 vv
clus                              HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK 27(20Q13.13) MUTATED                                  2
  AMP PEAK 27(20Q13.13) WILD-TYPE                                5
D27V9, multiclass
                                  clus
vv                                 AMP PEAK 27(20Q13.13) MUTATED
  FIBROLAMELLAR CARCINOMA                                      0
  HEPATOCELLULAR CARCINOMA                                   118
  HEPATOCHOLANGIOCARCINOMA (MIXED)                             2
                                  clus
vv                                 AMP PEAK 27(20Q13.13) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                        2
  HEPATOCELLULAR CARCINOMA                                     235
  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   104   7   1   5
  AMP PEAK 27(20Q13.13) WILD-TYPE 214   8   0  16
D27V10, multiclass
    clus
vv   AMP PEAK 27(20Q13.13) MUTATED AMP PEAK 27(20Q13.13) WILD-TYPE
  R0                           104                             214
  R1                             7                               8
  R2                             1                               0
  RX                             5                              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 27(20Q13.13) MUTATED                                  0    51
  AMP PEAK 27(20Q13.13) WILD-TYPE                                1   106
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 27(20Q13.13) MUTATED                           4    63
  AMP PEAK 27(20Q13.13) WILD-TYPE                        13   114
D27V11, multiclass
                                  clus
vv                                 AMP PEAK 27(20Q13.13) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                       51
  BLACK OR AFRICAN AMERICAN                                    4
  WHITE                                                       63
                                  clus
vv                                 AMP PEAK 27(20Q13.13) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               1
  ASIAN                                                        106
  BLACK OR AFRICAN AMERICAN                                     13
  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"
D27V12, binary
                                 cls
clus                                0   1
  AMP PEAK 27(20Q13.13) MUTATED     4 109
  AMP PEAK 27(20Q13.13) WILD-TYPE   9 223
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 27(20Q13.13) MUTATED      4  109
  AMP PEAK 27(20Q13.13) WILD-TYPE    9  223
                        clus
vv                       AMP PEAK 27(20Q13.13) MUTATED
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           109
                        clus
vv                       AMP PEAK 27(20Q13.13) WILD-TYPE
  HISPANIC OR LATINO                                   9
  NOT HISPANIC OR LATINO                             223
[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  52
  AMP PEAK 28(20Q13.33) WILD-TYPE 158  77
  AMP PEAK 28(20Q13.33) MUTATED AMP PEAK 28(20Q13.33) WILD-TYPE 
                            123                             235 
  AMP PEAK 28(20Q13.33) MUTATED AMP PEAK 28(20Q13.33) WILD-TYPE 
                             52                              77 
$`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        22.92         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 
       23.38        45.93         0.26        14.60        44.81        13.45 
TCGA-BW-A5NO TCGA-CC-5261 TCGA-CC-5264 TCGA-CC-A3M9 TCGA-CC-A3MB TCGA-CC-A3MC 
        0.66         3.19         3.35         9.86        10.36        11.93 
TCGA-CC-A5UC TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7II TCGA-CC-A7IL TCGA-CC-A8HU 
       11.41         8.94         7.13        13.12         9.14        11.31 
TCGA-CC-A8HV TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A 
        9.17         8.15        79.73       113.00         7.33         2.60 
TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EJ 
        0.46        21.76        12.95        45.11        49.15        33.04 
TCGA-DD-A39V TCGA-DD-A3A5 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4ND TCGA-DD-A4NN 
       21.14       102.74        13.78        30.61        90.28        29.56 
TCGA-DD-A4NO TCGA-DD-A4NR TCGA-DD-A4NV TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AAC8 
       73.81         0.30        78.84        35.67       114.35         0.53 
TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACI TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ 
       76.41        55.40        53.19        61.68        13.64        14.20 
TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACV TCGA-DD-AACX TCGA-DD-AACZ TCGA-DD-AAD0 
       59.31        51.35        50.33         5.59         5.62         4.50 
TCGA-DD-AAD6 TCGA-DD-AADA TCGA-DD-AADD TCGA-DD-AADF TCGA-DD-AADN TCGA-DD-AADO 
       22.09        40.54        40.47         3.78        29.52        14.89 
TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AAE0 TCGA-DD-AAE3 TCGA-DD-AAE6 
       15.58        18.21        19.30        18.25        18.61         4.64 
TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAEK TCGA-DD-AAVR 
       23.74        18.90        23.64        25.78        35.08        82.62 
TCGA-DD-AAVV TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7XO TCGA-ED-A82E TCGA-ED-A8O5 
       80.71        13.35         9.73        14.04        13.41        13.35 
TCGA-ED-A8O6 TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A3JL TCGA-ES-A2HS TCGA-FV-A23B 
        1.84        20.61        19.59         9.96        22.85        60.89 
TCGA-FV-A2QQ TCGA-FV-A3R2 TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25W TCGA-G3-A25X 
       23.97         6.38         0.39        13.68        30.74        58.49 
TCGA-G3-A5SM TCGA-G3-A7M6 TCGA-G3-A7M9 TCGA-G3-AAV1 TCGA-G3-AAV6 TCGA-HP-A5MZ 
       17.10        20.78         1.84        11.80         2.14         2.99 
TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75G TCGA-PD-A5DF TCGA-RG-A7D4 
       21.60        31.27        12.72        22.95        21.01        36.10 
TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WQ-A9G7 TCGA-WQ-AB4B 
       17.59        19.76        15.98        10.75         0.99        12.99 
TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZS-A9CD 
       22.78        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        49.84        47.74        18.25        11.74        38.40 
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        17.10 
TCGA-5R-AA1D TCGA-BC-4073 TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W 
       14.76        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         4.24         2.86 
TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3MA TCGA-CC-A5UD TCGA-CC-A7IF 
        3.39         4.24         3.32         9.96         9.99        21.34 
TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A8HT TCGA-CC-A9FS 
        9.83        12.00        12.56         8.61         4.60         6.94 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA 
       37.78        83.57        53.33        51.29        90.71        79.40 
TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EI TCGA-DD-A1EK 
       66.31        19.79        75.65        11.47         6.02        18.35 
TCGA-DD-A1EL TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 
       13.64        27.19        55.69         5.62        19.76        25.81 
TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A6 TCGA-DD-A3A8 
        7.66        70.06        17.59        20.12       107.11         0.36 
TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ 
       33.14        32.52        30.97        30.15        26.83        30.51 
TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NS TCGA-DD-A73A 
       39.78        56.25       108.76        12.26        80.75        23.93 
TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-AA3A TCGA-DD-AAC9 
        9.30        23.05        22.78         1.45        13.48        11.41 
TCGA-DD-AACA TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH 
       75.65        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-AACU 
       69.11         0.30         3.52        58.16        42.81        51.52 
TCGA-DD-AACW TCGA-DD-AACY TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 
       46.82        47.67        18.54        21.63        42.58        44.22 
TCGA-DD-AAD8 TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADE TCGA-DD-AADG TCGA-DD-AADI 
       40.08        40.83        13.97        39.52        37.64        35.67 
TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADP TCGA-DD-AADQ 
       35.05        34.49        20.91         0.39        15.06        14.33 
TCGA-DD-AADR TCGA-DD-AADV TCGA-DD-AADY TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE4 
       66.67        18.87        18.25        18.15        20.98        19.99 
TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEI 
       21.17        21.83        15.72        25.08        26.63        50.33 
TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVX 
       79.07        89.69        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 
       29.92        26.93        28.08        13.91         0.20        12.82 
TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KC 
        0.20        13.15         0.20        18.74        19.99         0.62 
TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R3 
       11.93        14.40        19.10        27.88         8.12        12.03 
TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V 
        0.03         0.33        81.73        51.06        53.79        28.27 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ 
       14.86        21.53        22.13        25.64         5.92        19.53 
TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A6UC TCGA-G3-A7M5 
       19.23        25.25        22.95        20.42        22.06        14.70 
TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV3 
       11.87        14.14        15.78        15.65        12.23        13.55 
TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB 
        0.89         8.75        11.87        22.92         1.02         2.20 
TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 
       37.71        20.75        17.06        16.83        11.80         2.14 
TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75H 
       29.79        13.97        12.03         9.57        16.67        24.56 
TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V 
       20.71         7.53        10.85        58.88        26.27        17.69 
TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK 
        3.09        21.04        19.33        19.04        15.39        15.52 
TCGA-T1-A6J8 TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7MF TCGA-UB-AA0V TCGA-WJ-A86L 
        0.76        16.44         1.71         7.04        10.32        11.34 
TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ 
       20.22        24.85        18.28        35.77        25.71        23.21 
TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CE TCGA-ZS-A9CF 
       35.87         0.69        25.15        12.99        40.80        79.30 
TCGA-ZS-A9CG 
       11.21 

  AMP PEAK 28(20Q13.33) MUTATED AMP PEAK 28(20Q13.33) WILD-TYPE 
                           0.26                            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 
                          18.25                           20.22 
[1] "0.3 - 114.3 (18.2)" "0.0 - 120.8 (20.2)"
[1] "hr=" "1.4"
D28V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE III STAGE IIIA
  AMP PEAK 28(20Q13.33) MUTATED        51       30         2         25
  AMP PEAK 28(20Q13.33) WILD-TYPE     120       55         1         35
                                 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                               51                             120
  STAGE II                              30                              55
  STAGE III                              2                               1
  STAGE IIIA                            25                              35
  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      53  34  33   5
  AMP PEAK 28(20Q13.33) WILD-TYPE   129  58  41   7
D28V4, multiclass
       clus
vv      AMP PEAK 28(20Q13.33) MUTATED AMP PEAK 28(20Q13.33) WILD-TYPE
  T0+T1                            53                             129
  T2                               34                              58
  T3                               33                              41
  T4                                5                               7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V5, binary
                                 cls
clus                                0   1
  AMP PEAK 28(20Q13.33) MUTATED    90   2
  AMP PEAK 28(20Q13.33) WILD-TYPE 160   1
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 28(20Q13.33) MUTATED     90    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                            90                             160
  1                             2                               1
[1] 2 2
[1] FALSE
D28V6, binary
                                 cls
clus                                0   1
  AMP PEAK 28(20Q13.33) MUTATED    96   3
  AMP PEAK 28(20Q13.33) WILD-TYPE 165   1
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 28(20Q13.33) MUTATED     96    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                            96                             165
  1                             3                               1
[1] 2 2
[1] FALSE
D28V7, binary
                                 cls
clus                                0   1
  AMP PEAK 28(20Q13.33) MUTATED    48  77
  AMP PEAK 28(20Q13.33) WILD-TYPE  67 170
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 28(20Q13.33) MUTATED     48   77
  AMP PEAK 28(20Q13.33) WILD-TYPE   67  170
        clus
vv       AMP PEAK 28(20Q13.33) MUTATED AMP PEAK 28(20Q13.33) WILD-TYPE
  FEMALE                            48                              67
  MALE                              77                             170
[1] 2 2
[1] FALSE
D28V8, binary
                                 cls
clus                                0   1
  AMP PEAK 28(20Q13.33) MUTATED   116   1
  AMP PEAK 28(20Q13.33) WILD-TYPE 220   6
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 28(20Q13.33) MUTATED    116    1
  AMP PEAK 28(20Q13.33) WILD-TYPE  220    6
     clus
vv    AMP PEAK 28(20Q13.33) MUTATED AMP PEAK 28(20Q13.33) WILD-TYPE
  NO                            116                             220
  YES                             1                               6
[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                        123
  AMP PEAK 28(20Q13.33) WILD-TYPE                      230
                                 vv
clus                              HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK 28(20Q13.33) MUTATED                                  2
  AMP PEAK 28(20Q13.33) WILD-TYPE                                5
D28V9, multiclass
                                  clus
vv                                 AMP PEAK 28(20Q13.33) MUTATED
  FIBROLAMELLAR CARCINOMA                                      0
  HEPATOCELLULAR CARCINOMA                                   123
  HEPATOCHOLANGIOCARCINOMA (MIXED)                             2
                                  clus
vv                                 AMP PEAK 28(20Q13.33) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                        2
  HEPATOCELLULAR CARCINOMA                                     230
  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   110   6   1   6
  AMP PEAK 28(20Q13.33) WILD-TYPE 208   9   0  15
D28V10, multiclass
    clus
vv   AMP PEAK 28(20Q13.33) MUTATED AMP PEAK 28(20Q13.33) WILD-TYPE
  R0                           110                             208
  R1                             6                               9
  R2                             1                               0
  RX                             6                              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 28(20Q13.33) MUTATED                                  0    56
  AMP PEAK 28(20Q13.33) WILD-TYPE                                1   101
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 28(20Q13.33) MUTATED                           4    63
  AMP PEAK 28(20Q13.33) WILD-TYPE                        13   114
D28V11, multiclass
                                  clus
vv                                 AMP PEAK 28(20Q13.33) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                       56
  BLACK OR AFRICAN AMERICAN                                    4
  WHITE                                                       63
                                  clus
vv                                 AMP PEAK 28(20Q13.33) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               1
  ASIAN                                                        101
  BLACK OR AFRICAN AMERICAN                                     13
  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"
D28V12, binary
                                 cls
clus                                0   1
  AMP PEAK 28(20Q13.33) MUTATED     4 114
  AMP PEAK 28(20Q13.33) WILD-TYPE   9 218
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 28(20Q13.33) MUTATED      4  114
  AMP PEAK 28(20Q13.33) WILD-TYPE    9  218
                        clus
vv                       AMP PEAK 28(20Q13.33) MUTATED
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           114
                        clus
vv                       AMP PEAK 28(20Q13.33) WILD-TYPE
  HISPANIC OR LATINO                                   9
  NOT HISPANIC OR LATINO                             218
[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    57  26
  AMP PEAK 29(XQ28) WILD-TYPE 172 103
  AMP PEAK 29(XQ28) MUTATED AMP PEAK 29(XQ28) WILD-TYPE 
                         83                         275 
  AMP PEAK 29(XQ28) MUTATED AMP PEAK 29(XQ28) WILD-TYPE 
                         26                         103 
$`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-5264 TCGA-CC-A3MA 
       17.10        27.52        12.72         0.66         3.35         9.96 
TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A9FS TCGA-DD-A114 
        8.94         7.13         9.83        12.00         6.94        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-A7M5 TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV3 
       20.42        22.06        14.70        15.65        12.23        13.55 
TCGA-G3-AAV5 TCGA-G3-AAV7 TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A6G5 TCGA-KR-A7K8 
        8.75        11.87         2.99        37.71        16.83        29.79 
TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-NI-A4U2 TCGA-O8-A75V 
       12.72         9.57        16.67        22.95        58.88        17.69 
TCGA-UB-A7ME TCGA-WQ-A9G7 TCGA-ZP-A9CV TCGA-ZS-A9CD TCGA-ZS-A9CG 
       15.98         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 
       49.84        18.25        11.74        38.40        20.81        22.92 
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        14.76         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        23.38 
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        45.93         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         4.24         2.86         3.19         3.39         4.24 
TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A5UD 
        3.32         9.86        10.36        11.93        11.41         9.99 
TCGA-CC-A7IF TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A7IL TCGA-CC-A8HT 
       21.34        13.12        12.56         8.61         9.14         4.60 
TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A115 TCGA-DD-A116 
       11.31         9.17         8.15        79.73        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-A39W TCGA-DD-A39X TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 
       27.19        55.69        19.76        25.81         7.66        70.06 
TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA 
       20.12       102.74       107.11         0.36        30.61        33.14 
TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NL 
       32.52        90.28        30.15        26.83        30.51        56.25 
TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS 
       29.56        73.81       108.76        12.26         0.30        80.75 
TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-AA3A 
       23.93         9.30        23.05         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-AACK TCGA-DD-AACL 
       63.48        12.00        15.42         6.41         0.30         3.52 
TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACU 
       58.16        42.81        61.68        13.64        14.20        51.52 
TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 
       50.33        46.82         5.59         5.62         4.50        18.54 
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-AADP TCGA-DD-AADQ 
       35.05        34.49        20.91         0.39        15.06        14.33 
TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADV TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 
       66.67        15.58        18.87        18.25        18.25        18.15 
TCGA-DD-AAE2 TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEB 
       20.98         4.64        21.17        21.83        18.90        15.72 
TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVR 
       25.08        26.63        23.64        50.33        35.08        82.62 
TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVV TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVZ 
       59.93        72.39        80.71        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        29.92        26.93        28.08        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        20.78        11.87 
TCGA-G3-A7M8 TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV1 TCGA-G3-AAV4 TCGA-G3-AAV6 
       14.14         1.84        15.78        11.80         0.89         2.14 
TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-AAU7 
       22.92         1.02         2.20        20.75        17.06        11.80 
TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75H 
        2.14        21.60        31.27        13.97        12.03        24.56 
TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A8LF TCGA-PD-A5DF TCGA-QA-A7B7 
       20.71         7.53        10.85        26.27        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        36.10 
TCGA-T1-A6J8 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7MF 
        0.76        17.59        19.76        16.44         1.71         7.04 
TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-WX-AA46 
       10.75        10.32        11.34        12.99        20.22        24.85 
TCGA-WX-AA47 TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 
       18.28        22.78        13.55        25.71        23.21        35.87 
TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CE TCGA-ZS-A9CF 
        0.69        25.15        12.99        40.80        79.30 

  AMP PEAK 29(XQ28) MUTATED AMP PEAK 29(XQ28) WILD-TYPE 
                       0.20                        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 
                      19.99                       19.76 
[1] "0.2 - 114.3 (20.0)" "0.0 - 120.8 (19.8)"
[1] "hr=" "1.2"
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     129       64         3         48          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                         129
  STAGE II                          21                          64
  STAGE III                          0                           3
  STAGE IIIA                        12                          48
  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   139  70  59  10
D29V4, multiclass
       clus
vv      AMP PEAK 29(XQ28) MUTATED AMP PEAK 29(XQ28) WILD-TYPE
  T0+T1                        43                         139
  T2                           22                          70
  T3                           15                          59
  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 196   3
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 29(XQ28) MUTATED     54    0
  AMP PEAK 29(XQ28) WILD-TYPE  196    3
   clus
vv  AMP PEAK 29(XQ28) MUTATED AMP PEAK 29(XQ28) WILD-TYPE
  0                        54                         196
  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 200   4
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 29(XQ28) MUTATED     61    0
  AMP PEAK 29(XQ28) WILD-TYPE  200    4
   clus
vv  AMP PEAK 29(XQ28) MUTATED AMP PEAK 29(XQ28) WILD-TYPE
  0                        61                         200
  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 100 179
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 29(XQ28) MUTATED     15   68
  AMP PEAK 29(XQ28) WILD-TYPE  100  179
        clus
vv       AMP PEAK 29(XQ28) MUTATED AMP PEAK 29(XQ28) WILD-TYPE
  FEMALE                        15                         100
  MALE                          68                         179
[1] 2 2
[1] FALSE
D29V8, binary
                             cls
clus                            0   1
  AMP PEAK 29(XQ28) MUTATED    76   2
  AMP PEAK 29(XQ28) WILD-TYPE 260   5
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 29(XQ28) MUTATED     76    2
  AMP PEAK 29(XQ28) WILD-TYPE  260    5
     clus
vv    AMP PEAK 29(XQ28) MUTATED AMP PEAK 29(XQ28) WILD-TYPE
  NO                         76                         260
  YES                         2                           5
[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                      270
                             vv
clus                          HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK 29(XQ28) MUTATED                                  0
  AMP PEAK 29(XQ28) WILD-TYPE                                7
D29V9, 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                                 270
  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 243  12   1  17
D29V10, multiclass
    clus
vv   AMP PEAK 29(XQ28) MUTATED AMP PEAK 29(XQ28) WILD-TYPE
  R0                        75                         243
  R1                         3                          12
  R2                         0                           1
  RX                         4                          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 29(XQ28) MUTATED                                  1    36
  AMP PEAK 29(XQ28) WILD-TYPE                                0   121
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 29(XQ28) MUTATED                           5    36
  AMP PEAK 29(XQ28) WILD-TYPE                        12   141
D29V11, 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                                                    121
  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"
D29V12, binary
                             cls
clus                            0   1
  AMP PEAK 29(XQ28) MUTATED     1  77
  AMP PEAK 29(XQ28) WILD-TYPE  12 255
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 29(XQ28) MUTATED      1   77
  AMP PEAK 29(XQ28) WILD-TYPE   12  255
                        clus
vv                       AMP PEAK 29(XQ28) MUTATED AMP PEAK 29(XQ28) WILD-TYPE
  HISPANIC OR LATINO                             1                          12
  NOT HISPANIC OR LATINO                        77                         255
[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   100  59
  DEL PEAK  1(1P36.31) WILD-TYPE 129  70
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                           159                            199 
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                            59                             70 
$`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        49.84        18.25        11.74        38.40 
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        23.38        45.93        14.60        36.66         2.86 
TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A5UC 
        3.19         3.39         4.24         9.96        10.36        11.41 
TCGA-CC-A5UD TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7IJ TCGA-CC-A7IL 
        9.99         7.13        21.34         9.83        12.56         9.14 
TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 
        6.94         8.15        79.73        53.33       113.00         7.33 
TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EB 
        2.60         0.46        21.76        51.29        90.71        66.31 
TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EJ TCGA-DD-A39X TCGA-DD-A39Z 
       12.95        45.11        49.15        33.04        55.69        19.76 
TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A9 TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ 
       25.81         7.66        30.61        30.15        26.83        30.51 
TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NR TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73F 
       29.56        73.81         0.30        23.93         9.30        35.67 
TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AACA TCGA-DD-AACC TCGA-DD-AACH 
      114.35        13.48         0.53        75.65        55.40         6.41 
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-AADD TCGA-DD-AADF TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK 
       13.97        40.47         3.78        35.67        35.05        34.49 
TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADR TCGA-DD-AADW 
        0.39        29.52        14.89        15.06        66.67        19.30 
TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAEH 
       18.25        18.25        18.15        20.98        18.61        25.78 
TCGA-DD-AAEK TCGA-DD-AAVQ TCGA-DD-AAVS TCGA-DD-AAVW TCGA-DD-AAVZ TCGA-DD-AAW0 
       35.08        89.69        59.93        76.18        62.47        66.25 
TCGA-ED-A4XI TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A82E 
       26.93        13.35         9.73         0.20        12.82        13.41 
TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK 
       13.35         1.84         0.20        19.59         0.62        11.93 
TCGA-ES-A2HS TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R3 
       22.85        60.89        23.97        19.10        27.88        12.03 
TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-G3-A25S TCGA-G3-A25V TCGA-G3-A25W 
        0.03         0.33        81.73        13.68        28.27        30.74 
TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A5SI TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A7M5 
       58.49        14.86        25.25        20.42        17.10        14.70 
TCGA-G3-A7M9 TCGA-G3-AAV1 TCGA-G3-AAV6 TCGA-GJ-A3OU TCGA-KR-A7K2 TCGA-KR-A7K7 
        1.84        11.80         2.14        22.92        21.60        31.27 
TCGA-LG-A9QC TCGA-MI-A75G TCGA-MI-A75H TCGA-O8-A75V TCGA-RC-A7S9 TCGA-RC-A7SH 
       13.97        22.95        24.56        17.69        21.04        15.39 
TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-T1-A6J8 TCGA-UB-A7MA TCGA-UB-A7MC TCGA-UB-A7ME 
       15.52        36.10         0.76        17.59        16.44        15.98 
TCGA-UB-A7MF TCGA-UB-AA0U TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-XR-A8TF TCGA-ZP-A9CY 
        7.04        10.75         0.99        12.99        22.78        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        22.92 
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        17.10        14.76 
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-5264 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MC TCGA-CC-A5UE 
        4.24         3.35         3.32         9.86        11.93         8.94 
TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IK TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV 
       12.00        13.12         8.61         4.60        11.31         9.17 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A1EA TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE 
       37.78        83.57        79.40        19.79        75.65        11.47 
TCGA-DD-A1EI TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39Y 
        6.02        18.35        13.64        21.14        27.19         5.62 
TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 
       70.06        17.59        20.12       102.74       107.11        13.78 
TCGA-DD-A3A8 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NK 
        0.36        33.14        32.52        90.28        30.97        39.78 
TCGA-DD-A4NL TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73C 
       56.25       108.76        12.26        80.75        78.84        23.05 
TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-AAC9 TCGA-DD-AACB TCGA-DD-AACD TCGA-DD-AACE 
       22.78         1.45        11.41        76.41        12.53        63.48 
TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACI TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACQ 
       12.00        15.42        53.19         3.52        58.16        14.20 
TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACX TCGA-DD-AACY 
       59.31        51.35        51.52        50.33         5.59        47.67 
TCGA-DD-AACZ TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD8 TCGA-DD-AADE TCGA-DD-AADG 
        5.62        21.63        42.58        40.08        39.52        37.64 
TCGA-DD-AADL TCGA-DD-AADQ TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADV TCGA-DD-AAE4 
       20.91        14.33        15.58        18.21        18.87        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-AAEG TCGA-DD-AAEI TCGA-DD-AAVP TCGA-DD-AAVR 
       25.08        26.63        23.64        50.33        79.07        82.62 
TCGA-DD-AAVU TCGA-DD-AAVV TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAW1 TCGA-DD-AAW2 
       72.39        80.71        56.48        64.77        65.39        49.48 
TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A7PZ TCGA-ED-A7XO 
       53.69        29.92        28.08        13.91         0.20        14.04 
TCGA-ED-A7XP TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A3JL TCGA-ES-A2HT 
       13.15        18.74        19.99        20.61         9.96        14.40 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25Z 
        8.12         6.38         0.39        51.06        53.79        21.53 
TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SJ 
       22.13        25.64         5.92        19.53        19.23        22.95 
TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV0 
       22.06        20.78        11.87        14.14        15.78        15.65 
TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV7 TCGA-GJ-A6C0 
       12.23        13.55         0.89         8.75        11.87         1.02 
TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 
        2.20         2.99        37.71        20.75        17.06        16.83 
TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QD TCGA-MI-A75C 
       11.80         2.14        29.79        12.72        12.03         9.57 
TCGA-MI-A75E TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF 
       16.67        20.71         7.53        10.85        58.88        26.27 
TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-UB-A7MB TCGA-UB-A7MD 
       21.01         3.09        19.33        19.04        19.76         1.71 
TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 TCGA-YA-A8S7 
       10.32        11.34        20.22        24.85        18.28        13.55 
TCGA-ZP-A9CV TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CF 
       35.77        35.87        25.15        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                           0.20 
  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 
                         19.59                          19.79 
[1] "0.0 - 114.3 (19.6)" "0.2 - 120.8 (19.8)"
[1] "hr=" "1.1"
D30V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IIIA
  DEL PEAK  1(1P36.31) MUTATED        75       37         1         25
  DEL PEAK  1(1P36.31) WILD-TYPE      96       48         2         35
                                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                              75                             96
  STAGE II                             37                             48
  STAGE III                             1                              2
  STAGE IIIA                           25                             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  1(1P36.31) MUTATED      81  39  33   7
  DEL PEAK  1(1P36.31) WILD-TYPE   101  53  41   5
D30V4, multiclass
       clus
vv      DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE
  T0+T1                           81                            101
  T2                              39                             53
  T3                              33                             41
  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 138   1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.31) MUTATED    112    2
  DEL PEAK  1(1P36.31) WILD-TYPE  138    1
   clus
vv  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE
  0                          112                            138
  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 138   1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.31) MUTATED    123    3
  DEL PEAK  1(1P36.31) WILD-TYPE  138    1
   clus
vv  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE
  0                          123                            138
  1                            3                              1
[1] 2 2
[1] FALSE
D30V7, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.31) MUTATED    57 104
  DEL PEAK  1(1P36.31) WILD-TYPE  58 143
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.31) MUTATED     57  104
  DEL PEAK  1(1P36.31) WILD-TYPE   58  143
        clus
vv       DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE
  FEMALE                           57                             58
  MALE                            104                            143
[1] 2 2
[1] FALSE
D30V8, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.31) MUTATED   150   1
  DEL PEAK  1(1P36.31) WILD-TYPE 186   6
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.31) MUTATED    150    1
  DEL PEAK  1(1P36.31) WILD-TYPE  186    6
     clus
vv    DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE
  NO                           150                            186
  YES                            1                              6
[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                        156
  DEL PEAK  1(1P36.31) WILD-TYPE                      197
                                vv
clus                             HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK  1(1P36.31) MUTATED                                  5
  DEL PEAK  1(1P36.31) WILD-TYPE                                2
D30V9, multiclass
                                  clus
vv                                 DEL PEAK  1(1P36.31) MUTATED
  FIBROLAMELLAR CARCINOMA                                     0
  HEPATOCELLULAR CARCINOMA                                  156
  HEPATOCHOLANGIOCARCINOMA (MIXED)                            5
                                  clus
vv                                 DEL PEAK  1(1P36.31) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                       2
  HEPATOCELLULAR CARCINOMA                                    197
  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   138  10   1  10
  DEL PEAK  1(1P36.31) WILD-TYPE 180   5   0  11
D30V10, multiclass
    clus
vv   DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE
  R0                          138                            180
  R1                           10                              5
  R2                            1                              0
  RX                           10                             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  1(1P36.31) MUTATED                                  0    78
  DEL PEAK  1(1P36.31) WILD-TYPE                                1    79
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  1(1P36.31) MUTATED                           4    75
  DEL PEAK  1(1P36.31) WILD-TYPE                        13   102
D30V11, multiclass
                                  clus
vv                                 DEL PEAK  1(1P36.31) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                      78
  BLACK OR AFRICAN AMERICAN                                   4
  WHITE                                                      75
                                  clus
vv                                 DEL PEAK  1(1P36.31) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        79
  BLACK OR AFRICAN AMERICAN                                    13
  WHITE                                                       102
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V12, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.31) MUTATED     5 150
  DEL PEAK  1(1P36.31) WILD-TYPE   8 182
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.31) MUTATED      5  150
  DEL PEAK  1(1P36.31) WILD-TYPE    8  182
                        clus
vv                       DEL PEAK  1(1P36.31) MUTATED
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                          150
                        clus
vv                       DEL PEAK  1(1P36.31) WILD-TYPE
  HISPANIC OR LATINO                                  8
  NOT HISPANIC OR LATINO                            182
[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    89  50
  DEL PEAK  2(1P36.11) WILD-TYPE 140  79
  DEL PEAK  2(1P36.11) MUTATED DEL PEAK  2(1P36.11) WILD-TYPE 
                           139                            219 
  DEL PEAK  2(1P36.11) MUTATED DEL PEAK  2(1P36.11) WILD-TYPE 
                            50                             79 
$`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        49.84        18.25        11.74        38.40 
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         4.24         2.86 
TCGA-CC-5261 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A7IE 
        3.19         9.96        10.36        11.41         9.99         7.13 
TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7IJ TCGA-CC-A7IL TCGA-CC-A8HV TCGA-CC-A9FS 
       21.34         9.83        12.56         9.14         9.17         6.94 
TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A 
        8.15        79.73        53.33       113.00         7.33         2.60 
TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A1E9 TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EJ 
        0.46        21.76        90.71        45.11        49.15        33.04 
TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A3A1 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NH 
       21.14        55.69         7.66        30.61        33.14        30.15 
TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A73B TCGA-DD-A73F 
       26.83        30.51        29.56        73.81         9.30        35.67 
TCGA-DD-A73G TCGA-DD-AAC8 TCGA-DD-AACA TCGA-DD-AACC TCGA-DD-AACJ TCGA-DD-AACK 
      114.35         0.53        75.65        55.40        69.11         0.30 
TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACW TCGA-DD-AAD0 TCGA-DD-AAD1 
       42.81        61.68        13.64        46.82         4.50        18.54 
TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADI 
       44.22        22.09        40.54        40.83        13.97        35.67 
TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADM TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADR 
       35.05        34.49         0.39        14.89        15.06        66.67 
TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE3 TCGA-DD-AAEE 
       19.30        18.25        18.25        18.15        18.61        26.63 
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-A66X TCGA-ED-A66Y TCGA-ED-A7PY TCGA-ED-A82E 
       66.25        29.92        13.35         9.73        12.82        13.41 
TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK 
       13.35         1.84         0.20        19.59         0.62        11.93 
TCGA-ES-A2HS TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A496 
       22.85        60.89        23.97        27.88        12.03         0.33 
TCGA-FV-A4ZP TCGA-G3-A25S TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A5SI 
       81.73        13.68        30.74        58.49        14.86        25.25 
TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A7M5 TCGA-G3-A7M9 TCGA-G3-AAV1 TCGA-G3-AAV6 
       20.42        17.10        14.70         1.84        11.80         2.14 
TCGA-GJ-A3OU TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-LG-A9QC TCGA-MI-A75G 
       22.92        21.60        31.27        12.72        13.97        22.95 
TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-T1-A6J8 TCGA-UB-A7MA TCGA-UB-A7MC 
       15.39        15.52        36.10         0.76        17.59        16.44 
TCGA-UB-A7MF TCGA-UB-AA0U TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-XR-A8TF TCGA-ZP-A9CZ 
        7.04        10.75         0.99        12.99        22.78        23.21 
TCGA-ZP-A9D1 
        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        22.92 
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        17.10        14.76 
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 
       23.38         1.12        69.57        44.42        45.93         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-5264 TCGA-CC-A1HT TCGA-CC-A3M9 
        0.66         3.39         4.24         3.35         3.32         9.86 
TCGA-CC-A3MC TCGA-CC-A5UE TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IK TCGA-CC-A8HT 
       11.93         8.94        12.00        13.12         8.61         4.60 
TCGA-CC-A8HU TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A11D TCGA-DD-A1EA TCGA-DD-A1EB 
       11.31        37.78        83.57        51.29        79.40        66.31 
TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EI TCGA-DD-A1EK 
       19.79        75.65        11.47        12.95         6.02        18.35 
TCGA-DD-A1EL TCGA-DD-A39W TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A2 
       13.64        27.19         5.62        19.76        25.81        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-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-AA3A TCGA-DD-AAC9 TCGA-DD-AACB TCGA-DD-AACD 
       22.78         1.45        13.48        11.41        76.41        12.53 
TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACL 
       63.48        12.00        15.42         6.41        53.19         3.52 
TCGA-DD-AACM TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACV 
       58.16        14.20        59.31        51.35        51.52        50.33 
TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD8 
        5.59        47.67         5.62        21.63        42.58        40.08 
TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADL TCGA-DD-AADN 
       40.47        39.52         3.78        37.64        20.91        29.52 
TCGA-DD-AADQ TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADV TCGA-DD-AAE2 TCGA-DD-AAE4 
       14.33        15.58        18.21        18.87        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-AAVP TCGA-DD-AAVR 
       25.08        23.64        25.78        50.33        79.07        82.62 
TCGA-DD-AAVV TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 
       80.71        56.48        64.77        65.39        49.48        53.69 
TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A7PX TCGA-ED-A7PZ TCGA-ED-A7XO 
       26.93        28.08        13.91         0.20         0.20        14.04 
TCGA-ED-A7XP TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A3JL TCGA-ES-A2HT 
       13.15        18.74        19.99        20.61         9.96        14.40 
TCGA-FV-A2QR TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A495 TCGA-FV-A4ZQ TCGA-G3-A25T 
       19.10         8.12         6.38         0.03         0.39        51.06 
TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI 
       53.79        28.27        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        22.06        20.78        11.87 
TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 
       14.14        15.78        15.65        12.23        13.55         0.89 
TCGA-G3-AAV5 TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 
        8.75        11.87         1.02         2.20         2.99        37.71 
TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K8 
       20.75        17.06        16.83        11.80         2.14        29.79 
TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A520 
       12.03         9.57        16.67        24.56        20.71         7.53 
TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 
       10.85        58.88        26.27        17.69        21.01         3.09 
TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-UB-A7MB TCGA-UB-A7MD TCGA-UB-A7ME 
       21.04        19.33        19.04        19.76         1.71        15.98 
TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 TCGA-YA-A8S7 
       10.32        11.34        20.22        24.85        18.28        13.55 
TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD 
       35.77        25.71        35.87        25.15        12.99        45.57 
TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       40.80        79.30        11.21 

  DEL PEAK  2(1P36.11) MUTATED DEL PEAK  2(1P36.11) WILD-TYPE 
                          0.20                           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 
                         18.61                          19.99 
[1] "0.2 - 114.3 (18.6)" "0.0 - 120.8 (20.0)"
[1] "hr=" "1"  
D31V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IIIA
  DEL PEAK  2(1P36.11) MUTATED        59       36         1         24
  DEL PEAK  2(1P36.11) WILD-TYPE     112       49         2         36
                                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                              59                            112
  STAGE II                             36                             49
  STAGE III                             1                              2
  STAGE IIIA                           24                             36
  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      64  39  33   5
  DEL PEAK  2(1P36.11) WILD-TYPE   118  53  41   7
D31V4, multiclass
       clus
vv      DEL PEAK  2(1P36.11) MUTATED DEL PEAK  2(1P36.11) WILD-TYPE
  T0+T1                           64                            118
  T2                              39                             53
  T3                              33                             41
  T4                               5                              7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V5, binary
                                cls
clus                               0   1
  DEL PEAK  2(1P36.11) MUTATED   100   3
  DEL PEAK  2(1P36.11) WILD-TYPE 150   0
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  2(1P36.11) MUTATED    100    3
  DEL PEAK  2(1P36.11) WILD-TYPE  150    0
   clus
vv  DEL PEAK  2(1P36.11) MUTATED DEL PEAK  2(1P36.11) WILD-TYPE
  0                          100                            150
  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 151   1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  2(1P36.11) MUTATED    110    3
  DEL PEAK  2(1P36.11) WILD-TYPE  151    1
   clus
vv  DEL PEAK  2(1P36.11) MUTATED DEL PEAK  2(1P36.11) WILD-TYPE
  0                          110                            151
  1                            3                              1
[1] 2 2
[1] FALSE
D31V7, binary
                                cls
clus                               0   1
  DEL PEAK  2(1P36.11) MUTATED    47  94
  DEL PEAK  2(1P36.11) WILD-TYPE  68 153
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  2(1P36.11) MUTATED     47   94
  DEL PEAK  2(1P36.11) WILD-TYPE   68  153
        clus
vv       DEL PEAK  2(1P36.11) MUTATED DEL PEAK  2(1P36.11) WILD-TYPE
  FEMALE                           47                             68
  MALE                             94                            153
[1] 2 2
[1] FALSE
D31V8, binary
                                cls
clus                               0   1
  DEL PEAK  2(1P36.11) MUTATED   131   3
  DEL PEAK  2(1P36.11) WILD-TYPE 205   4
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  2(1P36.11) MUTATED    131    3
  DEL PEAK  2(1P36.11) WILD-TYPE  205    4
     clus
vv    DEL PEAK  2(1P36.11) MUTATED DEL PEAK  2(1P36.11) WILD-TYPE
  NO                           131                            205
  YES                            3                              4
[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                        137
  DEL PEAK  2(1P36.11) WILD-TYPE                      216
                                vv
clus                             HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK  2(1P36.11) MUTATED                                  4
  DEL PEAK  2(1P36.11) WILD-TYPE                                3
D31V9, multiclass
                                  clus
vv                                 DEL PEAK  2(1P36.11) MUTATED
  FIBROLAMELLAR CARCINOMA                                     0
  HEPATOCELLULAR CARCINOMA                                  137
  HEPATOCHOLANGIOCARCINOMA (MIXED)                            4
                                  clus
vv                                 DEL PEAK  2(1P36.11) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                       2
  HEPATOCELLULAR CARCINOMA                                    216
  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   121   9   1   9
  DEL PEAK  2(1P36.11) WILD-TYPE 197   6   0  12
D31V10, multiclass
    clus
vv   DEL PEAK  2(1P36.11) MUTATED DEL PEAK  2(1P36.11) WILD-TYPE
  R0                          121                            197
  R1                            9                              6
  R2                            1                              0
  RX                            9                             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  2(1P36.11) MUTATED                                  0    71
  DEL PEAK  2(1P36.11) WILD-TYPE                                1    86
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  2(1P36.11) MUTATED                           4    65
  DEL PEAK  2(1P36.11) WILD-TYPE                        13   112
D31V11, multiclass
                                  clus
vv                                 DEL PEAK  2(1P36.11) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                      71
  BLACK OR AFRICAN AMERICAN                                   4
  WHITE                                                      65
                                  clus
vv                                 DEL PEAK  2(1P36.11) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        86
  BLACK OR AFRICAN AMERICAN                                    13
  WHITE                                                       112
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V12, binary
                                cls
clus                               0   1
  DEL PEAK  2(1P36.11) MUTATED     4 134
  DEL PEAK  2(1P36.11) WILD-TYPE   9 198
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  2(1P36.11) MUTATED      4  134
  DEL PEAK  2(1P36.11) WILD-TYPE    9  198
                        clus
vv                       DEL PEAK  2(1P36.11) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                          134
                        clus
vv                       DEL PEAK  2(1P36.11) WILD-TYPE
  HISPANIC OR LATINO                                  9
  NOT HISPANIC OR LATINO                            198
[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    30  20
  DEL PEAK  3(2Q22.1) WILD-TYPE 199 109
  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                           50                           308 
  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                           20                           109 
$`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        23.38         0.26 
TCGA-BD-A3EP TCGA-CC-5264 TCGA-CC-A7IG TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IL 
       13.45         3.35         9.83        13.12        12.56         9.14 
TCGA-DD-A115 TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39Y TCGA-DD-A3A1 TCGA-DD-A4NJ 
       83.57        13.64        21.14         5.62         7.66        30.51 
TCGA-DD-A73B TCGA-DD-AACE TCGA-DD-AACU TCGA-DD-AACZ TCGA-DD-AADI TCGA-DD-AADL 
        9.30        63.48        51.52         5.62        35.67        20.91 
TCGA-DD-AADN TCGA-DD-AADV TCGA-DD-AADW TCGA-DD-AAE2 TCGA-DD-AAE4 TCGA-DD-AAE6 
       29.52        18.87        19.30        20.98        19.99         4.64 
TCGA-DD-AAED TCGA-ED-A459 TCGA-ED-A66Y TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-FV-A3I1 
       25.08        29.92         9.73         0.20        14.04         8.12 
TCGA-G3-AAV7 TCGA-GJ-A9DB TCGA-KR-A7K2 TCGA-RC-A7SH TCGA-T1-A6J8 TCGA-UB-A7MF 
       11.87         2.20        21.60        15.39         0.76         7.04 
TCGA-WQ-AB4B TCGA-ZP-A9D2 
       12.99        25.15 

$`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        49.84        38.40        22.92 
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        17.10        14.76 
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        45.93        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         4.24         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         9.86         9.96 
TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IE 
       10.36        11.93        11.41         9.99         8.94         7.13 
TCGA-CC-A7IF TCGA-CC-A7IH TCGA-CC-A7IK TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV 
       21.34        12.00         8.61         4.60        11.31         9.17 
TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A116 TCGA-DD-A118 
        6.94         8.15        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        26.63 
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-AAVV TCGA-DD-AAVW TCGA-DD-AAVX 
       82.62        59.93        72.39        80.71        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-A7PX TCGA-ED-A7PY 
       26.93        28.08        13.91        13.35         0.20        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-A3I0 
       22.85        14.40        60.89        23.97        19.10        27.88 
TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ 
        6.38        12.03         0.03         0.33        81.73         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-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ 
       14.86        21.53        22.13        25.64         5.92        19.53 
TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC 
       19.23        25.25        22.95        20.42        17.10        22.06 
TCGA-G3-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-A7M9 TCGA-G3-AAUZ 
       14.70        20.78        11.87        14.14         1.84        15.78 
TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 
       15.65        11.80        12.23        13.55         0.89         8.75 
TCGA-G3-AAV6 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF 
        2.14        22.92         1.02         2.99        37.71        20.75 
TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-KR-A7K8 
       17.06        16.83        11.80         2.14        31.27        29.79 
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        22.95 
TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF 
       24.56        20.71         7.53        10.85        58.88        26.27 
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-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD 
       15.52        36.10        17.59        19.76        16.44         1.71 
TCGA-UB-A7ME TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WX-AA44 
       15.98        10.75        10.32        11.34         0.99        20.22 
TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY 
       24.85        18.28        22.78        13.55        35.77        25.71 
TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE 
       23.21        35.87         0.69        12.99        45.57        40.80 
TCGA-ZS-A9CF TCGA-ZS-A9CG 
       79.30        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 
                       13.545                        20.515 
[1] "0.2 - 120.8 (13.5)" "0.0 - 114.3 (20.5)"
[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     148       71         3         51
                               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                           148
  STAGE II                            14                            71
  STAGE III                            0                             3
  STAGE IIIA                           9                            51
  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   157  78  63  11
D32V4, multiclass
       clus
vv      DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  T0+T1                          25                           157
  T2                             14                            78
  T3                             11                            63
  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 216   3
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2Q22.1) MUTATED     34    0
  DEL PEAK  3(2Q22.1) WILD-TYPE  216    3
   clus
vv  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  0                          34                           216
  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 225   4
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2Q22.1) MUTATED     36    0
  DEL PEAK  3(2Q22.1) WILD-TYPE  225    4
   clus
vv  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  0                          36                           225
  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 100 211
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2Q22.1) MUTATED     15   36
  DEL PEAK  3(2Q22.1) WILD-TYPE  100  211
        clus
vv       DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  FEMALE                          15                           100
  MALE                            36                           211
[1] 2 2
[1] FALSE
D32V8, binary
                               cls
clus                              0   1
  DEL PEAK  3(2Q22.1) MUTATED    46   2
  DEL PEAK  3(2Q22.1) WILD-TYPE 290   5
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2Q22.1) MUTATED     46    2
  DEL PEAK  3(2Q22.1) WILD-TYPE  290    5
     clus
vv    DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  NO                           46                           290
  YES                           2                             5
[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                      303
                               vv
clus                            HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK  3(2Q22.1) MUTATED                                  1
  DEL PEAK  3(2Q22.1) WILD-TYPE                                6
D32V9, 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                                   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
  DEL PEAK  3(2Q22.1) MUTATED    47   0   0   4
  DEL PEAK  3(2Q22.1) WILD-TYPE 271  15   1  17
D32V10, multiclass
    clus
vv   DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  R0                          47                           271
  R1                           0                            15
  R2                           0                             1
  RX                           4                            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  3(2Q22.1) MUTATED                                  0    24
  DEL PEAK  3(2Q22.1) WILD-TYPE                                1   133
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  3(2Q22.1) MUTATED                           4    22
  DEL PEAK  3(2Q22.1) WILD-TYPE                        13   155
D32V11, 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                                                      133
  BLACK OR AFRICAN AMERICAN                                   13
  WHITE                                                      155
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V12, binary
                               cls
clus                              0   1
  DEL PEAK  3(2Q22.1) MUTATED     2  45
  DEL PEAK  3(2Q22.1) WILD-TYPE  11 287
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2Q22.1) MUTATED      2   45
  DEL PEAK  3(2Q22.1) WILD-TYPE   11  287
                        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                                11
  NOT HISPANIC OR LATINO                           287
[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  20
  DEL PEAK  4(2Q37.3) WILD-TYPE 190 109
  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                           59                           299 
  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                           20                           109 
$`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        49.84        13.02        10.78        23.38 
TCGA-BC-A216 TCGA-BC-A3KF TCGA-BC-A5W4 TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5264 
       44.42         0.26        17.98        13.45         0.66         3.35 
TCGA-CC-A3M9 TCGA-CC-A7II TCGA-CC-A7IL TCGA-DD-A113 TCGA-DD-A115 TCGA-DD-A11A 
        9.86        13.12         9.14        79.73        83.57         2.60 
TCGA-DD-A11C TCGA-DD-A1EB TCGA-DD-A1EL TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A4NA 
       21.76        66.31        13.64         5.62        19.76        33.14 
TCGA-DD-A4NJ TCGA-DD-A4NQ TCGA-DD-A73B TCGA-DD-AACE TCGA-DD-AACO TCGA-DD-AACU 
       30.51        12.26         9.30        63.48        61.68        51.52 
TCGA-DD-AAD5 TCGA-DD-AADC TCGA-DD-AADF TCGA-DD-AADI TCGA-DD-AADL TCGA-DD-AADN 
       44.22        13.97         3.78        35.67        20.91        29.52 
TCGA-DD-AADP TCGA-DD-AAED TCGA-DD-AAEG TCGA-ED-A459 TCGA-ED-A66Y TCGA-ED-A7PX 
       15.06        25.08        23.64        29.92         9.73         0.20 
TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A496 TCGA-G3-A5SI 
        0.20        14.04        27.88         8.12         0.33        25.25 
TCGA-G3-A7M9 TCGA-G3-AAV7 TCGA-GJ-A9DB TCGA-KR-A7K2 TCGA-RC-A7SH TCGA-RC-A7SK 
        1.84        11.87         2.20        21.60        15.39        15.52 
TCGA-T1-A6J8 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MF TCGA-WQ-AB4B 
        0.76        17.59        19.76         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 
       38.40        20.81        22.92         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        17.10        14.76         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        45.93 
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 
        4.24         2.86         3.19         3.39         4.24         3.32 
TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A5UE 
        9.96        10.36        11.93        11.41         9.99         8.94 
TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7IJ TCGA-CC-A7IK 
        7.13        21.34         9.83        12.00        12.56         8.61 
TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A114 
        4.60        11.31         9.17         6.94         8.15        37.78 
TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11D TCGA-DD-A1E9 
       53.33       113.00         7.33         0.46        51.29        90.71 
TCGA-DD-A1EA TCGA-DD-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-A39V TCGA-DD-A39W 
       49.15         6.02        33.04        18.35        21.14        27.19 
TCGA-DD-A39X TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 
       55.69        25.81         7.66        70.06        17.59        20.12 
TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NB 
      102.74       107.11        13.78         0.36        30.61        32.52 
TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NK TCGA-DD-A4NL 
       90.28        30.97        30.15        26.83        39.78        56.25 
TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV 
       29.56        73.81       108.76         0.30        80.75        78.84 
TCGA-DD-A73A TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G 
       23.93        23.05        22.78         1.45        35.67       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-AACG TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ 
       12.53        12.00        15.42         6.41        53.19        69.11 
TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACP TCGA-DD-AACQ 
        0.30         3.52        58.16        42.81        13.64        14.20 
TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY 
       59.31        51.35        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-AAD6 
        5.62         4.50        18.54        21.63        42.58        22.09 
TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADG 
       40.08        40.54        40.83        40.47        39.52        37.64 
TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADM TCGA-DD-AADO TCGA-DD-AADQ TCGA-DD-AADR 
       35.05        34.49         0.39        14.89        14.33        66.67 
TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADV TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 
       15.58        18.21        18.87        19.30        18.25        18.25 
TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE7 
       18.15        20.98        18.61        19.99         4.64        21.17 
TCGA-DD-AAE8 TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAEE TCGA-DD-AAEH 
       21.83        23.74        18.90        15.72        26.63        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-AAVV TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ 
       72.39        80.71        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        26.93        28.08 
TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A7PY TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 
       13.91        13.35        12.82        13.15        13.41        13.35 
TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB 
        1.84         0.20        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-A2QQ TCGA-FV-A2QR TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A4ZP 
       23.97        19.10         6.38        12.03         0.03        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-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC 
       19.53        19.23        22.95        20.42        17.10        22.06 
TCGA-G3-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV0 
       14.70        20.78        11.87        14.14        15.78        15.65 
TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 
       11.80        12.23        13.55         0.89         8.75         2.14 
TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG 
       22.92         1.02         2.99        37.71        20.75        17.06 
TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG 
       16.83        11.80         2.14        31.27        29.79        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        22.95        24.56 
TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V 
       20.71         7.53        10.85        58.88        26.27        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        36.10 
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-AA44 TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TF TCGA-YA-A8S7 
        0.99        20.22        24.85        18.28        22.78        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        35.87         0.69        25.15 
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  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                         0.20                          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 
                        15.39                         20.22 
[1] "0.2 - 83.6 (15.4)"  "0.0 - 120.8 (20.2)"
[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     146       66         3         49
                               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                           146
  STAGE II                            19                            66
  STAGE III                            0                             3
  STAGE IIIA                          11                            49
  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   156  72  61  11
D33V4, multiclass
       clus
vv      DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE
  T0+T1                          26                           156
  T2                             20                            72
  T3                             13                            61
  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 213   2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q37.3) MUTATED     37    1
  DEL PEAK  4(2Q37.3) WILD-TYPE  213    2
   clus
vv  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE
  0                          37                           213
  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 214   4
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q37.3) MUTATED     47    0
  DEL PEAK  4(2Q37.3) WILD-TYPE  214    4
   clus
vv  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE
  0                          47                           214
  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  95 207
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q37.3) MUTATED     20   40
  DEL PEAK  4(2Q37.3) WILD-TYPE   95  207
        clus
vv       DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE
  FEMALE                          20                            95
  MALE                            40                           207
[1] 2 2
[1] FALSE
D33V8, binary
                               cls
clus                              0   1
  DEL PEAK  4(2Q37.3) MUTATED    53   1
  DEL PEAK  4(2Q37.3) WILD-TYPE 283   6
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q37.3) MUTATED     53    1
  DEL PEAK  4(2Q37.3) WILD-TYPE  283    6
     clus
vv    DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE
  NO                           53                           283
  YES                           1                             6
[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                      296
                               vv
clus                            HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK  4(2Q37.3) MUTATED                                  3
  DEL PEAK  4(2Q37.3) WILD-TYPE                                4
D33V9, 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                                   296
  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 266  13   1  15
D33V10, multiclass
    clus
vv   DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE
  R0                          52                           266
  R1                           2                            13
  R2                           0                             1
  RX                           6                            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  4(2Q37.3) MUTATED                                  0    26
  DEL PEAK  4(2Q37.3) WILD-TYPE                                1   131
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  4(2Q37.3) MUTATED                           5    27
  DEL PEAK  4(2Q37.3) WILD-TYPE                        12   150
D33V11, 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                                                      131
  BLACK OR AFRICAN AMERICAN                                   12
  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"
D33V12, binary
                               cls
clus                              0   1
  DEL PEAK  4(2Q37.3) MUTATED     3  51
  DEL PEAK  4(2Q37.3) WILD-TYPE  10 281
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q37.3) MUTATED      3   51
  DEL PEAK  4(2Q37.3) WILD-TYPE   10  281
                        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                                10
  NOT HISPANIC OR LATINO                           281
[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    42  25
  DEL PEAK  5(3P13) WILD-TYPE 187 104
  DEL PEAK  5(3P13) MUTATED DEL PEAK  5(3P13) WILD-TYPE 
                         67                         291 
  DEL PEAK  5(3P13) MUTATED DEL PEAK  5(3P13) WILD-TYPE 
                         25                         104 
$`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        49.84        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        45.93         2.86 
TCGA-CC-5263 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IG 
        4.24         9.96        10.36         8.94         7.13         9.83 
TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A8HV TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A11A 
       13.12        12.56         9.17         8.15        79.73         2.60 
TCGA-DD-A1E9 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NO 
       90.71        30.61        33.14        30.15        26.83        73.81 
TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AACO TCGA-DD-AAD2 TCGA-DD-AADC TCGA-DD-AADJ 
      114.35        13.48        61.68        21.63        13.97        35.05 
TCGA-DD-AADO TCGA-DD-AADY TCGA-DD-AAE3 TCGA-DD-AAVQ TCGA-DD-AAVU TCGA-ED-A66Y 
       14.89        18.25        18.61        89.69        72.39         9.73 
TCGA-ED-A7PX TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A82E TCGA-ED-A97K TCGA-EP-A2KA 
        0.20         0.20        14.04        13.41         0.20        20.61 
TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-G3-A25T TCGA-G3-A25X TCGA-G3-A7M5 TCGA-G3-AAV1 
       27.88        12.03        51.06        58.49        14.70        11.80 
TCGA-G3-AAV6 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-LG-A9QC TCGA-RC-A7SH TCGA-UB-A7MC 
        2.14        21.60        31.27        13.97        15.39        16.44 
TCGA-UB-A7MD TCGA-UB-A7MF TCGA-WQ-AB4B TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZS-A9CE 
        1.71         7.04        12.99        35.87         0.69        40.80 
TCGA-ZS-A9CF 
       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        38.40 
TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-4R-AA8I TCGA-5C-A9VH 
       20.81        22.92         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 
       17.10        14.76         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        23.38         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-5264 TCGA-CC-A1HT TCGA-CC-A3M9 
        4.24         3.19         3.39         3.35         3.32         9.86 
TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A7IF TCGA-CC-A7IH TCGA-CC-A7IK 
       11.93        11.41         9.99        21.34        12.00         8.61 
TCGA-CC-A7IL TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A9FS TCGA-DD-A114 TCGA-DD-A115 
        9.14         4.60        11.31         6.94        37.78        83.57 
TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D 
       53.33       113.00         7.33         0.46        21.76        51.29 
TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF 
       79.40        66.31        19.79        75.65        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-A39Z TCGA-DD-A3A0 
       21.14        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-A3A7 TCGA-DD-A3A8 TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NJ 
       13.78         0.36        32.52        90.28        30.97        30.51 
TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR 
       39.78        56.25        29.56       108.76        12.26         0.30 
TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-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-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB 
        1.45        35.67         0.53        11.41        75.65        76.41 
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-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-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-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-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADK 
       40.47        39.52         3.78        37.64        35.67        34.49 
TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR 
       20.91         0.39        29.52        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        26.63        23.64        25.78 
TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVV 
       50.33        35.08        79.07        82.62        59.93        80.71 
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-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 
       49.48        53.69        29.92        26.93        28.08        13.91 
TCGA-ED-A66X TCGA-ED-A7PY TCGA-ED-A7XP TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-EP-A12J 
       13.35        12.82        13.15        13.35         1.84        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-A3I1 TCGA-FV-A3R2 
       14.40        60.89        23.97        19.10         8.12         6.38 
TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25U 
        0.03         0.33        81.73         0.39        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-A5SM TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-A7M9 
       17.10        22.06        20.78        11.87        14.14         1.84 
TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 
       15.78        15.65        12.23        13.55         0.89         8.75 
TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 
       11.87        22.92         1.02         2.20         2.99        37.71 
TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K8 
       20.75        17.06        16.83        11.80         2.14        29.79 
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        22.95        24.56 
TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V 
       20.71         7.53        10.85        58.88        26.27        17.69 
TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SK 
       21.01         3.09        21.04        19.33        19.04        15.52 
TCGA-RG-A7D4 TCGA-T1-A6J8 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7ME TCGA-UB-AA0U 
       36.10         0.76        17.59        19.76        15.98        10.75 
TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 
       10.32        11.34         0.99        20.22        24.85        18.28 
TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D2 
       22.78        13.55        35.77        25.71        23.21        25.15 
TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CG 
       12.99        45.57        11.21 

  DEL PEAK  5(3P13) MUTATED DEL PEAK  5(3P13) WILD-TYPE 
                       0.20                        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 
                      14.70                       20.42 
[1] "0.2 - 114.3 (14.7)" "0.0 - 120.8 (20.4)"
[1] "hr=" "1.1"
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     151       65         3         44          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                         151
  STAGE II                          20                          65
  STAGE III                          0                           3
  STAGE IIIA                        16                          44
  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   160  69  54   8
D34V4, multiclass
       clus
vv      DEL PEAK  5(3P13) MUTATED DEL PEAK  5(3P13) WILD-TYPE
  T0+T1                        22                         160
  T2                           23                          69
  T3                           20                          54
  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 203   2
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  5(3P13) MUTATED     47    1
  DEL PEAK  5(3P13) WILD-TYPE  203    2
   clus
vv  DEL PEAK  5(3P13) MUTATED DEL PEAK  5(3P13) WILD-TYPE
  0                        47                         203
  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 213   2
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  5(3P13) MUTATED     48    2
  DEL PEAK  5(3P13) WILD-TYPE  213    2
   clus
vv  DEL PEAK  5(3P13) MUTATED DEL PEAK  5(3P13) WILD-TYPE
  0                        48                         213
  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  85 208
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  5(3P13) MUTATED     30   39
  DEL PEAK  5(3P13) WILD-TYPE   85  208
        clus
vv       DEL PEAK  5(3P13) MUTATED DEL PEAK  5(3P13) WILD-TYPE
  FEMALE                        30                          85
  MALE                          39                         208
[1] 2 2
[1] FALSE
D34V8, binary
                             cls
clus                            0   1
  DEL PEAK  5(3P13) MUTATED    66   0
  DEL PEAK  5(3P13) WILD-TYPE 270   7
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  5(3P13) MUTATED     66    0
  DEL PEAK  5(3P13) WILD-TYPE  270    7
     clus
vv    DEL PEAK  5(3P13) MUTATED DEL PEAK  5(3P13) WILD-TYPE
  NO                         66                         270
  YES                         0                           7
[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                      289
                             vv
clus                          HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK  5(3P13) MUTATED                                  5
  DEL PEAK  5(3P13) WILD-TYPE                                2
D34V9, 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                                 289
  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 254  14   1  17
D34V10, multiclass
    clus
vv   DEL PEAK  5(3P13) MUTATED DEL PEAK  5(3P13) WILD-TYPE
  R0                        64                         254
  R1                         1                          14
  R2                         0                           1
  RX                         4                          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  5(3P13) MUTATED                                  0    32
  DEL PEAK  5(3P13) WILD-TYPE                                1   125
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  5(3P13) MUTATED                           4    33
  DEL PEAK  5(3P13) WILD-TYPE                        13   144
D34V11, 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                                                    125
  BLACK OR AFRICAN AMERICAN                                 13
  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"
D34V12, binary
                             cls
clus                            0   1
  DEL PEAK  5(3P13) MUTATED     2  64
  DEL PEAK  5(3P13) WILD-TYPE  11 268
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  5(3P13) MUTATED      2   64
  DEL PEAK  5(3P13) WILD-TYPE   11  268
                        clus
vv                       DEL PEAK  5(3P13) MUTATED DEL PEAK  5(3P13) WILD-TYPE
  HISPANIC OR LATINO                             2                          11
  NOT HISPANIC OR LATINO                        64                         268
[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    48  33
  DEL PEAK  6(4P16.3) WILD-TYPE 181  96
  DEL PEAK  6(4P16.3) MUTATED DEL PEAK  6(4P16.3) WILD-TYPE 
                           81                           277 
  DEL PEAK  6(4P16.3) MUTATED DEL PEAK  6(4P16.3) WILD-TYPE 
                           33                            96 
$`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        23.38         5.03 
TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BW-A5NO TCGA-CC-5264 TCGA-CC-A3MC TCGA-CC-A7IE 
       17.98        14.60         0.66         3.35        11.93         7.13 
TCGA-CC-A7IF TCGA-CC-A7II TCGA-CC-A7IK TCGA-CC-A7IL TCGA-CC-A8HV TCGA-CC-A9FW 
       21.34        13.12         8.61         9.14         9.17         8.15 
TCGA-DD-A114 TCGA-DD-A119 TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A39X TCGA-DD-A39Y 
       37.78         7.33         6.02        33.04        55.69         5.62 
TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NN TCGA-DD-A73A TCGA-DD-AAC8 TCGA-DD-AACE 
       26.83        30.51        29.56        23.93         0.53        63.48 
TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACP TCGA-DD-AACU 
       12.00        15.42        58.16        42.81        13.64        51.52 
TCGA-DD-AACY TCGA-DD-AAD5 TCGA-DD-AAD8 TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADV 
       47.67        44.22        40.08        13.97        40.47        18.87 
TCGA-DD-AAE8 TCGA-DD-AAED TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVQ TCGA-DD-AAVU 
       21.83        25.08        50.33        35.08        89.69        72.39 
TCGA-DD-AAVV TCGA-ED-A459 TCGA-ED-A7XO TCGA-ED-A8O6 TCGA-EP-A2KB TCGA-EP-A2KC 
       80.71        29.92        14.04         1.84        19.59         0.62 
TCGA-FV-A2QQ TCGA-FV-A4ZP TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25X TCGA-G3-A3CH 
       23.97        81.73        13.68        53.79        58.49        25.64 
TCGA-G3-A7M5 TCGA-G3-AAUZ TCGA-G3-AAV1 TCGA-G3-AAV4 TCGA-GJ-A3OU TCGA-HP-A5N0 
       14.70        15.78        11.80         0.89        22.92        37.71 
TCGA-K7-A5RG TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-MI-A75G TCGA-PD-A5DF TCGA-RG-A7D4 
       17.06        21.60        31.27        22.95        21.01        36.10 
TCGA-UB-A7MC TCGA-UB-A7ME TCGA-UB-A7MF TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-XR-A8TF 
       16.44        15.98         7.04        12.99        20.22        22.78 
TCGA-YA-A8S7 TCGA-ZP-A9D2 TCGA-ZS-A9CE 
       13.55        25.15        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        49.84        47.74 
TCGA-2Y-A9H5 TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA 
       18.25        11.74        38.40        20.81        22.92         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        17.10        14.76         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 
       45.93         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         4.24         2.86         3.19         3.39 
TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A5UC 
        4.24         3.32         9.86         9.96        10.36        11.41 
TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7IJ TCGA-CC-A8HT 
        9.99         8.94         9.83        12.00        12.56         4.60 
TCGA-CC-A8HU TCGA-CC-A9FS TCGA-DD-A113 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 
       11.31         6.94        79.73        83.57        53.33       113.00 
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-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-A1EH TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39Z 
       49.15        18.35        13.64        21.14        27.19        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-A4NK TCGA-DD-A4NL TCGA-DD-A4NO 
       90.28        30.97        30.15        39.78        56.25        73.81 
TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73B 
      108.76        12.26         0.30        80.75        78.84         9.30 
TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A 
       23.05        22.78         1.45        35.67       114.35        13.48 
TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACH 
       11.41        75.65        76.41        55.40        12.53         6.41 
TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACO TCGA-DD-AACQ 
       53.19        69.11         0.30         3.52        61.68        14.20 
TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACZ 
       59.31        51.35        50.33        46.82         5.59         5.62 
TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD6 TCGA-DD-AADA 
        4.50        18.54        21.63        42.58        22.09        40.54 
TCGA-DD-AADB TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ 
       40.83        39.52         3.78        37.64        35.67        35.05 
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-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-AAEA TCGA-DD-AAEB TCGA-DD-AAEE TCGA-DD-AAEG 
       21.17        23.74        18.90        15.72        26.63        23.64 
TCGA-DD-AAEH TCGA-DD-AAVP TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVW TCGA-DD-AAVX 
       25.78        79.07        82.62        59.93        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-A66Y TCGA-ED-A7PX 
       26.93        28.08        13.91        13.35         9.73         0.20 
TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A97K 
       12.82         0.20        13.15        13.41        13.35         0.20 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS 
       18.74        19.99        20.61         9.96        11.93        22.85 
TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 
       14.40        60.89        19.10        27.88         8.12         6.38 
TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25V 
       12.03         0.03         0.33         0.39        51.06        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-A5SM TCGA-G3-A6UC 
       19.23        25.25        22.95        20.42        17.10        22.06 
TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-A7M9 TCGA-G3-AAV0 TCGA-G3-AAV2 
       20.78        11.87        14.14         1.84        15.65        12.23 
TCGA-G3-AAV3 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB 
       13.55         8.75         2.14        11.87         1.02         2.20 
TCGA-HP-A5MZ TCGA-K7-A5RF TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K8 
        2.99        20.75        16.83        11.80         2.14        29.79 
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        24.56 
TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V 
       20.71         7.53        10.85        58.88        26.27        17.69 
TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK 
        3.09        21.04        19.33        19.04        15.39        15.52 
TCGA-T1-A6J8 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MD TCGA-UB-AA0U TCGA-UB-AA0V 
        0.76        17.59        19.76         1.71        10.75        10.32 
TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WX-AA46 TCGA-WX-AA47 TCGA-ZP-A9CV TCGA-ZP-A9CY 
       11.34         0.99        24.85        18.28        35.77        25.71 
TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CF 
       23.21        35.87         0.69        12.99        45.57        79.30 
TCGA-ZS-A9CG 
       11.21 

  DEL PEAK  6(4P16.3) MUTATED DEL PEAK  6(4P16.3) WILD-TYPE 
                         0.53                          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 
                        21.01                         19.53 
[1] "0.5 - 89.7 (21.0)"  "0.0 - 120.8 (19.5)"
[1] "hr=" "1.3"
D35V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IIIA
  DEL PEAK  6(4P16.3) MUTATED        35       19         0         18
  DEL PEAK  6(4P16.3) WILD-TYPE     136       66         3         42
                               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                             35                           136
  STAGE II                            19                            66
  STAGE III                            0                             3
  STAGE IIIA                          18                            42
  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      37  22  21   3
  DEL PEAK  6(4P16.3) WILD-TYPE   145  70  53   9
D35V4, multiclass
       clus
vv      DEL PEAK  6(4P16.3) MUTATED DEL PEAK  6(4P16.3) WILD-TYPE
  T0+T1                          37                           145
  T2                             22                            70
  T3                             21                            53
  T4                              3                             9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V5, binary
                               cls
clus                              0   1
  DEL PEAK  6(4P16.3) MUTATED    56   2
  DEL PEAK  6(4P16.3) WILD-TYPE 194   1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(4P16.3) MUTATED     56    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                          56                           194
  1                           2                             1
[1] 2 2
[1] FALSE
D35V6, binary
                               cls
clus                              0   1
  DEL PEAK  6(4P16.3) MUTATED    62   2
  DEL PEAK  6(4P16.3) WILD-TYPE 199   2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(4P16.3) MUTATED     62    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                          62                           199
  1                           2                             2
[1] 2 2
[1] FALSE
D35V7, binary
                               cls
clus                              0   1
  DEL PEAK  6(4P16.3) MUTATED    17  67
  DEL PEAK  6(4P16.3) WILD-TYPE  98 180
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(4P16.3) MUTATED     17   67
  DEL PEAK  6(4P16.3) WILD-TYPE   98  180
        clus
vv       DEL PEAK  6(4P16.3) MUTATED DEL PEAK  6(4P16.3) WILD-TYPE
  FEMALE                          17                            98
  MALE                            67                           180
[1] 2 2
[1] FALSE
D35V8, binary
                               cls
clus                              0   1
  DEL PEAK  6(4P16.3) MUTATED    78   2
  DEL PEAK  6(4P16.3) WILD-TYPE 258   5
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(4P16.3) MUTATED     78    2
  DEL PEAK  6(4P16.3) WILD-TYPE  258    5
     clus
vv    DEL PEAK  6(4P16.3) MUTATED DEL PEAK  6(4P16.3) WILD-TYPE
  NO                           78                           258
  YES                           2                             5
[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                         82
  DEL PEAK  6(4P16.3) WILD-TYPE                      271
                               vv
clus                            HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK  6(4P16.3) MUTATED                                  2
  DEL PEAK  6(4P16.3) WILD-TYPE                                5
D35V9, multiclass
                                  clus
vv                                 DEL PEAK  6(4P16.3) MUTATED
  FIBROLAMELLAR CARCINOMA                                    0
  HEPATOCELLULAR CARCINOMA                                  82
  HEPATOCHOLANGIOCARCINOMA (MIXED)                           2
                                  clus
vv                                 DEL PEAK  6(4P16.3) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                      2
  HEPATOCELLULAR CARCINOMA                                   271
  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    72   3   1   7
  DEL PEAK  6(4P16.3) WILD-TYPE 246  12   0  14
D35V10, multiclass
    clus
vv   DEL PEAK  6(4P16.3) MUTATED DEL PEAK  6(4P16.3) WILD-TYPE
  R0                          72                           246
  R1                           3                            12
  R2                           1                             0
  RX                           7                            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    44
  DEL PEAK  6(4P16.3) WILD-TYPE                                1   113
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  6(4P16.3) MUTATED                           6    32
  DEL PEAK  6(4P16.3) WILD-TYPE                        11   145
D35V11, multiclass
                                  clus
vv                                 DEL PEAK  6(4P16.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                     44
  BLACK OR AFRICAN AMERICAN                                  6
  WHITE                                                     32
                                  clus
vv                                 DEL PEAK  6(4P16.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                      113
  BLACK OR AFRICAN AMERICAN                                   11
  WHITE                                                      145
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V12, binary
                               cls
clus                              0   1
  DEL PEAK  6(4P16.3) MUTATED     6  75
  DEL PEAK  6(4P16.3) WILD-TYPE   7 257
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(4P16.3) MUTATED      6   75
  DEL PEAK  6(4P16.3) WILD-TYPE    7  257
                        clus
vv                       DEL PEAK  6(4P16.3) MUTATED
  HISPANIC OR LATINO                               6
  NOT HISPANIC OR LATINO                          75
                        clus
vv                       DEL PEAK  6(4P16.3) WILD-TYPE
  HISPANIC OR LATINO                                 7
  NOT HISPANIC OR LATINO                           257
[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   102  64
  DEL PEAK  7(4Q21.3) WILD-TYPE 127  65
  DEL PEAK  7(4Q21.3) MUTATED DEL PEAK  7(4Q21.3) WILD-TYPE 
                          166                           192 
  DEL PEAK  7(4Q21.3) MUTATED DEL PEAK  7(4Q21.3) WILD-TYPE 
                           64                            65 
$`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        49.84 
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        23.38         1.12         5.03        45.93         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         4.24 
TCGA-CC-5261 TCGA-CC-5263 TCGA-CC-5264 TCGA-CC-A3M9 TCGA-CC-A3MB TCGA-CC-A3MC 
        3.19         4.24         3.35         9.86        10.36        11.93 
TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7II 
        9.99         8.94         7.13        21.34         9.83        13.12 
TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A7IL TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FS 
       12.56         8.61         9.14        11.31         9.17         6.94 
TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A116 TCGA-DD-A119 TCGA-DD-A11A 
        8.15        79.73        37.78        53.33         7.33         2.60 
TCGA-DD-A1EB TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ 
       66.31        12.95        45.11        49.15         6.02        33.04 
TCGA-DD-A1EL TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A3A5 TCGA-DD-A3A9 TCGA-DD-A4ND 
       13.64        55.69         5.62       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-A73G TCGA-DD-AAC8 TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACE 
        9.30       114.35         0.53        76.41        55.40        63.48 
TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACP 
       12.00        15.42         3.52        58.16        42.81        13.64 
TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACZ TCGA-DD-AAD3 
       59.31        51.52        50.33        46.82         5.62        42.58 
TCGA-DD-AAD5 TCGA-DD-AAD8 TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADI 
       44.22        40.08        40.83        13.97        40.47        35.67 
TCGA-DD-AADL TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADR TCGA-DD-AADV TCGA-DD-AADY 
       20.91        14.89        15.06        66.67        18.87        18.25 
TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE6 TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAED 
       18.25        18.15         4.64        21.83        18.90        25.08 
TCGA-DD-AAEK TCGA-DD-AAVQ TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVV TCGA-DD-AAVW 
       35.08        89.69        59.93        72.39        80.71        76.18 
TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-ED-A459 TCGA-ED-A66X TCGA-ED-A7PX TCGA-ED-A7PY 
       62.47        66.25        29.92        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-A7M5 
       58.49        14.86        21.53        25.25        17.10        14.70 
TCGA-G3-A7M9 TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV4 TCGA-G3-AAV6 
        1.84        15.65        11.80        12.23         0.89         2.14 
TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-KR-A7K2 
       11.87        22.92         1.02        37.71        17.06        21.60 
TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC TCGA-MI-A75G TCGA-O8-A75V 
       31.27        29.79        12.72        13.97        22.95        17.69 
TCGA-RC-A7SB TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-T1-A6J8 TCGA-UB-A7MB 
       19.33        15.39        15.52        36.10         0.76        19.76 
TCGA-UB-A7MC TCGA-UB-A7ME TCGA-UB-A7MF TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA44 
       16.44        15.98         7.04         0.99        12.99        20.22 
TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9D2 TCGA-ZS-A9CE 
       22.78        13.55        25.15        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        38.40        22.92         1.18 
TCGA-2Y-A9HB TCGA-4R-AA8I TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4072 
        8.55         8.61        17.10        14.76         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-CC-A5UC TCGA-CC-A7IH 
        2.86         3.39         3.32         9.96        11.41        12.00 
TCGA-CC-A8HT TCGA-DD-A115 TCGA-DD-A118 TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D 
        4.60        83.57       113.00         0.46        21.76        51.29 
TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EK 
       90.71        79.40        19.79        75.65        11.47        18.35 
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-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A4NA 
       17.59        20.12       107.11        13.78         0.36        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-A73F TCGA-DD-AA3A TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACD TCGA-DD-AACH 
       35.67        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 
       26.63        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        26.93 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66Y TCGA-ED-A82E TCGA-ED-A8O6 TCGA-EP-A12J 
       28.08        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-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV3 
       22.06        20.78        11.87        14.14        15.78        13.55 
TCGA-G3-AAV5 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-K7-A5RF TCGA-K7-A6G5 TCGA-K7-AAU7 
        8.75         2.20         2.99        20.75        16.83        11.80 
TCGA-KR-A7K0 TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75H TCGA-MI-A75I 
        2.14        12.03         9.57        16.67        24.56        20.71 
TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-PD-A5DF TCGA-QA-A7B7 
        7.53        10.85        58.88        26.27        21.01         3.09 
TCGA-RC-A7S9 TCGA-RC-A7SF TCGA-UB-A7MA TCGA-UB-A7MD TCGA-UB-AA0U TCGA-UB-AA0V 
       21.04        19.04        17.59         1.71        10.75        10.32 
TCGA-WJ-A86L TCGA-WX-AA46 TCGA-WX-AA47 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ 
       11.34        24.85        18.28        35.77        25.71        23.21 
TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CF TCGA-ZS-A9CG 
       35.87         0.69        12.99        45.57        79.30        11.21 

  DEL PEAK  7(4Q21.3) MUTATED DEL PEAK  7(4Q21.3) WILD-TYPE 
                         0.20                          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 
                       17.835                        20.765 
[1] "0.2 - 120.8 (17.8)" "0.0 - 113.0 (20.8)"
[1] "hr=" "1.2"
D36V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IIIA
  DEL PEAK  7(4Q21.3) MUTATED        75       44         2         28
  DEL PEAK  7(4Q21.3) WILD-TYPE      96       41         1         32
                               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                             75                            96
  STAGE II                            44                            41
  STAGE III                            2                             1
  STAGE IIIA                          28                            32
  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      79  48  36   5
  DEL PEAK  7(4Q21.3) WILD-TYPE   103  44  38   7
D36V4, multiclass
       clus
vv      DEL PEAK  7(4Q21.3) MUTATED DEL PEAK  7(4Q21.3) WILD-TYPE
  T0+T1                          79                           103
  T2                             48                            44
  T3                             36                            38
  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   119   2
  DEL PEAK  7(4Q21.3) WILD-TYPE 131   1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(4Q21.3) MUTATED    119    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                         119                           131
  1                           2                             1
[1] 2 2
[1] FALSE
D36V6, binary
                               cls
clus                              0   1
  DEL PEAK  7(4Q21.3) MUTATED   132   3
  DEL PEAK  7(4Q21.3) WILD-TYPE 129   1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(4Q21.3) MUTATED    132    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                         132                           129
  1                           3                             1
[1] 2 2
[1] FALSE
D36V7, binary
                               cls
clus                              0   1
  DEL PEAK  7(4Q21.3) MUTATED    50 119
  DEL PEAK  7(4Q21.3) WILD-TYPE  65 128
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(4Q21.3) MUTATED     50  119
  DEL PEAK  7(4Q21.3) WILD-TYPE   65  128
        clus
vv       DEL PEAK  7(4Q21.3) MUTATED DEL PEAK  7(4Q21.3) WILD-TYPE
  FEMALE                          50                            65
  MALE                           119                           128
[1] 2 2
[1] FALSE
D36V8, binary
                               cls
clus                              0   1
  DEL PEAK  7(4Q21.3) MUTATED   156   3
  DEL PEAK  7(4Q21.3) WILD-TYPE 180   4
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(4Q21.3) MUTATED    156    3
  DEL PEAK  7(4Q21.3) WILD-TYPE  180    4
     clus
vv    DEL PEAK  7(4Q21.3) MUTATED DEL PEAK  7(4Q21.3) WILD-TYPE
  NO                          156                           180
  YES                           3                             4
[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                        166
  DEL PEAK  7(4Q21.3) WILD-TYPE                      187
                               vv
clus                            HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK  7(4Q21.3) MUTATED                                  3
  DEL PEAK  7(4Q21.3) WILD-TYPE                                4
D36V9, multiclass
                                  clus
vv                                 DEL PEAK  7(4Q21.3) MUTATED
  FIBROLAMELLAR CARCINOMA                                    0
  HEPATOCELLULAR CARCINOMA                                 166
  HEPATOCHOLANGIOCARCINOMA (MIXED)                           3
                                  clus
vv                                 DEL PEAK  7(4Q21.3) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                      2
  HEPATOCELLULAR CARCINOMA                                   187
  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   150   6   1  12
  DEL PEAK  7(4Q21.3) WILD-TYPE 168   9   0   9
D36V10, multiclass
    clus
vv   DEL PEAK  7(4Q21.3) MUTATED DEL PEAK  7(4Q21.3) WILD-TYPE
  R0                         150                           168
  R1                           6                             9
  R2                           1                             0
  RX                          12                             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    89
  DEL PEAK  7(4Q21.3) WILD-TYPE                                1    68
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  7(4Q21.3) MUTATED                           9    67
  DEL PEAK  7(4Q21.3) WILD-TYPE                         8   110
D36V11, multiclass
                                  clus
vv                                 DEL PEAK  7(4Q21.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                     89
  BLACK OR AFRICAN AMERICAN                                  9
  WHITE                                                     67
                                  clus
vv                                 DEL PEAK  7(4Q21.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                       68
  BLACK OR AFRICAN AMERICAN                                    8
  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"
D36V12, binary
                               cls
clus                              0   1
  DEL PEAK  7(4Q21.3) MUTATED    10 151
  DEL PEAK  7(4Q21.3) WILD-TYPE   3 181
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(4Q21.3) MUTATED     10  151
  DEL PEAK  7(4Q21.3) WILD-TYPE    3  181
                        clus
vv                       DEL PEAK  7(4Q21.3) MUTATED
  HISPANIC OR LATINO                              10
  NOT HISPANIC OR LATINO                         151
                        clus
vv                       DEL PEAK  7(4Q21.3) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           181
[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   102  65
  DEL PEAK  8(4Q22.3) WILD-TYPE 127  64
  DEL PEAK  8(4Q22.3) MUTATED DEL PEAK  8(4Q22.3) WILD-TYPE 
                          167                           191 
  DEL PEAK  8(4Q22.3) MUTATED DEL PEAK  8(4Q22.3) WILD-TYPE 
                           65                            64 
$`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        49.84 
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        23.38         1.12         5.03        45.93 
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         4.24 
TCGA-CC-5261 TCGA-CC-5263 TCGA-CC-5264 TCGA-CC-A3M9 TCGA-CC-A3MB TCGA-CC-A3MC 
        3.19         4.24         3.35         9.86        10.36        11.93 
TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7II 
        9.99         8.94         7.13        21.34         9.83        13.12 
TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A7IL TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FS 
       12.56         8.61         9.14        11.31         9.17         6.94 
TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A116 TCGA-DD-A119 TCGA-DD-A11A 
        8.15        79.73        37.78        53.33         7.33         2.60 
TCGA-DD-A11C TCGA-DD-A1EB TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI 
       21.76        66.31        12.95        45.11        49.15         6.02 
TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A3A0 TCGA-DD-A3A5 
       33.04        13.64        55.69         5.62        25.81       102.74 
TCGA-DD-A3A9 TCGA-DD-A4ND TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NN 
       30.61        90.28        30.15        26.83        30.51        29.56 
TCGA-DD-A4NO TCGA-DD-A4NQ TCGA-DD-A73B TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AAC8 
       73.81        12.26         9.30        35.67       114.35         0.53 
TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACL 
       76.41        55.40        63.48        12.00        15.42         3.52 
TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACP TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACV 
       58.16        42.81        13.64        59.31        51.52        50.33 
TCGA-DD-AACW TCGA-DD-AACZ TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD8 TCGA-DD-AADB 
       46.82         5.62        42.58        44.22        40.08        40.83 
TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADI TCGA-DD-AADL TCGA-DD-AADO TCGA-DD-AADP 
       13.97        40.47        35.67        20.91        14.89        15.06 
TCGA-DD-AADR TCGA-DD-AADV TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE6 
       66.67        18.87        18.25        18.25        18.15         4.64 
TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAED TCGA-DD-AAEK TCGA-DD-AAVQ TCGA-DD-AAVS 
       21.83        18.90        25.08        35.08        89.69        59.93 
TCGA-DD-AAVU TCGA-DD-AAVV TCGA-DD-AAVW TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-ED-A459 
       72.39        80.71        76.18        62.47        66.25        29.92 
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-A7M5 TCGA-G3-A7M9 TCGA-G3-AAV1 TCGA-G3-AAV2 
       25.25        17.10        14.70         1.84        11.80        12.23 
TCGA-G3-AAV4 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-HP-A5N0 TCGA-K7-A5RG 
        0.89         2.14        11.87        22.92        37.71        17.06 
TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC TCGA-MI-A75G 
       21.60        31.27        29.79        12.72        13.97        22.95 
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        36.10         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-WX-AA44 TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9D2 TCGA-ZS-A9CE 
       20.22        22.78        13.55        25.15        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        38.40        22.92         8.55 
TCGA-4R-AA8I TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-4073 
        8.61        17.10        14.76         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-CC-A5UC TCGA-CC-A7IH 
        2.86         3.39         3.32         9.96        11.41        12.00 
TCGA-CC-A8HT TCGA-DD-A115 TCGA-DD-A118 TCGA-DD-A11B TCGA-DD-A11D TCGA-DD-A1E9 
        4.60        83.57       113.00         0.46        51.29        90.71 
TCGA-DD-A1EA TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EK TCGA-DD-A39V 
       79.40        19.79        75.65        11.47        18.35        21.14 
TCGA-DD-A39W TCGA-DD-A39Z TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 
       27.19        19.76         7.66        70.06        17.59        20.12 
TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NF 
      107.11        13.78         0.36        33.14        32.52        30.97 
TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NP TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV 
       39.78        56.25       108.76         0.30        80.75        78.84 
TCGA-DD-A73A TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-AA3A TCGA-DD-AAC9 
       23.93        23.05        22.78         1.45        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        26.63        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        26.93        28.08        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        22.06        20.78        11.87 
TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV3 TCGA-G3-AAV5 TCGA-GJ-A6C0 
       14.14        15.78        15.65        13.55         8.75         1.02 
TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-K7-A5RF TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 
        2.20         2.99        20.75        16.83        11.80         2.14 
TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A520 
       12.03         9.57        16.67        24.56        20.71         7.53 
TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 
       10.85        58.88        26.27        21.01         3.09        21.04 
TCGA-RC-A7SF TCGA-UB-A7MA TCGA-UB-A7MD TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WJ-A86L 
       19.04        17.59         1.71        10.75        10.32        11.34 
TCGA-WX-AA46 TCGA-WX-AA47 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 
       24.85        18.28        35.77        25.71        23.21        35.87 
TCGA-ZP-A9D1 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CF TCGA-ZS-A9CG 
        0.69        12.99        45.57        79.30        11.21 

  DEL PEAK  8(4Q22.3) MUTATED DEL PEAK  8(4Q22.3) WILD-TYPE 
                         0.20                          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 
                        18.15                         20.71 
[1] "0.2 - 120.8 (18.1)" "0.0 - 113.0 (20.7)"
[1] "hr=" "1.2"
D37V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IIIA
  DEL PEAK  8(4Q22.3) MUTATED        77       44         2         28
  DEL PEAK  8(4Q22.3) WILD-TYPE      94       41         1         32
                               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                             77                            94
  STAGE II                            44                            41
  STAGE III                            2                             1
  STAGE IIIA                          28                            32
  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      81  47  36   5
  DEL PEAK  8(4Q22.3) WILD-TYPE   101  45  38   7
D37V4, multiclass
       clus
vv      DEL PEAK  8(4Q22.3) MUTATED DEL PEAK  8(4Q22.3) WILD-TYPE
  T0+T1                          81                           101
  T2                             47                            45
  T3                             36                            38
  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   120   2
  DEL PEAK  8(4Q22.3) WILD-TYPE 130   1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(4Q22.3) MUTATED    120    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                         120                           130
  1                           2                             1
[1] 2 2
[1] FALSE
D37V6, binary
                               cls
clus                              0   1
  DEL PEAK  8(4Q22.3) MUTATED   134   3
  DEL PEAK  8(4Q22.3) WILD-TYPE 127   1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(4Q22.3) MUTATED    134    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                         134                           127
  1                           3                             1
[1] 2 2
[1] FALSE
D37V7, binary
                               cls
clus                              0   1
  DEL PEAK  8(4Q22.3) MUTATED    50 120
  DEL PEAK  8(4Q22.3) WILD-TYPE  65 127
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(4Q22.3) MUTATED     50  120
  DEL PEAK  8(4Q22.3) WILD-TYPE   65  127
        clus
vv       DEL PEAK  8(4Q22.3) MUTATED DEL PEAK  8(4Q22.3) WILD-TYPE
  FEMALE                          50                            65
  MALE                           120                           127
[1] 2 2
[1] FALSE
D37V8, binary
                               cls
clus                              0   1
  DEL PEAK  8(4Q22.3) MUTATED   157   3
  DEL PEAK  8(4Q22.3) WILD-TYPE 179   4
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(4Q22.3) MUTATED    157    3
  DEL PEAK  8(4Q22.3) WILD-TYPE  179    4
     clus
vv    DEL PEAK  8(4Q22.3) MUTATED DEL PEAK  8(4Q22.3) WILD-TYPE
  NO                          157                           179
  YES                           3                             4
[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                        167
  DEL PEAK  8(4Q22.3) WILD-TYPE                      186
                               vv
clus                            HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK  8(4Q22.3) MUTATED                                  3
  DEL PEAK  8(4Q22.3) WILD-TYPE                                4
D37V9, multiclass
                                  clus
vv                                 DEL PEAK  8(4Q22.3) MUTATED
  FIBROLAMELLAR CARCINOMA                                    0
  HEPATOCELLULAR CARCINOMA                                 167
  HEPATOCHOLANGIOCARCINOMA (MIXED)                           3
                                  clus
vv                                 DEL PEAK  8(4Q22.3) 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  8(4Q22.3) MUTATED   151   6   1  12
  DEL PEAK  8(4Q22.3) WILD-TYPE 167   9   0   9
D37V10, multiclass
    clus
vv   DEL PEAK  8(4Q22.3) MUTATED DEL PEAK  8(4Q22.3) WILD-TYPE
  R0                         151                           167
  R1                           6                             9
  R2                           1                             0
  RX                          12                             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    88
  DEL PEAK  8(4Q22.3) WILD-TYPE                                1    69
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  8(4Q22.3) MUTATED                           9    69
  DEL PEAK  8(4Q22.3) WILD-TYPE                         8   108
D37V11, multiclass
                                  clus
vv                                 DEL PEAK  8(4Q22.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                     88
  BLACK OR AFRICAN AMERICAN                                  9
  WHITE                                                     69
                                  clus
vv                                 DEL PEAK  8(4Q22.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                       69
  BLACK OR AFRICAN AMERICAN                                    8
  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"
D37V12, binary
                               cls
clus                              0   1
  DEL PEAK  8(4Q22.3) MUTATED    10 153
  DEL PEAK  8(4Q22.3) WILD-TYPE   3 179
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(4Q22.3) MUTATED     10  153
  DEL PEAK  8(4Q22.3) WILD-TYPE    3  179
                        clus
vv                       DEL PEAK  8(4Q22.3) MUTATED
  HISPANIC OR LATINO                              10
  NOT HISPANIC OR LATINO                         153
                        clus
vv                       DEL PEAK  8(4Q22.3) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           179
[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    99  69
  DEL PEAK  9(4Q35.1) WILD-TYPE 130  60
  DEL PEAK  9(4Q35.1) MUTATED DEL PEAK  9(4Q35.1) WILD-TYPE 
                          168                           190 
  DEL PEAK  9(4Q35.1) MUTATED DEL PEAK  9(4Q35.1) WILD-TYPE 
                           69                            60 
$`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        49.84        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        45.93         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         4.24 
TCGA-CC-5261 TCGA-CC-5264 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB 
        3.19         3.35         3.32         9.86         9.96        10.36 
TCGA-CC-A3MC TCGA-CC-A5UD TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7II 
       11.93         9.99         7.13        21.34         9.83        13.12 
TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A7IL TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FS 
       12.56         8.61         9.14        11.31         9.17         6.94 
TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A116 TCGA-DD-A119 TCGA-DD-A11A 
        8.15        79.73        37.78        53.33         7.33         2.60 
TCGA-DD-A11B TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ 
        0.46        12.95        45.11        49.15         6.02        33.04 
TCGA-DD-A1EL TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A3A0 TCGA-DD-A3A2 
       13.64        27.19        55.69         5.62        25.81        70.06 
TCGA-DD-A3A9 TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NN TCGA-DD-A4NO 
       30.61        30.15        26.83        30.51        29.56        73.81 
TCGA-DD-A73B TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACE 
        9.30         0.53        11.41        76.41        55.40        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-AACN TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACV 
       42.81        13.64        14.20        59.31        51.52        50.33 
TCGA-DD-AACW TCGA-DD-AACZ TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD8 
       46.82         5.62        21.63        42.58        44.22        40.08 
TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADI TCGA-DD-AADK TCGA-DD-AADL 
       40.83        13.97        40.47        35.67        34.49        20.91 
TCGA-DD-AADM TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADR TCGA-DD-AADV TCGA-DD-AADW 
        0.39        14.89        15.06        66.67        18.87        19.30 
TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE6 TCGA-DD-AAE8 TCGA-DD-AAEB 
       18.25        18.25        18.15         4.64        21.83        15.72 
TCGA-DD-AAEE TCGA-DD-AAEK TCGA-DD-AAVQ TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW 
       26.63        35.08        89.69        59.93        72.39        76.18 
TCGA-DD-AAVY TCGA-DD-AAW0 TCGA-ED-A459 TCGA-ED-A66X TCGA-ED-A7PY TCGA-ED-A7PZ 
       64.77        66.25        29.92        13.35        12.82         0.20 
TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A8O5 TCGA-ED-A97K TCGA-EP-A2KB TCGA-EP-A2KC 
       14.04        13.15        13.35         0.20        19.59         0.62 
TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I1 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-G3-A25S 
       23.97        19.10         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-A7M5 
       58.49        14.86        21.53        25.25        17.10        14.70 
TCGA-G3-A7M9 TCGA-G3-AAV1 TCGA-G3-AAV4 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A3OU 
        1.84        11.80         0.89         2.14        11.87        22.92 
TCGA-K7-A5RG TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-LG-A9QC TCGA-MI-A75G TCGA-MI-A75I 
       17.06        21.60        31.27        13.97        22.95        20.71 
TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-RC-A7SB TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 
       58.88        26.27        19.33        15.39        15.52        36.10 
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-WX-AA44 TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9D2 TCGA-ZS-A9CE 
       12.99        20.22        22.78        13.55        25.15        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        38.40        22.92 
TCGA-2Y-A9HB TCGA-4R-AA8I TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4072 
        8.55         8.61        17.10        14.76         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        23.38 
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-CC-A5UC TCGA-CC-A5UE TCGA-CC-A7IH 
        2.86         3.39         4.24        11.41         8.94        12.00 
TCGA-CC-A8HT TCGA-DD-A115 TCGA-DD-A118 TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 
        4.60        83.57       113.00        21.76        51.29        90.71 
TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EK 
       79.40        66.31        19.79        75.65        11.47        18.35 
TCGA-DD-A39V TCGA-DD-A39Z TCGA-DD-A3A1 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 
       21.14        19.76         7.66        17.59        20.12       102.74 
TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND 
      107.11        13.78         0.36        33.14        32.52        90.28 
TCGA-DD-A4NF TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR 
       30.97        39.78        56.25       108.76        12.26         0.30 
TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E 
       80.75        78.84        23.93        23.05        22.78         1.45 
TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AACA TCGA-DD-AACD TCGA-DD-AACJ 
       35.67       114.35        13.48        75.65        12.53        69.11 
TCGA-DD-AACK TCGA-DD-AACO TCGA-DD-AACT TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AAD0 
        0.30        61.68        51.35         5.59        47.67         4.50 
TCGA-DD-AAD1 TCGA-DD-AAD6 TCGA-DD-AADA TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG 
       18.54        22.09        40.54        39.52         3.78        37.64 
TCGA-DD-AADJ TCGA-DD-AADN TCGA-DD-AADQ TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AAE2 
       35.05        29.52        14.33        15.58        18.21        20.98 
TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE7 TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAED 
       18.61        19.99        21.17        23.74        18.90        25.08 
TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAVP TCGA-DD-AAVR TCGA-DD-AAVV 
       23.64        25.78        50.33        79.07        82.62        80.71 
TCGA-DD-AAVX TCGA-DD-AAVZ TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A4XI 
       56.48        62.47        65.39        49.48        53.69        26.93 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A82E TCGA-ED-A8O6 
       28.08        13.91         9.73         0.20        13.41         1.84 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS 
       18.74        19.99        20.61         9.96        11.93        22.85 
TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A3I0 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 
       14.40        60.89        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-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV0 
       22.06        20.78        11.87        14.14        15.78        15.65 
TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV5 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ 
       12.23        13.55         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 
       37.71        20.75        16.83        11.80         2.14        29.79 
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        24.56         7.53 
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-WX-AA47 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 
       18.28        35.77        25.71        23.21        35.87         0.69 
TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CF TCGA-ZS-A9CG 
       12.99        45.57        79.30        11.21 

  DEL PEAK  9(4Q35.1) MUTATED DEL PEAK  9(4Q35.1) WILD-TYPE 
                         0.20                          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 
                       17.080                        21.025 
[1] "0.2 - 120.8 (17.1)" "0.0 - 114.3 (21.0)"
[1] "hr=" "1.6"
D38V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IIIA
  DEL PEAK  9(4Q35.1) MUTATED        74       46         2         31
  DEL PEAK  9(4Q35.1) WILD-TYPE      97       39         1         29
                               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                             74                            97
  STAGE II                            46                            39
  STAGE III                            2                             1
  STAGE IIIA                          31                            29
  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      78  49  40   4
  DEL PEAK  9(4Q35.1) WILD-TYPE   104  43  34   8
D38V4, multiclass
       clus
vv      DEL PEAK  9(4Q35.1) MUTATED DEL PEAK  9(4Q35.1) WILD-TYPE
  T0+T1                          78                           104
  T2                             49                            43
  T3                             40                            34
  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 127   1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(4Q35.1) MUTATED    123    2
  DEL PEAK  9(4Q35.1) WILD-TYPE  127    1
   clus
vv  DEL PEAK  9(4Q35.1) MUTATED DEL PEAK  9(4Q35.1) WILD-TYPE
  0                         123                           127
  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 127   1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(4Q35.1) MUTATED    134    3
  DEL PEAK  9(4Q35.1) WILD-TYPE  127    1
   clus
vv  DEL PEAK  9(4Q35.1) MUTATED DEL PEAK  9(4Q35.1) WILD-TYPE
  0                         134                           127
  1                           3                             1
[1] 2 2
[1] FALSE
D38V7, binary
                               cls
clus                              0   1
  DEL PEAK  9(4Q35.1) MUTATED    46 125
  DEL PEAK  9(4Q35.1) WILD-TYPE  69 122
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(4Q35.1) MUTATED     46  125
  DEL PEAK  9(4Q35.1) WILD-TYPE   69  122
        clus
vv       DEL PEAK  9(4Q35.1) MUTATED DEL PEAK  9(4Q35.1) WILD-TYPE
  FEMALE                          46                            69
  MALE                           125                           122
[1] 2 2
[1] FALSE
D38V8, binary
                               cls
clus                              0   1
  DEL PEAK  9(4Q35.1) MUTATED   157   3
  DEL PEAK  9(4Q35.1) WILD-TYPE 179   4
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(4Q35.1) MUTATED    157    3
  DEL PEAK  9(4Q35.1) WILD-TYPE  179    4
     clus
vv    DEL PEAK  9(4Q35.1) MUTATED DEL PEAK  9(4Q35.1) WILD-TYPE
  NO                          157                           179
  YES                           3                             4
[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                        168
  DEL PEAK  9(4Q35.1) WILD-TYPE                      185
                               vv
clus                            HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK  9(4Q35.1) MUTATED                                  3
  DEL PEAK  9(4Q35.1) WILD-TYPE                                4
D38V9, multiclass
                                  clus
vv                                 DEL PEAK  9(4Q35.1) MUTATED
  FIBROLAMELLAR CARCINOMA                                    0
  HEPATOCELLULAR CARCINOMA                                 168
  HEPATOCHOLANGIOCARCINOMA (MIXED)                           3
                                  clus
vv                                 DEL PEAK  9(4Q35.1) 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  9(4Q35.1) MUTATED   152   5   1  12
  DEL PEAK  9(4Q35.1) WILD-TYPE 166  10   0   9
D38V10, multiclass
    clus
vv   DEL PEAK  9(4Q35.1) MUTATED DEL PEAK  9(4Q35.1) WILD-TYPE
  R0                         152                           166
  R1                           5                            10
  R2                           1                             0
  RX                          12                             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    62
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  9(4Q35.1) MUTATED                          10    66
  DEL PEAK  9(4Q35.1) WILD-TYPE                         7   111
D38V11, multiclass
                                  clus
vv                                 DEL PEAK  9(4Q35.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                     95
  BLACK OR AFRICAN AMERICAN                                 10
  WHITE                                                     66
                                  clus
vv                                 DEL PEAK  9(4Q35.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                       62
  BLACK OR AFRICAN AMERICAN                                    7
  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"
D38V12, binary
                               cls
clus                              0   1
  DEL PEAK  9(4Q35.1) MUTATED     8 159
  DEL PEAK  9(4Q35.1) WILD-TYPE   5 173
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(4Q35.1) MUTATED      8  159
  DEL PEAK  9(4Q35.1) WILD-TYPE    5  173
                        clus
vv                       DEL PEAK  9(4Q35.1) MUTATED
  HISPANIC OR LATINO                               8
  NOT HISPANIC OR LATINO                         159
                        clus
vv                       DEL PEAK  9(4Q35.1) WILD-TYPE
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                           173
[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    84  48
  DEL PEAK 10(6Q27) WILD-TYPE 145  81
  DEL PEAK 10(6Q27) MUTATED DEL PEAK 10(6Q27) WILD-TYPE 
                        132                         226 
  DEL PEAK 10(6Q27) MUTATED DEL PEAK 10(6Q27) WILD-TYPE 
                         48                          81 
$`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        38.40 
TCGA-2Y-A9H8 TCGA-2Y-A9HA TCGA-4R-AA8I TCGA-5R-AA1C TCGA-5R-AAAM TCGA-BC-A10Q 
       20.81         1.18         8.61        17.10         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-CC-A7IF TCGA-CC-A7IL TCGA-CC-A9FS 
        9.86         9.96        11.93        21.34         9.14         6.94 
TCGA-CC-A9FW TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A 
        8.15        37.78        83.57       113.00         7.33         2.60 
TCGA-DD-A11C TCGA-DD-A1E9 TCGA-DD-A1EE TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI 
       21.76        90.71        11.47        45.11        49.15         6.02 
TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A39X TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A8 
       33.04        18.35        55.69        19.76        25.81         0.36 
TCGA-DD-A4NA TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NN TCGA-DD-A4NS 
       33.14        30.15        30.51        39.78        29.56        80.75 
TCGA-DD-A73E TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AACB TCGA-DD-AACD TCGA-DD-AACE 
        1.45        13.48         0.53        76.41        12.53        63.48 
TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACP TCGA-DD-AACU TCGA-DD-AACW TCGA-DD-AACY 
        6.41        53.19        13.64        51.52        46.82        47.67 
TCGA-DD-AAD0 TCGA-DD-AAD3 TCGA-DD-AAD8 TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADJ 
        4.50        42.58        40.08         3.78        37.64        35.05 
TCGA-DD-AADL TCGA-DD-AADN TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADV 
       20.91        29.52        15.06        14.33        66.67        18.87 
TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE9 TCGA-DD-AAEE 
       19.30        18.25        20.98        18.61        23.74        26.63 
TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAEK TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVY 
       23.64        25.78        35.08        59.93        72.39        64.77 
TCGA-DD-AAW0 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A66Y TCGA-ED-A7PX 
       66.25        49.48        53.69        29.92         9.73         0.20 
TCGA-ED-A7PZ TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J 
        0.20        13.41        13.35         1.84         0.20        18.74 
TCGA-EP-A3RK TCGA-ES-A2HS TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R2 
       11.93        22.85        60.89        19.10        27.88         6.38 
TCGA-FV-A496 TCGA-FV-A4ZP TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25X TCGA-G3-A25Y 
        0.33        81.73        13.68        51.06        58.49        14.86 
TCGA-G3-A3CG TCGA-G3-A5SL TCGA-G3-A6UC TCGA-G3-A7M5 TCGA-G3-A7M9 TCGA-G3-AAV1 
       22.13        20.42        22.06        14.70         1.84        11.80 
TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV6 TCGA-HP-A5N0 TCGA-LG-A6GG TCGA-MI-A75E 
       13.55         0.89         2.14        37.71        12.72        16.67 
TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-NI-A8LF TCGA-RC-A7SK TCGA-T1-A6J8 
       22.95        24.56        20.71        26.27        15.52         0.76 
TCGA-UB-A7MB TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WJ-A86L TCGA-ZS-A9CE TCGA-ZS-A9CF 
       19.76        15.98        10.75        11.34        40.80        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        49.84        47.74        22.92         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        14.76        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        23.38         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 
       45.93        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-5264 
        0.66         4.24         3.19         3.39         4.24         3.35 
TCGA-CC-A3MB TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IG 
       10.36        11.41         9.99         8.94         7.13         9.83 
TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A8HT TCGA-CC-A8HU 
       12.00        13.12        12.56         8.61         4.60        11.31 
TCGA-CC-A8HV TCGA-DD-A113 TCGA-DD-A116 TCGA-DD-A11B TCGA-DD-A11D TCGA-DD-A1EA 
        9.17        79.73        53.33         0.46        51.29        79.40 
TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EF TCGA-DD-A1EL TCGA-DD-A39V 
       66.31        19.79        75.65        12.95        13.64        21.14 
TCGA-DD-A39W TCGA-DD-A39Y TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 
       27.19         5.62         7.66        70.06        17.59        20.12 
TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NB TCGA-DD-A4ND 
      102.74       107.11        13.78        30.61        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-A73D 
        0.30        78.84        23.93         9.30        23.05        22.78 
TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACC TCGA-DD-AACF 
       35.67       114.35        11.41        75.65        55.40        12.00 
TCGA-DD-AACG TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN 
       15.42        69.11         0.30         3.52        58.16        42.81 
TCGA-DD-AACO TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACV TCGA-DD-AACX 
       61.68        14.20        59.31        51.35        50.33         5.59 
TCGA-DD-AACZ TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AADA 
        5.62        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-AADM TCGA-DD-AADO TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AAE0 TCGA-DD-AAE1 
        0.39        14.89        15.58        18.21        18.25        18.15 
TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEB 
       19.99         4.64        21.17        21.83        18.90        15.72 
TCGA-DD-AAED TCGA-DD-AAEI TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVV 
       25.08        50.33        79.07        89.69        82.62        80.71 
TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVZ TCGA-DD-AAW1 TCGA-ED-A4XI TCGA-ED-A5KG 
       76.18        56.48        62.47        65.39        26.93        28.08 
TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A7PY TCGA-ED-A7XO TCGA-ED-A7XP TCGA-EP-A26S 
       13.91        13.35        12.82        14.04        13.15        19.99 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-ES-A2HT TCGA-FV-A2QQ 
       20.61        19.59         0.62         9.96        14.40        23.97 
TCGA-FV-A3I1 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A4ZQ TCGA-G3-A25U TCGA-G3-A25V 
        8.12        12.03         0.03         0.39        53.79        28.27 
TCGA-G3-A25W TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
       30.74        21.53        25.64         5.92        19.53        19.23 
TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SM TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 
       25.25        22.95        17.10        20.78        11.87        14.14 
TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV5 TCGA-G3-AAV7 TCGA-GJ-A3OU 
       15.78        15.65        12.23         8.75        11.87        22.92 
TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 
        1.02         2.20         2.99        20.75        17.06        16.83 
TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A9QC 
       11.80         2.14        21.60        31.27        29.79        13.97 
TCGA-LG-A9QD TCGA-MI-A75C TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-O8-A75V 
       12.03         9.57         7.53        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-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7MF TCGA-UB-AA0V 
       36.10        17.59        16.44         1.71         7.04        10.32 
TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TF 
        0.99        12.99        20.22        24.85        18.28        22.78 
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        35.87         0.69 
TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CG 
       25.15        12.99        45.57        11.21 

  DEL PEAK 10(6Q27) MUTATED DEL PEAK 10(6Q27) WILD-TYPE 
                       0.20                        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 
                      20.09                       19.56 
[1] "0.2 - 120.8 (20.1)" "0.0 - 114.3 (19.6)"
[1] "hr=" "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     110       53         2         37          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                         110
  STAGE II                          32                          53
  STAGE III                          1                           2
  STAGE IIIA                        23                          37
  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   118  57  46   8
D39V4, multiclass
       clus
vv      DEL PEAK 10(6Q27) MUTATED DEL PEAK 10(6Q27) WILD-TYPE
  T0+T1                        64                         118
  T2                           35                          57
  T3                           28                          46
  T4                            4                           8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V5, binary
                             cls
clus                            0   1
  DEL PEAK 10(6Q27) MUTATED    93   2
  DEL PEAK 10(6Q27) WILD-TYPE 157   1
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 10(6Q27) MUTATED     93    2
  DEL PEAK 10(6Q27) WILD-TYPE  157    1
   clus
vv  DEL PEAK 10(6Q27) MUTATED DEL PEAK 10(6Q27) WILD-TYPE
  0                        93                         157
  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 158   1
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 10(6Q27) MUTATED    103    3
  DEL PEAK 10(6Q27) WILD-TYPE  158    1
   clus
vv  DEL PEAK 10(6Q27) MUTATED DEL PEAK 10(6Q27) WILD-TYPE
  0                       103                         158
  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  68 161
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 10(6Q27) MUTATED     47   86
  DEL PEAK 10(6Q27) WILD-TYPE   68  161
        clus
vv       DEL PEAK 10(6Q27) MUTATED DEL PEAK 10(6Q27) WILD-TYPE
  FEMALE                        47                          68
  MALE                          86                         161
[1] 2 2
[1] FALSE
D39V8, binary
                             cls
clus                            0   1
  DEL PEAK 10(6Q27) MUTATED   124   1
  DEL PEAK 10(6Q27) WILD-TYPE 212   6
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 10(6Q27) MUTATED    124    1
  DEL PEAK 10(6Q27) WILD-TYPE  212    6
     clus
vv    DEL PEAK 10(6Q27) MUTATED DEL PEAK 10(6Q27) WILD-TYPE
  NO                        124                         212
  YES                         1                           6
[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                      223
                             vv
clus                          HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK 10(6Q27) MUTATED                                  3
  DEL PEAK 10(6Q27) WILD-TYPE                                4
D39V9, 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                                 223
  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 199   9   0  16
D39V10, multiclass
    clus
vv   DEL PEAK 10(6Q27) MUTATED DEL PEAK 10(6Q27) WILD-TYPE
  R0                       119                         199
  R1                         6                           9
  R2                         1                           0
  RX                         5                          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 10(6Q27) MUTATED                                  0    62
  DEL PEAK 10(6Q27) WILD-TYPE                                1    95
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 10(6Q27) MUTATED                           4    65
  DEL PEAK 10(6Q27) WILD-TYPE                        13   112
D39V11, 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                                                     95
  BLACK OR AFRICAN AMERICAN                                 13
  WHITE                                                    112
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V12, binary
                             cls
clus                            0   1
  DEL PEAK 10(6Q27) MUTATED     2 126
  DEL PEAK 10(6Q27) WILD-TYPE  11 206
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 10(6Q27) MUTATED      2  126
  DEL PEAK 10(6Q27) WILD-TYPE   11  206
                        clus
vv                       DEL PEAK 10(6Q27) MUTATED DEL PEAK 10(6Q27) WILD-TYPE
  HISPANIC OR LATINO                             2                          11
  NOT HISPANIC OR LATINO                       126                         206
[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   155  84
  DEL PEAK 11(8P23.2) WILD-TYPE  74  45
  DEL PEAK 11(8P23.2) MUTATED DEL PEAK 11(8P23.2) WILD-TYPE 
                          239                           119 
  DEL PEAK 11(8P23.2) MUTATED DEL PEAK 11(8P23.2) WILD-TYPE 
                           84                            45 
$`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        49.84        47.74        18.25        11.74        38.40 
TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-5C-A9VH TCGA-5R-AA1C 
       22.92         1.18         8.55        13.02        10.59        17.10 
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        45.93         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         4.24         3.19         3.39 
TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MC TCGA-CC-A7IE TCGA-CC-A7IF 
        4.24         3.32         9.86        11.93         7.13        21.34 
TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IL TCGA-CC-A8HT 
        9.83        12.00        13.12        12.56         9.14         4.60 
TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A115 
       11.31         9.17         6.94         8.15        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        26.63        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        29.92        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-A7M5 
       22.13        19.53        22.95        20.42        22.06        14.70 
TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV4 
       20.78        11.87        15.78        15.65        12.23         0.89 
TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ 
        8.75         2.14        11.87         1.02         2.20         2.99 
TCGA-HP-A5N0 TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-LG-A9QC 
       37.71        16.83        11.80        21.60        31.27        13.97 
TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A8JO 
       12.03         9.57        16.67        24.56        20.71        10.85 
TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 
       58.88        26.27        17.69        21.01         3.09        21.04 
TCGA-RC-A7SF TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-T1-A6J8 TCGA-UB-A7MB TCGA-UB-A7MD 
       19.04        15.52        36.10         0.76        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-WX-AA44 TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 
       20.22        13.55        35.77        23.21        35.87        25.15 
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 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        14.76        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        23.38         1.12        69.57        17.98        18.48 
TCGA-BD-A2L6 TCGA-BD-A3ER TCGA-CC-5260 TCGA-CC-5264 TCGA-CC-A3MA TCGA-CC-A3MB 
       44.81        36.66         2.86         3.35         9.96        10.36 
TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IK TCGA-DD-A114 TCGA-DD-A11A 
       11.41         9.99         8.94         8.61        37.78         2.60 
TCGA-DD-A11B TCGA-DD-A11D TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED 
        0.46        51.29        79.40        66.31        19.79        75.65 
TCGA-DD-A1EH TCGA-DD-A39W TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A4 TCGA-DD-A3A5 
       49.15        27.19         7.66        70.06        20.12       102.74 
TCGA-DD-A3A6 TCGA-DD-A4NB TCGA-DD-A4NL TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A73B 
      107.11        32.52        56.25       108.76        12.26         9.30 
TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACF TCGA-DD-AACI 
       13.48         0.53        11.41        75.65        12.00        53.19 
TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACT TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX 
        0.30         3.52        51.35        50.33        46.82         5.59 
TCGA-DD-AAD6 TCGA-DD-AADJ TCGA-DD-AADL TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW 
       22.09        35.05        20.91        15.58        18.21        19.30 
TCGA-DD-AADY TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAEA TCGA-DD-AAEK 
       18.25        18.15        20.98        18.61        18.90        35.08 
TCGA-DD-AAVV TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAW1 TCGA-ED-A4XI TCGA-ED-A5KG 
       80.71        76.18        56.48        65.39        26.93        28.08 
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-A7M8 TCGA-G3-A7M9 TCGA-G3-AAV1 TCGA-G3-AAV3 TCGA-GJ-A3OU 
       17.10        14.14         1.84        11.80        13.55        22.92 
TCGA-K7-A5RF TCGA-K7-A5RG TCGA-KR-A7K0 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-MI-A75G 
       20.75        17.06         2.14        29.79        12.72        22.95 
TCGA-MR-A520 TCGA-RC-A7SB TCGA-RC-A7SH TCGA-UB-A7MA TCGA-UB-A7MC TCGA-UB-AA0V 
        7.53        19.33        15.39        17.59        16.44        10.32 
TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TF TCGA-ZP-A9CY TCGA-ZP-A9D1 
       24.85        18.28        22.78        25.71         0.69 

  DEL PEAK 11(8P23.2) MUTATED DEL PEAK 11(8P23.2) WILD-TYPE 
                         0.03                          0.20 
  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 
                        20.22                         19.23 
[1] "0.0 - 114.3 (20.2)" "0.2 - 120.8 (19.2)"
[1] "hr=" "1"  
D40V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IIIA
  DEL PEAK 11(8P23.2) MUTATED       119       55         0         36
  DEL PEAK 11(8P23.2) WILD-TYPE      52       30         3         24
                               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                            119                            52
  STAGE II                            55                            30
  STAGE III                            0                             3
  STAGE IIIA                          36                            24
  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     126  61  46   6
  DEL PEAK 11(8P23.2) WILD-TYPE    56  31  28   6
D40V4, multiclass
       clus
vv      DEL PEAK 11(8P23.2) MUTATED DEL PEAK 11(8P23.2) WILD-TYPE
  T0+T1                         126                            56
  T2                             61                            31
  T3                             46                            28
  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  88   0
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(8P23.2) MUTATED    162    3
  DEL PEAK 11(8P23.2) WILD-TYPE   88    0
   clus
vv  DEL PEAK 11(8P23.2) MUTATED DEL PEAK 11(8P23.2) WILD-TYPE
  0                         162                            88
  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  90   0
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(8P23.2) MUTATED    171    4
  DEL PEAK 11(8P23.2) WILD-TYPE   90    0
   clus
vv  DEL PEAK 11(8P23.2) MUTATED DEL PEAK 11(8P23.2) WILD-TYPE
  0                         171                            90
  1                           4                             0
[1] 2 2
[1] FALSE
D40V7, binary
                               cls
clus                              0   1
  DEL PEAK 11(8P23.2) MUTATED    73 168
  DEL PEAK 11(8P23.2) WILD-TYPE  42  79
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(8P23.2) MUTATED     73  168
  DEL PEAK 11(8P23.2) WILD-TYPE   42   79
        clus
vv       DEL PEAK 11(8P23.2) MUTATED DEL PEAK 11(8P23.2) WILD-TYPE
  FEMALE                          73                            42
  MALE                           168                            79
[1] 2 2
[1] FALSE
D40V8, binary
                               cls
clus                              0   1
  DEL PEAK 11(8P23.2) MUTATED   223   5
  DEL PEAK 11(8P23.2) WILD-TYPE 113   2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(8P23.2) MUTATED    223    5
  DEL PEAK 11(8P23.2) WILD-TYPE  113    2
     clus
vv    DEL PEAK 11(8P23.2) MUTATED DEL PEAK 11(8P23.2) WILD-TYPE
  NO                          223                           113
  YES                           5                             2
[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                        237
  DEL PEAK 11(8P23.2) WILD-TYPE                      116
                               vv
clus                            HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK 11(8P23.2) MUTATED                                  3
  DEL PEAK 11(8P23.2) WILD-TYPE                                4
D40V9, multiclass
                                  clus
vv                                 DEL PEAK 11(8P23.2) MUTATED
  FIBROLAMELLAR CARCINOMA                                    1
  HEPATOCELLULAR CARCINOMA                                 237
  HEPATOCHOLANGIOCARCINOMA (MIXED)                           3
                                  clus
vv                                 DEL PEAK 11(8P23.2) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                      1
  HEPATOCELLULAR CARCINOMA                                   116
  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  15
  DEL PEAK 11(8P23.2) WILD-TYPE 109   5   0   6
D40V10, multiclass
    clus
vv   DEL PEAK 11(8P23.2) MUTATED DEL PEAK 11(8P23.2) WILD-TYPE
  R0                         209                           109
  R1                          10                             5
  R2                           1                             0
  RX                          15                             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 11(8P23.2) MUTATED                                  1   101
  DEL PEAK 11(8P23.2) WILD-TYPE                                0    56
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 11(8P23.2) MUTATED                          13   119
  DEL PEAK 11(8P23.2) WILD-TYPE                         4    58
D40V11, multiclass
                                  clus
vv                                 DEL PEAK 11(8P23.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                    101
  BLACK OR AFRICAN AMERICAN                                 13
  WHITE                                                    119
                                  clus
vv                                 DEL PEAK 11(8P23.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                       56
  BLACK OR AFRICAN AMERICAN                                    4
  WHITE                                                       58
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V12, binary
                               cls
clus                              0   1
  DEL PEAK 11(8P23.2) MUTATED     9 220
  DEL PEAK 11(8P23.2) WILD-TYPE   4 112
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(8P23.2) MUTATED      9  220
  DEL PEAK 11(8P23.2) WILD-TYPE    4  112
                        clus
vv                       DEL PEAK 11(8P23.2) MUTATED
  HISPANIC OR LATINO                               9
  NOT HISPANIC OR LATINO                         220
                        clus
vv                       DEL PEAK 11(8P23.2) WILD-TYPE
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           112
[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   152  82
  DEL PEAK 12(8P12) WILD-TYPE  77  47
  DEL PEAK 12(8P12) MUTATED DEL PEAK 12(8P12) WILD-TYPE 
                        234                         124 
  DEL PEAK 12(8P12) MUTATED DEL PEAK 12(8P12) WILD-TYPE 
                         82                          47 
$`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        49.84        47.74        18.25        11.74        38.40 
TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-5C-A9VH TCGA-5R-AA1C 
       22.92         1.18         8.55        13.02        10.59        17.10 
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        45.93         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         4.24         3.19         3.39 
TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A7IE TCGA-CC-A7IF 
        4.24         3.32         9.86         9.96         7.13        21.34 
TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7IJ TCGA-CC-A7IL TCGA-CC-A8HT TCGA-CC-A8HU 
        9.83        12.00        12.56         9.14         4.60        11.31 
TCGA-CC-A8HV TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A115 TCGA-DD-A116 
        9.17         6.94         8.15        79.73        83.57        53.33 
TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11C TCGA-DD-A1E9 TCGA-DD-A1EE TCGA-DD-A1EF 
      113.00         7.33        21.76        90.71        11.47        12.95 
TCGA-DD-A1EG TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V 
       45.11         6.02        33.04        18.35        13.64        21.14 
TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A3 TCGA-DD-A3A5 TCGA-DD-A3A7 TCGA-DD-A3A8 
        5.62        19.76        17.59       102.74        13.78         0.36 
TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4ND TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK 
       30.61        33.14        90.28        30.15        30.51        39.78 
TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A 
       29.56        73.81         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-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACG 
        0.53        76.41        55.40        12.53        63.48        15.42 
TCGA-DD-AACH TCGA-DD-AACJ TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP 
        6.41        69.11        58.16        42.81        61.68        13.64 
TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 
       14.20        59.31         5.62         4.50        18.54        21.63 
TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC 
       42.58        44.22        40.08        40.54        40.83        13.97 
TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADK 
       40.47        39.52         3.78        37.64        35.67        34.49 
TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADV 
       29.52        14.89        15.06        14.33        66.67        18.87 
TCGA-DD-AAE0 TCGA-DD-AAE4 TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAE9 TCGA-DD-AAEB 
       18.25        19.99        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        26.63        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-AAVY 
       89.69        82.62        59.93        72.39        76.18        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        29.92        26.93 
TCGA-ED-A66X TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A8O6 TCGA-EP-A12J 
       13.35        12.82         0.20        14.04         1.84        18.74 
TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS 
       19.99        20.61         0.62         9.96        11.93        22.85 
TCGA-ES-A2HT TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 
       14.40        23.97        19.10        27.88         8.12         6.38 
TCGA-FV-A495 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25V TCGA-G3-A25W 
        0.03        81.73         0.39        13.68        28.27        30.74 
TCGA-G3-A25X TCGA-G3-A3CG TCGA-G3-A3CJ TCGA-G3-A5SL TCGA-G3-A6UC TCGA-G3-A7M5 
       58.49        22.13        19.53        20.42        22.06        14.70 
TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV2 
       20.78        11.87         1.84        15.78        15.65        12.23 
TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-HP-A5MZ TCGA-K7-A6G5 
        0.89         8.75         2.14        11.87         2.99        16.83 
TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD 
       11.80        21.60        31.27        29.79        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        24.56        20.71        10.85        26.27 
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        36.10         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-WX-AA44 TCGA-WX-AA47 TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CZ TCGA-ZP-A9D0 
       20.22        18.28        13.55        35.77        23.21        35.87 
TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       25.15        12.99        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        14.76        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        23.38         1.12        69.57        17.98        18.48 
TCGA-BD-A2L6 TCGA-BD-A3ER TCGA-CC-5260 TCGA-CC-5264 TCGA-CC-A3MB TCGA-CC-A3MC 
       44.81        36.66         2.86         3.35        10.36        11.93 
TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7II TCGA-CC-A7IK TCGA-DD-A114 
       11.41         9.99         8.94        13.12         8.61        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-AAVV TCGA-DD-AAVX TCGA-DD-AAW1 TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66Y 
       80.71        56.48        65.39        28.08        13.91         9.73 
TCGA-ED-A7PX TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A97K TCGA-EP-A2KB 
        0.20        13.15        13.41        13.35         0.20        19.59 
TCGA-FV-A23B TCGA-FV-A3R3 TCGA-FV-A496 TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25Y 
       60.89        12.03         0.33        51.06        53.79        14.86 
TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ 
       21.53        25.64         5.92        19.23        25.25        22.95 
TCGA-G3-A5SM TCGA-G3-A7M8 TCGA-G3-AAV1 TCGA-G3-AAV3 TCGA-GJ-A3OU TCGA-GJ-A6C0 
       17.10        14.14        11.80        13.55        22.92         1.02 
TCGA-GJ-A9DB TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-KR-A7K0 TCGA-LG-A6GG 
        2.20        37.71        20.75        17.06         2.14        12.72 
TCGA-MI-A75G TCGA-MR-A520 TCGA-NI-A4U2 TCGA-RC-A7SB TCGA-UB-A7MC TCGA-UB-AA0V 
       22.95         7.53        58.88        19.33        16.44        10.32 
TCGA-WX-AA46 TCGA-XR-A8TF TCGA-ZP-A9CY TCGA-ZP-A9D1 
       24.85        22.78        25.71         0.69 

  DEL PEAK 12(8P12) MUTATED DEL PEAK 12(8P12) WILD-TYPE 
                       0.03                        0.20 
  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 
                     19.875                      19.460 
[1] "0.0 - 114.3 (19.9)" "0.2 - 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       114       55         1         35          7
  DEL PEAK 12(8P12) WILD-TYPE      57       30         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                          114                          57
  STAGE II                          55                          30
  STAGE III                          1                           2
  STAGE IIIA                        35                          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     121  61  47   6
  DEL PEAK 12(8P12) WILD-TYPE    61  31  27   6
D41V4, multiclass
       clus
vv      DEL PEAK 12(8P12) MUTATED DEL PEAK 12(8P12) WILD-TYPE
  T0+T1                       121                          61
  T2                           61                          31
  T3                           47                          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  88   0
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 12(8P12) MUTATED    162    3
  DEL PEAK 12(8P12) WILD-TYPE   88    0
   clus
vv  DEL PEAK 12(8P12) MUTATED DEL PEAK 12(8P12) WILD-TYPE
  0                       162                          88
  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  94   0
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 12(8P12) MUTATED    167    4
  DEL PEAK 12(8P12) WILD-TYPE   94    0
   clus
vv  DEL PEAK 12(8P12) MUTATED DEL PEAK 12(8P12) WILD-TYPE
  0                       167                          94
  1                         4                           0
[1] 2 2
[1] FALSE
D41V7, binary
                             cls
clus                            0   1
  DEL PEAK 12(8P12) MUTATED    73 163
  DEL PEAK 12(8P12) WILD-TYPE  42  84
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 12(8P12) MUTATED     73  163
  DEL PEAK 12(8P12) WILD-TYPE   42   84
        clus
vv       DEL PEAK 12(8P12) MUTATED DEL PEAK 12(8P12) WILD-TYPE
  FEMALE                        73                          42
  MALE                         163                          84
[1] 2 2
[1] FALSE
D41V8, binary
                             cls
clus                            0   1
  DEL PEAK 12(8P12) MUTATED   217   6
  DEL PEAK 12(8P12) WILD-TYPE 119   1
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 12(8P12) MUTATED    217    6
  DEL PEAK 12(8P12) WILD-TYPE  119    1
     clus
vv    DEL PEAK 12(8P12) MUTATED DEL PEAK 12(8P12) WILD-TYPE
  NO                        217                         119
  YES                         6                           1
[1] 2 2
[1] FALSE
                             vv
clus                          FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  DEL PEAK 12(8P12) MUTATED                         1                      231
  DEL PEAK 12(8P12) WILD-TYPE                       1                      122
                             vv
clus                          HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK 12(8P12) MUTATED                                  4
  DEL PEAK 12(8P12) WILD-TYPE                                3
D41V9, multiclass
                                  clus
vv                                 DEL PEAK 12(8P12) MUTATED
  FIBROLAMELLAR CARCINOMA                                  1
  HEPATOCELLULAR CARCINOMA                               231
  HEPATOCHOLANGIOCARCINOMA (MIXED)                         4
                                  clus
vv                                 DEL PEAK 12(8P12) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                    1
  HEPATOCELLULAR CARCINOMA                                 122
  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   204  11   1  14
  DEL PEAK 12(8P12) WILD-TYPE 114   4   0   7
D41V10, multiclass
    clus
vv   DEL PEAK 12(8P12) MUTATED DEL PEAK 12(8P12) WILD-TYPE
  R0                       204                         114
  R1                        11                           4
  R2                         1                           0
  RX                        14                           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 12(8P12) MUTATED                                  1    99
  DEL PEAK 12(8P12) WILD-TYPE                                0    58
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 12(8P12) MUTATED                          13   116
  DEL PEAK 12(8P12) WILD-TYPE                         4    61
D41V11, multiclass
                                  clus
vv                                 DEL PEAK 12(8P12) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         1
  ASIAN                                                   99
  BLACK OR AFRICAN AMERICAN                               13
  WHITE                                                  116
                                  clus
vv                                 DEL PEAK 12(8P12) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                     58
  BLACK OR AFRICAN AMERICAN                                  4
  WHITE                                                     61
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V12, binary
                             cls
clus                            0   1
  DEL PEAK 12(8P12) MUTATED    10 214
  DEL PEAK 12(8P12) WILD-TYPE   3 118
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 12(8P12) MUTATED     10  214
  DEL PEAK 12(8P12) WILD-TYPE    3  118
                        clus
vv                       DEL PEAK 12(8P12) MUTATED DEL PEAK 12(8P12) WILD-TYPE
  HISPANIC OR LATINO                            10                           3
  NOT HISPANIC OR LATINO                       214                         118
[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  58
  DEL PEAK 13(9P21.3) WILD-TYPE 142  71
  DEL PEAK 13(9P21.3) MUTATED DEL PEAK 13(9P21.3) WILD-TYPE 
                          145                           213 
  DEL PEAK 13(9P21.3) MUTATED DEL PEAK 13(9P21.3) WILD-TYPE 
                           58                            71 
$`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        49.84 
TCGA-2Y-A9H5 TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-2Y-A9H8 TCGA-3K-AAZ8 TCGA-5C-A9VG 
       18.25        11.74        38.40        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         4.24 
TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UD 
        4.24         3.32         9.86        10.36        11.93         9.99 
TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7IJ TCGA-CC-A7IK 
        8.94         7.13        21.34         9.83        12.56         8.61 
TCGA-CC-A7IL TCGA-CC-A8HU TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A115 
        9.14        11.31         6.94         8.15        79.73        83.57 
TCGA-DD-A116 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A1EF 
       53.33         7.33         2.60         0.46        21.76        12.95 
TCGA-DD-A1EG TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39X TCGA-DD-A39Y 
       45.11         6.02        33.04        13.64        55.69         5.62 
TCGA-DD-A3A0 TCGA-DD-A3A9 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-A4NO TCGA-DD-A73F 
       25.81        30.61        90.28        26.83        73.81        35.67 
TCGA-DD-AA3A TCGA-DD-AACA TCGA-DD-AACC TCGA-DD-AACE TCGA-DD-AACG TCGA-DD-AACH 
       13.48        75.65        55.40        63.48        15.42         6.41 
TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACW TCGA-DD-AACZ 
       61.68        13.64        59.31        51.52        46.82         5.62 
TCGA-DD-AAD3 TCGA-DD-AADC TCGA-DD-AADE TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL 
       42.58        13.97        39.52        35.05        34.49        20.91 
TCGA-DD-AADN TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADS TCGA-DD-AADV TCGA-DD-AAE1 
       29.52        15.06        14.33        15.58        18.87        18.15 
TCGA-DD-AAE3 TCGA-DD-AAE6 TCGA-DD-AAE8 TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEK 
       18.61         4.64        21.83        25.08        26.63        35.08 
TCGA-DD-AAVQ TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVZ TCGA-DD-AAW0 
       89.69        59.93        72.39        76.18        62.47        66.25 
TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A66X TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-ED-A82E 
       29.92        26.93        13.35         0.20        13.15        13.41 
TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK 
        1.84         0.20        20.61        19.59         0.62        11.93 
TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A4ZP 
       60.89        23.97        27.88         8.12         6.38        81.73 
TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A3CJ TCGA-G3-A7M5 TCGA-G3-A7M7 TCGA-G3-AAV1 
       13.68        51.06        19.53        14.70        11.87        11.80 
TCGA-G3-AAV3 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A9DB TCGA-KR-A7K7 TCGA-KR-A7K8 
       13.55         2.14        11.87         2.20        31.27        29.79 
TCGA-MI-A75G TCGA-MI-A75I TCGA-NI-A8LF TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF 
       22.95        20.71        26.27        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        36.10         0.76        15.98         7.04 
TCGA-UB-AA0U TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-XR-A8TF TCGA-ZP-A9D0 TCGA-ZP-A9D1 
       10.75         0.99        12.99        22.78        35.87         0.69 
TCGA-ZP-A9D2 
       25.15 

$`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        22.92         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 
       17.10        14.76         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 
       23.38         1.12        69.57        44.42        45.93        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-5264 TCGA-CC-A3MA TCGA-CC-A5UC 
        2.86         3.19         3.39         3.35         9.96        11.41 
TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A8HT TCGA-CC-A8HV TCGA-DD-A114 TCGA-DD-A118 
       12.00        13.12         4.60         9.17        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-AAVV TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAW1 TCGA-DD-AAW2 
       82.62        80.71        56.48        64.77        65.39        49.48 
TCGA-DD-AAW3 TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY 
       53.69        28.08        13.91         9.73         0.20        12.82 
TCGA-ED-A7XO TCGA-ED-A8O5 TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A3JL TCGA-ES-A2HS 
       14.04        13.35        18.74        19.99         9.96        22.85 
TCGA-ES-A2HT TCGA-FV-A2QR TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ 
       14.40        19.10        12.03         0.03         0.33         0.39 
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-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ 
       22.13        25.64         5.92        19.23        25.25        22.95 
TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M8 TCGA-G3-A7M9 
       20.42        17.10        22.06        20.78        14.14         1.84 
TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-GJ-A3OU 
       15.78        15.65        12.23         0.89         8.75        22.92 
TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 
        1.02         2.99        37.71        20.75        17.06        16.83 
TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD 
       11.80         2.14        21.60        12.72        13.97        12.03 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75H TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 
        9.57        16.67        24.56         7.53        10.85        58.88 
TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC 
       17.69        21.01         3.09        17.59        19.76        16.44 
TCGA-UB-A7MD TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 
        1.71        10.32        11.34        20.22        24.85        18.28 
TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D4 TCGA-ZS-A9CD 
       13.55        35.77        25.71        23.21        12.99        45.57 
TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       40.80        79.30        11.21 

  DEL PEAK 13(9P21.3) MUTATED DEL PEAK 13(9P21.3) WILD-TYPE 
                         0.20                          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 
                        18.87                         20.12 
[1] "0.2 - 90.3 (18.9)"  "0.0 - 120.8 (20.1)"
[1] "hr=" "1.3"
D42V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IIIA
  DEL PEAK 13(9P21.3) MUTATED        65       35         0         28
  DEL PEAK 13(9P21.3) WILD-TYPE     106       50         3         32
                               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                             65                           106
  STAGE II                            35                            50
  STAGE III                            0                             3
  STAGE IIIA                          28                            32
  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      71  39  34   3
  DEL PEAK 13(9P21.3) WILD-TYPE   111  53  40   9
D42V4, multiclass
       clus
vv      DEL PEAK 13(9P21.3) MUTATED DEL PEAK 13(9P21.3) WILD-TYPE
  T0+T1                          71                           111
  T2                             39                            53
  T3                             34                            40
  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 149   1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(9P21.3) MUTATED    101    2
  DEL PEAK 13(9P21.3) WILD-TYPE  149    1
   clus
vv  DEL PEAK 13(9P21.3) MUTATED DEL PEAK 13(9P21.3) WILD-TYPE
  0                         101                           149
  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 155   2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(9P21.3) MUTATED    106    2
  DEL PEAK 13(9P21.3) WILD-TYPE  155    2
   clus
vv  DEL PEAK 13(9P21.3) MUTATED DEL PEAK 13(9P21.3) WILD-TYPE
  0                         106                           155
  1                           2                             2
[1] 2 2
[1] FALSE
D42V7, binary
                               cls
clus                              0   1
  DEL PEAK 13(9P21.3) MUTATED    42 105
  DEL PEAK 13(9P21.3) WILD-TYPE  73 142
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(9P21.3) MUTATED     42  105
  DEL PEAK 13(9P21.3) WILD-TYPE   73  142
        clus
vv       DEL PEAK 13(9P21.3) MUTATED DEL PEAK 13(9P21.3) WILD-TYPE
  FEMALE                          42                            73
  MALE                           105                           142
[1] 2 2
[1] FALSE
D42V8, binary
                               cls
clus                              0   1
  DEL PEAK 13(9P21.3) MUTATED   136   2
  DEL PEAK 13(9P21.3) WILD-TYPE 200   5
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(9P21.3) MUTATED    136    2
  DEL PEAK 13(9P21.3) WILD-TYPE  200    5
     clus
vv    DEL PEAK 13(9P21.3) MUTATED DEL PEAK 13(9P21.3) WILD-TYPE
  NO                          136                           200
  YES                           2                             5
[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                        144
  DEL PEAK 13(9P21.3) WILD-TYPE                      209
                               vv
clus                            HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK 13(9P21.3) MUTATED                                  3
  DEL PEAK 13(9P21.3) WILD-TYPE                                4
D42V9, multiclass
                                  clus
vv                                 DEL PEAK 13(9P21.3) MUTATED
  FIBROLAMELLAR CARCINOMA                                    0
  HEPATOCELLULAR CARCINOMA                                 144
  HEPATOCHOLANGIOCARCINOMA (MIXED)                           3
                                  clus
vv                                 DEL PEAK 13(9P21.3) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                      2
  HEPATOCELLULAR CARCINOMA                                   209
  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   129   8   1   7
  DEL PEAK 13(9P21.3) WILD-TYPE 189   7   0  14
D42V10, multiclass
    clus
vv   DEL PEAK 13(9P21.3) MUTATED DEL PEAK 13(9P21.3) WILD-TYPE
  R0                         129                           189
  R1                           8                             7
  R2                           1                             0
  RX                           7                            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 13(9P21.3) MUTATED                                  1    74
  DEL PEAK 13(9P21.3) WILD-TYPE                                0    83
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 13(9P21.3) MUTATED                           7    64
  DEL PEAK 13(9P21.3) WILD-TYPE                        10   113
D42V11, multiclass
                                  clus
vv                                 DEL PEAK 13(9P21.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                     74
  BLACK OR AFRICAN AMERICAN                                  7
  WHITE                                                     64
                                  clus
vv                                 DEL PEAK 13(9P21.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                       83
  BLACK OR AFRICAN AMERICAN                                   10
  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"
D42V12, binary
                               cls
clus                              0   1
  DEL PEAK 13(9P21.3) MUTATED     3 140
  DEL PEAK 13(9P21.3) WILD-TYPE  10 192
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(9P21.3) MUTATED      3  140
  DEL PEAK 13(9P21.3) WILD-TYPE   10  192
                        clus
vv                       DEL PEAK 13(9P21.3) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                         140
                        clus
vv                       DEL PEAK 13(9P21.3) WILD-TYPE
  HISPANIC OR LATINO                                10
  NOT HISPANIC OR LATINO                           192
[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    69  45
  DEL PEAK 14(9Q31.3) WILD-TYPE 160  84
  DEL PEAK 14(9Q31.3) MUTATED DEL PEAK 14(9Q31.3) WILD-TYPE 
                          114                           244 
  DEL PEAK 14(9Q31.3) MUTATED DEL PEAK 14(9Q31.3) WILD-TYPE 
                           45                            84 
$`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        49.84        18.25        11.74 
TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-5C-A9VH 
       20.81        22.92         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 
       45.93        17.98        14.60         4.24         2.86         3.32 
TCGA-CC-A3M9 TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UE TCGA-CC-A7IF TCGA-CC-A7IJ 
        9.86        10.36        11.93         8.94        21.34        12.56 
TCGA-CC-A7IL TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A116 TCGA-DD-A119 TCGA-DD-A11A 
        9.14         8.15        79.73        53.33         7.33         2.60 
TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EI TCGA-DD-A1EJ 
        0.46        21.76        12.95        45.11         6.02        33.04 
TCGA-DD-A1EK TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NI 
       18.35        55.69         5.62        30.61        33.14        26.83 
TCGA-DD-A4NJ TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-AA3A TCGA-DD-AACB TCGA-DD-AACD 
       30.51        29.56        73.81        13.48        76.41        12.53 
TCGA-DD-AACE TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACU TCGA-DD-AACZ TCGA-DD-AAD3 
       63.48        61.68        13.64        51.52         5.62        42.58 
TCGA-DD-AAD8 TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADO TCGA-DD-AADV 
       40.08        35.05        34.49        20.91        14.89        18.87 
TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAED TCGA-DD-AAEK TCGA-DD-AAVQ TCGA-DD-AAVU 
       21.83        18.90        25.08        35.08        89.69        72.39 
TCGA-DD-AAVW TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-ED-A459 TCGA-ED-A66X TCGA-ED-A7PX 
       76.18        62.47        66.25        29.92        13.35         0.20 
TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-EP-A2KC TCGA-EP-A3RK TCGA-FV-A2QQ TCGA-FV-A3I0 
        0.20        13.15         0.62        11.93        23.97        27.88 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A4ZP TCGA-G3-A25S TCGA-G3-A25T 
        8.12         6.38        12.03        81.73        13.68        51.06 
TCGA-G3-A3CH TCGA-G3-A7M5 TCGA-G3-AAV1 TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB 
       25.64        14.70        11.80        11.87         1.02         2.20 
TCGA-MI-A75G TCGA-MI-A75I TCGA-PD-A5DF TCGA-RC-A7SB TCGA-RC-A7SH TCGA-RC-A7SK 
       22.95        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 
       36.10         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        35.87        25.15        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        38.40         8.55         8.61 
TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-A10T 
        0.66        17.10        14.76         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        23.38         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-5264 
       36.66         0.66         3.19         3.39         4.24         3.35 
TCGA-CC-A3MA TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A7IE TCGA-CC-A7IG TCGA-CC-A7IH 
        9.96        11.41         9.99         7.13         9.83        12.00 
TCGA-CC-A7II TCGA-CC-A7IK TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FS 
       13.12         8.61         4.60        11.31         9.17         6.94 
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        26.63        23.64        25.78 
TCGA-DD-AAEI TCGA-DD-AAVP TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVV TCGA-DD-AAVX 
       50.33        79.07        82.62        59.93        80.71        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        26.93        28.08 
TCGA-ED-A627 TCGA-ED-A66Y TCGA-ED-A7PY TCGA-ED-A7XO TCGA-ED-A82E TCGA-ED-A8O5 
       13.91         9.73        12.82        14.04        13.41        13.35 
TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB 
        1.84         0.20        18.74        19.99        20.61        19.59 
TCGA-EP-A3JL TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A495 
        9.96        22.85        14.40        60.89        19.10         0.03 
TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X 
        0.33         0.39        53.79        28.27        30.74        58.49 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
       14.86        21.53        22.13         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        22.06        20.78 
TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV2 
       11.87        14.14         1.84        15.78        15.65        12.23 
TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-GJ-A3OU TCGA-HP-A5MZ 
       13.55         0.89         8.75         2.14        22.92         2.99 
TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 
       37.71        20.75        17.06        16.83        11.80         2.14 
TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD 
       21.60        31.27        29.79        12.72        13.97        12.03 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75H TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 
        9.57        16.67        24.56         7.53        10.85        58.88 
TCGA-NI-A8LF TCGA-O8-A75V TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SF TCGA-UB-A7MA 
       26.27        17.69         3.09        21.04        19.04        17.59 
TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WX-AA44 
       16.44         1.71        10.32        11.34         0.99        20.22 
TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY 
       24.85        18.28        22.78        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 
                         0.20                          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 
                       19.545                        19.775 
[1] "0.2 - 89.7 (19.5)"  "0.0 - 120.8 (19.8)"
[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     125       54         3         43
                               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                           125
  STAGE II                            31                            54
  STAGE III                            0                             3
  STAGE IIIA                          17                            43
  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   130  56  52   6
D43V4, multiclass
       clus
vv      DEL PEAK 14(9Q31.3) MUTATED DEL PEAK 14(9Q31.3) WILD-TYPE
  T0+T1                          52                           130
  T2                             36                            56
  T3                             22                            52
  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 178   0
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(9Q31.3) MUTATED     72    3
  DEL PEAK 14(9Q31.3) WILD-TYPE  178    0
   clus
vv  DEL PEAK 14(9Q31.3) MUTATED DEL PEAK 14(9Q31.3) WILD-TYPE
  0                          72                           178
  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 185   1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(9Q31.3) MUTATED     76    3
  DEL PEAK 14(9Q31.3) WILD-TYPE  185    1
   clus
vv  DEL PEAK 14(9Q31.3) MUTATED DEL PEAK 14(9Q31.3) WILD-TYPE
  0                          76                           185
  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  80 166
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(9Q31.3) MUTATED     35   81
  DEL PEAK 14(9Q31.3) WILD-TYPE   80  166
        clus
vv       DEL PEAK 14(9Q31.3) MUTATED DEL PEAK 14(9Q31.3) WILD-TYPE
  FEMALE                          35                            80
  MALE                            81                           166
[1] 2 2
[1] FALSE
D43V8, binary
                               cls
clus                              0   1
  DEL PEAK 14(9Q31.3) MUTATED   106   2
  DEL PEAK 14(9Q31.3) WILD-TYPE 230   5
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(9Q31.3) MUTATED    106    2
  DEL PEAK 14(9Q31.3) WILD-TYPE  230    5
     clus
vv    DEL PEAK 14(9Q31.3) MUTATED DEL PEAK 14(9Q31.3) WILD-TYPE
  NO                          106                           230
  YES                           2                             5
[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                      239
                               vv
clus                            HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK 14(9Q31.3) MUTATED                                  2
  DEL PEAK 14(9Q31.3) WILD-TYPE                                5
D43V9, 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                                   239
  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 221   8   0  13
D43V10, multiclass
    clus
vv   DEL PEAK 14(9Q31.3) MUTATED DEL PEAK 14(9Q31.3) WILD-TYPE
  R0                          97                           221
  R1                           7                             8
  R2                           1                             0
  RX                           8                            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 14(9Q31.3) MUTATED                                  0    53
  DEL PEAK 14(9Q31.3) WILD-TYPE                                1   104
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 14(9Q31.3) MUTATED                           6    57
  DEL PEAK 14(9Q31.3) WILD-TYPE                        11   120
D43V11, 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                                                      104
  BLACK OR AFRICAN AMERICAN                                   11
  WHITE                                                      120
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V12, binary
                               cls
clus                              0   1
  DEL PEAK 14(9Q31.3) MUTATED     2 113
  DEL PEAK 14(9Q31.3) WILD-TYPE  11 219
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(9Q31.3) MUTATED      2  113
  DEL PEAK 14(9Q31.3) WILD-TYPE   11  219
                        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                                11
  NOT HISPANIC OR LATINO                           219
[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    57  37
  DEL PEAK 15(10Q23.31) WILD-TYPE 172  92
  DEL PEAK 15(10Q23.31) MUTATED DEL PEAK 15(10Q23.31) WILD-TYPE 
                             94                             264 
  DEL PEAK 15(10Q23.31) MUTATED DEL PEAK 15(10Q23.31) WILD-TYPE 
                             37                              92 
$`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        22.92         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        23.38        44.42        45.93 
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-5264 TCGA-CC-A1HT TCGA-CC-A3MA TCGA-CC-A3MB 
        2.86         4.24         3.35         3.32         9.96        10.36 
TCGA-CC-A3MC TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7II TCGA-CC-A8HT TCGA-DD-A114 
       11.93         9.99         8.94        13.12         4.60        37.78 
TCGA-DD-A115 TCGA-DD-A118 TCGA-DD-A11A TCGA-DD-A11C TCGA-DD-A1EG TCGA-DD-A1EL 
       83.57       113.00         2.60        21.76        45.11        13.64 
TCGA-DD-A39Y TCGA-DD-A3A0 TCGA-DD-A4NA TCGA-DD-A4NI TCGA-DD-A4NQ TCGA-DD-AACG 
        5.62        25.81        33.14        26.83        12.26        15.42 
TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACM TCGA-DD-AACO TCGA-DD-AACQ TCGA-DD-AACU 
        6.41        53.19        58.16        61.68        14.20        51.52 
TCGA-DD-AACV TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD8 
       50.33         5.62         4.50        42.58        44.22        40.08 
TCGA-DD-AADA TCGA-DD-AADL TCGA-DD-AADN TCGA-DD-AADR TCGA-DD-AADY TCGA-DD-AAE2 
       40.54        20.91        29.52        66.67        18.25        20.98 
TCGA-DD-AAE8 TCGA-ED-A459 TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7XO TCGA-ED-A8O6 
       21.83        29.92         9.73         0.20        14.04         1.84 
TCGA-ED-A97K TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A496 TCGA-G3-A25T 
        0.20        23.97        19.10        27.88         0.33        51.06 
TCGA-G3-A25U TCGA-G3-A25X TCGA-G3-A5SJ TCGA-G3-A7M5 TCGA-G3-AAV1 TCGA-G3-AAV4 
       53.79        58.49        22.95        14.70        11.80         0.89 
TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-NI-A4U2 TCGA-PD-A5DF 
       37.71        17.06        21.60        31.27        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        36.10        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        49.84        18.25        11.74 
TCGA-2Y-A9H7 TCGA-2Y-A9H8 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-4R-AA8I 
       38.40        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        17.10        14.76         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         4.24 
TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-A3M9 TCGA-CC-A5UC TCGA-CC-A7IE TCGA-CC-A7IF 
        3.19         3.39         9.86        11.41         7.13        21.34 
TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A7IL TCGA-CC-A8HU 
        9.83        12.00        12.56         8.61         9.14        11.31 
TCGA-CC-A8HV TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A116 TCGA-DD-A119 
        9.17         6.94         8.15        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        26.63 
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-AAVV TCGA-DD-AAVW TCGA-DD-AAVX 
       82.62        59.93        72.39        80.71        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 
       26.93        28.08        13.91        13.35        12.82         0.20 
TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
       13.15        13.41        13.35        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-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A4ZP 
       60.89         8.12         6.38        12.03         0.03        81.73 
TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z 
        0.39        13.68        28.27        30.74        14.86        21.53 
TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI 
       22.13        25.64         5.92        19.53        19.23        25.25 
TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 
       20.42        17.10        22.06        20.78        11.87        14.14 
TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV5 
        1.84        15.78        15.65        12.23        13.55         8.75 
TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ 
        2.14        11.87        22.92         1.02         2.20         2.99 
TCGA-K7-A5RF TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K8 TCGA-LG-A6GG 
       20.75        16.83        11.80         2.14        29.79        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        22.95        24.56 
TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A8LF TCGA-O8-A75V TCGA-RC-A7S9 
       20.71         7.53        10.85        26.27        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-AA0U TCGA-UB-AA0V TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA44 
        7.04        10.75        10.32         0.99        12.99        20.22 
TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TF TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ 
       24.85        18.28        22.78        35.77        25.71        23.21 
TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CF TCGA-ZS-A9CG 
       35.87        25.15        12.99        45.57        79.30        11.21 

  DEL PEAK 15(10Q23.31) MUTATED DEL PEAK 15(10Q23.31) WILD-TYPE 
                           0.20                            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 
                         20.335                          19.675 
[1] "0.2 - 113.0 (20.3)" "0.0 - 120.8 (19.7)"
[1] "hr=" "1.3"
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     135       62         3         39
                                 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                             135
  STAGE II                              23                              62
  STAGE III                              0                               3
  STAGE IIIA                            21                              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 15(10Q23.31) MUTATED      38  27  22   7
  DEL PEAK 15(10Q23.31) WILD-TYPE   144  65  52   5
D44V4, multiclass
       clus
vv      DEL PEAK 15(10Q23.31) MUTATED DEL PEAK 15(10Q23.31) WILD-TYPE
  T0+T1                            38                             144
  T2                               27                              65
  T3                               22                              52
  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 186   1
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 15(10Q23.31) MUTATED     64    2
  DEL PEAK 15(10Q23.31) WILD-TYPE  186    1
   clus
vv  DEL PEAK 15(10Q23.31) MUTATED DEL PEAK 15(10Q23.31) WILD-TYPE
  0                            64                             186
  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 190   4
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 15(10Q23.31) MUTATED     71    0
  DEL PEAK 15(10Q23.31) WILD-TYPE  190    4
   clus
vv  DEL PEAK 15(10Q23.31) MUTATED DEL PEAK 15(10Q23.31) WILD-TYPE
  0                            71                             190
  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  85 182
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 15(10Q23.31) MUTATED     30   65
  DEL PEAK 15(10Q23.31) WILD-TYPE   85  182
        clus
vv       DEL PEAK 15(10Q23.31) MUTATED DEL PEAK 15(10Q23.31) WILD-TYPE
  FEMALE                            30                              85
  MALE                              65                             182
[1] 2 2
[1] FALSE
D44V8, binary
                                 cls
clus                                0   1
  DEL PEAK 15(10Q23.31) MUTATED    91   1
  DEL PEAK 15(10Q23.31) WILD-TYPE 245   6
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 15(10Q23.31) MUTATED     91    1
  DEL PEAK 15(10Q23.31) WILD-TYPE  245    6
     clus
vv    DEL PEAK 15(10Q23.31) MUTATED DEL PEAK 15(10Q23.31) WILD-TYPE
  NO                             91                             245
  YES                             1                               6
[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                      262
                                 vv
clus                              HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK 15(10Q23.31) MUTATED                                  4
  DEL PEAK 15(10Q23.31) WILD-TYPE                                3
D44V9, 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                                     262
  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 237  11   1  13
D44V10, multiclass
    clus
vv   DEL PEAK 15(10Q23.31) MUTATED DEL PEAK 15(10Q23.31) WILD-TYPE
  R0                            81                             237
  R1                             4                              11
  R2                             0                               1
  RX                             8                              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 15(10Q23.31) MUTATED                                  0    46
  DEL PEAK 15(10Q23.31) WILD-TYPE                                1   111
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 15(10Q23.31) MUTATED                          10    38
  DEL PEAK 15(10Q23.31) WILD-TYPE                         7   139
D44V11, 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                                                        111
  BLACK OR AFRICAN AMERICAN                                      7
  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"
D44V12, binary
                                 cls
clus                                0   1
  DEL PEAK 15(10Q23.31) MUTATED     3  85
  DEL PEAK 15(10Q23.31) WILD-TYPE  10 247
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 15(10Q23.31) MUTATED      3   85
  DEL PEAK 15(10Q23.31) WILD-TYPE   10  247
                        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                                  10
  NOT HISPANIC OR LATINO                             247
[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    61  40
  DEL PEAK 16(10Q26.13) WILD-TYPE 168  89
  DEL PEAK 16(10Q26.13) MUTATED DEL PEAK 16(10Q26.13) WILD-TYPE 
                            101                             257 
  DEL PEAK 16(10Q26.13) MUTATED DEL PEAK 16(10Q26.13) WILD-TYPE 
                             40                              89 
$`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        22.92 
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 
       23.38         5.03        45.93        22.36        17.98        18.48 
TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5260 TCGA-CC-5264 TCGA-CC-A1HT TCGA-CC-A3M9 
       13.45         0.66         2.86         3.35         3.32         9.86 
TCGA-CC-A3MA TCGA-CC-A3MC TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7II TCGA-CC-A7IJ 
        9.96        11.93         9.99         8.94        13.12        12.56 
TCGA-CC-A8HT TCGA-CC-A8HV TCGA-CC-A9FW TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A11A 
        4.60         9.17         8.15        37.78        83.57         2.60 
TCGA-DD-A11C TCGA-DD-A1EB TCGA-DD-A1EG TCGA-DD-A1EL TCGA-DD-A39Y TCGA-DD-A3A0 
       21.76        66.31        45.11        13.64         5.62        25.81 
TCGA-DD-A4NA TCGA-DD-A4NI TCGA-DD-A4NQ TCGA-DD-A73F TCGA-DD-AACG TCGA-DD-AACI 
       33.14        26.83        12.26        35.67        15.42        53.19 
TCGA-DD-AACM TCGA-DD-AACO TCGA-DD-AACQ TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACZ 
       58.16        61.68        14.20        51.52        50.33         5.62 
TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADL TCGA-DD-AADM 
       42.58        44.22        40.08        40.54        20.91         0.39 
TCGA-DD-AADN TCGA-DD-AADR TCGA-DD-AADY TCGA-DD-AAE2 TCGA-DD-AAE8 TCGA-ED-A459 
       29.52        66.67        18.25        20.98        21.83        29.92 
TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7XO TCGA-ED-A8O6 TCGA-ED-A97K TCGA-FV-A2QQ 
        9.73         0.20        14.04         1.84         0.20        23.97 
TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A496 TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25X 
       19.10        27.88         0.33        51.06        53.79        58.49 
TCGA-G3-A25Y TCGA-G3-A5SJ TCGA-G3-A7M5 TCGA-G3-AAV1 TCGA-G3-AAV4 TCGA-K7-A5RG 
       14.86        22.95        14.70        11.80         0.89        17.06 
TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-PD-A5DF 
       21.60        31.27        29.79        10.85        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        36.10        19.76         1.71 
TCGA-UB-AA0U TCGA-WQ-A9G7 TCGA-YA-A8S7 TCGA-ZP-A9D1 TCGA-ZS-A9CE 
       10.75         0.99        13.55         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        49.84        18.25        11.74        38.40        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 
       17.10        14.76        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         4.24         3.19         3.39 
TCGA-CC-5263 TCGA-CC-A3MB TCGA-CC-A5UC TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IG 
        4.24        10.36        11.41         7.13        21.34         9.83 
TCGA-CC-A7IH TCGA-CC-A7IK TCGA-CC-A7IL TCGA-CC-A8HU TCGA-CC-A9FS TCGA-DD-A113 
       12.00         8.61         9.14        11.31         6.94        79.73 
TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11D TCGA-DD-A1E9 
       53.33       113.00         7.33         0.46        51.29        90.71 
TCGA-DD-A1EA TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EH 
       79.40        19.79        75.65        11.47        12.95        49.15 
TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39X 
        6.02        33.04        18.35        21.14        27.19        55.69 
TCGA-DD-A39Z TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 
       19.76         7.66        70.06        17.59        20.12       102.74 
TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NB TCGA-DD-A4ND 
      107.11        13.78         0.36        30.61        32.52        90.28 
TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN 
       30.97        30.15        30.51        39.78        56.25        29.56 
TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A 
       73.81       108.76         0.30        80.75        78.84        23.93 
TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73G TCGA-DD-AA3A 
        9.30        23.05        22.78         1.45       114.35        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-AACJ TCGA-DD-AACK TCGA-DD-AACL 
       63.48        12.00         6.41        69.11         0.30         3.52 
TCGA-DD-AACN TCGA-DD-AACP TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACW TCGA-DD-AACX 
       42.81        13.64        59.31        51.35        46.82         5.59 
TCGA-DD-AACY TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD6 TCGA-DD-AADB 
       47.67         4.50        18.54        21.63        22.09        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-AADO TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADS 
       35.05        34.49        14.89        15.06        14.33        15.58 
TCGA-DD-AADU TCGA-DD-AADV TCGA-DD-AADW TCGA-DD-AAE0 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-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB 
       19.99         4.64        21.17        23.74        18.90        15.72 
TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAEK 
       25.08        26.63        23.64        25.78        50.33        35.08 
TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVV 
       79.07        89.69        82.62        59.93        72.39        80.71 
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        26.93        28.08        13.91        13.35 
TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-EP-A12J 
       12.82         0.20        13.15        13.41        13.35        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-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 
       22.85        14.40        60.89         8.12         6.38        12.03 
TCGA-FV-A495 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25V TCGA-G3-A25W 
        0.03        81.73         0.39        13.68        28.27        30.74 
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        22.06        20.78        11.87 
TCGA-G3-A7M8 TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV3 
       14.14         1.84        15.78        15.65        12.23        13.55 
TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB 
        8.75         2.14        11.87        22.92         1.02         2.20 
TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 
        2.99        37.71        20.75        16.83        11.80         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        22.95 
TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A520 TCGA-NI-A8LF TCGA-O8-A75V TCGA-RC-A7S9 
       24.56        20.71         7.53        26.27        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-AA44 TCGA-WX-AA46 
        7.04        10.32        11.34        12.99        20.22        24.85 
TCGA-WX-AA47 TCGA-XR-A8TF TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 
       18.28        22.78        35.77        25.71        23.21        35.87 
TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CF TCGA-ZS-A9CG 
       25.15        12.99        45.57        79.30        11.21 

  DEL PEAK 16(10Q26.13) MUTATED DEL PEAK 16(10Q26.13) WILD-TYPE 
                           0.20                            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 
                          19.10                           19.99 
[1] "0.2 - 83.6 (19.1)"  "0.0 - 120.8 (20.0)"
[1] "hr=" "1.4"
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     130       59         3         40
                                 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                             130
  STAGE II                              26                              59
  STAGE III                              0                               3
  STAGE IIIA                            20                              40
  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   139  63  51   5
D45V4, multiclass
       clus
vv      DEL PEAK 16(10Q26.13) MUTATED DEL PEAK 16(10Q26.13) WILD-TYPE
  T0+T1                            43                             139
  T2                               29                              63
  T3                               23                              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"
D45V5, binary
                                 cls
clus                                0   1
  DEL PEAK 16(10Q26.13) MUTATED    70   2
  DEL PEAK 16(10Q26.13) WILD-TYPE 180   1
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 16(10Q26.13) MUTATED     70    2
  DEL PEAK 16(10Q26.13) WILD-TYPE  180    1
   clus
vv  DEL PEAK 16(10Q26.13) MUTATED DEL PEAK 16(10Q26.13) WILD-TYPE
  0                            70                             180
  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 186   4
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 16(10Q26.13) MUTATED     75    0
  DEL PEAK 16(10Q26.13) WILD-TYPE  186    4
   clus
vv  DEL PEAK 16(10Q26.13) MUTATED DEL PEAK 16(10Q26.13) WILD-TYPE
  0                            75                             186
  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  82 178
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 16(10Q26.13) MUTATED     33   69
  DEL PEAK 16(10Q26.13) WILD-TYPE   82  178
        clus
vv       DEL PEAK 16(10Q26.13) MUTATED DEL PEAK 16(10Q26.13) WILD-TYPE
  FEMALE                            33                              82
  MALE                              69                             178
[1] 2 2
[1] FALSE
D45V8, binary
                                 cls
clus                                0   1
  DEL PEAK 16(10Q26.13) MUTATED    98   1
  DEL PEAK 16(10Q26.13) WILD-TYPE 238   6
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 16(10Q26.13) MUTATED     98    1
  DEL PEAK 16(10Q26.13) WILD-TYPE  238    6
     clus
vv    DEL PEAK 16(10Q26.13) MUTATED DEL PEAK 16(10Q26.13) WILD-TYPE
  NO                             98                             238
  YES                             1                               6
[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                      256
                                 vv
clus                              HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK 16(10Q26.13) MUTATED                                  4
  DEL PEAK 16(10Q26.13) WILD-TYPE                                3
D45V9, 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                                     256
  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 231  10   1  13
D45V10, multiclass
    clus
vv   DEL PEAK 16(10Q26.13) MUTATED DEL PEAK 16(10Q26.13) WILD-TYPE
  R0                            87                             231
  R1                             5                              10
  R2                             0                               1
  RX                             8                              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 16(10Q26.13) MUTATED                                  0    48
  DEL PEAK 16(10Q26.13) WILD-TYPE                                1   109
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 16(10Q26.13) MUTATED                          10    42
  DEL PEAK 16(10Q26.13) WILD-TYPE                         7   135
D45V11, 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                                                        109
  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"
D45V12, binary
                                 cls
clus                                0   1
  DEL PEAK 16(10Q26.13) MUTATED     3  92
  DEL PEAK 16(10Q26.13) WILD-TYPE  10 240
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 16(10Q26.13) MUTATED      3   92
  DEL PEAK 16(10Q26.13) WILD-TYPE   10  240
                        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                                  10
  NOT HISPANIC OR LATINO                             240
[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    43  27
  DEL PEAK 17(11Q14.1) WILD-TYPE 186 102
  DEL PEAK 17(11Q14.1) MUTATED DEL PEAK 17(11Q14.1) WILD-TYPE 
                            70                            288 
  DEL PEAK 17(11Q14.1) MUTATED DEL PEAK 17(11Q14.1) WILD-TYPE 
                            27                            102 
$`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        49.84        13.02        10.78 
TCGA-5C-AAPD TCGA-5R-AA1D TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10S TCGA-BC-A112 
        0.66        14.76        27.91        37.32        46.78         5.03 
TCGA-BC-A217 TCGA-BC-A3KF TCGA-CC-5263 TCGA-CC-5264 TCGA-CC-A3M9 TCGA-CC-A3MC 
       45.93         0.26         4.24         3.35         9.86        11.93 
TCGA-CC-A5UD TCGA-CC-A7IG TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A7IL TCGA-CC-A8HU 
        9.99         9.83        12.56         8.61         9.14        11.31 
TCGA-DD-A113 TCGA-DD-A11A TCGA-DD-A1E9 TCGA-DD-A1EF TCGA-DD-A1EJ TCGA-DD-A39X 
       79.73         2.60        90.71        12.95        33.04        55.69 
TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-A73B TCGA-DD-AACB TCGA-DD-AACP 
       32.52        90.28        26.83         9.30        76.41        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-AAE3 TCGA-DD-AAE6 TCGA-DD-AAED 
       14.89        15.06        18.25        18.61         4.64        25.08 
TCGA-DD-AAEK TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A8O6 TCGA-EP-A2KC TCGA-FV-A2QQ 
       35.08         0.20        14.04         1.84         0.62        23.97 
TCGA-FV-A4ZP TCGA-G3-A25S TCGA-G3-A5SJ TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV6 
       81.73        13.68        22.95        11.80        12.23         2.14 
TCGA-K7-A5RG TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RG-A7D4 
       17.06        21.60        31.27        19.33        19.04        36.10 
TCGA-UB-A7MA TCGA-UB-A7MC TCGA-UB-A7MF TCGA-YA-A8S7 
       17.59        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        38.40 
TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-4R-AA8I TCGA-5C-A9VH 
       20.81        22.92         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 
       17.10         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        23.38         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         4.24         2.86         3.19 
TCGA-CC-5262 TCGA-CC-A1HT TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A5UC TCGA-CC-A5UE 
        3.39         3.32         9.96        10.36        11.41         8.94 
TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A8HT TCGA-CC-A8HV 
        7.13        21.34        12.00        13.12         4.60         9.17 
TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 
        6.94         8.15        37.78        83.57        53.33       113.00 
TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1EA TCGA-DD-A1EB 
        7.33         0.46        21.76        51.29        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-A1EL TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39Y TCGA-DD-A39Z 
       18.35        13.64        21.14        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-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NF 
      107.11        13.78         0.36        30.61        33.14        30.97 
TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO 
       30.15        30.51        39.78        56.25        29.56        73.81 
TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A 
      108.76        12.26         0.30        80.75        78.84        23.93 
TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A 
       23.05        22.78         1.45        35.67       114.35        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-AACQ TCGA-DD-AACS 
        3.52        58.16        42.81        61.68        14.20        59.31 
TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACZ TCGA-DD-AAD0 
       51.35        51.52        46.82         5.59         5.62         4.50 
TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC 
       18.54        21.63        42.58        40.54        40.83        13.97 
TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK 
       39.52         3.78        37.64        35.67        35.05        34.49 
TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS 
       20.91         0.39        29.52        14.33        66.67        15.58 
TCGA-DD-AADU TCGA-DD-AADV TCGA-DD-AADW TCGA-DD-AAE0 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-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-AAVP TCGA-DD-AAVQ 
       26.63        23.64        25.78        50.33        79.07        89.69 
TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVV TCGA-DD-AAVW TCGA-DD-AAVX 
       82.62        59.93        72.39        80.71        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-A66X TCGA-ED-A66Y 
       29.92        26.93        28.08        13.91        13.35         9.73 
TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A97K 
        0.20        12.82        13.15        13.41        13.35         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-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 
       22.85        14.40        60.89        19.10        27.88         8.12 
TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25T 
        6.38        12.03         0.03         0.33         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-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M7 
       20.42        17.10        22.06        14.70        20.78        11.87 
TCGA-G3-A7M8 TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV3 TCGA-G3-AAV4 
       14.14         1.84        15.78        15.65        13.55         0.89 
TCGA-G3-AAV5 TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ 
        8.75        11.87        22.92         1.02         2.20         2.99 
TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K8 
       37.71        20.75        16.83        11.80         2.14        29.79 
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        22.95 
TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF 
       24.56        20.71         7.53        10.85        58.88        26.27 
TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SH TCGA-RC-A7SK 
       17.69        21.01         3.09        21.04        15.39        15.52 
TCGA-T1-A6J8 TCGA-UB-A7MB TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0U TCGA-UB-AA0V 
        0.76        19.76         1.71        15.98        10.75        10.32 
TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 
       11.34         0.99        12.99        20.22        24.85        18.28 
TCGA-XR-A8TF TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 
       22.78        35.77        25.71        23.21        35.87         0.69 
TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       25.15        12.99        45.57        40.80        79.30        11.21 

  DEL PEAK 17(11Q14.1) MUTATED DEL PEAK 17(11Q14.1) WILD-TYPE 
                          0.20                           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 
                        17.325                         20.170 
[1] "0.2 - 90.7 (17.3)"  "0.0 - 120.8 (20.2)"
[1] "hr=" "1.2"
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     142       70         3         41
                                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                            142
  STAGE II                             15                             70
  STAGE III                             0                              3
  STAGE IIIA                           19                             41
  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   151  74  52  11
D46V4, multiclass
       clus
vv      DEL PEAK 17(11Q14.1) MUTATED DEL PEAK 17(11Q14.1) WILD-TYPE
  T0+T1                           31                            151
  T2                              18                             74
  T3                              22                             52
  T4                               1                             11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V5, binary
                                cls
clus                               0   1
  DEL PEAK 17(11Q14.1) MUTATED    53   2
  DEL PEAK 17(11Q14.1) WILD-TYPE 197   1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 17(11Q14.1) MUTATED     53    2
  DEL PEAK 17(11Q14.1) WILD-TYPE  197    1
   clus
vv  DEL PEAK 17(11Q14.1) MUTATED DEL PEAK 17(11Q14.1) WILD-TYPE
  0                           53                            197
  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 205   3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 17(11Q14.1) MUTATED     56    1
  DEL PEAK 17(11Q14.1) WILD-TYPE  205    3
   clus
vv  DEL PEAK 17(11Q14.1) MUTATED DEL PEAK 17(11Q14.1) WILD-TYPE
  0                           56                            205
  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  92 198
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 17(11Q14.1) MUTATED     23   49
  DEL PEAK 17(11Q14.1) WILD-TYPE   92  198
        clus
vv       DEL PEAK 17(11Q14.1) MUTATED DEL PEAK 17(11Q14.1) WILD-TYPE
  FEMALE                           23                             92
  MALE                             49                            198
[1] 2 2
[1] FALSE
D46V8, binary
                                cls
clus                               0   1
  DEL PEAK 17(11Q14.1) MUTATED    67   1
  DEL PEAK 17(11Q14.1) WILD-TYPE 269   6
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 17(11Q14.1) MUTATED     67    1
  DEL PEAK 17(11Q14.1) WILD-TYPE  269    6
     clus
vv    DEL PEAK 17(11Q14.1) MUTATED DEL PEAK 17(11Q14.1) WILD-TYPE
  NO                            67                            269
  YES                            1                              6
[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                      285
                                vv
clus                             HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK 17(11Q14.1) MUTATED                                  3
  DEL PEAK 17(11Q14.1) WILD-TYPE                                4
D46V9, 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                                    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
  DEL PEAK 17(11Q14.1) MUTATED    63   5   0   4
  DEL PEAK 17(11Q14.1) WILD-TYPE 255  10   1  17
D46V10, multiclass
    clus
vv   DEL PEAK 17(11Q14.1) MUTATED DEL PEAK 17(11Q14.1) WILD-TYPE
  R0                           63                            255
  R1                            5                             10
  R2                            0                              1
  RX                            4                             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 17(11Q14.1) MUTATED                                  0    33
  DEL PEAK 17(11Q14.1) WILD-TYPE                                1   124
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 17(11Q14.1) MUTATED                           5    34
  DEL PEAK 17(11Q14.1) WILD-TYPE                        12   143
D46V11, 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                                                       124
  BLACK OR AFRICAN AMERICAN                                    12
  WHITE                                                       143
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V12, binary
                                cls
clus                               0   1
  DEL PEAK 17(11Q14.1) MUTATED     5  63
  DEL PEAK 17(11Q14.1) WILD-TYPE   8 269
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 17(11Q14.1) MUTATED      5   63
  DEL PEAK 17(11Q14.1) WILD-TYPE    8  269
                        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                                  8
  NOT HISPANIC OR LATINO                            269
[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    57  33
  DEL PEAK 18(11Q24.2) WILD-TYPE 172  96
  DEL PEAK 18(11Q24.2) MUTATED DEL PEAK 18(11Q24.2) WILD-TYPE 
                            90                            268 
  DEL PEAK 18(11Q24.2) MUTATED DEL PEAK 18(11Q24.2) WILD-TYPE 
                            33                             96 
$`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        49.84        13.02        10.78 
TCGA-5C-AAPD TCGA-5R-AA1D TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10S TCGA-BC-A112 
        0.66        14.76        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-5264 
       45.93         0.26        14.60         0.66         4.24         3.35 
TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MC TCGA-CC-A5UD TCGA-CC-A7IG TCGA-CC-A7IJ 
        9.86         9.96        11.93         9.99         9.83        12.56 
TCGA-CC-A7IK TCGA-CC-A7IL TCGA-CC-A8HU TCGA-CC-A8HV TCGA-DD-A113 TCGA-DD-A11A 
        8.61         9.14        11.31         9.17        79.73         2.60 
TCGA-DD-A1E9 TCGA-DD-A1EF TCGA-DD-A1EJ TCGA-DD-A39X TCGA-DD-A4NB TCGA-DD-A4ND 
       90.71        12.95        33.04        55.69        32.52        90.28 
TCGA-DD-A4NI TCGA-DD-A4NN TCGA-DD-A73B TCGA-DD-A73E TCGA-DD-AACB TCGA-DD-AACI 
       26.83        29.56         9.30         1.45        76.41        53.19 
TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACV TCGA-DD-AACY TCGA-DD-AAD5 TCGA-DD-AAD6 
       61.68        13.64        50.33        47.67        44.22        22.09 
TCGA-DD-AAD8 TCGA-DD-AADD TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADY TCGA-DD-AAE2 
       40.08        40.47        14.89        15.06        18.25        20.98 
TCGA-DD-AAE3 TCGA-DD-AAE6 TCGA-DD-AAED TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVV 
       18.61         4.64        25.08        35.08        79.07        80.71 
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-A25U TCGA-G3-A5SJ TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 
       13.68        53.79        22.95        15.65        11.80        12.23 
TCGA-G3-AAV6 TCGA-GJ-A6C0 TCGA-K7-A5RG TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-PD-A5DF 
        2.14         1.02        17.06        21.60        31.27        21.01 
TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MC TCGA-UB-A7ME 
       19.33        19.04        36.10        17.59        16.44        15.98 
TCGA-UB-A7MF TCGA-WQ-AB4B TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CZ TCGA-ZP-A9D0 
        7.04        12.99        22.78        13.55        23.21        35.87 

$`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        38.40 
TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-4R-AA8I TCGA-5C-A9VH 
       20.81        22.92         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 
       17.10         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        23.38         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         4.24         2.86         3.19         3.39         3.32 
TCGA-CC-A3MB TCGA-CC-A5UC TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IH 
       10.36        11.41         8.94         7.13        21.34        12.00 
TCGA-CC-A7II TCGA-CC-A8HT TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A114 TCGA-DD-A115 
       13.12         4.60         6.94         8.15        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-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV 
       73.81       108.76        12.26         0.30        80.75        78.84 
TCGA-DD-A73A TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A 
       23.93        23.05        22.78        35.67       114.35        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-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-AACS TCGA-DD-AACT TCGA-DD-AACU 
       58.16        42.81        14.20        59.31        51.35        51.52 
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-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADE TCGA-DD-AADF 
       42.58        40.54        40.83        13.97        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-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-AADW TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE4 TCGA-DD-AAE7 TCGA-DD-AAE8 
       19.30        18.25        18.15        19.99        21.17        21.83 
TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEH 
       23.74        18.90        15.72        26.63        23.64        25.78 
TCGA-DD-AAEI TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW 
       50.33        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        29.92        26.93        28.08        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-A25V TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z 
       51.06        28.27        30.74        58.49        14.86        21.53 
TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI 
       22.13        25.64         5.92        19.53        19.23        25.25 
TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M7 
       20.42        17.10        22.06        14.70        20.78        11.87 
TCGA-G3-A7M8 TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 
       14.14         1.84        15.78        13.55         0.89         8.75 
TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF 
       11.87        22.92         2.20         2.99        37.71        20.75 
TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC 
       16.83        11.80         2.14        29.79        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        22.95        24.56        20.71 
TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-QA-A7B7 
        7.53        10.85        58.88        26.27        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-AA44 TCGA-WX-AA46 
       10.75        10.32        11.34         0.99        20.22        24.85 
TCGA-WX-AA47 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZP-A9D4 
       18.28        35.77        25.71         0.69        25.15        12.99 
TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       45.57        40.80        79.30        11.21 

  DEL PEAK 18(11Q24.2) MUTATED DEL PEAK 18(11Q24.2) WILD-TYPE 
                          0.20                           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                         20.055 
[1] "0.2 - 90.7 (17.9)"  "0.0 - 120.8 (20.1)"
[1] "hr=" "1.1"
D47V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IIIA
  DEL PEAK 18(11Q24.2) MUTATED        38       21         0         21
  DEL PEAK 18(11Q24.2) WILD-TYPE     133       64         3         39
                                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                              38                            133
  STAGE II                             21                             64
  STAGE III                             0                              3
  STAGE IIIA                           21                             39
  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      42  24  24   2
  DEL PEAK 18(11Q24.2) WILD-TYPE   140  68  50  10
D47V4, multiclass
       clus
vv      DEL PEAK 18(11Q24.2) MUTATED DEL PEAK 18(11Q24.2) WILD-TYPE
  T0+T1                           42                            140
  T2                              24                             68
  T3                              24                             50
  T4                               2                             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V5, binary
                                cls
clus                               0   1
  DEL PEAK 18(11Q24.2) MUTATED    65   2
  DEL PEAK 18(11Q24.2) WILD-TYPE 185   1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(11Q24.2) MUTATED     65    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                           65                            185
  1                            2                              1
[1] 2 2
[1] FALSE
D47V6, binary
                                cls
clus                               0   1
  DEL PEAK 18(11Q24.2) MUTATED    70   1
  DEL PEAK 18(11Q24.2) WILD-TYPE 191   3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(11Q24.2) MUTATED     70    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                           70                            191
  1                            1                              3
[1] 2 2
[1] FALSE
D47V7, binary
                                cls
clus                               0   1
  DEL PEAK 18(11Q24.2) MUTATED    29  63
  DEL PEAK 18(11Q24.2) WILD-TYPE  86 184
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(11Q24.2) MUTATED     29   63
  DEL PEAK 18(11Q24.2) WILD-TYPE   86  184
        clus
vv       DEL PEAK 18(11Q24.2) MUTATED DEL PEAK 18(11Q24.2) WILD-TYPE
  FEMALE                           29                             86
  MALE                             63                            184
[1] 2 2
[1] FALSE
D47V8, binary
                                cls
clus                               0   1
  DEL PEAK 18(11Q24.2) MUTATED    87   1
  DEL PEAK 18(11Q24.2) WILD-TYPE 249   6
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(11Q24.2) MUTATED     87    1
  DEL PEAK 18(11Q24.2) WILD-TYPE  249    6
     clus
vv    DEL PEAK 18(11Q24.2) MUTATED DEL PEAK 18(11Q24.2) WILD-TYPE
  NO                            87                            249
  YES                            1                              6
[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                         88
  DEL PEAK 18(11Q24.2) WILD-TYPE                      265
                                vv
clus                             HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK 18(11Q24.2) MUTATED                                  3
  DEL PEAK 18(11Q24.2) WILD-TYPE                                4
D47V9, multiclass
                                  clus
vv                                 DEL PEAK 18(11Q24.2) MUTATED
  FIBROLAMELLAR CARCINOMA                                     1
  HEPATOCELLULAR CARCINOMA                                   88
  HEPATOCHOLANGIOCARCINOMA (MIXED)                            3
                                  clus
vv                                 DEL PEAK 18(11Q24.2) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                       1
  HEPATOCELLULAR CARCINOMA                                    265
  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    80   5   0   6
  DEL PEAK 18(11Q24.2) WILD-TYPE 238  10   1  15
D47V10, multiclass
    clus
vv   DEL PEAK 18(11Q24.2) MUTATED DEL PEAK 18(11Q24.2) WILD-TYPE
  R0                           80                            238
  R1                            5                             10
  R2                            0                              1
  RX                            6                             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 18(11Q24.2) MUTATED                                  0    44
  DEL PEAK 18(11Q24.2) WILD-TYPE                                1   113
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 18(11Q24.2) MUTATED                           7    41
  DEL PEAK 18(11Q24.2) WILD-TYPE                        10   136
D47V11, multiclass
                                  clus
vv                                 DEL PEAK 18(11Q24.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                      44
  BLACK OR AFRICAN AMERICAN                                   7
  WHITE                                                      41
                                  clus
vv                                 DEL PEAK 18(11Q24.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                       113
  BLACK OR AFRICAN AMERICAN                                    10
  WHITE                                                       136
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V12, binary
                                cls
clus                               0   1
  DEL PEAK 18(11Q24.2) MUTATED     6  82
  DEL PEAK 18(11Q24.2) WILD-TYPE   7 250
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(11Q24.2) MUTATED      6   82
  DEL PEAK 18(11Q24.2) WILD-TYPE    7  250
                        clus
vv                       DEL PEAK 18(11Q24.2) MUTATED
  HISPANIC OR LATINO                                6
  NOT HISPANIC OR LATINO                           82
                        clus
vv                       DEL PEAK 18(11Q24.2) WILD-TYPE
  HISPANIC OR LATINO                                  7
  NOT HISPANIC OR LATINO                            250
[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    45  27
  DEL PEAK 19(12P12.1) WILD-TYPE 184 102
  DEL PEAK 19(12P12.1) MUTATED DEL PEAK 19(12P12.1) WILD-TYPE 
                            72                            286 
  DEL PEAK 19(12P12.1) MUTATED DEL PEAK 19(12P12.1) WILD-TYPE 
                            27                            102 
$`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        23.38        45.93 
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         9.96 
TCGA-CC-A3MC TCGA-CC-A5UE TCGA-CC-A7IK TCGA-CC-A7IL TCGA-CC-A8HT TCGA-CC-A8HV 
       11.93         8.94         8.61         9.14         4.60         9.17 
TCGA-DD-A119 TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39X 
        7.33        45.11        49.15        33.04        13.64        55.69 
TCGA-DD-A39Y TCGA-DD-A3A1 TCGA-DD-A3A7 TCGA-DD-A4NA TCGA-DD-A4NH TCGA-DD-A4NI 
        5.62         7.66        13.78        33.14        30.15        26.83 
TCGA-DD-A4NJ TCGA-DD-A4NO TCGA-DD-A73F TCGA-DD-AACE TCGA-DD-AACG TCGA-DD-AACN 
       30.51        73.81        35.67        63.48        15.42        42.81 
TCGA-DD-AACU TCGA-DD-AACY TCGA-DD-AAD5 TCGA-DD-AAD8 TCGA-DD-AADD TCGA-DD-AADJ 
       51.52        47.67        44.22        40.08        40.47        35.05 
TCGA-DD-AADM TCGA-DD-AADO TCGA-DD-AAE3 TCGA-DD-AAEE TCGA-DD-AAEI TCGA-DD-AAEK 
        0.39        14.89        18.61        26.63        50.33        35.08 
TCGA-DD-AAVP TCGA-DD-AAVU TCGA-DD-AAVV TCGA-ED-A7XP TCGA-EP-A2KC TCGA-FV-A3I1 
       79.07        72.39        80.71        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        20.78        15.65 
TCGA-G3-AAV3 TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-K7-AAU7 TCGA-MI-A75G TCGA-MI-A75I 
       13.55        11.87         1.02        11.80        22.95        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        49.84        47.74 
TCGA-2Y-A9H5 TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA 
       18.25        11.74        38.40        20.81        22.92         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        17.10        14.76 
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         4.24         2.86         3.19         3.39         4.24 
TCGA-CC-5264 TCGA-CC-A3M9 TCGA-CC-A3MB TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A7IE 
        3.35         9.86        10.36        11.41         9.99         7.13 
TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A8HU 
       21.34         9.83        12.00        13.12        12.56        11.31 
TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 
        6.94         8.15        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        29.92        26.93 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY 
       28.08        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-A7M5 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-A7M9 
       17.10        22.06        14.70        11.87        14.14         1.84 
TCGA-G3-AAUZ TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 
       15.78        11.80        12.23         0.89         8.75         2.14 
TCGA-GJ-A3OU TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG 
       22.92         2.20         2.99        37.71        20.75        17.06 
TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG 
       16.83         2.14        21.60        31.27        29.79        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        24.56         7.53 
TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SB 
       58.88        26.27        17.69         3.09        21.04        19.33 
TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC 
       19.04        15.39        36.10        17.59        19.76        16.44 
TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-A7MF TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-A9G7 
        1.71        15.98         7.04        10.32        11.34         0.99 
TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TF TCGA-YA-A8S7 
       12.99        20.22        24.85        18.28        22.78        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        35.87        25.15        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 
                          0.26                           0.03 
  DEL PEAK 19(12P12.1) MUTATED DEL PEAK 19(12P12.1) WILD-TYPE 
                         80.71                         120.82 
  DEL PEAK 19(12P12.1) MUTATED DEL PEAK 19(12P12.1) WILD-TYPE 
                        16.815                         19.890 
[1] "0.3 - 80.7 (16.8)"  "0.0 - 120.8 (19.9)"
[1] "hr=" "1.2"
D48V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IIIA
  DEL PEAK 19(12P12.1) MUTATED        30       18         1         10
  DEL PEAK 19(12P12.1) WILD-TYPE     141       67         2         50
                                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                            141
  STAGE II                             18                             67
  STAGE III                             1                              2
  STAGE IIIA                           10                             50
  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  23  15   3
  DEL PEAK 19(12P12.1) WILD-TYPE   149  69  59   9
D48V4, multiclass
       clus
vv      DEL PEAK 19(12P12.1) MUTATED DEL PEAK 19(12P12.1) WILD-TYPE
  T0+T1                           33                            149
  T2                              23                             69
  T3                              15                             59
  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    51   2
  DEL PEAK 19(12P12.1) WILD-TYPE 199   1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(12P12.1) MUTATED     51    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                           51                            199
  1                            2                              1
[1] 2 2
[1] FALSE
D48V6, binary
                                cls
clus                               0   1
  DEL PEAK 19(12P12.1) MUTATED    56   2
  DEL PEAK 19(12P12.1) WILD-TYPE 205   2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(12P12.1) MUTATED     56    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                           56                            205
  1                            2                              2
[1] 2 2
[1] FALSE
D48V7, binary
                                cls
clus                               0   1
  DEL PEAK 19(12P12.1) MUTATED    22  52
  DEL PEAK 19(12P12.1) WILD-TYPE  93 195
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(12P12.1) MUTATED     22   52
  DEL PEAK 19(12P12.1) WILD-TYPE   93  195
        clus
vv       DEL PEAK 19(12P12.1) MUTATED DEL PEAK 19(12P12.1) WILD-TYPE
  FEMALE                           22                             93
  MALE                             52                            195
[1] 2 2
[1] FALSE
D48V8, binary
                                cls
clus                               0   1
  DEL PEAK 19(12P12.1) MUTATED    69   0
  DEL PEAK 19(12P12.1) WILD-TYPE 267   7
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(12P12.1) MUTATED     69    0
  DEL PEAK 19(12P12.1) WILD-TYPE  267    7
     clus
vv    DEL PEAK 19(12P12.1) MUTATED DEL PEAK 19(12P12.1) WILD-TYPE
  NO                            69                            267
  YES                            0                              7
[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                         72
  DEL PEAK 19(12P12.1) WILD-TYPE                      281
                                vv
clus                             HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK 19(12P12.1) MUTATED                                  1
  DEL PEAK 19(12P12.1) WILD-TYPE                                6
D48V9, multiclass
                                  clus
vv                                 DEL PEAK 19(12P12.1) MUTATED
  FIBROLAMELLAR CARCINOMA                                     1
  HEPATOCELLULAR CARCINOMA                                   72
  HEPATOCHOLANGIOCARCINOMA (MIXED)                            1
                                  clus
vv                                 DEL PEAK 19(12P12.1) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                       1
  HEPATOCELLULAR CARCINOMA                                    281
  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    61   4   1   6
  DEL PEAK 19(12P12.1) WILD-TYPE 257  11   0  15
D48V10, multiclass
    clus
vv   DEL PEAK 19(12P12.1) MUTATED DEL PEAK 19(12P12.1) WILD-TYPE
  R0                           61                            257
  R1                            4                             11
  R2                            1                              0
  RX                            6                             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 19(12P12.1) MUTATED                                  0    34
  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   145
D48V11, multiclass
                                  clus
vv                                 DEL PEAK 19(12P12.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                      34
  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                                                       145
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V12, binary
                                cls
clus                               0   1
  DEL PEAK 19(12P12.1) MUTATED     3  65
  DEL PEAK 19(12P12.1) WILD-TYPE  10 267
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(12P12.1) MUTATED      3   65
  DEL PEAK 19(12P12.1) WILD-TYPE   10  267
                        clus
vv                       DEL PEAK 19(12P12.1) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           65
                        clus
vv                       DEL PEAK 19(12P12.1) WILD-TYPE
  HISPANIC OR LATINO                                 10
  NOT HISPANIC OR LATINO                            267
[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    27  25
  DEL PEAK 20(12Q24.33) WILD-TYPE 202 104
  DEL PEAK 20(12Q24.33) MUTATED DEL PEAK 20(12Q24.33) WILD-TYPE 
                             52                             306 
  DEL PEAK 20(12Q24.33) MUTATED DEL PEAK 20(12Q24.33) WILD-TYPE 
                             25                             104 
$`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        45.93 
TCGA-BC-A5W4 TCGA-CC-5260 TCGA-CC-A1HT TCGA-CC-A3MA TCGA-CC-A3MC TCGA-CC-A5UD 
       17.98         2.86         3.32         9.96        11.93         9.99 
TCGA-CC-A5UE TCGA-CC-A7IL TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EL TCGA-DD-A39X 
        8.94         9.14        45.11        49.15        13.64        55.69 
TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A5 TCGA-DD-A3A9 TCGA-DD-A4NI TCGA-DD-A4NJ 
       19.76        25.81       102.74        30.61        26.83        30.51 
TCGA-DD-A4NO TCGA-DD-AAC8 TCGA-DD-AACA TCGA-DD-AACE TCGA-DD-AACG TCGA-DD-AACN 
       73.81         0.53        75.65        63.48        15.42        42.81 
TCGA-DD-AACU TCGA-DD-AAD3 TCGA-DD-AAD8 TCGA-DD-AADF TCGA-DD-AADM TCGA-DD-AADY 
       51.52        42.58        40.08         3.78         0.39        18.25 
TCGA-DD-AAE3 TCGA-DD-AAEK TCGA-DD-AAVU TCGA-ED-A459 TCGA-ED-A82E TCGA-ED-A97K 
       18.61        35.08        72.39        29.92        13.41         0.20 
TCGA-EP-A2KC TCGA-FV-A3I1 TCGA-FV-A496 TCGA-G3-A25W TCGA-G3-A25Y TCGA-MI-A75G 
        0.62         8.12         0.33        30.74        14.86        22.95 
TCGA-NI-A8LF TCGA-RC-A7SB TCGA-RC-A7SK TCGA-ZP-A9D1 
       26.27        19.33        15.52         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        49.84        47.74        18.25        11.74 
TCGA-2Y-A9H7 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-4R-AA8I TCGA-5C-A9VG 
       38.40        22.92         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        17.10        14.76         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        23.38         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         4.24         3.19 
TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-5264 TCGA-CC-A3M9 TCGA-CC-A3MB TCGA-CC-A5UC 
        3.39         4.24         3.35         9.86        10.36        11.41 
TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IJ 
        7.13        21.34         9.83        12.00        13.12        12.56 
TCGA-CC-A7IK TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FS TCGA-CC-A9FW 
        8.61         4.60        11.31         9.17         6.94         8.15 
TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 
       79.73        37.78        83.57        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-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EI 
       66.31        19.79        75.65        11.47        12.95         6.02 
TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39Y TCGA-DD-A3A1 
       33.04        18.35        21.14        27.19         5.62         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-A4ND TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NK 
       33.14        32.52        90.28        30.97        30.15        39.78 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS 
       56.25        29.56       108.76        12.26         0.30        80.75 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E 
       78.84        23.93         9.30        23.05        22.78         1.45 
TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC9 TCGA-DD-AACB TCGA-DD-AACC 
       35.67       114.35        13.48        11.41        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-AACY TCGA-DD-AACZ 
       51.35        50.33        46.82         5.59        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-AADG TCGA-DD-AADI 
       40.83        13.97        40.47        39.52        37.64        35.67 
TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP 
       35.05        34.49        20.91        29.52        14.89        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        26.63 
TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR 
       23.64        25.78        50.33        79.07        89.69        82.62 
TCGA-DD-AAVS TCGA-DD-AAVV TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ 
       59.93        80.71        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        26.93        28.08 
TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ 
       13.91        13.35         9.73         0.20        12.82         0.20 
TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-EP-A12J TCGA-EP-A26S 
       14.04        13.15        13.35         1.84        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-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R2 TCGA-FV-A3R3 
       60.89        23.97        19.10        27.88         6.38        12.03 
TCGA-FV-A495 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U 
        0.03        81.73         0.39        13.68        51.06        53.79 
TCGA-G3-A25V TCGA-G3-A25X TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI 
       28.27        58.49        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-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-A7M9 
       22.06        14.70        20.78        11.87        14.14         1.84 
TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 
       15.78        15.65        11.80        12.23        13.55         0.89 
TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB 
        8.75         2.14        11.87        22.92         1.02         2.20 
TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 
        2.99        37.71        20.75        17.06        16.83        11.80 
TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC 
        2.14        21.60        31.27        29.79        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        24.56        20.71         7.53 
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        36.10         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-AA44 TCGA-WX-AA46 TCGA-WX-AA47 
       11.34         0.99        12.99        20.22        24.85        18.28 
TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 
       22.78        13.55        35.77        25.71        23.21        35.87 
TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       25.15        12.99        45.57        40.80        79.30        11.21 

  DEL PEAK 20(12Q24.33) MUTATED DEL PEAK 20(12Q24.33) WILD-TYPE 
                           0.20                            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 
                         20.285                          19.675 
[1] "0.2 - 102.7 (20.3)" "0.0 - 120.8 (19.7)"
[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     151       70         1         51
                                 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                             151
  STAGE II                              15                              70
  STAGE III                              2                               1
  STAGE IIIA                             9                              51
  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   160  76  61   9
D49V4, multiclass
       clus
vv      DEL PEAK 20(12Q24.33) MUTATED DEL PEAK 20(12Q24.33) WILD-TYPE
  T0+T1                            22                             160
  T2                               16                              76
  T3                               13                              61
  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 210   3
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 20(12Q24.33) MUTATED     40    0
  DEL PEAK 20(12Q24.33) WILD-TYPE  210    3
   clus
vv  DEL PEAK 20(12Q24.33) MUTATED DEL PEAK 20(12Q24.33) WILD-TYPE
  0                            40                             210
  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 218   2
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 20(12Q24.33) MUTATED     43    2
  DEL PEAK 20(12Q24.33) WILD-TYPE  218    2
   clus
vv  DEL PEAK 20(12Q24.33) MUTATED DEL PEAK 20(12Q24.33) WILD-TYPE
  0                            43                             218
  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  94 214
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 20(12Q24.33) MUTATED     21   33
  DEL PEAK 20(12Q24.33) WILD-TYPE   94  214
        clus
vv       DEL PEAK 20(12Q24.33) MUTATED DEL PEAK 20(12Q24.33) WILD-TYPE
  FEMALE                            21                              94
  MALE                              33                             214
[1] 2 2
[1] FALSE
D49V8, binary
                                 cls
clus                                0   1
  DEL PEAK 20(12Q24.33) MUTATED    49   1
  DEL PEAK 20(12Q24.33) WILD-TYPE 287   6
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 20(12Q24.33) MUTATED     49    1
  DEL PEAK 20(12Q24.33) WILD-TYPE  287    6
     clus
vv    DEL PEAK 20(12Q24.33) MUTATED DEL PEAK 20(12Q24.33) WILD-TYPE
  NO                             49                             287
  YES                             1                               6
[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                      300
                                 vv
clus                              HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK 20(12Q24.33) MUTATED                                  1
  DEL PEAK 20(12Q24.33) WILD-TYPE                                6
D49V9, 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                                     300
  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 269  14   1  18
D49V10, multiclass
    clus
vv   DEL PEAK 20(12Q24.33) MUTATED DEL PEAK 20(12Q24.33) WILD-TYPE
  R0                            49                             269
  R1                             1                              14
  R2                             0                               1
  RX                             3                              18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 20(12Q24.33) MUTATED                                  0    28
  DEL PEAK 20(12Q24.33) WILD-TYPE                                1   129
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 20(12Q24.33) MUTATED                           3    22
  DEL PEAK 20(12Q24.33) WILD-TYPE                        14   155
D49V11, 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                                                        129
  BLACK OR AFRICAN AMERICAN                                     14
  WHITE                                                        155
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V12, binary
                                 cls
clus                                0   1
  DEL PEAK 20(12Q24.33) MUTATED     2  50
  DEL PEAK 20(12Q24.33) WILD-TYPE  11 282
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 20(12Q24.33) MUTATED      2   50
  DEL PEAK 20(12Q24.33) WILD-TYPE   11  282
                        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                                  11
  NOT HISPANIC OR LATINO                             282
[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   101  71
  DEL PEAK 21(13Q14.2) WILD-TYPE 128  58
  DEL PEAK 21(13Q14.2) MUTATED DEL PEAK 21(13Q14.2) WILD-TYPE 
                           172                            186 
  DEL PEAK 21(13Q14.2) MUTATED DEL PEAK 21(13Q14.2) WILD-TYPE 
                            71                             58 
$`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 
       23.38         1.12         5.03        45.93         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         4.24         2.86 
TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-5264 TCGA-CC-A1HT TCGA-CC-A3M9 
        3.19         3.39         4.24         3.35         3.32         9.86 
TCGA-CC-A3MA TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A5UE TCGA-CC-A7IF TCGA-CC-A7IG 
        9.96        11.93        11.41         8.94        21.34         9.83 
TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A7IL TCGA-CC-A8HU TCGA-CC-A8HV 
       13.12        12.56         8.61         9.14        11.31         9.17 
TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 
        6.94         8.15        79.73        37.78        83.57        53.33 
TCGA-DD-A118 TCGA-DD-A11A TCGA-DD-A11C TCGA-DD-A1EF TCGA-DD-A1EI TCGA-DD-A1EK 
      113.00         2.60        21.76        12.95         6.02        18.35 
TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A3A0 TCGA-DD-A3A5 TCGA-DD-A3A9 TCGA-DD-A4NA 
       55.69         5.62        25.81       102.74        30.61        33.14 
TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NQ TCGA-DD-A4NR 
       30.15        30.51        29.56        73.81        12.26         0.30 
TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AACF 
        1.45        35.67       114.35        13.48         0.53        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-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-AAD1 TCGA-DD-AAD8 TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADF TCGA-DD-AADI 
       18.54        40.08        13.97        40.47         3.78        35.67 
TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADO TCGA-DD-AADR TCGA-DD-AADV 
       34.49        20.91         0.39        14.89        66.67        18.87 
TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 
       19.30        18.25        18.25        20.98        18.61        19.99 
TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEI 
       21.83        18.90        25.08        26.63        23.64        50.33 
TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVV TCGA-ED-A459 TCGA-ED-A4XI 
       35.08        79.07        89.69        80.71        29.92        26.93 
TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-EP-A3RK 
        9.73         0.20         0.20        14.04        13.15        11.93 
TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A495 TCGA-G3-A25S TCGA-G3-A25T 
       27.88         8.12         6.38         0.03        13.68        51.06 
TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A3CH TCGA-G3-A5SI TCGA-G3-A5SM TCGA-G3-A7M5 
       58.49        14.86        25.64        25.25        17.10        14.70 
TCGA-G3-A7M6 TCGA-G3-AAUZ TCGA-G3-AAV4 TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 
       20.78        15.78         0.89        11.87        22.92         1.02 
TCGA-GJ-A9DB TCGA-K7-A5RG TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-MI-A75G TCGA-MI-A75I 
        2.20        17.06        21.60        29.79        22.95        20.71 
TCGA-MR-A8JO TCGA-NI-A8LF TCGA-PD-A5DF TCGA-RC-A7S9 TCGA-RC-A7SF TCGA-RC-A7SH 
       10.85        26.27        21.01        21.04        19.04        15.39 
TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MC TCGA-UB-A7MF TCGA-UB-AA0U 
       15.52        36.10        17.59        16.44         7.04        10.75 
TCGA-WJ-A86L TCGA-WX-AA44 TCGA-WX-AA47 TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CY 
       11.34        20.22        18.28        22.78        13.55        25.71 
TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZS-A9CE TCGA-ZS-A9CG 
       23.21        35.87        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        49.84 
TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-2Y-A9H9 TCGA-2Y-A9HB TCGA-5C-AAPD TCGA-5R-AA1C 
       11.74        38.40        22.92         8.55         0.66        17.10 
TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10S TCGA-BC-A10U 
       14.76         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-CC-A5UD TCGA-CC-A7IE TCGA-CC-A7IH TCGA-CC-A8HT 
       36.66        10.36         9.99         7.13        12.00         4.60 
TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB 
        7.33         0.46        51.29        90.71        79.40        66.31 
TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EJ 
       19.79        75.65        11.47        45.11        49.15        33.04 
TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39Z TCGA-DD-A3A1 TCGA-DD-A3A2 
       13.64        21.14        27.19        19.76         7.66        70.06 
TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A4NB 
       17.59        20.12       107.11        13.78         0.36        32.52 
TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NI TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NP 
       90.28        30.97        26.83        39.78        56.25       108.76 
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-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-AACJ TCGA-DD-AACK TCGA-DD-AACT TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY 
       69.11         0.30        51.35        46.82         5.59        47.67 
TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 
        5.62         4.50        21.63        42.58        44.22        22.09 
TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADE TCGA-DD-AADG TCGA-DD-AADJ TCGA-DD-AADN 
       40.54        40.83        39.52        37.64        35.05        29.52 
TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AAE1 TCGA-DD-AAE6 
       15.06        14.33        15.58        18.21        18.15         4.64 
TCGA-DD-AAE7 TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAEH TCGA-DD-AAVR TCGA-DD-AAVS 
       21.17        23.74        15.72        25.78        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-A5KG TCGA-ED-A627 TCGA-ED-A66X 
       65.39        49.48        53.69        28.08        13.91        13.35 
TCGA-ED-A7PY TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J 
       12.82        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-ES-A2HS 
       19.99        20.61        19.59         0.62         9.96        22.85 
TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3R3 TCGA-FV-A496 
       14.40        60.89        23.97        19.10        12.03         0.33 
TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Z 
       81.73         0.39        53.79        28.27        30.74        21.53 
TCGA-G3-A3CG TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SJ TCGA-G3-A5SL 
       22.13         5.92        19.53        19.23        22.95        20.42 
TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-A7M9 TCGA-G3-AAV0 TCGA-G3-AAV1 
       22.06        11.87        14.14         1.84        15.65        11.80 
TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-HP-A5MZ TCGA-HP-A5N0 
       12.23        13.55         8.75         2.14         2.99        37.71 
TCGA-K7-A5RF TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG 
       20.75        16.83        11.80         2.14        31.27        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        24.56         7.53 
TCGA-NI-A4U2 TCGA-O8-A75V TCGA-QA-A7B7 TCGA-RC-A7SB TCGA-T1-A6J8 TCGA-UB-A7MB 
       58.88        17.69         3.09        19.33         0.76        19.76 
TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0V TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA46 
        1.71        15.98        10.32         0.99        12.99        24.85 
TCGA-ZP-A9CV TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CF 
       35.77         0.69        25.15        12.99        45.57        79.30 

  DEL PEAK 21(13Q14.2) MUTATED DEL PEAK 21(13Q14.2) WILD-TYPE 
                          0.03                           0.20 
  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 
                        18.315                         21.155 
[1] "0.0 - 120.8 (18.3)" "0.2 - 108.8 (21.2)"
[1] "hr=" "1.5"
D50V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IIIA
  DEL PEAK 21(13Q14.2) MUTATED        74       49         1         29
  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                              74                             97
  STAGE II                             49                             36
  STAGE III                             1                              2
  STAGE IIIA                           29                             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      78  52  34  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                           78                            104
  T2                              52                             40
  T3                              34                             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   124   1
  DEL PEAK 21(13Q14.2) WILD-TYPE 126   2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(13Q14.2) MUTATED    124    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                          124                            126
  1                            1                              2
[1] 2 2
[1] FALSE
D50V6, binary
                                cls
clus                               0   1
  DEL PEAK 21(13Q14.2) MUTATED   126   2
  DEL PEAK 21(13Q14.2) WILD-TYPE 135   2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(13Q14.2) MUTATED    126    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                          126                            135
  1                            2                              2
[1] 2 2
[1] FALSE
D50V7, binary
                                cls
clus                               0   1
  DEL PEAK 21(13Q14.2) MUTATED    62 112
  DEL PEAK 21(13Q14.2) WILD-TYPE  53 135
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(13Q14.2) MUTATED     62  112
  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                           62                             53
  MALE                            112                            135
[1] 2 2
[1] FALSE
D50V8, binary
                                cls
clus                               0   1
  DEL PEAK 21(13Q14.2) MUTATED   162   4
  DEL PEAK 21(13Q14.2) WILD-TYPE 174   3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(13Q14.2) MUTATED    162    4
  DEL PEAK 21(13Q14.2) WILD-TYPE  174    3
     clus
vv    DEL PEAK 21(13Q14.2) MUTATED DEL PEAK 21(13Q14.2) WILD-TYPE
  NO                           162                            174
  YES                            4                              3
[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                        169
  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
D50V9, multiclass
                                  clus
vv                                 DEL PEAK 21(13Q14.2) MUTATED
  FIBROLAMELLAR CARCINOMA                                     1
  HEPATOCELLULAR CARCINOMA                                  169
  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   149   8   0  13
  DEL PEAK 21(13Q14.2) WILD-TYPE 169   7   1   8
D50V10, multiclass
    clus
vv   DEL PEAK 21(13Q14.2) MUTATED DEL PEAK 21(13Q14.2) WILD-TYPE
  R0                          149                            169
  R1                            8                              7
  R2                            0                              1
  RX                           13                              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    87
  DEL PEAK 21(13Q14.2) WILD-TYPE                                1    70
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 21(13Q14.2) MUTATED                           9    76
  DEL PEAK 21(13Q14.2) WILD-TYPE                         8   101
D50V11, multiclass
                                  clus
vv                                 DEL PEAK 21(13Q14.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                      87
  BLACK OR AFRICAN AMERICAN                                   9
  WHITE                                                      76
                                  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"
D50V12, binary
                                cls
clus                               0   1
  DEL PEAK 21(13Q14.2) MUTATED     7 161
  DEL PEAK 21(13Q14.2) WILD-TYPE   6 171
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(13Q14.2) MUTATED      7  161
  DEL PEAK 21(13Q14.2) WILD-TYPE    6  171
                        clus
vv                       DEL PEAK 21(13Q14.2) MUTATED
  HISPANIC OR LATINO                                7
  NOT HISPANIC OR LATINO                          161
                        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  49
  DEL PEAK 22(14Q23.3) WILD-TYPE 152  80
  DEL PEAK 22(14Q23.3) MUTATED DEL PEAK 22(14Q23.3) WILD-TYPE 
                           126                            232 
  DEL PEAK 22(14Q23.3) MUTATED DEL PEAK 22(14Q23.3) WILD-TYPE 
                            49                             80 
$`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        49.84 
TCGA-2Y-A9H4 TCGA-2Y-A9H9 TCGA-5C-A9VG TCGA-5C-AAPD TCGA-BC-4073 TCGA-BC-A10Q 
       47.74        22.92        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-5264 TCGA-CC-A1HT TCGA-CC-A3MA 
        4.24         2.86         3.19         3.35         3.32         9.96 
TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IG TCGA-CC-A7II 
       10.36        11.93         8.94         7.13         9.83        13.12 
TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV TCGA-DD-A113 
       12.56         8.61         4.60        11.31         9.17        79.73 
TCGA-DD-A115 TCGA-DD-A118 TCGA-DD-A11A TCGA-DD-A11C TCGA-DD-A1E9 TCGA-DD-A1EG 
       83.57       113.00         2.60        21.76        90.71        45.11 
TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A3A1 
        6.02        33.04        13.64        55.69         5.62         7.66 
TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NB TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NO 
       13.78        30.61        32.52        30.15        26.83        73.81 
TCGA-DD-A4NQ TCGA-DD-A73F TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AACA TCGA-DD-AACE 
       12.26        35.67        13.48         0.53        75.65        63.48 
TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACN TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACV 
       15.42         6.41        42.81        59.31        51.52        50.33 
TCGA-DD-AACX TCGA-DD-AACZ TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AADB TCGA-DD-AADD 
        5.59         5.62        44.22        22.09        40.83        40.47 
TCGA-DD-AADF TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADR 
        3.78        20.91         0.39        29.52        14.89        66.67 
TCGA-DD-AADV TCGA-DD-AADW TCGA-DD-AAE0 TCGA-DD-AAE3 TCGA-DD-AAE6 TCGA-DD-AAE8 
       18.87        19.30        18.25        18.61         4.64        21.83 
TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAVP TCGA-DD-AAVU TCGA-DD-AAVV 
       25.08        26.63        23.64        79.07        72.39        80.71 
TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A7PX TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-ED-A82E 
       53.69        29.92         0.20         0.20        13.15        13.41 
TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A2KB TCGA-EP-A3RK TCGA-FV-A3I0 
        1.84         0.20        18.74        19.59        11.93        27.88 
TCGA-FV-A4ZP TCGA-G3-A25S TCGA-G3-A25X TCGA-G3-A3CH TCGA-G3-A5SM TCGA-G3-A7M9 
       81.73        13.68        58.49        25.64        17.10         1.84 
TCGA-G3-AAV1 TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-K7-A5RG TCGA-KR-A7K7 TCGA-NI-A8LF 
       11.80        11.87         1.02        17.06        31.27        26.27 
TCGA-PD-A5DF TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MC 
       21.01        19.04        15.39        15.52        36.10        16.44 
TCGA-UB-A7MF TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-XR-A8TF TCGA-ZP-A9D2 
        7.04         0.99        12.99        20.22        22.78        25.15 

$`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        38.40        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        17.10        14.76         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        23.38        69.57        45.93        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-CC-A5UC TCGA-CC-A5UD TCGA-CC-A7IF TCGA-CC-A7IH 
        4.24         9.86        11.41         9.99        21.34        12.00 
TCGA-CC-A7IL TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A114 TCGA-DD-A116 TCGA-DD-A119 
        9.14         6.94         8.15        37.78        53.33         7.33 
TCGA-DD-A11B TCGA-DD-A11D TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED 
        0.46        51.29        79.40        66.31        19.79        75.65 
TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EK TCGA-DD-A39V TCGA-DD-A39W 
       11.47        12.95        49.15        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-A4NJ 
      107.11         0.36        33.14        90.28        30.97        30.51 
TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NP TCGA-DD-A4NR TCGA-DD-A4NS 
       39.78        56.25        29.56       108.76         0.30        80.75 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E 
       78.84        23.93         9.30        23.05        22.78         1.45 
TCGA-DD-A73G TCGA-DD-AAC9 TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACF 
      114.35        11.41        76.41        55.40        12.53        12.00 
TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACO 
       53.19        69.11         0.30         3.52        58.16        61.68 
TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACT TCGA-DD-AACW TCGA-DD-AACY TCGA-DD-AAD0 
       13.64        14.20        51.35        46.82        47.67         4.50 
TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADC 
       18.54        21.63        42.58        40.08        40.54        13.97 
TCGA-DD-AADE TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADP 
       39.52        37.64        35.67        35.05        34.49        15.06 
TCGA-DD-AADQ TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADY TCGA-DD-AAE1 TCGA-DD-AAE2 
       14.33        15.58        18.21        18.25        18.15        20.98 
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-AAEK TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVW 
       50.33        35.08        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-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PY 
       26.93        28.08        13.91        13.35         9.73        12.82 
TCGA-ED-A7XO TCGA-ED-A8O5 TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3JL 
       14.04        13.35        19.99        20.61         0.62         9.96 
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-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25T 
        6.38        12.03         0.03         0.33         0.39        51.06 
TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG 
       53.79        28.27        30.74        14.86        21.53        22.13 
TCGA-G3-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-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ 
       22.06        14.70        20.78        11.87        14.14        15.78 
TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 
       15.65        12.23        13.55         0.89         8.75         2.14 
TCGA-GJ-A3OU TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A6G5 
       22.92         2.20         2.99        37.71        20.75        16.83 
TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC 
       11.80         2.14        21.60        29.79        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        22.95        24.56        20.71 
TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-O8-A75V TCGA-QA-A7B7 TCGA-RC-A7S9 
        7.53        10.85        58.88        17.69         3.09        21.04 
TCGA-RC-A7SB TCGA-T1-A6J8 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MD TCGA-UB-A7ME 
       19.33         0.76        17.59        19.76         1.71        15.98 
TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WX-AA46 TCGA-WX-AA47 TCGA-YA-A8S7 
       10.75        10.32        11.34        24.85        18.28        13.55 
TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D4 
       35.77        25.71        23.21        35.87         0.69        12.99 
TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       45.57        40.80        79.30        11.21 

  DEL PEAK 22(14Q23.3) MUTATED DEL PEAK 22(14Q23.3) WILD-TYPE 
                          0.20                           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 
                        18.805                         20.055 
[1] "0.2 - 113.0 (18.8)" "0.0 - 120.8 (20.1)"
[1] "hr=" "1.2"
D51V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IIIA
  DEL PEAK 22(14Q23.3) MUTATED        55       34         0         25
  DEL PEAK 22(14Q23.3) WILD-TYPE     116       51         3         35
                                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                              55                            116
  STAGE II                             34                             51
  STAGE III                             0                              3
  STAGE IIIA                           25                             35
  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      56  38  30   5
  DEL PEAK 22(14Q23.3) WILD-TYPE   126  54  44   7
D51V4, multiclass
       clus
vv      DEL PEAK 22(14Q23.3) MUTATED DEL PEAK 22(14Q23.3) WILD-TYPE
  T0+T1                           56                            126
  T2                              38                             54
  T3                              30                             44
  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    96   1
  DEL PEAK 22(14Q23.3) WILD-TYPE 154   2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 22(14Q23.3) MUTATED     96    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                           96                            154
  1                            1                              2
[1] 2 2
[1] FALSE
D51V6, binary
                                cls
clus                               0   1
  DEL PEAK 22(14Q23.3) MUTATED   100   2
  DEL PEAK 22(14Q23.3) WILD-TYPE 161   2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 22(14Q23.3) MUTATED    100    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                          100                            161
  1                            2                              2
[1] 2 2
[1] FALSE
D51V7, binary
                                cls
clus                               0   1
  DEL PEAK 22(14Q23.3) MUTATED    37  92
  DEL PEAK 22(14Q23.3) WILD-TYPE  78 155
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 22(14Q23.3) MUTATED     37   92
  DEL PEAK 22(14Q23.3) WILD-TYPE   78  155
        clus
vv       DEL PEAK 22(14Q23.3) MUTATED DEL PEAK 22(14Q23.3) WILD-TYPE
  FEMALE                           37                             78
  MALE                             92                            155
[1] 2 2
[1] FALSE
D51V8, binary
                                cls
clus                               0   1
  DEL PEAK 22(14Q23.3) MUTATED   121   2
  DEL PEAK 22(14Q23.3) WILD-TYPE 215   5
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 22(14Q23.3) MUTATED    121    2
  DEL PEAK 22(14Q23.3) WILD-TYPE  215    5
     clus
vv    DEL PEAK 22(14Q23.3) MUTATED DEL PEAK 22(14Q23.3) WILD-TYPE
  NO                           121                            215
  YES                            2                              5
[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                        124
  DEL PEAK 22(14Q23.3) WILD-TYPE                      229
                                vv
clus                             HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK 22(14Q23.3) MUTATED                                  4
  DEL PEAK 22(14Q23.3) WILD-TYPE                                3
D51V9, multiclass
                                  clus
vv                                 DEL PEAK 22(14Q23.3) MUTATED
  FIBROLAMELLAR CARCINOMA                                     1
  HEPATOCELLULAR CARCINOMA                                  124
  HEPATOCHOLANGIOCARCINOMA (MIXED)                            4
                                  clus
vv                                 DEL PEAK 22(14Q23.3) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                       1
  HEPATOCELLULAR CARCINOMA                                    229
  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   112   5   0   9
  DEL PEAK 22(14Q23.3) WILD-TYPE 206  10   1  12
D51V10, multiclass
    clus
vv   DEL PEAK 22(14Q23.3) MUTATED DEL PEAK 22(14Q23.3) WILD-TYPE
  R0                          112                            206
  R1                            5                             10
  R2                            0                              1
  RX                            9                             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 22(14Q23.3) MUTATED                                  0    69
  DEL PEAK 22(14Q23.3) WILD-TYPE                                1    88
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 22(14Q23.3) MUTATED                           7    51
  DEL PEAK 22(14Q23.3) WILD-TYPE                        10   126
D51V11, multiclass
                                  clus
vv                                 DEL PEAK 22(14Q23.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                      69
  BLACK OR AFRICAN AMERICAN                                   7
  WHITE                                                      51
                                  clus
vv                                 DEL PEAK 22(14Q23.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        88
  BLACK OR AFRICAN AMERICAN                                    10
  WHITE                                                       126
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V12, binary
                                cls
clus                               0   1
  DEL PEAK 22(14Q23.3) MUTATED     6 117
  DEL PEAK 22(14Q23.3) WILD-TYPE   7 215
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 22(14Q23.3) MUTATED      6  117
  DEL PEAK 22(14Q23.3) WILD-TYPE    7  215
                        clus
vv                       DEL PEAK 22(14Q23.3) MUTATED
  HISPANIC OR LATINO                                6
  NOT HISPANIC OR LATINO                          117
                        clus
vv                       DEL PEAK 22(14Q23.3) WILD-TYPE
  HISPANIC OR LATINO                                  7
  NOT HISPANIC OR LATINO                            215
[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    82  46
  DEL PEAK 23(14Q32.33) WILD-TYPE 147  83
  DEL PEAK 23(14Q32.33) MUTATED DEL PEAK 23(14Q32.33) WILD-TYPE 
                            128                             230 
  DEL PEAK 23(14Q32.33) MUTATED DEL PEAK 23(14Q32.33) WILD-TYPE 
                             46                              83 
$`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        49.84 
TCGA-2Y-A9H4 TCGA-2Y-A9H6 TCGA-2Y-A9H9 TCGA-5C-A9VG TCGA-5C-AAPD TCGA-BC-A10Q 
       47.74        11.74        22.92        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        45.93         0.26 
TCGA-BC-A3KG TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5264 TCGA-CC-A1HT 
       22.36         4.24         2.86         3.19         3.35         3.32 
TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UE TCGA-CC-A7II TCGA-CC-A7IJ 
        9.96        10.36        11.93         8.94        13.12        12.56 
TCGA-CC-A7IK TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV TCGA-DD-A113 TCGA-DD-A115 
        8.61         4.60        11.31         9.17        79.73        83.57 
TCGA-DD-A11A TCGA-DD-A11C TCGA-DD-A1E9 TCGA-DD-A1EG TCGA-DD-A1EJ TCGA-DD-A1EL 
        2.60        21.76        90.71        45.11        33.04        13.64 
TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A3A1 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NB 
       55.69         5.62         7.66        13.78        30.61        32.52 
TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NO TCGA-DD-A4NQ TCGA-DD-A73G 
       30.15        26.83        30.51        73.81        12.26       114.35 
TCGA-DD-AA3A TCGA-DD-AACA TCGA-DD-AACE TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI 
       13.48        75.65        63.48        15.42         6.41        53.19 
TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACX TCGA-DD-AACZ 
       42.81        61.68        59.31        51.52         5.59         5.62 
TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AADB TCGA-DD-AADD TCGA-DD-AADF TCGA-DD-AADL 
       44.22        22.09        40.83        40.47         3.78        20.91 
TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADR TCGA-DD-AADV TCGA-DD-AADW 
        0.39        29.52        14.89        66.67        18.87        19.30 
TCGA-DD-AAE0 TCGA-DD-AAE6 TCGA-DD-AAE8 TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEG 
       18.25         4.64        21.83        25.08        26.63        23.64 
TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVU TCGA-DD-AAVV TCGA-DD-AAW3 TCGA-ED-A459 
       35.08        79.07        72.39        80.71        53.69        29.92 
TCGA-ED-A7PX TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O6 TCGA-ED-A97K 
        0.20         0.20        13.15        13.41         1.84         0.20 
TCGA-EP-A12J TCGA-EP-A2KB TCGA-EP-A3RK TCGA-FV-A3I0 TCGA-FV-A495 TCGA-FV-A4ZP 
       18.74        19.59        11.93        27.88         0.03        81.73 
TCGA-G3-A25S TCGA-G3-A25X TCGA-G3-A3CH TCGA-G3-A5SM TCGA-G3-A7M9 TCGA-G3-AAV1 
       13.68        58.49        25.64        17.10         1.84        11.80 
TCGA-G3-AAV3 TCGA-G3-AAV7 TCGA-K7-A5RG TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-NI-A8LF 
       13.55        11.87        17.06        31.27        29.79        26.27 
TCGA-QA-A7B7 TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB 
        3.09        15.39        15.52        36.10        17.59        19.76 
TCGA-UB-A7MC TCGA-UB-A7MF TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA44 
       16.44         7.04        11.34         0.99        12.99        20.22 
TCGA-ZP-A9D0 TCGA-ZP-A9D2 
       35.87        25.15 

$`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        38.40        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        17.10        14.76         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        23.38 
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-CC-A5UC TCGA-CC-A5UD TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IG 
        9.86        11.41         9.99         7.13        21.34         9.83 
TCGA-CC-A7IH TCGA-CC-A7IL TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A114 TCGA-DD-A116 
       12.00         9.14         6.94         8.15        37.78        53.33 
TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11D TCGA-DD-A1EA TCGA-DD-A1EB 
      113.00         7.33         0.46        51.29        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-A3A2 
       18.35        21.14        27.19        19.76        25.81        70.06 
TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A8 TCGA-DD-A4NA 
       17.59        20.12       102.74       107.11         0.36        33.14 
TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NP 
       90.28        30.97        39.78        56.25        29.56       108.76 
TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C 
        0.30        80.75        78.84        23.93         9.30        23.05 
TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACB 
       22.78         1.45        35.67         0.53        11.41        76.41 
TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACF TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL 
       55.40        12.53        12.00        69.11         0.30         3.52 
TCGA-DD-AACM TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACT TCGA-DD-AACV TCGA-DD-AACW 
       58.16        13.64        14.20        51.35        50.33        46.82 
TCGA-DD-AACY TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD8 
       47.67         4.50        18.54        21.63        42.58        40.08 
TCGA-DD-AADA TCGA-DD-AADC TCGA-DD-AADE TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ 
       40.54        13.97        39.52        37.64        35.67        35.05 
TCGA-DD-AADK TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADY 
       34.49        15.06        14.33        15.58        18.21        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-AAEH TCGA-DD-AAEI TCGA-DD-AAVQ TCGA-DD-AAVR 
       18.90        15.72        25.78        50.33        89.69        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-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X 
       65.39        49.48        26.93        28.08        13.91        13.35 
TCGA-ED-A66Y TCGA-ED-A7PY TCGA-ED-A7XO TCGA-ED-A8O5 TCGA-EP-A26S TCGA-EP-A2KA 
        9.73        12.82        14.04        13.35        19.99        20.61 
TCGA-EP-A2KC TCGA-EP-A3JL TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ 
        0.62         9.96        22.85        14.40        60.89        23.97 
TCGA-FV-A2QR TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A496 TCGA-FV-A4ZQ 
       19.10         8.12         6.38        12.03         0.33         0.39 
TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z 
       51.06        53.79        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-A6UC TCGA-G3-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 
       20.42        22.06        14.70        20.78        11.87        14.14 
TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 
       15.78        15.65        12.23         0.89         8.75         2.14 
TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF 
       22.92         1.02         2.20         2.99        37.71        20.75 
TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-LG-A6GG TCGA-LG-A9QC 
       16.83        11.80         2.14        21.60        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        22.95        24.56        20.71 
TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-O8-A75V TCGA-PD-A5DF TCGA-RC-A7S9 
        7.53        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-WX-AA47 TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CV 
       10.32        24.85        18.28        22.78        13.55        35.77 
TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D1 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE 
       25.71        23.21         0.69        12.99        45.57        40.80 
TCGA-ZS-A9CF TCGA-ZS-A9CG 
       79.30        11.21 

  DEL PEAK 23(14Q32.33) MUTATED DEL PEAK 23(14Q32.33) WILD-TYPE 
                           0.03                            0.30 
  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 
                         19.085                          19.990 
[1] "0.0 - 114.3 (19.1)" "0.3 - 120.8 (20.0)"
[1] "hr=" "1.1"
D52V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE III STAGE IIIA
  DEL PEAK 23(14Q32.33) MUTATED        52       40         0         22
  DEL PEAK 23(14Q32.33) WILD-TYPE     119       45         3         38
                                 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                               52                             119
  STAGE II                              40                              45
  STAGE III                              0                               3
  STAGE IIIA                            22                              38
  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      54  44  28   5
  DEL PEAK 23(14Q32.33) WILD-TYPE   128  48  46   7
D52V4, multiclass
       clus
vv      DEL PEAK 23(14Q32.33) MUTATED DEL PEAK 23(14Q32.33) WILD-TYPE
  T0+T1                            54                             128
  T2                               44                              48
  T3                               28                              46
  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    92   1
  DEL PEAK 23(14Q32.33) WILD-TYPE 158   2
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 23(14Q32.33) MUTATED     92    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                            92                             158
  1                             1                               2
[1] 2 2
[1] FALSE
D52V6, binary
                                 cls
clus                                0   1
  DEL PEAK 23(14Q32.33) MUTATED    98   2
  DEL PEAK 23(14Q32.33) WILD-TYPE 163   2
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 23(14Q32.33) MUTATED     98    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                            98                             163
  1                             2                               2
[1] 2 2
[1] FALSE
D52V7, binary
                                 cls
clus                                0   1
  DEL PEAK 23(14Q32.33) MUTATED    41  90
  DEL PEAK 23(14Q32.33) WILD-TYPE  74 157
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 23(14Q32.33) MUTATED     41   90
  DEL PEAK 23(14Q32.33) WILD-TYPE   74  157
        clus
vv       DEL PEAK 23(14Q32.33) MUTATED DEL PEAK 23(14Q32.33) WILD-TYPE
  FEMALE                            41                              74
  MALE                              90                             157
[1] 2 2
[1] FALSE
D52V8, binary
                                 cls
clus                                0   1
  DEL PEAK 23(14Q32.33) MUTATED   123   2
  DEL PEAK 23(14Q32.33) WILD-TYPE 213   5
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 23(14Q32.33) MUTATED    123    2
  DEL PEAK 23(14Q32.33) WILD-TYPE  213    5
     clus
vv    DEL PEAK 23(14Q32.33) MUTATED DEL PEAK 23(14Q32.33) WILD-TYPE
  NO                            123                             213
  YES                             2                               5
[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                        125
  DEL PEAK 23(14Q32.33) WILD-TYPE                      228
                                 vv
clus                              HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK 23(14Q32.33) MUTATED                                  5
  DEL PEAK 23(14Q32.33) WILD-TYPE                                2
D52V9, multiclass
                                  clus
vv                                 DEL PEAK 23(14Q32.33) MUTATED
  FIBROLAMELLAR CARCINOMA                                      1
  HEPATOCELLULAR CARCINOMA                                   125
  HEPATOCHOLANGIOCARCINOMA (MIXED)                             5
                                  clus
vv                                 DEL PEAK 23(14Q32.33) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                        1
  HEPATOCELLULAR CARCINOMA                                     228
  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   114   6   0   9
  DEL PEAK 23(14Q32.33) WILD-TYPE 204   9   1  12
D52V10, multiclass
    clus
vv   DEL PEAK 23(14Q32.33) MUTATED DEL PEAK 23(14Q32.33) WILD-TYPE
  R0                           114                             204
  R1                             6                               9
  R2                             0                               1
  RX                             9                              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 23(14Q32.33) MUTATED                                  0    65
  DEL PEAK 23(14Q32.33) WILD-TYPE                                1    92
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 23(14Q32.33) MUTATED                           8    55
  DEL PEAK 23(14Q32.33) WILD-TYPE                         9   122
D52V11, multiclass
                                  clus
vv                                 DEL PEAK 23(14Q32.33) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                       65
  BLACK OR AFRICAN AMERICAN                                    8
  WHITE                                                       55
                                  clus
vv                                 DEL PEAK 23(14Q32.33) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               1
  ASIAN                                                         92
  BLACK OR AFRICAN AMERICAN                                      9
  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"
D52V12, binary
                                 cls
clus                                0   1
  DEL PEAK 23(14Q32.33) MUTATED     5 119
  DEL PEAK 23(14Q32.33) WILD-TYPE   8 213
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 23(14Q32.33) MUTATED      5  119
  DEL PEAK 23(14Q32.33) WILD-TYPE    8  213
                        clus
vv                       DEL PEAK 23(14Q32.33) MUTATED
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                           119
                        clus
vv                       DEL PEAK 23(14Q32.33) WILD-TYPE
  HISPANIC OR LATINO                                   8
  NOT HISPANIC OR LATINO                             213
[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    40  35
  DEL PEAK 24(15Q26.3) WILD-TYPE 189  94
  DEL PEAK 24(15Q26.3) MUTATED DEL PEAK 24(15Q26.3) WILD-TYPE 
                            75                            283 
  DEL PEAK 24(15Q26.3) MUTATED DEL PEAK 24(15Q26.3) WILD-TYPE 
                            35                             94 
$`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-5264 TCGA-CC-A3MA 
       44.42        17.98        14.60         4.24         3.35         9.96 
TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A7IG TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IK 
       11.41         9.99         9.83        13.12        12.56         8.61 
TCGA-CC-A8HV TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A11C TCGA-DD-A1E9 
        9.17        79.73        37.78        83.57        21.76        90.71 
TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39Y TCGA-DD-A3A5 TCGA-DD-A4NA 
        6.02        33.04        13.64         5.62       102.74        33.14 
TCGA-DD-A4NQ TCGA-DD-A73B TCGA-DD-A73F TCGA-DD-AAC8 TCGA-DD-AACG TCGA-DD-AACH 
       12.26         9.30        35.67         0.53        15.42         6.41 
TCGA-DD-AACL TCGA-DD-AACS TCGA-DD-AADB TCGA-DD-AADF TCGA-DD-AADK TCGA-DD-AADV 
        3.52        59.31        40.83         3.78        34.49        18.87 
TCGA-DD-AAE1 TCGA-DD-AAE4 TCGA-DD-AAE7 TCGA-DD-AAEK TCGA-DD-AAVQ TCGA-DD-AAVV 
       18.15        19.99        21.17        35.08        89.69        80.71 
TCGA-DD-AAVX TCGA-ED-A459 TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A82E TCGA-EP-A2KB 
       56.48        29.92         9.73         0.20        13.41        19.59 
TCGA-FV-A3I0 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-G3-A25Z TCGA-G3-A5SI TCGA-G3-A5SM 
       27.88         0.33        81.73        21.53        25.25        17.10 
TCGA-G3-A7M9 TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV4 TCGA-G3-AAV6 TCGA-G3-AAV7 
        1.84        15.65        11.80         0.89         2.14        11.87 
TCGA-GJ-A3OU TCGA-K7-A5RG TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-NI-A8LF TCGA-RG-A7D4 
       22.92        17.06        21.60        31.27        26.27        36.10 
TCGA-WQ-A9G7 TCGA-YA-A8S7 TCGA-ZS-A9CF 
        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        49.84        47.74 
TCGA-2Y-A9H5 TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB 
       18.25        11.74        38.40        22.92         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        17.10        14.76         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        23.38         1.12        69.57        45.93 
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-CC-A5UE TCGA-CC-A7IE 
        3.32         9.86        10.36        11.93         8.94         7.13 
TCGA-CC-A7IF TCGA-CC-A7IH TCGA-CC-A7IL TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A9FS 
       21.34        12.00         9.14         4.60        11.31         6.94 
TCGA-CC-A9FW TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B 
        8.15        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-A1EK TCGA-DD-A39V TCGA-DD-A39W 
       12.95        45.11        49.15        18.35        21.14        27.19 
TCGA-DD-A39X TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 
       55.69        19.76        25.81         7.66        70.06        17.59 
TCGA-DD-A3A4 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NB 
       20.12       107.11        13.78         0.36        30.61        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-A4NR TCGA-DD-A4NS 
       56.25        29.56        73.81       108.76         0.30        80.75 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73G 
       78.84        23.93        23.05        22.78         1.45       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-AACI TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACM 
       63.48        12.00        53.19        69.11         0.30        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-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-AADC TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADG TCGA-DD-AADI 
       40.54        13.97        40.47        39.52        37.64        35.67 
TCGA-DD-AADJ TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP 
       35.05        20.91         0.39        29.52        14.89        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-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE6 TCGA-DD-AAE8 TCGA-DD-AAE9 
       18.25        20.98        18.61         4.64        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        26.63        23.64        25.78 
TCGA-DD-AAEI TCGA-DD-AAVP TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW 
       50.33        79.07        82.62        59.93        72.39        76.18 
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 
       26.93        28.08        13.91        13.35        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-A2KA TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS 
       19.99        20.61         0.62         9.96        11.93        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-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U 
       12.03         0.03         0.39        13.68        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-A5SJ TCGA-G3-A5SL TCGA-G3-A6UC 
        5.92        19.53        19.23        22.95        20.42        22.06 
TCGA-G3-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV2 
       14.70        20.78        11.87        14.14        15.78        12.23 
TCGA-G3-AAV3 TCGA-G3-AAV5 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 
       13.55         8.75         1.02         2.20         2.99        37.71 
TCGA-K7-A5RF TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K8 TCGA-LG-A6GG 
       20.75        16.83        11.80         2.14        29.79        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        22.95        24.56 
TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-O8-A75V TCGA-PD-A5DF 
       20.71         7.53        10.85        58.88        17.69        21.01 
TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK 
        3.09        21.04        19.33        19.04        15.39        15.52 
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-UB-AA0V TCGA-WJ-A86L TCGA-WQ-AB4B TCGA-WX-AA44 
        7.04        10.75        10.32        11.34        12.99        20.22 
TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TF TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ 
       24.85        18.28        22.78        35.77        25.71        23.21 
TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE 
       35.87         0.69        25.15        12.99        45.57        40.80 
TCGA-ZS-A9CG 
       11.21 

  DEL PEAK 24(15Q26.3) MUTATED DEL PEAK 24(15Q26.3) WILD-TYPE 
                          0.20                           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                          20.42 
[1] "0.2 - 102.7 (17.1)" "0.0 - 120.8 (20.4)"
[1] "hr=" "1.6"
D53V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IIIA
  DEL PEAK 24(15Q26.3) MUTATED        27       27         1         15
  DEL PEAK 24(15Q26.3) WILD-TYPE     144       58         2         45
                                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                              27                            144
  STAGE II                             27                             58
  STAGE III                             1                              2
  STAGE IIIA                           15                             45
  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      29  27  20   1
  DEL PEAK 24(15Q26.3) WILD-TYPE   153  65  54  11
D53V4, multiclass
       clus
vv      DEL PEAK 24(15Q26.3) MUTATED DEL PEAK 24(15Q26.3) WILD-TYPE
  T0+T1                           29                            153
  T2                              27                             65
  T3                              20                             54
  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    53   2
  DEL PEAK 24(15Q26.3) WILD-TYPE 197   1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(15Q26.3) MUTATED     53    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                           53                            197
  1                            2                              1
[1] 2 2
[1] FALSE
D53V6, binary
                                cls
clus                               0   1
  DEL PEAK 24(15Q26.3) MUTATED    65   0
  DEL PEAK 24(15Q26.3) WILD-TYPE 196   4
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(15Q26.3) MUTATED     65    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                           65                            196
  1                            0                              4
[1] 2 2
[1] FALSE
D53V7, binary
                                cls
clus                               0   1
  DEL PEAK 24(15Q26.3) MUTATED    25  52
  DEL PEAK 24(15Q26.3) WILD-TYPE  90 195
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(15Q26.3) MUTATED     25   52
  DEL PEAK 24(15Q26.3) WILD-TYPE   90  195
        clus
vv       DEL PEAK 24(15Q26.3) MUTATED DEL PEAK 24(15Q26.3) WILD-TYPE
  FEMALE                           25                             90
  MALE                             52                            195
[1] 2 2
[1] FALSE
D53V8, binary
                                cls
clus                               0   1
  DEL PEAK 24(15Q26.3) MUTATED    72   1
  DEL PEAK 24(15Q26.3) WILD-TYPE 264   6
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(15Q26.3) MUTATED     72    1
  DEL PEAK 24(15Q26.3) WILD-TYPE  264    6
     clus
vv    DEL PEAK 24(15Q26.3) MUTATED DEL PEAK 24(15Q26.3) WILD-TYPE
  NO                            72                            264
  YES                            1                              6
[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                         74
  DEL PEAK 24(15Q26.3) WILD-TYPE                      279
                                vv
clus                             HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK 24(15Q26.3) MUTATED                                  3
  DEL PEAK 24(15Q26.3) WILD-TYPE                                4
D53V9, multiclass
                                  clus
vv                                 DEL PEAK 24(15Q26.3) MUTATED
  FIBROLAMELLAR CARCINOMA                                     0
  HEPATOCELLULAR CARCINOMA                                   74
  HEPATOCHOLANGIOCARCINOMA (MIXED)                            3
                                  clus
vv                                 DEL PEAK 24(15Q26.3) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                       2
  HEPATOCELLULAR CARCINOMA                                    279
  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    69   2   0   6
  DEL PEAK 24(15Q26.3) WILD-TYPE 249  13   1  15
D53V10, multiclass
    clus
vv   DEL PEAK 24(15Q26.3) MUTATED DEL PEAK 24(15Q26.3) WILD-TYPE
  R0                           69                            249
  R1                            2                             13
  R2                            0                              1
  RX                            6                             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 24(15Q26.3) MUTATED                                  0    39
  DEL PEAK 24(15Q26.3) WILD-TYPE                                1   118
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 24(15Q26.3) MUTATED                           5    33
  DEL PEAK 24(15Q26.3) WILD-TYPE                        12   144
D53V11, multiclass
                                  clus
vv                                 DEL PEAK 24(15Q26.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                      39
  BLACK OR AFRICAN AMERICAN                                   5
  WHITE                                                      33
                                  clus
vv                                 DEL PEAK 24(15Q26.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                       118
  BLACK OR AFRICAN AMERICAN                                    12
  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"
D53V12, binary
                                cls
clus                               0   1
  DEL PEAK 24(15Q26.3) MUTATED     3  70
  DEL PEAK 24(15Q26.3) WILD-TYPE  10 262
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(15Q26.3) MUTATED      3   70
  DEL PEAK 24(15Q26.3) WILD-TYPE   10  262
                        clus
vv                       DEL PEAK 24(15Q26.3) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           70
                        clus
vv                       DEL PEAK 24(15Q26.3) WILD-TYPE
  HISPANIC OR LATINO                                 10
  NOT HISPANIC OR LATINO                            262
[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  59
  DEL PEAK 25(16Q23.1) WILD-TYPE 130  70
  DEL PEAK 25(16Q23.1) MUTATED DEL PEAK 25(16Q23.1) WILD-TYPE 
                           158                            200 
  DEL PEAK 25(16Q23.1) MUTATED DEL PEAK 25(16Q23.1) WILD-TYPE 
                            59                             70 
$`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        49.84        18.25        38.40        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        23.38         1.12        44.42        45.93        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         4.24         2.86 
TCGA-CC-5261 TCGA-CC-5263 TCGA-CC-5264 TCGA-CC-A3M9 TCGA-CC-A3MB TCGA-CC-A3MC 
        3.19         4.24         3.35         9.86        10.36        11.93 
TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IG 
       11.41         9.99         8.94         7.13        21.34         9.83 
TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A113 
        4.60        11.31         9.17         6.94         8.15        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-AAVV TCGA-DD-AAVW 
       79.07        89.69        59.93        72.39        80.71        76.18 
TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-ED-A459 TCGA-ED-A5KG TCGA-ED-A66X TCGA-ED-A66Y 
       62.47        66.25        29.92        28.08        13.35         9.73 
TCGA-ED-A7PY TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-EP-A2KB TCGA-ES-A2HS TCGA-FV-A23B 
       12.82        13.35         1.84        19.59        22.85        60.89 
TCGA-FV-A2QQ TCGA-FV-A3I0 TCGA-FV-A3R2 TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25X 
       23.97        27.88         6.38        13.68        53.79        58.49 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A5SI TCGA-G3-A7M5 TCGA-G3-A7M9 
       14.86        21.53        25.64        25.25        14.70         1.84 
TCGA-G3-AAUZ TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG 
       15.78         2.14        11.87        31.27        29.79        12.72 
TCGA-MI-A75G TCGA-MI-A75I TCGA-NI-A8LF TCGA-O8-A75V TCGA-QA-A7B7 TCGA-RC-A7SB 
       22.95        20.71        26.27        17.69         3.09        19.33 
TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RG-A7D4 TCGA-T1-A6J8 TCGA-UB-A7MA TCGA-UB-A7MB 
       19.04        15.39        36.10         0.76        17.59        19.76 
TCGA-UB-A7MF TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-XR-A8TF TCGA-ZP-A9CZ 
        7.04        10.75        11.34         0.99        22.78        23.21 
TCGA-ZP-A9D1 TCGA-ZS-A9CG 
        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        22.92 
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        17.10        14.76 
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-CC-A7IH TCGA-CC-A7II 
       36.66         3.39         3.32         9.96        12.00        13.12 
TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A7IL TCGA-DD-A115 TCGA-DD-A118 TCGA-DD-A119 
       12.56         8.61         9.14        83.57       113.00         7.33 
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-A1EG TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V 
       75.65        11.47        45.11        18.35        13.64        21.14 
TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 
       27.19        55.69        25.81         7.66        70.06        17.59 
TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A4NA TCGA-DD-A4NB 
       20.12       102.74       107.11        13.78        33.14        32.52 
TCGA-DD-A4NF TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NP TCGA-DD-A4NR TCGA-DD-A4NS 
       30.97        39.78        56.25       108.76         0.30        80.75 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73G 
       78.84        23.93        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-AACD 
       13.48         0.53        11.41        75.65        76.41        12.53 
TCGA-DD-AACE TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACT TCGA-DD-AACX TCGA-DD-AACY 
       63.48        69.11         0.30        51.35         5.59        47.67 
TCGA-DD-AAD2 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADC TCGA-DD-AADD 
       21.63        44.22        22.09        40.08        13.97        40.47 
TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADN TCGA-DD-AADQ TCGA-DD-AADS 
       39.52         3.78        37.64        29.52        14.33        15.58 
TCGA-DD-AADU TCGA-DD-AADY TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE7 
       18.21        18.25        20.98        18.61        19.99        21.17 
TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAEE TCGA-DD-AAEI TCGA-DD-AAVR 
       23.74        18.90        15.72        26.63        50.33        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        26.93 
TCGA-ED-A627 TCGA-ED-A7PX TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E 
       13.91         0.20         0.20        14.04        13.15        13.41 
TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3JL 
        0.20        18.74        19.99        20.61         0.62         9.96 
TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A2QR TCGA-FV-A3I1 TCGA-FV-A3R3 TCGA-FV-A495 
       11.93        14.40        19.10         8.12        12.03         0.03 
TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25V TCGA-G3-A25W 
        0.33        81.73         0.39        51.06        28.27        30.74 
TCGA-G3-A3CG TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SJ TCGA-G3-A5SL 
       22.13         5.92        19.53        19.23        22.95        20.42 
TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAV0 
       17.10        22.06        20.78        11.87        14.14        15.65 
TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-GJ-A3OU 
       11.80        12.23        13.55         0.89         8.75        22.92 
TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG 
        1.02         2.20         2.99        37.71        20.75        17.06 
TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-LG-A9QC TCGA-LG-A9QD 
       16.83        11.80         2.14        21.60        13.97        12.03 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75H TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 
        9.57        16.67        24.56         7.53        10.85        58.88 
TCGA-PD-A5DF TCGA-RC-A7S9 TCGA-RC-A7SK TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME 
       21.01        21.04        15.52        16.44         1.71        15.98 
TCGA-UB-AA0V TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 TCGA-YA-A8S7 
       10.32        12.99        20.22        24.85        18.28        13.55 
TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD 
       35.77        25.71        35.87        25.15        12.99        45.57 
TCGA-ZS-A9CE TCGA-ZS-A9CF 
       40.80        79.30 

  DEL PEAK 25(16Q23.1) MUTATED DEL PEAK 25(16Q23.1) WILD-TYPE 
                          0.36                           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 
                         19.17                          20.17 
[1] "0.4 - 90.3 (19.2)"  "0.0 - 120.8 (20.2)"
[1] "hr=" "1.3"
D54V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IIIA
  DEL PEAK 25(16Q23.1) MUTATED        67       50         1         25
  DEL PEAK 25(16Q23.1) WILD-TYPE     104       35         2         35
                                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                              67                            104
  STAGE II                             50                             35
  STAGE III                             1                              2
  STAGE IIIA                           25                             35
  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      73  51  31   6
  DEL PEAK 25(16Q23.1) WILD-TYPE   109  41  43   6
D54V4, multiclass
       clus
vv      DEL PEAK 25(16Q23.1) MUTATED DEL PEAK 25(16Q23.1) WILD-TYPE
  T0+T1                           73                            109
  T2                              51                             41
  T3                              31                             43
  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   120   2
  DEL PEAK 25(16Q23.1) WILD-TYPE 130   1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(16Q23.1) MUTATED    120    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                          120                            130
  1                            2                              1
[1] 2 2
[1] FALSE
D54V6, binary
                                cls
clus                               0   1
  DEL PEAK 25(16Q23.1) MUTATED   126   2
  DEL PEAK 25(16Q23.1) WILD-TYPE 135   2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(16Q23.1) MUTATED    126    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                          126                            135
  1                            2                              2
[1] 2 2
[1] FALSE
D54V7, binary
                                cls
clus                               0   1
  DEL PEAK 25(16Q23.1) MUTATED    56 105
  DEL PEAK 25(16Q23.1) WILD-TYPE  59 142
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(16Q23.1) MUTATED     56  105
  DEL PEAK 25(16Q23.1) WILD-TYPE   59  142
        clus
vv       DEL PEAK 25(16Q23.1) MUTATED DEL PEAK 25(16Q23.1) WILD-TYPE
  FEMALE                           56                             59
  MALE                            105                            142
[1] 2 2
[1] FALSE
D54V8, binary
                                cls
clus                               0   1
  DEL PEAK 25(16Q23.1) MUTATED   150   2
  DEL PEAK 25(16Q23.1) WILD-TYPE 186   5
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(16Q23.1) MUTATED    150    2
  DEL PEAK 25(16Q23.1) WILD-TYPE  186    5
     clus
vv    DEL PEAK 25(16Q23.1) MUTATED DEL PEAK 25(16Q23.1) WILD-TYPE
  NO                           150                            186
  YES                            2                              5
[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                        158
  DEL PEAK 25(16Q23.1) WILD-TYPE                      195
                                vv
clus                             HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK 25(16Q23.1) MUTATED                                  3
  DEL PEAK 25(16Q23.1) WILD-TYPE                                4
D54V9, multiclass
                                  clus
vv                                 DEL PEAK 25(16Q23.1) MUTATED
  FIBROLAMELLAR CARCINOMA                                     0
  HEPATOCELLULAR CARCINOMA                                  158
  HEPATOCHOLANGIOCARCINOMA (MIXED)                            3
                                  clus
vv                                 DEL PEAK 25(16Q23.1) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                       2
  HEPATOCELLULAR CARCINOMA                                    195
  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   143   7   0  11
  DEL PEAK 25(16Q23.1) WILD-TYPE 175   8   1  10
D54V10, multiclass
    clus
vv   DEL PEAK 25(16Q23.1) MUTATED DEL PEAK 25(16Q23.1) WILD-TYPE
  R0                          143                            175
  R1                            7                              8
  R2                            0                              1
  RX                           11                             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 25(16Q23.1) MUTATED                                  0    91
  DEL PEAK 25(16Q23.1) WILD-TYPE                                1    66
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 25(16Q23.1) MUTATED                           7    59
  DEL PEAK 25(16Q23.1) WILD-TYPE                        10   118
D54V11, multiclass
                                  clus
vv                                 DEL PEAK 25(16Q23.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                      91
  BLACK OR AFRICAN AMERICAN                                   7
  WHITE                                                      59
                                  clus
vv                                 DEL PEAK 25(16Q23.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        66
  BLACK OR AFRICAN AMERICAN                                    10
  WHITE                                                       118
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V12, binary
                                cls
clus                               0   1
  DEL PEAK 25(16Q23.1) MUTATED     7 149
  DEL PEAK 25(16Q23.1) WILD-TYPE   6 183
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(16Q23.1) MUTATED      7  149
  DEL PEAK 25(16Q23.1) WILD-TYPE    6  183
                        clus
vv                       DEL PEAK 25(16Q23.1) MUTATED
  HISPANIC OR LATINO                                7
  NOT HISPANIC OR LATINO                          149
                        clus
vv                       DEL PEAK 25(16Q23.1) WILD-TYPE
  HISPANIC OR LATINO                                  6
  NOT HISPANIC OR LATINO                            183
[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   127  90
  DEL PEAK 26(17P13.1) WILD-TYPE 102  39
  DEL PEAK 26(17P13.1) MUTATED DEL PEAK 26(17P13.1) WILD-TYPE 
                           217                            141 
  DEL PEAK 26(17P13.1) MUTATED DEL PEAK 26(17P13.1) WILD-TYPE 
                            90                             39 
$`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        22.92         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        23.38         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        45.93         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         4.24         2.86 
TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-5264 TCGA-CC-A1HT TCGA-CC-A3MA 
        3.19         3.39         4.24         3.35         3.32         9.96 
TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IF 
       10.36        11.93        11.41         9.99         8.94        21.34 
TCGA-CC-A7IG TCGA-CC-A7II TCGA-CC-A7IK TCGA-CC-A7IL TCGA-CC-A8HT TCGA-CC-A8HU 
        9.83        13.12         8.61         9.14         4.60        11.31 
TCGA-CC-A8HV TCGA-CC-A9FS TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 
        9.17         6.94        37.78        83.57        53.33       113.00 
TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1EA TCGA-DD-A1EB 
        7.33         2.60        21.76        51.29        79.40        66.31 
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-A39Y TCGA-DD-A3A0 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A7 
        5.62        25.81        17.59        20.12       102.74        13.78 
TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ 
       30.61        33.14        32.52        30.15        26.83        30.51 
TCGA-DD-A4NO TCGA-DD-A4NQ TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73E TCGA-DD-AAC9 
       73.81        12.26        23.93         9.30         1.45        11.41 
TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG 
       75.65        76.41        55.40        63.48        12.00        15.42 
TCGA-DD-AACH TCGA-DD-AACJ TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACQ TCGA-DD-AACS 
        6.41        69.11         3.52        58.16        14.20        59.31 
TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACX TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 
       51.52        50.33         5.59         5.62         4.50        18.54 
TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADB TCGA-DD-AADC 
       42.58        44.22        22.09        40.08        40.83        13.97 
TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADL TCGA-DD-AADN 
       40.47        39.52         3.78        37.64        20.91        29.52 
TCGA-DD-AADR TCGA-DD-AADV TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 
       66.67        18.87        19.30        18.25        18.25        18.15 
TCGA-DD-AAE2 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEB 
       20.98        19.99         4.64        21.83        18.90        15.72 
TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ 
       25.08        26.63        50.33        35.08        79.07        89.69 
TCGA-DD-AAVR TCGA-DD-AAVU TCGA-DD-AAVV TCGA-DD-AAVW TCGA-DD-AAW1 TCGA-ED-A459 
       82.62        72.39        80.71        76.18        65.39        29.92 
TCGA-ED-A7PX TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O6 
        0.20         0.20        14.04        13.15        13.41         1.84 
TCGA-ED-A97K TCGA-EP-A2KC TCGA-ES-A2HS TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR 
        0.20         0.62        22.85        60.89        23.97        19.10 
TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP 
       27.88         8.12         6.38         0.03         0.33        81.73 
TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z 
       13.68        53.79        28.27        30.74        14.86        21.53 
TCGA-G3-A3CH TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A7M5 
       25.64        25.25        22.95        20.42        17.10        14.70 
TCGA-G3-A7M6 TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV1 TCGA-G3-AAV4 TCGA-G3-AAV5 
       20.78         1.84        15.78        11.80         0.89         8.75 
TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5N0 TCGA-K7-AAU7 
       11.87        22.92         1.02         2.20        37.71        11.80 
TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-LG-A6GG TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I 
        2.14        21.60        12.72        16.67        22.95        20.71 
TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7SB 
       58.88        26.27        17.69        21.01         3.09        19.33 
TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-T1-A6J8 TCGA-UB-A7MB TCGA-UB-A7MC 
       15.39        15.52        36.10         0.76        19.76        16.44 
TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-A7MF TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-AB4B 
        1.71        15.98         7.04        10.75        11.34        12.99 
TCGA-WX-AA44 TCGA-YA-A8S7 TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CE 
       20.22        13.55         0.69        25.15        12.99        40.80 
TCGA-ZS-A9CF 
       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        49.84        11.74 
TCGA-2Y-A9H7 TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5R-AA1C 
       38.40         8.55        13.02        10.78        10.59        17.10 
TCGA-5R-AA1D TCGA-BC-A10Q TCGA-BC-A10S TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A69I 
       14.76        37.32        46.78         2.99        25.32        12.72 
TCGA-BD-A3ER TCGA-CC-A3M9 TCGA-CC-A7IE TCGA-CC-A7IH TCGA-CC-A7IJ TCGA-CC-A9FW 
       36.66         9.86         7.13        12.00        12.56         8.15 
TCGA-DD-A113 TCGA-DD-A11B TCGA-DD-A1E9 TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE 
       79.73         0.46        90.71        19.79        75.65        11.47 
TCGA-DD-A1EF TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Z TCGA-DD-A3A1 
       12.95        21.14        27.19        55.69        19.76         7.66 
TCGA-DD-A3A2 TCGA-DD-A3A6 TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NK 
       70.06       107.11         0.36        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-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-AACD TCGA-DD-AACI TCGA-DD-AACK TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP 
       12.53        53.19         0.30        42.81        61.68        13.64 
TCGA-DD-AACT TCGA-DD-AACW TCGA-DD-AACY TCGA-DD-AAD2 TCGA-DD-AADA TCGA-DD-AADI 
       51.35        46.82        47.67        21.63        40.54        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-AADU TCGA-DD-AAE3 TCGA-DD-AAE7 TCGA-DD-AAE9 TCGA-DD-AAEG 
       15.58        18.21        18.61        21.17        23.74        23.64 
TCGA-DD-AAEH TCGA-DD-AAVS TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 
       25.78        59.93        56.48        64.77        62.47        66.25 
TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X 
       49.48        53.69        26.93        28.08        13.91        13.35 
TCGA-ED-A66Y TCGA-ED-A7PY TCGA-ED-A8O5 TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
        9.73        12.82        13.35        18.74        19.99        20.61 
TCGA-EP-A2KB TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A3R3 TCGA-FV-A4ZQ 
       19.59         9.96        11.93        14.40        12.03         0.39 
TCGA-G3-A25T TCGA-G3-A25X TCGA-G3-A3CG TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
       51.06        58.49        22.13         5.92        19.53        19.23 
TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV3 
       22.06        11.87        14.14        15.65        12.23        13.55 
TCGA-G3-AAV6 TCGA-HP-A5MZ TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-KR-A7K7 
        2.14         2.99        20.75        17.06        16.83        31.27 
TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75H TCGA-MR-A520 
       29.79        13.97        12.03         9.57        24.56         7.53 
TCGA-MR-A8JO TCGA-RC-A7S9 TCGA-RC-A7SF TCGA-UB-A7MA TCGA-UB-AA0V TCGA-WQ-A9G7 
       10.85        21.04        19.04        17.59        10.32         0.99 
TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TF TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ 
       24.85        18.28        22.78        35.77        25.71        23.21 
TCGA-ZP-A9D0 TCGA-ZS-A9CD TCGA-ZS-A9CG 
       35.87        45.57        11.21 

  DEL PEAK 26(17P13.1) MUTATED DEL PEAK 26(17P13.1) WILD-TYPE 
                          0.03                           0.30 
  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 
                         19.10                          20.61 
[1] "0.0 - 120.8 (19.1)" "0.3 - 114.3 (20.6)"
[1] "hr=" "1.7"
D55V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IIIA
  DEL PEAK 26(17P13.1) MUTATED        91       57         2         38
  DEL PEAK 26(17P13.1) WILD-TYPE      80       28         1         22
                                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                              91                             80
  STAGE II                             57                             28
  STAGE III                             2                              1
  STAGE IIIA                           38                             22
  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      98 63 47 11
  DEL PEAK 26(17P13.1) WILD-TYPE    84 29 27  1
D55V4, multiclass
       clus
vv      DEL PEAK 26(17P13.1) MUTATED DEL PEAK 26(17P13.1) WILD-TYPE
  T0+T1                           98                             84
  T2                              63                             29
  T3                              47                             27
  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   152   3
  DEL PEAK 26(17P13.1) WILD-TYPE  98   0
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(17P13.1) MUTATED    152    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                          152                             98
  1                            3                              0
[1] 2 2
[1] FALSE
D55V6, binary
                                cls
clus                               0   1
  DEL PEAK 26(17P13.1) MUTATED   161   4
  DEL PEAK 26(17P13.1) WILD-TYPE 100   0
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(17P13.1) MUTATED    161    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                          161                            100
  1                            4                              0
[1] 2 2
[1] FALSE
D55V7, binary
                                cls
clus                               0   1
  DEL PEAK 26(17P13.1) MUTATED    67 153
  DEL PEAK 26(17P13.1) WILD-TYPE  48  94
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(17P13.1) MUTATED     67  153
  DEL PEAK 26(17P13.1) WILD-TYPE   48   94
        clus
vv       DEL PEAK 26(17P13.1) MUTATED DEL PEAK 26(17P13.1) WILD-TYPE
  FEMALE                           67                             48
  MALE                            153                             94
[1] 2 2
[1] FALSE
D55V8, binary
                                cls
clus                               0   1
  DEL PEAK 26(17P13.1) MUTATED   204   4
  DEL PEAK 26(17P13.1) WILD-TYPE 132   3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(17P13.1) MUTATED    204    4
  DEL PEAK 26(17P13.1) WILD-TYPE  132    3
     clus
vv    DEL PEAK 26(17P13.1) MUTATED DEL PEAK 26(17P13.1) WILD-TYPE
  NO                           204                            132
  YES                            4                              3
[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                        214
  DEL PEAK 26(17P13.1) WILD-TYPE                      139
                                vv
clus                             HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK 26(17P13.1) MUTATED                                  5
  DEL PEAK 26(17P13.1) WILD-TYPE                                2
D55V9, multiclass
                                  clus
vv                                 DEL PEAK 26(17P13.1) MUTATED
  FIBROLAMELLAR CARCINOMA                                     1
  HEPATOCELLULAR CARCINOMA                                  214
  HEPATOCHOLANGIOCARCINOMA (MIXED)                            5
                                  clus
vv                                 DEL PEAK 26(17P13.1) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                       1
  HEPATOCELLULAR CARCINOMA                                    139
  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   190  10   1  16
  DEL PEAK 26(17P13.1) WILD-TYPE 128   5   0   5
D55V10, multiclass
    clus
vv   DEL PEAK 26(17P13.1) MUTATED DEL PEAK 26(17P13.1) WILD-TYPE
  R0                          190                            128
  R1                           10                              5
  R2                            1                              0
  RX                           16                              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   104
  DEL PEAK 26(17P13.1) WILD-TYPE                                1    53
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 26(17P13.1) MUTATED                          12    99
  DEL PEAK 26(17P13.1) WILD-TYPE                         5    78
D55V11, multiclass
                                  clus
vv                                 DEL PEAK 26(17P13.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                     104
  BLACK OR AFRICAN AMERICAN                                  12
  WHITE                                                      99
                                  clus
vv                                 DEL PEAK 26(17P13.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        53
  BLACK OR AFRICAN AMERICAN                                     5
  WHITE                                                        78
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V12, binary
                                cls
clus                               0   1
  DEL PEAK 26(17P13.1) MUTATED     9 201
  DEL PEAK 26(17P13.1) WILD-TYPE   4 131
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(17P13.1) MUTATED      9  201
  DEL PEAK 26(17P13.1) WILD-TYPE    4  131
                        clus
vv                       DEL PEAK 26(17P13.1) MUTATED
  HISPANIC OR LATINO                                9
  NOT HISPANIC OR LATINO                          201
                        clus
vv                       DEL PEAK 26(17P13.1) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            131
[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  81
  DEL PEAK 27(17P11.2) WILD-TYPE 124  48
  DEL PEAK 27(17P11.2) MUTATED DEL PEAK 27(17P11.2) WILD-TYPE 
                           186                            172 
  DEL PEAK 27(17P11.2) MUTATED DEL PEAK 27(17P11.2) WILD-TYPE 
                            81                             48 
$`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        22.92         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 
       23.38         1.12        69.57         5.03        45.93         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         4.24         3.19         3.39         4.24         3.32 
TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A5UE TCGA-CC-A7IE 
        9.96        10.36        11.93        11.41         8.94         7.13 
TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7II TCGA-CC-A7IK TCGA-CC-A7IL TCGA-CC-A8HT 
       21.34         9.83        13.12         8.61         9.14         4.60 
TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FS TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 
       11.31         9.17         6.94        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        26.63 
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-AAVV TCGA-DD-AAW1 TCGA-ED-A459 TCGA-ED-A7PX TCGA-ED-A82E TCGA-ED-A8O6 
       80.71        65.39        29.92         0.20        13.41         1.84 
TCGA-ED-A97K TCGA-EP-A2KC TCGA-ES-A2HS TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR 
        0.20         0.62        22.85        60.89        23.97        19.10 
TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A495 TCGA-FV-A4ZP TCGA-G3-A25S 
       27.88         8.12         6.38         0.03        81.73        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-A5SL TCGA-G3-A5SM TCGA-G3-A7M6 TCGA-G3-A7M9 TCGA-G3-AAUZ 
       25.64        20.42        17.10        20.78         1.84        15.78 
TCGA-G3-AAV1 TCGA-G3-AAV5 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5N0 
       11.80         8.75        22.92         1.02         2.20        37.71 
TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-LG-A6GG TCGA-MI-A75E TCGA-MI-A75G 
       11.80         2.14        21.60        12.72        16.67        22.95 
TCGA-MI-A75I TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7SB 
       20.71        58.88        26.27        21.01         3.09        19.33 
TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-T1-A6J8 TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD 
       15.52        36.10         0.76        19.76        16.44         1.71 
TCGA-UB-A7ME TCGA-UB-A7MF TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-AB4B TCGA-WX-AA44 
       15.98         7.04        10.75        11.34        12.99        20.22 
TCGA-YA-A8S7 TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CE TCGA-ZS-A9CF 
       13.55         0.69        25.15        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        49.84        47.74 
TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-4R-AA8I TCGA-5C-A9VG 
       11.74        38.40         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        17.10        14.76        37.32        46.78         2.99 
TCGA-BC-A10X TCGA-BC-A216 TCGA-BC-A69I TCGA-BD-A3ER TCGA-CC-5260 TCGA-CC-5264 
       25.32        44.42        12.72        36.66         2.86         3.35 
TCGA-CC-A3M9 TCGA-CC-A5UD TCGA-CC-A7IH TCGA-CC-A7IJ TCGA-CC-A9FW TCGA-DD-A113 
        9.86         9.99        12.00        12.56         8.15        79.73 
TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A1E9 TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE 
        2.60         0.46        90.71        19.79        75.65        11.47 
TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Z 
       12.95        49.15        21.14        27.19        55.69        19.76 
TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A6 TCGA-DD-A3A8 TCGA-DD-A3A9 
       25.81         7.66        70.06       107.11         0.36        30.61 
TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NP 
       90.28        30.97        39.78        56.25        29.56       108.76 
TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73C TCGA-DD-A73D 
        0.30        80.75        78.84        23.93        23.05        22.78 
TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AACB TCGA-DD-AACD 
       35.67       114.35        13.48         0.53        76.41        12.53 
TCGA-DD-AACF TCGA-DD-AACI TCGA-DD-AACK TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP 
       12.00        53.19         0.30        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-AACY TCGA-DD-AAD2 TCGA-DD-AADA TCGA-DD-AADD TCGA-DD-AADI TCGA-DD-AADK 
       47.67        21.63        40.54        40.47        35.67        34.49 
TCGA-DD-AADM TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU 
        0.39        15.06        14.33        66.67        15.58        18.21 
TCGA-DD-AAE1 TCGA-DD-AAE3 TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAE9 
       18.15        18.61         4.64        21.17        21.83        23.74 
TCGA-DD-AAED TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAVS TCGA-DD-AAVW TCGA-DD-AAVX 
       25.08        23.64        25.78        59.93        76.18        56.48 
TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A4XI 
       64.77        62.47        66.25        49.48        53.69        26.93 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PY TCGA-ED-A7PZ 
       28.08        13.91        13.35         9.73        12.82         0.20 
TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A8O5 TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
       14.04        13.15        13.35        18.74        19.99        20.61 
TCGA-EP-A2KB TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A3R3 TCGA-FV-A496 
       19.59         9.96        11.93        14.40        12.03         0.33 
TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25X TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
        0.39        51.06        58.49         5.92        19.53        19.23 
TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A6UC TCGA-G3-A7M5 TCGA-G3-A7M7 TCGA-G3-A7M8 
       25.25        22.95        22.06        14.70        11.87        14.14 
TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV6 TCGA-G3-AAV7 
       15.65        12.23        13.55         0.89         2.14        11.87 
TCGA-HP-A5MZ TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-KR-A7K7 TCGA-KR-A7K8 
        2.99        20.75        17.06        16.83        31.27        29.79 
TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75H TCGA-MR-A520 TCGA-MR-A8JO 
       13.97        12.03         9.57        24.56         7.53        10.85 
TCGA-O8-A75V TCGA-RC-A7S9 TCGA-RC-A7SF TCGA-RC-A7SH TCGA-UB-A7MA TCGA-UB-AA0V 
       17.69        21.04        19.04        15.39        17.59        10.32 
TCGA-WQ-A9G7 TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TF TCGA-ZP-A9CV TCGA-ZP-A9CY 
        0.99        24.85        18.28        22.78        35.77        25.71 
TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZS-A9CD TCGA-ZS-A9CG 
       23.21        35.87        45.57        11.21 

  DEL PEAK 27(17P11.2) MUTATED DEL PEAK 27(17P11.2) WILD-TYPE 
                          0.03                           0.20 
  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 
                          19.2                           20.3 
[1] "0.0 - 120.8 (19.2)" "0.2 - 114.3 (20.3)"
[1] "hr=" "1.7"
D56V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IIIA
  DEL PEAK 27(17P11.2) MUTATED        73       50         1         35
  DEL PEAK 27(17P11.2) WILD-TYPE      98       35         2         25
                                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                              73                             98
  STAGE II                             50                             35
  STAGE III                             1                              2
  STAGE IIIA                           35                             25
  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      80  56  43   9
  DEL PEAK 27(17P11.2) WILD-TYPE   102  36  31   3
D56V4, multiclass
       clus
vv      DEL PEAK 27(17P11.2) MUTATED DEL PEAK 27(17P11.2) WILD-TYPE
  T0+T1                           80                            102
  T2                              56                             36
  T3                              43                             31
  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   129   3
  DEL PEAK 27(17P11.2) WILD-TYPE 121   0
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(17P11.2) MUTATED    129    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                          129                            121
  1                            3                              0
[1] 2 2
[1] FALSE
D56V6, binary
                                cls
clus                               0   1
  DEL PEAK 27(17P11.2) MUTATED   135   3
  DEL PEAK 27(17P11.2) WILD-TYPE 126   1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(17P11.2) MUTATED    135    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                          135                            126
  1                            3                              1
[1] 2 2
[1] FALSE
D56V7, binary
                                cls
clus                               0   1
  DEL PEAK 27(17P11.2) MUTATED    60 129
  DEL PEAK 27(17P11.2) WILD-TYPE  55 118
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(17P11.2) MUTATED     60  129
  DEL PEAK 27(17P11.2) WILD-TYPE   55  118
        clus
vv       DEL PEAK 27(17P11.2) MUTATED DEL PEAK 27(17P11.2) WILD-TYPE
  FEMALE                           60                             55
  MALE                            129                            118
[1] 2 2
[1] FALSE
D56V8, binary
                                cls
clus                               0   1
  DEL PEAK 27(17P11.2) MUTATED   176   4
  DEL PEAK 27(17P11.2) WILD-TYPE 160   3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(17P11.2) MUTATED    176    4
  DEL PEAK 27(17P11.2) WILD-TYPE  160    3
     clus
vv    DEL PEAK 27(17P11.2) MUTATED DEL PEAK 27(17P11.2) WILD-TYPE
  NO                           176                            160
  YES                            4                              3
[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                        183
  DEL PEAK 27(17P11.2) WILD-TYPE                      170
                                vv
clus                             HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK 27(17P11.2) MUTATED                                  5
  DEL PEAK 27(17P11.2) WILD-TYPE                                2
D56V9, multiclass
                                  clus
vv                                 DEL PEAK 27(17P11.2) MUTATED
  FIBROLAMELLAR CARCINOMA                                     1
  HEPATOCELLULAR CARCINOMA                                  183
  HEPATOCHOLANGIOCARCINOMA (MIXED)                            5
                                  clus
vv                                 DEL PEAK 27(17P11.2) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                       1
  HEPATOCELLULAR CARCINOMA                                    170
  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   161  10   1  14
  DEL PEAK 27(17P11.2) WILD-TYPE 157   5   0   7
D56V10, multiclass
    clus
vv   DEL PEAK 27(17P11.2) MUTATED DEL PEAK 27(17P11.2) WILD-TYPE
  R0                          161                            157
  R1                           10                              5
  R2                            1                              0
  RX                           14                              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    84
  DEL PEAK 27(17P11.2) WILD-TYPE                                1    73
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 27(17P11.2) MUTATED                          10    91
  DEL PEAK 27(17P11.2) WILD-TYPE                         7    86
D56V11, multiclass
                                  clus
vv                                 DEL PEAK 27(17P11.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                      84
  BLACK OR AFRICAN AMERICAN                                  10
  WHITE                                                      91
                                  clus
vv                                 DEL PEAK 27(17P11.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        73
  BLACK OR AFRICAN AMERICAN                                     7
  WHITE                                                        86
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V12, binary
                                cls
clus                               0   1
  DEL PEAK 27(17P11.2) MUTATED     8 172
  DEL PEAK 27(17P11.2) WILD-TYPE   5 160
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(17P11.2) MUTATED      8  172
  DEL PEAK 27(17P11.2) WILD-TYPE    5  160
                        clus
vv                       DEL PEAK 27(17P11.2) MUTATED
  HISPANIC OR LATINO                                8
  NOT HISPANIC OR LATINO                          172
                        clus
vv                       DEL PEAK 27(17P11.2) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                            160
[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    60  30
  DEL PEAK 28(18Q21.2) WILD-TYPE 169  99
  DEL PEAK 28(18Q21.2) MUTATED DEL PEAK 28(18Q21.2) WILD-TYPE 
                            90                            268 
  DEL PEAK 28(18Q21.2) MUTATED DEL PEAK 28(18Q21.2) WILD-TYPE 
                            30                             99 
$`DEL PEAK 28(18Q21.2) MUTATED`
TCGA-2Y-A9H3 TCGA-2Y-A9H5 TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1D TCGA-BC-A10R 
       49.84        18.25        10.59         0.66        14.76        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        45.93         0.26        10.36 
TCGA-CC-A5UD TCGA-CC-A7IK TCGA-CC-A8HV TCGA-DD-A118 TCGA-DD-A11A TCGA-DD-A11B 
        9.99         8.61         9.17       113.00         2.60         0.46 
TCGA-DD-A1EF TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A3A4 
       12.95        33.04        13.64        55.69         5.62        20.12 
TCGA-DD-A3A9 TCGA-DD-A4NB TCGA-DD-A4NI TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A73B 
       30.61        32.52        26.83        29.56        73.81         9.30 
TCGA-DD-A73E TCGA-DD-A73G TCGA-DD-AAC8 TCGA-DD-AACB TCGA-DD-AACE TCGA-DD-AACI 
        1.45       114.35         0.53        76.41        63.48        53.19 
TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACV TCGA-DD-AACX TCGA-DD-AACZ 
       42.81        61.68        13.64        50.33         5.59         5.62 
TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AADA TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADO 
       44.22        22.09        40.54        35.67        35.05        14.89 
TCGA-DD-AADV TCGA-DD-AADW TCGA-DD-AAE0 TCGA-DD-AAE2 TCGA-DD-AAEG TCGA-DD-AAEK 
       18.87        19.30        18.25        20.98        23.64        35.08 
TCGA-DD-AAVP TCGA-DD-AAVV TCGA-ED-A459 TCGA-ED-A66X TCGA-ED-A7XP TCGA-ED-A82E 
       79.07        80.71        29.92        13.35        13.15        13.41 
TCGA-ED-A8O6 TCGA-ES-A2HS TCGA-FV-A3I0 TCGA-FV-A3R2 TCGA-FV-A496 TCGA-G3-A25S 
        1.84        22.85        27.88         6.38         0.33        13.68 
TCGA-G3-A7M5 TCGA-G3-AAV1 TCGA-G3-AAV6 TCGA-GJ-A3OU TCGA-KR-A7K7 TCGA-MI-A75G 
       14.70        11.80         2.14        22.92        31.27        22.95 
TCGA-MR-A8JO TCGA-NI-A8LF TCGA-QA-A7B7 TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK 
       10.85        26.27         3.09        19.04        15.39        15.52 
TCGA-RG-A7D4 TCGA-T1-A6J8 TCGA-UB-A7MC TCGA-UB-A7MF TCGA-WX-AA44 TCGA-WX-AA47 
       36.10         0.76        16.44         7.04        20.22        18.28 
TCGA-YA-A8S7 TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       13.55        23.21        35.87        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        38.40        20.81        22.92         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        17.10         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 
       23.38         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-5264 
        4.24         2.86         3.19         3.39         4.24         3.35 
TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A5UE 
        3.32         9.86         9.96        11.93        11.41         8.94 
TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IJ 
        7.13        21.34         9.83        12.00        13.12        12.56 
TCGA-CC-A7IL TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A113 
        9.14         4.60        11.31         6.94         8.15        79.73 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A119 TCGA-DD-A11C TCGA-DD-A11D 
       37.78        83.57        53.33         7.33        21.76        51.29 
TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE 
       90.71        79.40        66.31        19.79        75.65        11.47 
TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EK TCGA-DD-A39V TCGA-DD-A39W 
       45.11        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-A3A5 
       19.76        25.81         7.66        70.06        17.59       102.74 
TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A4NA TCGA-DD-A4ND TCGA-DD-A4NF 
      107.11        13.78         0.36        33.14        90.28        30.97 
TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NP TCGA-DD-A4NQ 
       30.15        30.51        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-A73F TCGA-DD-AA3A TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACC TCGA-DD-AACD 
       35.67        13.48        11.41        75.65        55.40        12.53 
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-AACQ TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACW 
       58.16        14.20        59.31        51.35        51.52        46.82 
TCGA-DD-AACY TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD8 
       47.67         4.50        18.54        21.63        42.58        40.08 
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-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADP TCGA-DD-AADQ 
       34.49        20.91         0.39        29.52        15.06        14.33 
TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADY TCGA-DD-AAE1 TCGA-DD-AAE3 
       66.67        15.58        18.21        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-AAEH TCGA-DD-AAEI TCGA-DD-AAVQ 
       15.72        25.08        26.63        25.78        50.33        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        26.93 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ 
       28.08        13.91         9.73         0.20        12.82         0.20 
TCGA-ED-A7XO TCGA-ED-A8O5 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
       14.04        13.35         0.20        18.74        19.99        20.61 
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-A3I1 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A4ZP 
       23.97        19.10         8.12        12.03         0.03        81.73 
TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X 
        0.39        51.06        53.79        28.27        30.74        58.49 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ 
       14.86        21.53        22.13        25.64         5.92        19.53 
TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC 
       19.23        25.25        22.95        20.42        17.10        22.06 
TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV0 
       20.78        11.87        14.14         1.84        15.78        15.65 
TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV7 TCGA-GJ-A6C0 
       12.23        13.55         0.89         8.75        11.87         1.02 
TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 
        2.20         2.99        37.71        20.75        17.06        16.83 
TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC 
       11.80         2.14        21.60        29.79        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        24.56        20.71         7.53 
TCGA-NI-A4U2 TCGA-O8-A75V TCGA-PD-A5DF TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-UB-A7MA 
       58.88        17.69        21.01        21.04        19.33        17.59 
TCGA-UB-A7MB TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WJ-A86L 
       19.76         1.71        15.98        10.75        10.32        11.34 
TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA46 TCGA-XR-A8TF TCGA-ZP-A9CV TCGA-ZP-A9CY 
        0.99        12.99        24.85        22.78        35.77        25.71 
TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD 
        0.69        25.15        12.99        45.57 

  DEL PEAK 28(18Q21.2) MUTATED DEL PEAK 28(18Q21.2) WILD-TYPE 
                          0.26                           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 
                        18.955                         19.890 
[1] "0.3 - 114.3 (19.0)" "0.0 - 120.8 (19.9)"
[1] "hr=" "1"  
D57V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IIIA
  DEL PEAK 28(18Q21.2) MUTATED        44       22         0         16
  DEL PEAK 28(18Q21.2) WILD-TYPE     127       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                              44                            127
  STAGE II                             22                             63
  STAGE III                             0                              3
  STAGE IIIA                           16                             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      48  24  18   2
  DEL PEAK 28(18Q21.2) WILD-TYPE   134  68  56  10
D57V4, multiclass
       clus
vv      DEL PEAK 28(18Q21.2) MUTATED DEL PEAK 28(18Q21.2) WILD-TYPE
  T0+T1                           48                            134
  T2                              24                             68
  T3                              18                             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    63   1
  DEL PEAK 28(18Q21.2) WILD-TYPE 187   2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 28(18Q21.2) MUTATED     63    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                           63                            187
  1                            1                              2
[1] 2 2
[1] FALSE
D57V6, binary
                                cls
clus                               0   1
  DEL PEAK 28(18Q21.2) MUTATED    67   2
  DEL PEAK 28(18Q21.2) WILD-TYPE 194   2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 28(18Q21.2) MUTATED     67    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                           67                            194
  1                            2                              2
[1] 2 2
[1] FALSE
D57V7, binary
                                cls
clus                               0   1
  DEL PEAK 28(18Q21.2) MUTATED    34  58
  DEL PEAK 28(18Q21.2) WILD-TYPE  81 189
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 28(18Q21.2) MUTATED     34   58
  DEL PEAK 28(18Q21.2) WILD-TYPE   81  189
        clus
vv       DEL PEAK 28(18Q21.2) MUTATED DEL PEAK 28(18Q21.2) WILD-TYPE
  FEMALE                           34                             81
  MALE                             58                            189
[1] 2 2
[1] FALSE
D57V8, binary
                                cls
clus                               0   1
  DEL PEAK 28(18Q21.2) MUTATED    80   4
  DEL PEAK 28(18Q21.2) WILD-TYPE 256   3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 28(18Q21.2) MUTATED     80    4
  DEL PEAK 28(18Q21.2) WILD-TYPE  256    3
     clus
vv    DEL PEAK 28(18Q21.2) MUTATED DEL PEAK 28(18Q21.2) WILD-TYPE
  NO                            80                            256
  YES                            4                              3
[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                         88
  DEL PEAK 28(18Q21.2) WILD-TYPE                      265
                                vv
clus                             HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK 28(18Q21.2) MUTATED                                  2
  DEL PEAK 28(18Q21.2) WILD-TYPE                                5
D57V9, multiclass
                                  clus
vv                                 DEL PEAK 28(18Q21.2) MUTATED
  FIBROLAMELLAR CARCINOMA                                     2
  HEPATOCELLULAR CARCINOMA                                   88
  HEPATOCHOLANGIOCARCINOMA (MIXED)                            2
                                  clus
vv                                 DEL PEAK 28(18Q21.2) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                       0
  HEPATOCELLULAR CARCINOMA                                    265
  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    82   2   0   8
  DEL PEAK 28(18Q21.2) WILD-TYPE 236  13   1  13
D57V10, multiclass
    clus
vv   DEL PEAK 28(18Q21.2) MUTATED DEL PEAK 28(18Q21.2) WILD-TYPE
  R0                           82                            236
  R1                            2                             13
  R2                            0                              1
  RX                            8                             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    41
  DEL PEAK 28(18Q21.2) WILD-TYPE                                1   116
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 28(18Q21.2) MUTATED                           5    46
  DEL PEAK 28(18Q21.2) WILD-TYPE                        12   131
D57V11, multiclass
                                  clus
vv                                 DEL PEAK 28(18Q21.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                      41
  BLACK OR AFRICAN AMERICAN                                   5
  WHITE                                                      46
                                  clus
vv                                 DEL PEAK 28(18Q21.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                       116
  BLACK OR AFRICAN AMERICAN                                    12
  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"
D57V12, binary
                                cls
clus                               0   1
  DEL PEAK 28(18Q21.2) MUTATED     5  82
  DEL PEAK 28(18Q21.2) WILD-TYPE   8 250
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 28(18Q21.2) MUTATED      5   82
  DEL PEAK 28(18Q21.2) WILD-TYPE    8  250
                        clus
vv                       DEL PEAK 28(18Q21.2) MUTATED
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                           82
                        clus
vv                       DEL PEAK 28(18Q21.2) WILD-TYPE
  HISPANIC OR LATINO                                  8
  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    49  34
  DEL PEAK 29(19P13.3) WILD-TYPE 180  95
  DEL PEAK 29(19P13.3) MUTATED DEL PEAK 29(19P13.3) WILD-TYPE 
                            83                            275 
  DEL PEAK 29(19P13.3) MUTATED DEL PEAK 29(19P13.3) WILD-TYPE 
                            34                             95 
$`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        49.84 
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-CC-A5UD 
       18.48         4.24         4.24         3.32        11.93         9.99 
TCGA-CC-A5UE TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7II TCGA-CC-A7IK TCGA-CC-A7IL 
        8.94        21.34         9.83        13.12         8.61         9.14 
TCGA-DD-A113 TCGA-DD-A118 TCGA-DD-A11A TCGA-DD-A1EG TCGA-DD-A1EI TCGA-DD-A1EJ 
       79.73       113.00         2.60        45.11         6.02        33.04 
TCGA-DD-A1EL TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A3A9 TCGA-DD-A4NJ TCGA-DD-A4NQ 
       13.64        55.69         5.62        30.61        30.51        12.26 
TCGA-DD-A73D TCGA-DD-AACB TCGA-DD-AACE TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACL 
       22.78        76.41        63.48        15.42         6.41         3.52 
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-AACZ TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADB TCGA-DD-AADC 
        5.62        44.22        22.09        40.08        40.83        13.97 
TCGA-DD-AADD TCGA-DD-AADL TCGA-DD-AADV TCGA-DD-AAE6 TCGA-DD-AAE8 TCGA-DD-AAEG 
       40.47        20.91        18.87         4.64        21.83        23.64 
TCGA-DD-AAVR TCGA-DD-AAVV TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A7PZ TCGA-ED-A7XO 
       82.62        80.71        29.92        26.93         0.20        14.04 
TCGA-ED-A8O6 TCGA-ED-A97K TCGA-FV-A3I1 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-G3-A25S 
        1.84         0.20         8.12         0.33        81.73        13.68 
TCGA-G3-A25X TCGA-G3-A3CH TCGA-G3-A5SM TCGA-G3-A7M6 TCGA-G3-AAV1 TCGA-G3-AAV7 
       58.49        25.64        17.10        20.78        11.80        11.87 
TCGA-MI-A75C TCGA-NI-A8LF TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-T1-A6J8 
        9.57        26.27        15.52        36.10         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        38.40        20.81        22.92 
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        17.10 
TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R 
       14.76         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        23.38         1.12 
TCGA-BC-A110 TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69I 
       69.57        44.42        45.93        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-5264 TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A5UC 
        3.39         3.35         9.86         9.96        10.36        11.41 
TCGA-CC-A7IE TCGA-CC-A7IH TCGA-CC-A7IJ TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV 
        7.13        12.00        12.56         4.60        11.31         9.17 
TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A119 
        6.94         8.15        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-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EK 
       19.79        75.65        11.47        12.95        49.15        18.35 
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-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-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-A73E 
       80.75        78.84        23.93         9.30        23.05         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-AACC TCGA-DD-AACD TCGA-DD-AACF TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK 
       55.40        12.53        12.00        53.19        69.11         0.30 
TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACT TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY 
       58.16        42.81        51.35        46.82         5.59        47.67 
TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AADA TCGA-DD-AADE 
        4.50        18.54        21.63        42.58        40.54        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-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-AAE7 TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB 
       18.61        19.99        21.17        23.74        18.90        15.72 
TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP 
       25.08        26.63        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-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A5KG 
       62.47        66.25        65.39        49.48        53.69        28.08 
TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7XP 
       13.91        13.35         9.73         0.20        12.82        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-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 
       23.97        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-A25Y 
        0.39        51.06        53.79        28.27        30.74        14.86 
TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI 
       21.53        22.13         5.92        19.53        19.23        25.25 
TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A6UC TCGA-G3-A7M5 TCGA-G3-A7M7 TCGA-G3-A7M8 
       22.95        20.42        22.06        14.70        11.87        14.14 
TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 
        1.84        15.78        15.65        12.23        13.55         0.89 
TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ 
        8.75         2.14        22.92         1.02         2.20         2.99 
TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 
       37.71        20.75        17.06        16.83        11.80         2.14 
TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD 
       21.60        31.27        29.79        12.72        13.97        12.03 
TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO 
       16.67        22.95        24.56        20.71         7.53        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-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD 
       19.04        15.39        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-A9G7 
       15.98         7.04        10.75        10.32        11.34         0.99 
TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TF TCGA-YA-A8S7 
       12.99        20.22        24.85        18.28        22.78        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        35.87         0.69        25.15 
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 29(19P13.3) MUTATED DEL PEAK 29(19P13.3) WILD-TYPE 
                          0.20                           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 
                         17.10                          19.99 
[1] "0.2 - 113.0 (17.1)" "0.0 - 120.8 (20.0)"
[1] "hr=" "1.3"
D58V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IIIA
  DEL PEAK 29(19P13.3) MUTATED        35       26         0         15
  DEL PEAK 29(19P13.3) WILD-TYPE     136       59         3         45
                                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                            136
  STAGE II                             26                             59
  STAGE III                             0                              3
  STAGE IIIA                           15                             45
  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  27  16   5
  DEL PEAK 29(19P13.3) WILD-TYPE   145  65  58   7
D58V4, multiclass
       clus
vv      DEL PEAK 29(19P13.3) MUTATED DEL PEAK 29(19P13.3) WILD-TYPE
  T0+T1                           37                            145
  T2                              27                             65
  T3                              16                             58
  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    62   1
  DEL PEAK 29(19P13.3) WILD-TYPE 188   2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(19P13.3) MUTATED     62    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                           62                            188
  1                            1                              2
[1] 2 2
[1] FALSE
D58V6, binary
                                cls
clus                               0   1
  DEL PEAK 29(19P13.3) MUTATED    69   1
  DEL PEAK 29(19P13.3) WILD-TYPE 192   3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(19P13.3) MUTATED     69    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                           69                            192
  1                            1                              3
[1] 2 2
[1] FALSE
D58V7, binary
                                cls
clus                               0   1
  DEL PEAK 29(19P13.3) MUTATED    24  61
  DEL PEAK 29(19P13.3) WILD-TYPE  91 186
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(19P13.3) MUTATED     24   61
  DEL PEAK 29(19P13.3) WILD-TYPE   91  186
        clus
vv       DEL PEAK 29(19P13.3) MUTATED DEL PEAK 29(19P13.3) WILD-TYPE
  FEMALE                           24                             91
  MALE                             61                            186
[1] 2 2
[1] FALSE
D58V8, binary
                                cls
clus                               0   1
  DEL PEAK 29(19P13.3) MUTATED    76   1
  DEL PEAK 29(19P13.3) WILD-TYPE 260   6
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(19P13.3) MUTATED     76    1
  DEL PEAK 29(19P13.3) WILD-TYPE  260    6
     clus
vv    DEL PEAK 29(19P13.3) MUTATED DEL PEAK 29(19P13.3) WILD-TYPE
  NO                            76                            260
  YES                            1                              6
[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                         84
  DEL PEAK 29(19P13.3) WILD-TYPE                      269
                                vv
clus                             HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK 29(19P13.3) MUTATED                                  1
  DEL PEAK 29(19P13.3) WILD-TYPE                                6
D58V9, multiclass
                                  clus
vv                                 DEL PEAK 29(19P13.3) MUTATED
  FIBROLAMELLAR CARCINOMA                                     0
  HEPATOCELLULAR CARCINOMA                                   84
  HEPATOCHOLANGIOCARCINOMA (MIXED)                            1
                                  clus
vv                                 DEL PEAK 29(19P13.3) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                       2
  HEPATOCELLULAR CARCINOMA                                    269
  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    77   3   0   4
  DEL PEAK 29(19P13.3) WILD-TYPE 241  12   1  17
D58V10, multiclass
    clus
vv   DEL PEAK 29(19P13.3) MUTATED DEL PEAK 29(19P13.3) WILD-TYPE
  R0                           77                            241
  R1                            3                             12
  R2                            0                              1
  RX                            4                             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 29(19P13.3) MUTATED                                  0    51
  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   146
D58V11, multiclass
                                  clus
vv                                 DEL PEAK 29(19P13.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                      51
  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                                                       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"
D58V12, binary
                                cls
clus                               0   1
  DEL PEAK 29(19P13.3) MUTATED     3  81
  DEL PEAK 29(19P13.3) WILD-TYPE  10 251
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(19P13.3) MUTATED      3   81
  DEL PEAK 29(19P13.3) WILD-TYPE   10  251
                        clus
vv                       DEL PEAK 29(19P13.3) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           81
                        clus
vv                       DEL PEAK 29(19P13.3) WILD-TYPE
  HISPANIC OR LATINO                                 10
  NOT HISPANIC OR LATINO                            251
[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    17  10
  DEL PEAK 30(20P12.1) WILD-TYPE 212 119
  DEL PEAK 30(20P12.1) MUTATED DEL PEAK 30(20P12.1) WILD-TYPE 
                            27                            331 
  DEL PEAK 30(20P12.1) MUTATED DEL PEAK 30(20P12.1) WILD-TYPE 
                            10                            119 
$`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        14.76         1.12        11.93 
TCGA-CC-A7IH TCGA-CC-A7IL TCGA-CC-A9FS TCGA-DD-A1EK TCGA-DD-A39V TCGA-DD-A39Y 
       12.00         9.14         6.94        18.35        21.14         5.62 
TCGA-DD-A3A3 TCGA-DD-A3A5 TCGA-DD-A4NO TCGA-DD-A4NQ TCGA-DD-A73F TCGA-DD-AACS 
       17.59       102.74        73.81        12.26        35.67        59.31 
TCGA-DD-AACX TCGA-DD-AACZ TCGA-DD-AAD5 TCGA-DD-AADA TCGA-DD-AADJ TCGA-DD-AADM 
        5.59         5.62        44.22        40.54        35.05         0.39 
TCGA-ED-A7PX TCGA-ED-A97K TCGA-MR-A8JO 
        0.20         0.20        10.85 

$`DEL PEAK 30(20P12.1) WILD-TYPE`
TCGA-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        49.84 
TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H7 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA 
       47.74        18.25        38.40        20.81        22.92         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        17.10         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        23.38        69.57         5.03 
TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H 
       44.42        45.93         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-5264 
        4.24         2.86         3.19         3.39         4.24         3.35 
TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A5UC TCGA-CC-A5UD 
        3.32         9.86         9.96        10.36        11.41         9.99 
TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7II TCGA-CC-A7IJ 
        8.94         7.13        21.34         9.83        13.12        12.56 
TCGA-CC-A7IK TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FW TCGA-DD-A113 
        8.61         4.60        11.31         9.17         8.15        79.73 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A 
       37.78        83.57        53.33       113.00         7.33         2.60 
TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB 
        0.46        21.76        51.29        90.71        79.40        66.31 
TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH 
       19.79        75.65        11.47        12.95        45.11        49.15 
TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Z 
        6.02        33.04        13.64        27.19        55.69        19.76 
TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A4 TCGA-DD-A3A6 TCGA-DD-A3A7 
       25.81         7.66        70.06        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-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN 
       30.15        26.83        30.51        39.78        56.25        29.56 
TCGA-DD-A4NP TCGA-DD-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-A73D TCGA-DD-A73E TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 
       23.05        22.78         1.45       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-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-AACT TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACY TCGA-DD-AAD0 
       51.35        51.52        50.33        46.82        47.67         4.50 
TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADB 
       18.54        21.63        42.58        22.09        40.08        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-AADL TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ 
       34.49        20.91        29.52        14.89        15.06        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-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 
       26.63        23.64        25.78        50.33        35.08        79.07 
TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVV TCGA-DD-AAVW 
       89.69        82.62        59.93        72.39        80.71        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        29.92        26.93        28.08        13.91        13.35 
TCGA-ED-A66Y TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E 
        9.73        12.82         0.20        14.04        13.15        13.41 
TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB 
       13.35         1.84        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-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-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-A7M5 TCGA-G3-A7M6 
       22.95        20.42        17.10        22.06        14.70        20.78 
TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 
       11.87        14.14         1.84        15.78        15.65        11.80 
TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 
       12.23        13.55         0.89         8.75         2.14        11.87 
TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF 
       22.92         1.02         2.20         2.99        37.71        20.75 
TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 
       17.06        16.83        11.80         2.14        21.60        31.27 
TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E 
       29.79        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 
       22.95        24.56        20.71         7.53        58.88        26.27 
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        36.10         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-AA44 TCGA-WX-AA46 TCGA-WX-AA47 
       11.34         0.99        12.99        20.22        24.85        18.28 
TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 
       22.78        13.55        35.77        25.71        23.21        35.87 
TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CF 
        0.69        25.15        12.99        45.57        40.80        79.30 
TCGA-ZS-A9CG 
       11.21 

  DEL PEAK 30(20P12.1) MUTATED DEL PEAK 30(20P12.1) WILD-TYPE 
                          0.20                           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 
                         12.00                          20.22 
[1] "0.2 - 102.7 (12.0)" "0.0 - 120.8 (20.2)"
[1] "hr=" "1.3"
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     159       78         2         55
                                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                            159
  STAGE II                              7                             78
  STAGE III                             1                              2
  STAGE IIIA                            5                             55
  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   170  85  67  11
D59V4, multiclass
       clus
vv      DEL PEAK 30(20P12.1) MUTATED DEL PEAK 30(20P12.1) WILD-TYPE
  T0+T1                           12                            170
  T2                               7                             85
  T3                               7                             67
  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 228   3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(20P12.1) MUTATED     22    0
  DEL PEAK 30(20P12.1) WILD-TYPE  228    3
   clus
vv  DEL PEAK 30(20P12.1) MUTATED DEL PEAK 30(20P12.1) WILD-TYPE
  0                           22                            228
  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 239   3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(20P12.1) MUTATED     22    1
  DEL PEAK 30(20P12.1) WILD-TYPE  239    3
   clus
vv  DEL PEAK 30(20P12.1) MUTATED DEL PEAK 30(20P12.1) WILD-TYPE
  0                           22                            239
  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 105 230
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(20P12.1) MUTATED     10   17
  DEL PEAK 30(20P12.1) WILD-TYPE  105  230
        clus
vv       DEL PEAK 30(20P12.1) MUTATED DEL PEAK 30(20P12.1) WILD-TYPE
  FEMALE                           10                            105
  MALE                             17                            230
[1] 2 2
[1] FALSE
D59V8, binary
                                cls
clus                               0   1
  DEL PEAK 30(20P12.1) MUTATED    24   2
  DEL PEAK 30(20P12.1) WILD-TYPE 312   5
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(20P12.1) MUTATED     24    2
  DEL PEAK 30(20P12.1) WILD-TYPE  312    5
     clus
vv    DEL PEAK 30(20P12.1) MUTATED DEL PEAK 30(20P12.1) WILD-TYPE
  NO                            24                            312
  YES                            2                              5
[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                      328
                                vv
clus                             HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK 30(20P12.1) MUTATED                                  1
  DEL PEAK 30(20P12.1) WILD-TYPE                                6
D59V9, 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                                    328
  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 293  15   1  19
D59V10, multiclass
    clus
vv   DEL PEAK 30(20P12.1) MUTATED DEL PEAK 30(20P12.1) WILD-TYPE
  R0                           25                            293
  R1                            0                             15
  R2                            0                              1
  RX                            2                             19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 30(20P12.1) MUTATED                                  0    15
  DEL PEAK 30(20P12.1) WILD-TYPE                                1   142
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 30(20P12.1) MUTATED                           1    11
  DEL PEAK 30(20P12.1) WILD-TYPE                        16   166
D59V11, 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                                                       142
  BLACK OR AFRICAN AMERICAN                                    16
  WHITE                                                       166
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V12, binary
                                cls
clus                               0   1
  DEL PEAK 30(20P12.1) MUTATED     1  25
  DEL PEAK 30(20P12.1) WILD-TYPE  12 307
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(20P12.1) MUTATED      1   25
  DEL PEAK 30(20P12.1) WILD-TYPE   12  307
                        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                                 12
  NOT HISPANIC OR LATINO                            307
[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  28
  DEL PEAK 31(22Q12.1) WILD-TYPE 184 101
  DEL PEAK 31(22Q12.1) MUTATED DEL PEAK 31(22Q12.1) WILD-TYPE 
                            73                            285 
  DEL PEAK 31(22Q12.1) MUTATED DEL PEAK 31(22Q12.1) WILD-TYPE 
                            28                            101 
$`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        49.84        47.74         1.18        10.78 
TCGA-5R-AA1D TCGA-BC-A10Q TCGA-BC-A10T TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A5W4 
       14.76        37.32        27.52        45.93         0.26        17.98 
TCGA-BC-A69H TCGA-BC-A8YO TCGA-BD-A3EP TCGA-CC-5260 TCGA-CC-5264 TCGA-CC-A1HT 
       14.60        18.48        13.45         2.86         3.35         3.32 
TCGA-CC-A5UD TCGA-CC-A7IK TCGA-CC-A8HU TCGA-CC-A8HV TCGA-DD-A113 TCGA-DD-A114 
        9.99         8.61        11.31         9.17        79.73        37.78 
TCGA-DD-A11A TCGA-DD-A1EB TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A3A4 TCGA-DD-A3A6 
        2.60        66.31        55.69         5.62        20.12       107.11 
TCGA-DD-A4NB TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A73B 
       32.52        26.83        30.51        73.81       108.76         9.30 
TCGA-DD-AAC8 TCGA-DD-AACZ TCGA-DD-AAD5 TCGA-DD-AADF TCGA-DD-AADJ TCGA-DD-AADQ 
        0.53         5.62        44.22         3.78        35.05        14.33 
TCGA-DD-AADS TCGA-DD-AAE3 TCGA-DD-AAEE TCGA-DD-AAVR TCGA-ED-A459 TCGA-ED-A66Y 
       15.58        18.61        26.63        82.62        29.92         9.73 
TCGA-ED-A7PX TCGA-ED-A7XO TCGA-ED-A7XP TCGA-EP-A2KB TCGA-FV-A495 TCGA-FV-A4ZP 
        0.20        14.04        13.15        19.59         0.03        81.73 
TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A5SI TCGA-G3-A7M5 TCGA-G3-A7M9 TCGA-G3-AAV3 
       13.68        51.06        25.25        14.70         1.84        13.55 
TCGA-K7-A5RG TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-MI-A75G TCGA-MI-A75I 
       17.06        11.80        21.60        31.27        22.95        20.71 
TCGA-MR-A8JO TCGA-QA-A7B7 TCGA-RG-A7D4 TCGA-T1-A6J8 TCGA-UB-A7MC TCGA-WQ-AB4B 
       10.85         3.09        36.10         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        38.40 
TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-4R-AA8I TCGA-5C-A9VH 
       20.81        22.92         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        17.10         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        23.38         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         4.24         3.19         3.39         4.24 
TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A5UE 
        9.86         9.96        10.36        11.93        11.41         8.94 
TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IJ 
        7.13        21.34         9.83        12.00        13.12        12.56 
TCGA-CC-A7IL TCGA-CC-A8HT TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A115 TCGA-DD-A116 
        9.14         4.60         6.94         8.15        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-AAVV TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 
       80.71        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        26.93        28.08        13.91 
TCGA-ED-A66X TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 
       13.35        12.82         0.20        13.41        13.35         1.84 
TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3JL 
        0.20        18.74        19.99        20.61         0.62         9.96 
TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR 
       11.93        22.85        14.40        60.89        23.97        19.10 
TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A496 TCGA-FV-A4ZQ 
       27.88         8.12         6.38        12.03         0.33         0.39 
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-A7M8 
       20.42        17.10        22.06        20.78        11.87        14.14 
TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV4 TCGA-G3-AAV5 
       15.78        15.65        11.80        12.23         0.89         8.75 
TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ 
        2.14        11.87        22.92         1.02         2.20         2.99 
TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K8 TCGA-LG-A6GG 
       37.71        20.75        16.83         2.14        29.79        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        24.56         7.53 
TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-RC-A7S9 TCGA-RC-A7SB 
       58.88        26.27        17.69        21.01        21.04        19.33 
TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MD 
       19.04        15.39        15.52        17.59        19.76         1.71 
TCGA-UB-A7ME TCGA-UB-A7MF TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-A9G7 
       15.98         7.04        10.75        10.32        11.34         0.99 
TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CV 
       20.22        24.85        18.28        22.78        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        35.87         0.69        25.15        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                           0.20 
  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 
                         17.06                          20.22 
[1] "0.0 - 120.8 (17.1)" "0.2 - 114.3 (20.2)"
[1] "hr=" "1.1"
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     144       60         3         46
                                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                            144
  STAGE II                             25                             60
  STAGE III                             0                              3
  STAGE IIIA                           14                             46
  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   154  63  59   9
D60V4, multiclass
       clus
vv      DEL PEAK 31(22Q12.1) MUTATED DEL PEAK 31(22Q12.1) WILD-TYPE
  T0+T1                           28                            154
  T2                              29                             63
  T3                              15                             59
  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 202   3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(22Q12.1) MUTATED     48    0
  DEL PEAK 31(22Q12.1) WILD-TYPE  202    3
   clus
vv  DEL PEAK 31(22Q12.1) MUTATED DEL PEAK 31(22Q12.1) WILD-TYPE
  0                           48                            202
  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 204   3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(22Q12.1) MUTATED     57    1
  DEL PEAK 31(22Q12.1) WILD-TYPE  204    3
   clus
vv  DEL PEAK 31(22Q12.1) MUTATED DEL PEAK 31(22Q12.1) WILD-TYPE
  0                           57                            204
  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  88 199
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(22Q12.1) MUTATED     27   48
  DEL PEAK 31(22Q12.1) WILD-TYPE   88  199
        clus
vv       DEL PEAK 31(22Q12.1) MUTATED DEL PEAK 31(22Q12.1) WILD-TYPE
  FEMALE                           27                             88
  MALE                             48                            199
[1] 2 2
[1] FALSE
D60V8, binary
                                cls
clus                               0   1
  DEL PEAK 31(22Q12.1) MUTATED    68   2
  DEL PEAK 31(22Q12.1) WILD-TYPE 268   5
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(22Q12.1) MUTATED     68    2
  DEL PEAK 31(22Q12.1) WILD-TYPE  268    5
     clus
vv    DEL PEAK 31(22Q12.1) MUTATED DEL PEAK 31(22Q12.1) WILD-TYPE
  NO                            68                            268
  YES                            2                              5
[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                      282
                                vv
clus                             HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK 31(22Q12.1) MUTATED                                  2
  DEL PEAK 31(22Q12.1) WILD-TYPE                                5
D60V9, 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                                    282
  HEPATOCHOLANGIOCARCINOMA (MIXED)                              5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 31(22Q12.1) MUTATED    61   5   0   8
  DEL PEAK 31(22Q12.1) WILD-TYPE 257  10   1  13
D60V10, multiclass
    clus
vv   DEL PEAK 31(22Q12.1) MUTATED DEL PEAK 31(22Q12.1) WILD-TYPE
  R0                           61                            257
  R1                            5                             10
  R2                            0                              1
  RX                            8                             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 31(22Q12.1) MUTATED                                  0    25
  DEL PEAK 31(22Q12.1) WILD-TYPE                                1   132
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 31(22Q12.1) MUTATED                           8    41
  DEL PEAK 31(22Q12.1) WILD-TYPE                         9   136
D60V11, 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                                                       132
  BLACK OR AFRICAN AMERICAN                                     9
  WHITE                                                       136
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V12, binary
                                cls
clus                               0   1
  DEL PEAK 31(22Q12.1) MUTATED     5  64
  DEL PEAK 31(22Q12.1) WILD-TYPE   8 268
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(22Q12.1) MUTATED      5   64
  DEL PEAK 31(22Q12.1) WILD-TYPE    8  268
                        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                                  8
  NOT HISPANIC OR LATINO                            268
[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    44  33
  DEL PEAK 32(22Q13.32) WILD-TYPE 185  96
  DEL PEAK 32(22Q13.32) MUTATED DEL PEAK 32(22Q13.32) WILD-TYPE 
                             77                             281 
  DEL PEAK 32(22Q13.32) MUTATED DEL PEAK 32(22Q13.32) WILD-TYPE 
                             33                              96 
$`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        49.84        47.74        10.78        14.76 
TCGA-BC-A10Q TCGA-BC-A10T TCGA-BC-A10Y TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG 
       37.32        27.52        23.38        45.93         0.26        22.36 
TCGA-BC-A5W4 TCGA-BC-A8YO TCGA-BD-A3EP TCGA-CC-5260 TCGA-CC-5264 TCGA-CC-A1HT 
       17.98        18.48        13.45         2.86         3.35         3.32 
TCGA-CC-A3M9 TCGA-CC-A5UD TCGA-CC-A7IK TCGA-CC-A8HU TCGA-DD-A113 TCGA-DD-A114 
        9.86         9.99         8.61        11.31        79.73        37.78 
TCGA-DD-A115 TCGA-DD-A1EB TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A3A5 TCGA-DD-A3A6 
       83.57        66.31        55.69         5.62       102.74       107.11 
TCGA-DD-A3A7 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NO 
       13.78        33.14        32.52        26.83        30.51        73.81 
TCGA-DD-A4NP TCGA-DD-A73B TCGA-DD-AAC8 TCGA-DD-AACZ TCGA-DD-AADD TCGA-DD-AADF 
      108.76         9.30         0.53         5.62        40.47         3.78 
TCGA-DD-AADQ TCGA-DD-AADS TCGA-DD-AADV TCGA-DD-AAE3 TCGA-DD-AAEE TCGA-ED-A459 
       14.33        15.58        18.87        18.61        26.63        29.92 
TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7XO TCGA-ED-A7XP TCGA-EP-A2KB TCGA-FV-A2QR 
        9.73         0.20        14.04        13.15        19.59        19.10 
TCGA-FV-A4ZP TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A3CJ TCGA-G3-A5SI TCGA-G3-A7M5 
       81.73        13.68        51.06        19.53        25.25        14.70 
TCGA-G3-A7M9 TCGA-G3-AAV3 TCGA-K7-A5RG TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-KR-A7K7 
        1.84        13.55        17.06        11.80        21.60        31.27 
TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-PD-A5DF TCGA-QA-A7B7 
       22.95        20.71        10.85        58.88        21.01         3.09 
TCGA-RG-A7D4 TCGA-T1-A6J8 TCGA-UB-A7MC TCGA-WQ-AB4B TCGA-ZS-A9CF 
       36.10         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        38.40 
TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-4R-AA8I 
       20.81        22.92         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        17.10         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         4.24         3.19         3.39         4.24 
TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A5UE TCGA-CC-A7IE 
        9.96        10.36        11.93        11.41         8.94         7.13 
TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IL 
       21.34         9.83        12.00        13.12        12.56         9.14 
TCGA-CC-A8HT TCGA-CC-A8HV TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A116 TCGA-DD-A118 
        4.60         9.17         6.94         8.15        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-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-A3A4 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH 
       20.12         0.36        30.61        90.28        30.97        30.15 
TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS 
       39.78        56.25        29.56        12.26         0.30        80.75 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F 
       78.84        23.93        23.05        22.78         1.45        35.67 
TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC 
      114.35        13.48        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-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-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-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-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-AADN TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADR 
       20.91         0.39        29.52        14.89        15.06        66.67 
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-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-AAEG TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAEK 
       15.72        25.08        23.64        25.78        50.33        35.08 
TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVV 
       79.07        89.69        82.62        59.93        72.39        80.71 
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        26.93        28.08        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-A3I0 TCGA-FV-A3I1 
       22.85        14.40        60.89        23.97        27.88         8.12 
TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25U 
        6.38        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-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM 
       25.64         5.92        19.23        22.95        20.42        17.10 
TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV0 
       22.06        20.78        11.87        14.14        15.78        15.65 
TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 
       11.80        12.23         0.89         8.75         2.14        11.87 
TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF 
       22.92         1.02         2.20         2.99        37.71        20.75 
TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD 
       16.83         2.14        29.79        12.72        13.97        12.03 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75H TCGA-MR-A520 TCGA-NI-A8LF TCGA-O8-A75V 
        9.57        16.67        24.56         7.53        26.27        17.69 
TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-UB-A7MA 
       21.04        19.33        19.04        15.39        15.52        17.59 
TCGA-UB-A7MB TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-A7MF TCGA-UB-AA0U TCGA-UB-AA0V 
       19.76         1.71        15.98         7.04        10.75        10.32 
TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TF 
       11.34         0.99        20.22        24.85        18.28        22.78 
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        35.87         0.69 
TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CG 
       25.15        12.99        45.57        40.80        11.21 

  DEL PEAK 32(22Q13.32) MUTATED DEL PEAK 32(22Q13.32) WILD-TYPE 
                           0.20                            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 
                          19.10                           19.99 
[1] "0.2 - 120.8 (19.1)" "0.0 - 114.3 (20.0)"
[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     145       62         2         44
                                 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                             145
  STAGE II                              23                              62
  STAGE III                              1                               2
  STAGE IIIA                            16                              44
  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   155  64  55   7
D61V4, multiclass
       clus
vv      DEL PEAK 32(22Q13.32) MUTATED DEL PEAK 32(22Q13.32) WILD-TYPE
  T0+T1                            27                             155
  T2                               28                              64
  T3                               19                              55
  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 198   2
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 32(22Q13.32) MUTATED     52    1
  DEL PEAK 32(22Q13.32) WILD-TYPE  198    2
   clus
vv  DEL PEAK 32(22Q13.32) MUTATED DEL PEAK 32(22Q13.32) WILD-TYPE
  0                            52                             198
  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 201   3
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 32(22Q13.32) MUTATED     60    1
  DEL PEAK 32(22Q13.32) WILD-TYPE  201    3
   clus
vv  DEL PEAK 32(22Q13.32) MUTATED DEL PEAK 32(22Q13.32) WILD-TYPE
  0                            60                             201
  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  87 196
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 32(22Q13.32) MUTATED     28   51
  DEL PEAK 32(22Q13.32) WILD-TYPE   87  196
        clus
vv       DEL PEAK 32(22Q13.32) MUTATED DEL PEAK 32(22Q13.32) WILD-TYPE
  FEMALE                            28                              87
  MALE                              51                             196
[1] 2 2
[1] FALSE
D61V8, binary
                                 cls
clus                                0   1
  DEL PEAK 32(22Q13.32) MUTATED    74   2
  DEL PEAK 32(22Q13.32) WILD-TYPE 262   5
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 32(22Q13.32) MUTATED     74    2
  DEL PEAK 32(22Q13.32) WILD-TYPE  262    5
     clus
vv    DEL PEAK 32(22Q13.32) MUTATED DEL PEAK 32(22Q13.32) WILD-TYPE
  NO                             74                             262
  YES                             2                               5
[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                      278
                                 vv
clus                              HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK 32(22Q13.32) MUTATED                                  2
  DEL PEAK 32(22Q13.32) WILD-TYPE                                5
D61V9, 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                                     278
  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 255  10   1  12
D61V10, multiclass
    clus
vv   DEL PEAK 32(22Q13.32) MUTATED DEL PEAK 32(22Q13.32) WILD-TYPE
  R0                            63                             255
  R1                             5                              10
  R2                             0                               1
  RX                             9                              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 32(22Q13.32) MUTATED                                  1    24
  DEL PEAK 32(22Q13.32) WILD-TYPE                                0   133
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 32(22Q13.32) MUTATED                           7    45
  DEL PEAK 32(22Q13.32) WILD-TYPE                        10   132
D61V11, 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                                                        133
  BLACK OR AFRICAN AMERICAN                                     10
  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"
D61V12, binary
                                 cls
clus                                0   1
  DEL PEAK 32(22Q13.32) MUTATED     5  66
  DEL PEAK 32(22Q13.32) WILD-TYPE   8 266
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 32(22Q13.32) MUTATED      5   66
  DEL PEAK 32(22Q13.32) WILD-TYPE    8  266
                        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                                   8
  NOT HISPANIC OR LATINO                             266
[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    39  27
  DEL PEAK 33(XQ26.2) WILD-TYPE 190 102
  DEL PEAK 33(XQ26.2) MUTATED DEL PEAK 33(XQ26.2) WILD-TYPE 
                           66                           292 
  DEL PEAK 33(XQ26.2) MUTATED DEL PEAK 33(XQ26.2) WILD-TYPE 
                           27                           102 
$`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        45.93 
TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-A3MA 
        0.26        22.36        17.98         4.24         2.86         9.96 
TCGA-CC-A3MB TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A7IE TCGA-CC-A7IJ TCGA-CC-A7IL 
       10.36        11.41         9.99         7.13        12.56         9.14 
TCGA-CC-A8HU TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A11B TCGA-DD-A4NA TCGA-DD-A4NO 
       11.31        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        26.63        72.39        29.92         0.20         0.20 
TCGA-ED-A97K TCGA-FV-A3I0 TCGA-G3-A7M5 TCGA-G3-AAV4 TCGA-G3-AAV6 TCGA-GJ-A6C0 
        0.20        27.88        14.70         0.89         2.14         1.02 
TCGA-KR-A7K7 TCGA-LG-A9QC TCGA-QA-A7B7 TCGA-RC-A7SB TCGA-RC-A7SH TCGA-RC-A7SK 
       31.27        13.97         3.09        19.33        15.39        15.52 
TCGA-T1-A6J8 TCGA-UB-A7MC TCGA-UB-A7MF TCGA-WX-AA47 TCGA-ZP-A9D2 TCGA-ZS-A9CF 
        0.76        16.44         7.04        18.28        25.15        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        49.84        47.74 
TCGA-2Y-A9H5 TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA 
       18.25        11.74        38.40        20.81        22.92         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        17.10 
TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10S 
       14.76         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        23.38        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-5264 
       36.66         0.66         3.19         3.39         4.24         3.35 
TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MC TCGA-CC-A5UE TCGA-CC-A7IF TCGA-CC-A7IG 
        3.32         9.86        11.93         8.94        21.34         9.83 
TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IK TCGA-CC-A8HT TCGA-CC-A8HV TCGA-CC-A9FS 
       12.00        13.12         8.61         4.60         9.17         6.94 
TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A 
        8.15        79.73        37.78       113.00         7.33         2.60 
TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC 
       21.76        51.29        90.71        79.40        66.31        19.79 
TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI 
       75.65        11.47        12.95        45.11        49.15         6.02 
TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39X 
       33.04        18.35        13.64        21.14        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-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 
       20.12       102.74       107.11        13.78         0.36        30.61 
TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ 
       32.52        90.28        30.97        30.15        26.83        30.51 
TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR 
       39.78        56.25        29.56       108.76        12.26         0.30 
TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E 
       80.75        78.84        23.93        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-AACI 
       55.40        12.53        63.48        12.00         6.41        53.19 
TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACP TCGA-DD-AACQ 
       69.11         0.30         3.52        58.16        13.64        14.20 
TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD0 
       59.31        51.35         5.59        47.67         5.62         4.50 
TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD6 TCGA-DD-AADA TCGA-DD-AADD 
       18.54        21.63        42.58        22.09        40.54        40.47 
TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK 
       39.52         3.78        37.64        35.67        35.05        34.49 
TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU 
        0.39        29.52        14.33        66.67        15.58        18.21 
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-AAE8 TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAEG 
       21.17        21.83        23.74        18.90        15.72        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-AAVV TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ 
       59.93        80.71        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        26.93        28.08 
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        22.06        20.78        11.87 
TCGA-G3-A7M8 TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 
       14.14         1.84        15.78        15.65        11.80        12.23 
TCGA-G3-AAV3 TCGA-G3-AAV5 TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A9DB TCGA-HP-A5MZ 
       13.55         8.75        11.87        22.92         2.20         2.99 
TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K0 
       37.71        20.75        17.06        16.83        11.80         2.14 
TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E 
       21.60        29.79        12.72        12.03         9.57        16.67 
TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 
       22.95        24.56        20.71         7.53        10.85        58.88 
TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-RC-A7S9 TCGA-RC-A7SF TCGA-RG-A7D4 
       26.27        17.69        21.01        21.04        19.04        36.10 
TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0U TCGA-UB-AA0V 
       17.59        19.76         1.71        15.98        10.75        10.32 
TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-WX-AA46 TCGA-XR-A8TF 
       11.34         0.99        12.99        20.22        24.85        22.78 
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        35.87         0.69 
TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CG 
       12.99        45.57        40.80        11.21 

  DEL PEAK 33(XQ26.2) MUTATED DEL PEAK 33(XQ26.2) WILD-TYPE 
                         0.20                          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                        20.515 
[1] "0.2 - 114.3 (15.5)" "0.0 - 120.8 (20.5)"
[1] "hr=" "1.4"
D62V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IIIA
  DEL PEAK 33(XQ26.2) MUTATED        27       17         0         15
  DEL PEAK 33(XQ26.2) WILD-TYPE     144       68         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                           144
  STAGE II                            17                            68
  STAGE III                            0                             3
  STAGE IIIA                          15                            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  17   1
  DEL PEAK 33(XQ26.2) WILD-TYPE   154  72  57  11
D62V4, multiclass
       clus
vv      DEL PEAK 33(XQ26.2) MUTATED DEL PEAK 33(XQ26.2) WILD-TYPE
  T0+T1                          28                           154
  T2                             20                            72
  T3                             17                            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 203   2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 33(XQ26.2) MUTATED     47    1
  DEL PEAK 33(XQ26.2) WILD-TYPE  203    2
   clus
vv  DEL PEAK 33(XQ26.2) MUTATED DEL PEAK 33(XQ26.2) WILD-TYPE
  0                          47                           203
  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 207   4
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 33(XQ26.2) MUTATED     54    0
  DEL PEAK 33(XQ26.2) WILD-TYPE  207    4
   clus
vv  DEL PEAK 33(XQ26.2) MUTATED DEL PEAK 33(XQ26.2) WILD-TYPE
  0                          54                           207
  1                           0                             4
[1] 2 2
[1] FALSE
D62V7, binary
                               cls
clus                              0   1
  DEL PEAK 33(XQ26.2) MUTATED    19  47
  DEL PEAK 33(XQ26.2) WILD-TYPE  96 200
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 33(XQ26.2) MUTATED     19   47
  DEL PEAK 33(XQ26.2) WILD-TYPE   96  200
        clus
vv       DEL PEAK 33(XQ26.2) MUTATED DEL PEAK 33(XQ26.2) WILD-TYPE
  FEMALE                          19                            96
  MALE                            47                           200
[1] 2 2
[1] FALSE
D62V8, binary
                               cls
clus                              0   1
  DEL PEAK 33(XQ26.2) MUTATED    61   3
  DEL PEAK 33(XQ26.2) WILD-TYPE 275   4
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 33(XQ26.2) MUTATED     61    3
  DEL PEAK 33(XQ26.2) WILD-TYPE  275    4
     clus
vv    DEL PEAK 33(XQ26.2) MUTATED DEL PEAK 33(XQ26.2) WILD-TYPE
  NO                           61                           275
  YES                           3                             4
[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                         63
  DEL PEAK 33(XQ26.2) WILD-TYPE                      290
                               vv
clus                            HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK 33(XQ26.2) MUTATED                                  3
  DEL PEAK 33(XQ26.2) WILD-TYPE                                4
D62V9, multiclass
                                  clus
vv                                 DEL PEAK 33(XQ26.2) MUTATED
  FIBROLAMELLAR CARCINOMA                                    0
  HEPATOCELLULAR CARCINOMA                                  63
  HEPATOCHOLANGIOCARCINOMA (MIXED)                           3
                                  clus
vv                                 DEL PEAK 33(XQ26.2) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                      2
  HEPATOCELLULAR CARCINOMA                                   290
  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    59   1   0   6
  DEL PEAK 33(XQ26.2) WILD-TYPE 259  14   1  15
D62V10, multiclass
    clus
vv   DEL PEAK 33(XQ26.2) MUTATED DEL PEAK 33(XQ26.2) WILD-TYPE
  R0                          59                           259
  R1                           1                            14
  R2                           0                             1
  RX                           6                            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 33(XQ26.2) MUTATED                                  0    39
  DEL PEAK 33(XQ26.2) WILD-TYPE                                1   118
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 33(XQ26.2) MUTATED                           1    26
  DEL PEAK 33(XQ26.2) WILD-TYPE                        16   151
D62V11, multiclass
                                  clus
vv                                 DEL PEAK 33(XQ26.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                     39
  BLACK OR AFRICAN AMERICAN                                  1
  WHITE                                                     26
                                  clus
vv                                 DEL PEAK 33(XQ26.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                      118
  BLACK OR AFRICAN AMERICAN                                   16
  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"
D62V12, binary
                               cls
clus                              0   1
  DEL PEAK 33(XQ26.2) MUTATED     2  60
  DEL PEAK 33(XQ26.2) WILD-TYPE  11 272
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 33(XQ26.2) MUTATED      2   60
  DEL PEAK 33(XQ26.2) WILD-TYPE   11  272
                        clus
vv                       DEL PEAK 33(XQ26.2) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          60
                        clus
vv                       DEL PEAK 33(XQ26.2) WILD-TYPE
  HISPANIC OR LATINO                                11
  NOT HISPANIC OR LATINO                           272
[1] 2 2
[1] FALSE
