[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/22506983/LIHC-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/LIHC-TP/22531241/transformed.cor.cli.txt"

nPatients in clinical file=377, in cluster file=370, common to both=370
[1]  61 370
[1] "AMP PEAK  1(1Q21.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  1(1Q21.3) MUTATED AMP PEAK  1(1Q21.3) WILD-TYPE 
                          271                            99 
  AMP PEAK  1(1Q21.3) MUTATED AMP PEAK  1(1Q21.3) WILD-TYPE 
                          271                            99 
[1] "AMP PEAK  2(1Q42.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  2(1Q42.2) MUTATED AMP PEAK  2(1Q42.2) WILD-TYPE 
                          268                           102 
  AMP PEAK  2(1Q42.2) MUTATED AMP PEAK  2(1Q42.2) WILD-TYPE 
                          268                           102 
[1] "AMP PEAK  3(2P24.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  3(2P24.1) MUTATED AMP PEAK  3(2P24.1) WILD-TYPE 
                           65                           305 
  AMP PEAK  3(2P24.1) MUTATED AMP PEAK  3(2P24.1) WILD-TYPE 
                           65                           305 
[1] "AMP PEAK  4(2Q33.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  4(2Q33.1) MUTATED AMP PEAK  4(2Q33.1) WILD-TYPE 
                           64                           306 
  AMP PEAK  4(2Q33.1) MUTATED AMP PEAK  4(2Q33.1) WILD-TYPE 
                           64                           306 
[1] "AMP PEAK  5(3Q26.31) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  5(3Q26.31) MUTATED AMP PEAK  5(3Q26.31) WILD-TYPE 
                            77                            293 
  AMP PEAK  5(3Q26.31) MUTATED AMP PEAK  5(3Q26.31) WILD-TYPE 
                            77                            293 
[1] "AMP PEAK  6(4P14) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  6(4P14) MUTATED AMP PEAK  6(4P14) WILD-TYPE 
                         54                         316 
  AMP PEAK  6(4P14) MUTATED AMP PEAK  6(4P14) WILD-TYPE 
                         54                         316 
[1] "AMP PEAK  7(5P15.33) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  7(5P15.33) MUTATED AMP PEAK  7(5P15.33) WILD-TYPE 
                           163                            207 
  AMP PEAK  7(5P15.33) MUTATED AMP PEAK  7(5P15.33) WILD-TYPE 
                           163                            207 
[1] "AMP PEAK  8(5Q35.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  8(5Q35.3) MUTATED AMP PEAK  8(5Q35.3) WILD-TYPE 
                          135                           235 
  AMP PEAK  8(5Q35.3) MUTATED AMP PEAK  8(5Q35.3) WILD-TYPE 
                          135                           235 
[1] "AMP PEAK  9(6P25.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  9(6P25.2) MUTATED AMP PEAK  9(6P25.2) WILD-TYPE 
                          159                           211 
  AMP PEAK  9(6P25.2) MUTATED AMP PEAK  9(6P25.2) WILD-TYPE 
                          159                           211 
[1] "AMP PEAK 10(6P21.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 10(6P21.1) MUTATED AMP PEAK 10(6P21.1) WILD-TYPE 
                          158                           212 
  AMP PEAK 10(6P21.1) MUTATED AMP PEAK 10(6P21.1) WILD-TYPE 
                          158                           212 
[1] "AMP PEAK 11(6Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 11(6Q12) MUTATED AMP PEAK 11(6Q12) WILD-TYPE 
                        109                         261 
  AMP PEAK 11(6Q12) MUTATED AMP PEAK 11(6Q12) WILD-TYPE 
                        109                         261 
[1] "AMP PEAK 12(6Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 12(6Q12) MUTATED AMP PEAK 12(6Q12) WILD-TYPE 
                         83                         287 
  AMP PEAK 12(6Q12) MUTATED AMP PEAK 12(6Q12) WILD-TYPE 
                         83                         287 
[1] "AMP PEAK 13(7Q31.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 13(7Q31.2) MUTATED AMP PEAK 13(7Q31.2) WILD-TYPE 
                          120                           250 
  AMP PEAK 13(7Q31.2) MUTATED AMP PEAK 13(7Q31.2) WILD-TYPE 
                          120                           250 
[1] "AMP PEAK 14(8Q24.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 14(8Q24.21) MUTATED AMP PEAK 14(8Q24.21) WILD-TYPE 
                           231                            139 
  AMP PEAK 14(8Q24.21) MUTATED AMP PEAK 14(8Q24.21) WILD-TYPE 
                           231                            139 
[1] "AMP PEAK 15(9Q34.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 15(9Q34.2) MUTATED AMP PEAK 15(9Q34.2) WILD-TYPE 
                           47                           323 
  AMP PEAK 15(9Q34.2) MUTATED AMP PEAK 15(9Q34.2) WILD-TYPE 
                           47                           323 
[1] "AMP PEAK 16(10P15.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 16(10P15.1) MUTATED AMP PEAK 16(10P15.1) WILD-TYPE 
                            72                            298 
  AMP PEAK 16(10P15.1) MUTATED AMP PEAK 16(10P15.1) WILD-TYPE 
                            72                            298 
[1] "AMP PEAK 17(11Q13.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 17(11Q13.3) MUTATED AMP PEAK 17(11Q13.3) WILD-TYPE 
                            57                            313 
  AMP PEAK 17(11Q13.3) MUTATED AMP PEAK 17(11Q13.3) WILD-TYPE 
                            57                            313 
[1] "AMP PEAK 18(13Q32.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 18(13Q32.3) MUTATED AMP PEAK 18(13Q32.3) WILD-TYPE 
                            67                            303 
  AMP PEAK 18(13Q32.3) MUTATED AMP PEAK 18(13Q32.3) WILD-TYPE 
                            67                            303 
[1] "AMP PEAK 19(13Q33.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 19(13Q33.3) MUTATED AMP PEAK 19(13Q33.3) WILD-TYPE 
                            67                            303 
  AMP PEAK 19(13Q33.3) MUTATED AMP PEAK 19(13Q33.3) WILD-TYPE 
                            67                            303 
[1] "AMP PEAK 20(15Q26.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 20(15Q26.3) MUTATED AMP PEAK 20(15Q26.3) WILD-TYPE 
                            54                            316 
  AMP PEAK 20(15Q26.3) MUTATED AMP PEAK 20(15Q26.3) WILD-TYPE 
                            54                            316 
[1] "AMP PEAK 21(17P11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 21(17P11.2) MUTATED AMP PEAK 21(17P11.2) WILD-TYPE 
                            46                            324 
  AMP PEAK 21(17P11.2) MUTATED AMP PEAK 21(17P11.2) WILD-TYPE 
                            46                            324 
[1] "AMP PEAK 22(17Q25.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 22(17Q25.3) MUTATED AMP PEAK 22(17Q25.3) WILD-TYPE 
                           145                            225 
  AMP PEAK 22(17Q25.3) MUTATED AMP PEAK 22(17Q25.3) WILD-TYPE 
                           145                            225 
[1] "AMP PEAK 23(19P13.12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 23(19P13.12) MUTATED AMP PEAK 23(19P13.12) WILD-TYPE 
                             69                             301 
  AMP PEAK 23(19P13.12) MUTATED AMP PEAK 23(19P13.12) WILD-TYPE 
                             69                             301 
[1] "AMP PEAK 24(19Q13.11) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 24(19Q13.11) MUTATED AMP PEAK 24(19Q13.11) WILD-TYPE 
                             91                             279 
  AMP PEAK 24(19Q13.11) MUTATED AMP PEAK 24(19Q13.11) WILD-TYPE 
                             91                             279 
[1] "AMP PEAK 25(20Q13.13) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 25(20Q13.13) MUTATED AMP PEAK 25(20Q13.13) WILD-TYPE 
                            124                             246 
  AMP PEAK 25(20Q13.13) MUTATED AMP PEAK 25(20Q13.13) WILD-TYPE 
                            124                             246 
[1] "AMP PEAK 26(20Q13.33) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 26(20Q13.33) MUTATED AMP PEAK 26(20Q13.33) WILD-TYPE 
                            128                             242 
  AMP PEAK 26(20Q13.33) MUTATED AMP PEAK 26(20Q13.33) WILD-TYPE 
                            128                             242 
[1] "AMP PEAK 27(XQ28) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 27(XQ28) MUTATED AMP PEAK 27(XQ28) WILD-TYPE 
                         87                         283 
  AMP PEAK 27(XQ28) MUTATED AMP PEAK 27(XQ28) WILD-TYPE 
                         87                         283 
[1] "DEL PEAK  1(1P36.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                           162                            208 
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                           162                            208 
[1] "DEL PEAK  2(1P36.11) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  2(1P36.11) MUTATED DEL PEAK  2(1P36.11) WILD-TYPE 
                           142                            228 
  DEL PEAK  2(1P36.11) MUTATED DEL PEAK  2(1P36.11) WILD-TYPE 
                           142                            228 
[1] "DEL PEAK  3(2Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                           52                           318 
  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                           52                           318 
[1] "DEL PEAK  4(2Q37.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                           62                           308 
  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                           62                           308 
[1] "DEL PEAK  5(3P13) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  5(3P13) MUTATED DEL PEAK  5(3P13) WILD-TYPE 
                         73                         297 
  DEL PEAK  5(3P13) MUTATED DEL PEAK  5(3P13) WILD-TYPE 
                         73                         297 
[1] "DEL PEAK  6(4P16.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  6(4P16.3) MUTATED DEL PEAK  6(4P16.3) WILD-TYPE 
                           85                           285 
  DEL PEAK  6(4P16.3) MUTATED DEL PEAK  6(4P16.3) WILD-TYPE 
                           85                           285 
[1] "DEL PEAK  7(4Q21.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  7(4Q21.3) MUTATED DEL PEAK  7(4Q21.3) WILD-TYPE 
                          171                           199 
  DEL PEAK  7(4Q21.3) MUTATED DEL PEAK  7(4Q21.3) WILD-TYPE 
                          171                           199 
[1] "DEL PEAK  8(4Q24) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  8(4Q24) MUTATED DEL PEAK  8(4Q24) WILD-TYPE 
                        173                         197 
  DEL PEAK  8(4Q24) MUTATED DEL PEAK  8(4Q24) WILD-TYPE 
                        173                         197 
[1] "DEL PEAK  9(4Q35.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  9(4Q35.1) MUTATED DEL PEAK  9(4Q35.1) WILD-TYPE 
                          172                           198 
  DEL PEAK  9(4Q35.1) MUTATED DEL PEAK  9(4Q35.1) WILD-TYPE 
                          172                           198 
[1] "DEL PEAK 10(6Q27) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 10(6Q27) MUTATED DEL PEAK 10(6Q27) WILD-TYPE 
                        136                         234 
  DEL PEAK 10(6Q27) MUTATED DEL PEAK 10(6Q27) WILD-TYPE 
                        136                         234 
[1] "DEL PEAK 11(7Q36.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 11(7Q36.3) MUTATED DEL PEAK 11(7Q36.3) WILD-TYPE 
                           34                           336 
  DEL PEAK 11(7Q36.3) MUTATED DEL PEAK 11(7Q36.3) WILD-TYPE 
                           34                           336 
[1] "DEL PEAK 12(8P23.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 12(8P23.2) MUTATED DEL PEAK 12(8P23.2) WILD-TYPE 
                          247                           123 
  DEL PEAK 12(8P23.2) MUTATED DEL PEAK 12(8P23.2) WILD-TYPE 
                          247                           123 
[1] "DEL PEAK 13(8P12) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 13(8P12) MUTATED DEL PEAK 13(8P12) WILD-TYPE 
                        242                         128 
  DEL PEAK 13(8P12) MUTATED DEL PEAK 13(8P12) WILD-TYPE 
                        242                         128 
[1] "DEL PEAK 14(9P21.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 14(9P21.3) MUTATED DEL PEAK 14(9P21.3) WILD-TYPE 
                          150                           220 
  DEL PEAK 14(9P21.3) MUTATED DEL PEAK 14(9P21.3) WILD-TYPE 
                          150                           220 
[1] "DEL PEAK 15(9Q31.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 15(9Q31.3) MUTATED DEL PEAK 15(9Q31.3) WILD-TYPE 
                          119                           251 
  DEL PEAK 15(9Q31.3) MUTATED DEL PEAK 15(9Q31.3) WILD-TYPE 
                          119                           251 
[1] "DEL PEAK 16(10Q23.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(10Q23.31) WILD-TYPE 
                             97                             273 
  DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(10Q23.31) WILD-TYPE 
                             97                             273 
[1] "DEL PEAK 17(10Q26.13) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 17(10Q26.13) MUTATED DEL PEAK 17(10Q26.13) WILD-TYPE 
                            105                             265 
  DEL PEAK 17(10Q26.13) MUTATED DEL PEAK 17(10Q26.13) WILD-TYPE 
                            105                             265 
[1] "DEL PEAK 18(11Q14.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 18(11Q14.1) MUTATED DEL PEAK 18(11Q14.1) WILD-TYPE 
                            77                            293 
  DEL PEAK 18(11Q14.1) MUTATED DEL PEAK 18(11Q14.1) WILD-TYPE 
                            77                            293 
[1] "DEL PEAK 19(11Q23.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 19(11Q23.3) MUTATED DEL PEAK 19(11Q23.3) WILD-TYPE 
                            93                            277 
  DEL PEAK 19(11Q23.3) MUTATED DEL PEAK 19(11Q23.3) WILD-TYPE 
                            93                            277 
[1] "DEL PEAK 20(12P12.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 20(12P12.1) MUTATED DEL PEAK 20(12P12.1) WILD-TYPE 
                            78                            292 
  DEL PEAK 20(12P12.1) MUTATED DEL PEAK 20(12P12.1) WILD-TYPE 
                            78                            292 
[1] "DEL PEAK 21(12Q24.33) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 21(12Q24.33) MUTATED DEL PEAK 21(12Q24.33) WILD-TYPE 
                             59                             311 
  DEL PEAK 21(12Q24.33) MUTATED DEL PEAK 21(12Q24.33) WILD-TYPE 
                             59                             311 
[1] "DEL PEAK 22(13Q14.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 22(13Q14.2) MUTATED DEL PEAK 22(13Q14.2) WILD-TYPE 
                           179                            191 
  DEL PEAK 22(13Q14.2) MUTATED DEL PEAK 22(13Q14.2) WILD-TYPE 
                           179                            191 
[1] "DEL PEAK 23(14Q23.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 23(14Q23.3) MUTATED DEL PEAK 23(14Q23.3) WILD-TYPE 
                           131                            239 
  DEL PEAK 23(14Q23.3) MUTATED DEL PEAK 23(14Q23.3) WILD-TYPE 
                           131                            239 
[1] "DEL PEAK 24(14Q32.33) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 24(14Q32.33) MUTATED DEL PEAK 24(14Q32.33) WILD-TYPE 
                            133                             237 
  DEL PEAK 24(14Q32.33) MUTATED DEL PEAK 24(14Q32.33) WILD-TYPE 
                            133                             237 
[1] "DEL PEAK 25(15Q26.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 25(15Q26.3) MUTATED DEL PEAK 25(15Q26.3) WILD-TYPE 
                            79                            291 
  DEL PEAK 25(15Q26.3) MUTATED DEL PEAK 25(15Q26.3) WILD-TYPE 
                            79                            291 
[1] "DEL PEAK 26(16Q23.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 26(16Q23.1) MUTATED DEL PEAK 26(16Q23.1) WILD-TYPE 
                           162                            208 
  DEL PEAK 26(16Q23.1) MUTATED DEL PEAK 26(16Q23.1) WILD-TYPE 
                           162                            208 
[1] "DEL PEAK 27(17P13.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 27(17P13.1) MUTATED DEL PEAK 27(17P13.1) WILD-TYPE 
                           226                            144 
  DEL PEAK 27(17P13.1) MUTATED DEL PEAK 27(17P13.1) WILD-TYPE 
                           226                            144 
[1] "DEL PEAK 28(17P11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 28(17P11.2) MUTATED DEL PEAK 28(17P11.2) WILD-TYPE 
                           195                            175 
  DEL PEAK 28(17P11.2) MUTATED DEL PEAK 28(17P11.2) WILD-TYPE 
                           195                            175 
[1] "DEL PEAK 29(18Q21.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 29(18Q21.2) MUTATED DEL PEAK 29(18Q21.2) WILD-TYPE 
                            94                            276 
  DEL PEAK 29(18Q21.2) MUTATED DEL PEAK 29(18Q21.2) WILD-TYPE 
                            94                            276 
[1] "DEL PEAK 30(19P13.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 30(19P13.3) MUTATED DEL PEAK 30(19P13.3) WILD-TYPE 
                            87                            283 
  DEL PEAK 30(19P13.3) MUTATED DEL PEAK 30(19P13.3) WILD-TYPE 
                            87                            283 
[1] "DEL PEAK 31(20P12.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 31(20P12.1) MUTATED DEL PEAK 31(20P12.1) WILD-TYPE 
                            29                            341 
  DEL PEAK 31(20P12.1) MUTATED DEL PEAK 31(20P12.1) WILD-TYPE 
                            29                            341 
[1] "DEL PEAK 32(22Q12.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 32(22Q12.1) MUTATED DEL PEAK 32(22Q12.1) WILD-TYPE 
                            79                            291 
  DEL PEAK 32(22Q12.1) MUTATED DEL PEAK 32(22Q12.1) WILD-TYPE 
                            79                            291 
[1] "DEL PEAK 33(22Q13.32) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 33(22Q13.32) MUTATED DEL PEAK 33(22Q13.32) WILD-TYPE 
                             83                             287 
  DEL PEAK 33(22Q13.32) MUTATED DEL PEAK 33(22Q13.32) WILD-TYPE 
                             83                             287 
[1] "DEL PEAK 34(XQ26.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 34(XQ26.2) MUTATED DEL PEAK 34(XQ26.2) WILD-TYPE 
                           67                           303 
  DEL PEAK 34(XQ26.2) MUTATED DEL PEAK 34(XQ26.2) WILD-TYPE 
                           67                           303 
[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 370 columns.

[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=63,	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=218,	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=9,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY_N_STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY_M_STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'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 370 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=63, binary=FALSE, numeric=TRUE
PATHOLOGIC_STAGE, nv=9, binary=FALSE, numeric=FALSE
PATHOLOGY_T_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T1  T2  T3  T4 
183  95  77  12 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
183  95  77  12 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T1  T2  T3  T4 
183  95  77  12 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
183  95  77  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(1Q21.3) MUTATION ANALYSIS
D1V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  1(1Q21.3) MUTATED   164 102
  AMP PEAK  1(1Q21.3) WILD-TYPE  71  27
  AMP PEAK  1(1Q21.3) MUTATED AMP PEAK  1(1Q21.3) WILD-TYPE 
                          266                            98 
  AMP PEAK  1(1Q21.3) MUTATED AMP PEAK  1(1Q21.3) WILD-TYPE 
                          102                            27 
$`AMP PEAK  1(1Q21.3) MUTATED`
TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A112 TCGA-BD-A3ER TCGA-DD-A3A8 
       11.74        38.40         8.61         5.03        36.66         0.36 
TCGA-DD-A4NI TCGA-DD-AADV TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG 
       26.83        18.87        21.17        21.83        18.90        23.64 
TCGA-EP-A3JL TCGA-FV-A3I1 TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC 
        9.96         8.12        81.73        30.74        22.13        22.06 
TCGA-G3-A7M9 TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H TCGA-T1-A6J8 
        1.84         2.14        31.27        12.72        24.56         0.76 
TCGA-UB-A7MF TCGA-XR-A8TG TCGA-ZP-A9D1 TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX 
        7.04        29.52         0.69        63.75        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-A9H5 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-3K-AAZ8 TCGA-5C-A9VG 
       18.25        20.81        22.92         1.18        13.02        10.78 
TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10U 
       10.59         0.66        17.10        37.32        10.13        27.52 
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-A69I TCGA-BC-A8YO TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5261 
       14.60        12.72        18.48         0.66         4.24         3.19 
TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-5264 TCGA-CC-A1HT TCGA-CC-A3MA TCGA-CC-A3MB 
        3.39         4.24         3.35         3.32         9.96        10.36 
TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IF 
       11.93        11.41         9.99         8.94         7.13        21.34 
TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7IK TCGA-CC-A7IL TCGA-CC-A8HT TCGA-CC-A8HU 
        9.83        12.00         8.61         9.14         4.60        11.31 
TCGA-CC-A8HV TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A118 TCGA-DD-A119 
        9.17         8.15        79.73        37.78       113.00         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-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-A3A9 TCGA-DD-A4NF 
       25.81         7.66        17.59        13.78        30.61        30.97 
TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NR 
       30.15        30.51        39.78        29.56        73.81         0.30 
TCGA-DD-A4NV TCGA-DD-A73B TCGA-DD-A73D TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A 
       78.84         9.30        22.78        35.67       114.35        13.48 
TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACE TCGA-DD-AACF 
        0.53        11.41        76.41        55.40        71.80        12.00 
TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN 
        6.41        53.19        69.11         3.52        58.16        42.81 
TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACU 
       61.68        13.64        14.20        59.31        51.35        51.52 
TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD0 
       50.33        46.82         5.59        47.67         5.62         4.50 
TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADC 
       21.63        42.58        44.22        40.08        40.54        13.97 
TCGA-DD-AADD TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK 
       40.47         3.78        37.64        35.67        35.05        34.49 
TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADR TCGA-DD-AADW 
       20.91         0.39        14.89        15.06        66.67        19.30 
TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE3 TCGA-DD-AAE6 TCGA-DD-AAE9 
       18.25        18.25        18.15        18.61         4.64        23.74 
TCGA-DD-AAEB TCGA-DD-AAEH TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR 
       15.72        25.78        35.08        90.48        89.69        82.62 
TCGA-DD-AAVS TCGA-DD-AAVV TCGA-DD-AAVW TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 
       59.93        80.71        76.18        64.77        62.47        66.25 
TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A66X 
       65.39        60.99        53.69        29.92        26.93        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-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR 
        0.62        11.93        14.40        60.89        23.97        19.10 
TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25X 
       12.03         0.03         0.33        13.68        53.79        58.49 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SL 
       14.86        21.53        19.53        19.23        25.25        20.42 
TCGA-G3-A5SM TCGA-G3-A7M6 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV3 
       17.10        20.78        15.78        15.65        11.80        13.55 
TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 
        0.89        11.64         2.14        11.87        28.90         1.02 
TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A6G5 TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A9QC 
        2.99        37.71        16.83        27.25        29.79        13.97 
TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I TCGA-NI-A8LF TCGA-O8-A75V TCGA-QA-A7B7 
       16.67        22.95        20.71        26.27        17.69         3.09 
TCGA-RC-A7S9 TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB 
       21.04        15.39        15.52        36.10        27.88        19.76 
TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-A9G7 
       16.44         1.71        15.98        10.75        11.34         0.99 
TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-WX-AA47 TCGA-XR-A8TD TCGA-XR-A8TE TCGA-XR-A8TF 
       12.99        20.22        18.28        33.86        30.41        22.78 
TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 
       13.55        35.77        23.21        35.87        25.15        12.99 
TCGA-ZS-A9CD TCGA-ZS-A9CG 
       45.57        11.21 

$`AMP PEAK  1(1Q21.3) WILD-TYPE`
TCGA-2Y-A9GV TCGA-BC-A110 TCGA-BC-A5W4 TCGA-DD-A4ND TCGA-ES-A2HS TCGA-FV-A3R2 
       83.24        69.57        17.98        90.28        22.62         6.38 
TCGA-K7-A5RF TCGA-UB-AA0V TCGA-ZS-A9CE TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9H4 
       20.75        10.32        40.80        23.80        53.39        47.74 
TCGA-2Y-A9HB TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10S 
        8.55        14.76         1.51        48.99        27.91        46.78 
TCGA-BC-A10T TCGA-BC-A10X TCGA-BC-A3KF TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-CC-5260 
       27.52        25.32         0.26        44.81        13.45         2.86 
TCGA-CC-A3M9 TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A9FS TCGA-DD-A115 TCGA-DD-A116 
        9.86        13.12        12.56         6.94        83.57        53.33 
TCGA-DD-A11A TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EI TCGA-DD-A3A2 TCGA-DD-A3A4 
        2.60        19.79        75.65         6.02        70.06        20.12 
TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NL TCGA-DD-A4NP 
      102.74       107.11        33.14        32.52        56.25       108.76 
TCGA-DD-A4NQ TCGA-DD-A4NS TCGA-DD-A73A TCGA-DD-A73C TCGA-DD-A73E TCGA-DD-AACA 
       12.26        80.75        23.93        23.05         1.45        75.65 
TCGA-DD-AACD TCGA-DD-AACG TCGA-DD-AACK TCGA-DD-AAD1 TCGA-DD-AAD6 TCGA-DD-AADB 
       12.53        15.42         0.30        18.54        22.09        40.83 
TCGA-DD-AADE TCGA-DD-AADN TCGA-DD-AADQ TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AAE2 
       39.52        29.52        14.33        15.58        18.21        20.98 
TCGA-DD-AAE4 TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEI TCGA-DD-AAVU TCGA-DD-AAVX 
       19.99        25.08        26.63        50.33        72.39        56.48 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A7PX TCGA-ED-A97K TCGA-FV-A3I0 TCGA-FV-A4ZQ 
       28.08        13.91         0.20         0.20        27.88         0.39 
TCGA-G3-A25T TCGA-G3-A25V TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A5SJ TCGA-G3-A7M5 
       51.06        28.27        25.64         5.92        22.95        14.70 
TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAV2 TCGA-GJ-A9DB TCGA-K7-A5RG TCGA-K7-AAU7 
       11.87        14.14        12.23         2.20        17.06        11.80 
TCGA-LG-A9QD TCGA-MI-A75C TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-PD-A5DF 
       12.03         9.57         7.53        10.85        58.88        21.01 
TCGA-RC-A6M4 TCGA-RC-A6M5 TCGA-RC-A6M6 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-WX-AA46 
        0.72         0.49         0.30        19.33        19.04        24.85 
TCGA-ZP-A9CY TCGA-ZS-A9CF 
       25.71        79.30 

  AMP PEAK  1(1Q21.3) MUTATED AMP PEAK  1(1Q21.3) WILD-TYPE 
                         0.03                          0.20 
  AMP PEAK  1(1Q21.3) MUTATED AMP PEAK  1(1Q21.3) WILD-TYPE 
                       120.82                        108.76 
  AMP PEAK  1(1Q21.3) MUTATED AMP PEAK  1(1Q21.3) WILD-TYPE 
                       19.415                        20.865 
[1] "0.0 - 120.8 (19.4)" "0.2 - 108.8 (20.9)"
[1] "hr=" "1.6"
D1V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IIIA
  AMP PEAK  1(1Q21.3) MUTATED       123       68         2         43
  AMP PEAK  1(1Q21.3) WILD-TYPE      50       19         1         19
                               vv
clus                            STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK  1(1Q21.3) MUTATED            8          5        2         0
  AMP PEAK  1(1Q21.3) WILD-TYPE          1          2        0         1
                               vv
clus                            STAGE IVB
  AMP PEAK  1(1Q21.3) MUTATED           2
  AMP PEAK  1(1Q21.3) WILD-TYPE         0
D1V3, multiclass
            clus
vv           AMP PEAK  1(1Q21.3) MUTATED AMP PEAK  1(1Q21.3) WILD-TYPE
  STAGE I                            123                            50
  STAGE II                            68                            19
  STAGE III                            2                             1
  STAGE IIIA                          43                            19
  STAGE IIIB                           8                             1
  STAGE IIIC                           5                             2
  STAGE IV                             2                             0
  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                             T1  T2  T3  T4
  AMP PEAK  1(1Q21.3) MUTATED   131  73  56   9
  AMP PEAK  1(1Q21.3) WILD-TYPE  52  22  21   3
D1V4, multiclass
    clus
vv   AMP PEAK  1(1Q21.3) MUTATED AMP PEAK  1(1Q21.3) WILD-TYPE
  T1                         131                            52
  T2                          73                            22
  T3                          56                            21
  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"
D1V5, binary
                               cls
clus                              0   1
  AMP PEAK  1(1Q21.3) MUTATED   190   1
  AMP PEAK  1(1Q21.3) WILD-TYPE  64   2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1Q21.3) MUTATED    190    1
  AMP PEAK  1(1Q21.3) WILD-TYPE   64    2
   clus
vv  AMP PEAK  1(1Q21.3) MUTATED AMP PEAK  1(1Q21.3) WILD-TYPE
  0                         190                            64
  1                           1                             2
[1] 2 2
[1] FALSE
D1V6, binary
                               cls
clus                              0   1
  AMP PEAK  1(1Q21.3) MUTATED   197   4
  AMP PEAK  1(1Q21.3) WILD-TYPE  69   0
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1Q21.3) MUTATED    197    4
  AMP PEAK  1(1Q21.3) WILD-TYPE   69    0
   clus
vv  AMP PEAK  1(1Q21.3) MUTATED AMP PEAK  1(1Q21.3) WILD-TYPE
  0                         197                            69
  1                           4                             0
[1] 2 2
[1] FALSE
D1V7, binary
                               cls
clus                              0   1
  AMP PEAK  1(1Q21.3) MUTATED    89 182
  AMP PEAK  1(1Q21.3) WILD-TYPE  29  70
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1Q21.3) MUTATED     89  182
  AMP PEAK  1(1Q21.3) WILD-TYPE   29   70
        clus
vv       AMP PEAK  1(1Q21.3) MUTATED AMP PEAK  1(1Q21.3) WILD-TYPE
  FEMALE                          89                            29
  MALE                           182                            70
[1] 2 2
[1] FALSE
D1V8, binary
                               cls
clus                              0   1
  AMP PEAK  1(1Q21.3) MUTATED   252   6
  AMP PEAK  1(1Q21.3) WILD-TYPE  86   3
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1Q21.3) MUTATED    252    6
  AMP PEAK  1(1Q21.3) WILD-TYPE   86    3
     clus
vv    AMP PEAK  1(1Q21.3) MUTATED AMP PEAK  1(1Q21.3) WILD-TYPE
  NO                          252                            86
  YES                           6                             3
[1] 2 2
[1] FALSE
                               vv
clus                            FIBROLAMELLAR CARCINOMA
  AMP PEAK  1(1Q21.3) MUTATED                         0
  AMP PEAK  1(1Q21.3) WILD-TYPE                       3
                               vv
clus                            HEPATOCELLULAR CARCINOMA
  AMP PEAK  1(1Q21.3) MUTATED                        267
  AMP PEAK  1(1Q21.3) WILD-TYPE                       93
                               vv
clus                            HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK  1(1Q21.3) MUTATED                                  4
  AMP PEAK  1(1Q21.3) WILD-TYPE                                3
D1V9, multiclass
                                  clus
vv                                 AMP PEAK  1(1Q21.3) MUTATED
  FIBROLAMELLAR CARCINOMA                                    0
  HEPATOCELLULAR CARCINOMA                                 267
  HEPATOCHOLANGIOCARCINOMA (MIXED)                           4
                                  clus
vv                                 AMP PEAK  1(1Q21.3) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                      3
  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  1(1Q21.3) MUTATED   238  10   1  17
  AMP PEAK  1(1Q21.3) WILD-TYPE  86   7   0   4
D1V10, multiclass
    clus
vv   AMP PEAK  1(1Q21.3) MUTATED AMP PEAK  1(1Q21.3) WILD-TYPE
  R0                         238                            86
  R1                          10                             7
  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  1(1Q21.3) MUTATED                                  2   123
  AMP PEAK  1(1Q21.3) WILD-TYPE                                0    35
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  1(1Q21.3) MUTATED                          12   125
  AMP PEAK  1(1Q21.3) WILD-TYPE                         5    58
D1V11, multiclass
                                  clus
vv                                 AMP PEAK  1(1Q21.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           2
  ASIAN                                                    123
  BLACK OR AFRICAN AMERICAN                                 12
  WHITE                                                    125
                                  clus
vv                                 AMP PEAK  1(1Q21.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                       35
  BLACK OR AFRICAN AMERICAN                                    5
  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"
D1V12, binary
                               cls
clus                              0   1
  AMP PEAK  1(1Q21.3) MUTATED    12 245
  AMP PEAK  1(1Q21.3) WILD-TYPE   4  90
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1Q21.3) MUTATED     12  245
  AMP PEAK  1(1Q21.3) WILD-TYPE    4   90
                        clus
vv                       AMP PEAK  1(1Q21.3) MUTATED
  HISPANIC OR LATINO                              12
  NOT HISPANIC OR LATINO                         245
                        clus
vv                       AMP PEAK  1(1Q21.3) WILD-TYPE
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                            90
[1] 2 2
[1] FALSE

Clustering(2) Variable = AMP PEAK  2(1Q42.2) MUTATION ANALYSIS
D2V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  2(1Q42.2) MUTATED   169  94
  AMP PEAK  2(1Q42.2) WILD-TYPE  66  35
  AMP PEAK  2(1Q42.2) MUTATED AMP PEAK  2(1Q42.2) WILD-TYPE 
                          263                           101 
  AMP PEAK  2(1Q42.2) MUTATED AMP PEAK  2(1Q42.2) WILD-TYPE 
                           94                            35 
$`AMP PEAK  2(1Q42.2) MUTATED`
TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-BC-A112 TCGA-BC-A5W4 TCGA-BD-A3ER TCGA-DD-A3A8 
       11.74        38.40         5.03        17.98        36.66         0.36 
TCGA-DD-A4NI TCGA-DD-AADV TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG 
       26.83        18.87        21.17        21.83        18.90        23.64 
TCGA-EP-A3JL TCGA-FV-A3I1 TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC TCGA-G3-A7M9 
        9.96         8.12        30.74        22.13        22.06         1.84 
TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H TCGA-T1-A6J8 TCGA-UB-A7MF 
        2.14        31.27        12.72        24.56         0.76         7.04 
TCGA-XR-A8TG TCGA-ZP-A9D1 TCGA-ZS-A9CE TCGA-2Y-A9GS TCGA-2Y-A9GU TCGA-2Y-A9GW 
       29.52         0.69        40.80        23.80        63.75        41.79 
TCGA-2Y-A9GX TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 
       80.28        27.88       120.82        40.41        56.91        49.84 
TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-5C-A9VG 
       18.25        20.81        22.92         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-A10Y TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KG TCGA-BC-A69H 
       27.52        23.38        44.42        45.93        22.36        14.60 
TCGA-BC-A69I TCGA-BW-A5NO TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5264 TCGA-CC-A3M9 
       12.72         0.66         3.19         3.39         3.35         9.86 
TCGA-CC-A3MA TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IF 
        9.96        11.93        11.41         8.94         7.13        21.34 
TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7IK TCGA-CC-A7IL TCGA-CC-A8HT TCGA-CC-A8HU 
        9.83        12.00         8.61         9.14         4.60        11.31 
TCGA-CC-A8HV TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A118 TCGA-DD-A119 
        9.17         8.15        79.73        37.78       113.00         7.33 
TCGA-DD-A11B TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EE TCGA-DD-A1EF 
        0.46        51.29        90.71        79.40        11.47        12.95 
TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V 
       45.11        49.15        33.04        18.35        13.64        21.14 
TCGA-DD-A39W TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A3 
       27.19         5.62        19.76        25.81         7.66        17.59 
TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NF TCGA-DD-A4NH 
       13.78        30.61        33.14        32.52        30.97        30.15 
TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NQ TCGA-DD-A4NR 
       30.51        39.78        29.56        73.81        12.26         0.30 
TCGA-DD-A4NV TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A 
       78.84        22.78         1.45        35.67       114.35        13.48 
TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE 
        0.53        11.41        76.41        55.40        12.53        71.80 
TCGA-DD-AACF TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACL TCGA-DD-AACM 
       12.00         6.41        53.19        69.11         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-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD8 
        4.50        18.54        21.63        42.58        44.22        40.08 
TCGA-DD-AADA TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI 
       40.54        13.97        40.47         3.78        37.64        35.67 
TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADO TCGA-DD-AADP 
       35.05        34.49        20.91         0.39        14.89        15.06 
TCGA-DD-AADR TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 
       66.67        18.21        19.30        18.25        18.25        18.15 
TCGA-DD-AAE6 TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEH TCGA-DD-AAEK 
        4.64        23.74        15.72        25.08        25.78        35.08 
TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVV TCGA-DD-AAVW 
       90.48        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        60.99        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-A3RK 
       18.74        19.99        20.61        19.59         0.62        11.93 
TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3R3 TCGA-FV-A495 
       14.40        60.89        23.97        19.10        12.03         0.03 
TCGA-FV-A496 TCGA-G3-A25S TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CJ 
        0.33        13.68        58.49        14.86        21.53        19.53 
TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A7M6 TCGA-G3-AAV0 
       19.23        25.25        20.42        17.10        20.78        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        11.64         2.14 
TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A6G5 TCGA-KR-A7K2 
       11.87        28.90         2.99        37.71        16.83        27.25 
TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I 
       29.79        13.97         9.57        16.67        22.95        20.71 
TCGA-MR-A8JO TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A6M4 TCGA-RC-A7S9 
       10.85        17.69        21.01         3.09         0.72        21.04 
TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MC TCGA-UB-A7MD 
       19.04        15.39        36.10        27.88        16.44         1.71 
TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA44 
       15.98        10.75        11.34         0.99        12.99        20.22 
TCGA-WX-AA47 TCGA-XR-A8TD TCGA-XR-A8TF TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ 
       18.28        33.86        22.78        35.77        25.71        23.21 
TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CG 
       35.87        25.15        12.99        45.57        11.21 

$`AMP PEAK  2(1Q42.2) WILD-TYPE`
TCGA-2Y-A9GV TCGA-4R-AA8I TCGA-BC-A110 TCGA-DD-A4ND TCGA-ES-A2HS TCGA-FV-A3R2 
       83.24         8.61        69.57        90.28        22.62         6.38 
TCGA-FV-A4ZP TCGA-K7-A5RF TCGA-UB-AA0V TCGA-2Y-A9GT TCGA-2Y-A9GY TCGA-2Y-A9H4 
       81.73        20.75        10.32        53.39        24.89        47.74 
TCGA-2Y-A9HA TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10S 
        1.18        14.76         1.51        48.99        27.91        46.78 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Z TCGA-BC-A3KF TCGA-BC-A8YO TCGA-BD-A2L6 
        2.99        25.32         1.12         0.26        18.48        44.81 
TCGA-BD-A3EP TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3MB 
       13.45         4.24         2.86         4.24         3.32        10.36 
TCGA-CC-A5UD TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A9FS TCGA-DD-A115 TCGA-DD-A116 
        9.99        13.12        12.56         6.94        83.57        53.33 
TCGA-DD-A11A TCGA-DD-A11C TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EI 
        2.60        21.76        66.31        19.79        75.65         6.02 
TCGA-DD-A39X TCGA-DD-A3A2 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A4NL 
       55.69        70.06        20.12       102.74       107.11        56.25 
TCGA-DD-A4NP TCGA-DD-A4NS TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-AACA 
      108.76        80.75        23.93         9.30        23.05        75.65 
TCGA-DD-AACG TCGA-DD-AACK TCGA-DD-AAD6 TCGA-DD-AADB TCGA-DD-AADE TCGA-DD-AADN 
       15.42         0.30        22.09        40.83        39.52        29.52 
TCGA-DD-AADQ TCGA-DD-AADS TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAEE 
       14.33        15.58        20.98        18.61        19.99        26.63 
TCGA-DD-AAEI TCGA-DD-AAVU TCGA-DD-AAVX TCGA-ED-A627 TCGA-ED-A7PX TCGA-ED-A97K 
       50.33        72.39        56.48        13.91         0.20         0.20 
TCGA-FV-A3I0 TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A3CH 
       27.88         0.39        51.06        53.79        28.27        25.64 
TCGA-G3-A3CI TCGA-G3-A5SJ TCGA-G3-A7M5 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ 
        5.92        22.95        14.70        11.87        14.14        15.78 
TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-K7-A5RG TCGA-K7-AAU7 TCGA-LG-A9QD TCGA-MR-A520 
        1.02         2.20        17.06        11.80        12.03         7.53 
TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-RC-A6M5 TCGA-RC-A6M6 TCGA-RC-A7SB TCGA-RC-A7SK 
       58.88        26.27         0.49         0.30        19.33        15.52 
TCGA-UB-A7MB TCGA-WX-AA46 TCGA-XR-A8TE TCGA-YA-A8S7 TCGA-ZS-A9CF 
       19.76        24.85        30.41        13.55        79.30 

  AMP PEAK  2(1Q42.2) MUTATED AMP PEAK  2(1Q42.2) WILD-TYPE 
                         0.03                          0.20 
  AMP PEAK  2(1Q42.2) MUTATED AMP PEAK  2(1Q42.2) WILD-TYPE 
                       120.82                        108.76 
  AMP PEAK  2(1Q42.2) MUTATED AMP PEAK  2(1Q42.2) WILD-TYPE 
                        19.59                         19.99 
[1] "0.0 - 120.8 (19.6)" "0.2 - 108.8 (20.0)"
[1] "hr=" "1.2"
D2V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IIIA
  AMP PEAK  2(1Q42.2) MUTATED       123       66         2         39
  AMP PEAK  2(1Q42.2) WILD-TYPE      50       21         1         23
                               vv
clus                            STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK  2(1Q42.2) MUTATED            9          5        2         0
  AMP PEAK  2(1Q42.2) WILD-TYPE          0          2        0         1
                               vv
clus                            STAGE IVB
  AMP PEAK  2(1Q42.2) MUTATED           2
  AMP PEAK  2(1Q42.2) WILD-TYPE         0
D2V3, multiclass
            clus
vv           AMP PEAK  2(1Q42.2) MUTATED AMP PEAK  2(1Q42.2) WILD-TYPE
  STAGE I                            123                            50
  STAGE II                            66                            21
  STAGE III                            2                             1
  STAGE IIIA                          39                            23
  STAGE IIIB                           9                             0
  STAGE IIIC                           5                             2
  STAGE IV                             2                             0
  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                             T1  T2  T3  T4
  AMP PEAK  2(1Q42.2) MUTATED   132  73  52   9
  AMP PEAK  2(1Q42.2) WILD-TYPE  51  22  25   3
D2V4, multiclass
    clus
vv   AMP PEAK  2(1Q42.2) MUTATED AMP PEAK  2(1Q42.2) WILD-TYPE
  T1                         132                            51
  T2                          73                            22
  T3                          52                            25
  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"
D2V5, binary
                               cls
clus                              0   1
  AMP PEAK  2(1Q42.2) MUTATED   188   2
  AMP PEAK  2(1Q42.2) WILD-TYPE  66   1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q42.2) MUTATED    188    2
  AMP PEAK  2(1Q42.2) WILD-TYPE   66    1
   clus
vv  AMP PEAK  2(1Q42.2) MUTATED AMP PEAK  2(1Q42.2) WILD-TYPE
  0                         188                            66
  1                           2                             1
[1] 2 2
[1] FALSE
D2V6, binary
                               cls
clus                              0   1
  AMP PEAK  2(1Q42.2) MUTATED   197   4
  AMP PEAK  2(1Q42.2) WILD-TYPE  69   0
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q42.2) MUTATED    197    4
  AMP PEAK  2(1Q42.2) WILD-TYPE   69    0
   clus
vv  AMP PEAK  2(1Q42.2) MUTATED AMP PEAK  2(1Q42.2) WILD-TYPE
  0                         197                            69
  1                           4                             0
[1] 2 2
[1] FALSE
D2V7, binary
                               cls
clus                              0   1
  AMP PEAK  2(1Q42.2) MUTATED    88 180
  AMP PEAK  2(1Q42.2) WILD-TYPE  30  72
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q42.2) MUTATED     88  180
  AMP PEAK  2(1Q42.2) WILD-TYPE   30   72
        clus
vv       AMP PEAK  2(1Q42.2) MUTATED AMP PEAK  2(1Q42.2) WILD-TYPE
  FEMALE                          88                            30
  MALE                           180                            72
[1] 2 2
[1] FALSE
D2V8, binary
                               cls
clus                              0   1
  AMP PEAK  2(1Q42.2) MUTATED   248   6
  AMP PEAK  2(1Q42.2) WILD-TYPE  90   3
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q42.2) MUTATED    248    6
  AMP PEAK  2(1Q42.2) WILD-TYPE   90    3
     clus
vv    AMP PEAK  2(1Q42.2) MUTATED AMP PEAK  2(1Q42.2) WILD-TYPE
  NO                          248                            90
  YES                           6                             3
[1] 2 2
[1] FALSE
                               vv
clus                            FIBROLAMELLAR CARCINOMA
  AMP PEAK  2(1Q42.2) MUTATED                         2
  AMP PEAK  2(1Q42.2) WILD-TYPE                       1
                               vv
clus                            HEPATOCELLULAR CARCINOMA
  AMP PEAK  2(1Q42.2) MUTATED                        262
  AMP PEAK  2(1Q42.2) WILD-TYPE                       98
                               vv
clus                            HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK  2(1Q42.2) MUTATED                                  4
  AMP PEAK  2(1Q42.2) WILD-TYPE                                3
D2V9, multiclass
                                  clus
vv                                 AMP PEAK  2(1Q42.2) MUTATED
  FIBROLAMELLAR CARCINOMA                                    2
  HEPATOCELLULAR CARCINOMA                                 262
  HEPATOCHOLANGIOCARCINOMA (MIXED)                           4
                                  clus
vv                                 AMP PEAK  2(1Q42.2) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                      1
  HEPATOCELLULAR CARCINOMA                                    98
  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(1Q42.2) MUTATED   236  12   1  14
  AMP PEAK  2(1Q42.2) WILD-TYPE  88   5   0   7
D2V10, multiclass
    clus
vv   AMP PEAK  2(1Q42.2) MUTATED AMP PEAK  2(1Q42.2) WILD-TYPE
  R0                         236                            88
  R1                          12                             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
  AMP PEAK  2(1Q42.2) MUTATED                                  2   121
  AMP PEAK  2(1Q42.2) WILD-TYPE                                0    37
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  2(1Q42.2) MUTATED                          12   125
  AMP PEAK  2(1Q42.2) WILD-TYPE                         5    58
D2V11, multiclass
                                  clus
vv                                 AMP PEAK  2(1Q42.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           2
  ASIAN                                                    121
  BLACK OR AFRICAN AMERICAN                                 12
  WHITE                                                    125
                                  clus
vv                                 AMP PEAK  2(1Q42.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                       37
  BLACK OR AFRICAN AMERICAN                                    5
  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"
D2V12, binary
                               cls
clus                              0   1
  AMP PEAK  2(1Q42.2) MUTATED    11 243
  AMP PEAK  2(1Q42.2) WILD-TYPE   5  92
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q42.2) MUTATED     11  243
  AMP PEAK  2(1Q42.2) WILD-TYPE    5   92
                        clus
vv                       AMP PEAK  2(1Q42.2) MUTATED
  HISPANIC OR LATINO                              11
  NOT HISPANIC OR LATINO                         243
                        clus
vv                       AMP PEAK  2(1Q42.2) WILD-TYPE
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                            92
[1] 2 2
[1] FALSE

Clustering(3) Variable = AMP PEAK  3(2P24.1) MUTATION ANALYSIS
D3V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  3(2P24.1) MUTATED    32  31
  AMP PEAK  3(2P24.1) WILD-TYPE 203  98
  AMP PEAK  3(2P24.1) MUTATED AMP PEAK  3(2P24.1) WILD-TYPE 
                           63                           301 
  AMP PEAK  3(2P24.1) MUTATED AMP PEAK  3(2P24.1) WILD-TYPE 
                           31                            98 
$`AMP PEAK  3(2P24.1) MUTATED`
TCGA-BC-A112 TCGA-BC-A5W4 TCGA-ES-A2HS TCGA-G3-A25W TCGA-G3-A7M9 TCGA-LG-A6GG 
        5.03        17.98        22.62        30.74         1.84        12.72 
TCGA-XR-A8TG TCGA-2Y-A9GU TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H2 TCGA-2Y-A9H4 
       29.52        63.75        24.89        27.88        56.91        47.74 
TCGA-2Y-A9H5 TCGA-5R-AA1C TCGA-BC-4072 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T 
       18.25        17.10        48.99        37.32        10.13        27.52 
TCGA-BW-A5NO TCGA-CC-5263 TCGA-CC-5264 TCGA-CC-A3M9 TCGA-CC-A7IE TCGA-CC-A7IG 
        0.66         4.24         3.35         9.86         7.13         9.83 
TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-DD-A113 TCGA-DD-A115 TCGA-DD-A11A TCGA-DD-A1E9 
       12.56         8.61        79.73        83.57         2.60        90.71 
TCGA-DD-A1EG TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39X TCGA-DD-A3A9 TCGA-DD-A4NA 
       45.11        33.04        13.64        55.69        30.61        33.14 
TCGA-DD-A4NO TCGA-DD-A73B TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-AA3A 
       73.81         9.30        22.78         1.45        35.67        13.48 
TCGA-DD-AACB TCGA-DD-AACI TCGA-DD-AAD6 TCGA-DD-AADF TCGA-DD-AADN TCGA-DD-AADO 
       76.41        53.19        22.09         3.78        29.52        14.89 
TCGA-DD-AADR TCGA-DD-AAE2 TCGA-ED-A7PY TCGA-ED-A82E TCGA-ED-A8O6 TCGA-EP-A2KA 
       66.67        20.98        12.82        13.41         1.84        20.61 
TCGA-G3-A25T TCGA-G3-A25Z TCGA-G3-AAV0 TCGA-G3-AAV4 TCGA-G3-AAV6 TCGA-UB-A7MA 
       51.06        21.53        15.65         0.89         2.14        27.88 
TCGA-UB-A7MB TCGA-WJ-A86L TCGA-ZS-A9CF 
       19.76        11.34        79.30 

$`AMP PEAK  3(2P24.1) WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BD-A3ER 
       83.24        11.74        38.40         8.61        69.57        36.66 
TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV TCGA-DD-AAE7 TCGA-DD-AAE8 
        0.36        90.28        26.83        18.87        21.17        21.83 
TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A4ZP 
       18.90        23.64         9.96         8.12         6.38        81.73 
TCGA-G3-A3CG TCGA-G3-A6UC TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-MI-A75H 
       22.13        22.06        20.75         2.14        31.27        24.56 
TCGA-T1-A6J8 TCGA-UB-A7MF TCGA-UB-AA0V TCGA-ZP-A9D1 TCGA-ZS-A9CE TCGA-2Y-A9GS 
        0.76         7.04        10.32         0.69        40.80        23.80 
TCGA-2Y-A9GT TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H3 
       53.39        41.79        80.28       120.82        40.41        49.84 
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-AA1D TCGA-5R-AAAM TCGA-BC-4073 TCGA-BC-A10S 
       10.59         0.66        14.76         1.51        27.91        46.78 
TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A216 
       27.52         2.99        25.32        23.38         1.12        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-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
       44.81        13.45         4.24         2.86         3.19         3.39 
TCGA-CC-A1HT TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A5UD 
        3.32         9.96        10.36        11.93        11.41         9.99 
TCGA-CC-A5UE TCGA-CC-A7IF TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IL TCGA-CC-A8HT 
        8.94        21.34        12.00        13.12         9.14         4.60 
TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A114 TCGA-DD-A116 
       11.31         9.17         6.94         8.15        37.78        53.33 
TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1EA 
      113.00         7.33         0.46        21.76        51.29        79.40 
TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-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-A39Y TCGA-DD-A39Z 
        6.02        18.35        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-A4NB TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NJ 
      107.11        13.78        32.52        30.97        30.15        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-A73G TCGA-DD-AAC8 
       80.75        78.84        23.93        23.05       114.35         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        71.80        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-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD8 
        4.50        18.54        21.63        42.58        44.22        40.08 
TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADG 
       40.54        40.83        13.97        40.47        39.52        37.64 
TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADP 
       35.67        35.05        34.49        20.91         0.39        15.06 
TCGA-DD-AADQ TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 
       14.33        15.58        18.21        19.30        18.25        18.25 
TCGA-DD-AAE1 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE9 TCGA-DD-AAEB 
       18.15        18.61        19.99         4.64        23.74        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        90.48 
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        60.99 
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-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A8O5 
        9.73         0.20         0.20        14.04        13.15        13.35 
TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK 
        0.20        18.74        19.99        19.59         0.62        11.93 
TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R3 
       14.40        60.89        23.97        19.10        27.88        12.03 
TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25V 
        0.03         0.33         0.39        13.68        53.79        28.27 
TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
       58.49        14.86        25.64         5.92        19.53        19.23 
TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A7M5 TCGA-G3-A7M6 
       25.25        22.95        20.42        17.10        14.70        20.78 
TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 
       11.87        14.14        15.78        11.80        12.23        13.55 
TCGA-G3-AAV5 TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ 
       11.64        11.87        28.90         1.02         2.20         2.99 
TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-KR-A7K8 
       37.71        17.06        16.83        11.80        27.25        29.79 
TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I 
       13.97        12.03         9.57        16.67        22.95        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-A6M4 TCGA-RC-A6M5 TCGA-RC-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SB 
        3.09         0.72         0.49         0.30        21.04        19.33 
TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MC TCGA-UB-A7MD 
       19.04        15.39        15.52        36.10        16.44         1.71 
TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-WX-AA46 
       15.98        10.75         0.99        12.99        20.22        24.85 
TCGA-WX-AA47 TCGA-XR-A8TD TCGA-XR-A8TE TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CV 
       18.28        33.86        30.41        22.78        13.55        35.77 
TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD 
       25.71        23.21        35.87        25.15        12.99        45.57 
TCGA-ZS-A9CG 
       11.21 

  AMP PEAK  3(2P24.1) MUTATED AMP PEAK  3(2P24.1) WILD-TYPE 
                         0.66                          0.03 
  AMP PEAK  3(2P24.1) MUTATED AMP PEAK  3(2P24.1) WILD-TYPE 
                        90.71                        120.82 
  AMP PEAK  3(2P24.1) MUTATED AMP PEAK  3(2P24.1) WILD-TYPE 
                        20.98                         19.59 
[1] "0.7 - 90.7 (21.0)"  "0.0 - 120.8 (19.6)"
[1] "hr=" "1.5"
D3V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IIIA
  AMP PEAK  3(2P24.1) MUTATED        25       14         0         16
  AMP PEAK  3(2P24.1) WILD-TYPE     148       73         3         46
                               vv
clus                            STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK  3(2P24.1) MUTATED            2          2        1         0
  AMP PEAK  3(2P24.1) WILD-TYPE          7          5        1         1
                               vv
clus                            STAGE IVB
  AMP PEAK  3(2P24.1) MUTATED           1
  AMP PEAK  3(2P24.1) WILD-TYPE         1
D3V3, multiclass
            clus
vv           AMP PEAK  3(2P24.1) MUTATED AMP PEAK  3(2P24.1) WILD-TYPE
  STAGE I                             25                           148
  STAGE II                            14                            73
  STAGE III                            0                             3
  STAGE IIIA                          16                            46
  STAGE IIIB                           2                             7
  STAGE IIIC                           2                             5
  STAGE IV                             1                             1
  STAGE IVA                            0                             1
  STAGE IVB                            1                             1
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  AMP PEAK  3(2P24.1) MUTATED    26  17  20   2
  AMP PEAK  3(2P24.1) WILD-TYPE 157  78  57  10
D3V4, multiclass
    clus
vv   AMP PEAK  3(2P24.1) MUTATED AMP PEAK  3(2P24.1) WILD-TYPE
  T1                          26                           157
  T2                          17                            78
  T3                          20                            57
  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"
D3V5, binary
                               cls
clus                              0   1
  AMP PEAK  3(2P24.1) MUTATED    42   2
  AMP PEAK  3(2P24.1) WILD-TYPE 212   1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(2P24.1) MUTATED     42    2
  AMP PEAK  3(2P24.1) WILD-TYPE  212    1
   clus
vv  AMP PEAK  3(2P24.1) MUTATED AMP PEAK  3(2P24.1) WILD-TYPE
  0                          42                           212
  1                           2                             1
[1] 2 2
[1] FALSE
D3V6, binary
                               cls
clus                              0   1
  AMP PEAK  3(2P24.1) MUTATED    43   2
  AMP PEAK  3(2P24.1) WILD-TYPE 223   2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(2P24.1) MUTATED     43    2
  AMP PEAK  3(2P24.1) WILD-TYPE  223    2
   clus
vv  AMP PEAK  3(2P24.1) MUTATED AMP PEAK  3(2P24.1) WILD-TYPE
  0                          43                           223
  1                           2                             2
[1] 2 2
[1] FALSE
D3V7, binary
                               cls
clus                              0   1
  AMP PEAK  3(2P24.1) MUTATED    32  33
  AMP PEAK  3(2P24.1) WILD-TYPE  86 219
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(2P24.1) MUTATED     32   33
  AMP PEAK  3(2P24.1) WILD-TYPE   86  219
        clus
vv       AMP PEAK  3(2P24.1) MUTATED AMP PEAK  3(2P24.1) WILD-TYPE
  FEMALE                          32                            86
  MALE                            33                           219
[1] 2 2
[1] FALSE
D3V8, binary
                               cls
clus                              0   1
  AMP PEAK  3(2P24.1) MUTATED    60   1
  AMP PEAK  3(2P24.1) WILD-TYPE 278   8
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(2P24.1) MUTATED     60    1
  AMP PEAK  3(2P24.1) WILD-TYPE  278    8
     clus
vv    AMP PEAK  3(2P24.1) MUTATED AMP PEAK  3(2P24.1) WILD-TYPE
  NO                           60                           278
  YES                           1                             8
[1] 2 2
[1] FALSE
                               vv
clus                            FIBROLAMELLAR CARCINOMA
  AMP PEAK  3(2P24.1) MUTATED                         0
  AMP PEAK  3(2P24.1) WILD-TYPE                       3
                               vv
clus                            HEPATOCELLULAR CARCINOMA
  AMP PEAK  3(2P24.1) MUTATED                         63
  AMP PEAK  3(2P24.1) WILD-TYPE                      297
                               vv
clus                            HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK  3(2P24.1) MUTATED                                  2
  AMP PEAK  3(2P24.1) WILD-TYPE                                5
D3V9, multiclass
                                  clus
vv                                 AMP PEAK  3(2P24.1) MUTATED
  FIBROLAMELLAR CARCINOMA                                    0
  HEPATOCELLULAR CARCINOMA                                  63
  HEPATOCHOLANGIOCARCINOMA (MIXED)                           2
                                  clus
vv                                 AMP PEAK  3(2P24.1) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                      3
  HEPATOCELLULAR CARCINOMA                                   297
  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  3(2P24.1) MUTATED    56   5   0   4
  AMP PEAK  3(2P24.1) WILD-TYPE 268  12   1  17
D3V10, multiclass
    clus
vv   AMP PEAK  3(2P24.1) MUTATED AMP PEAK  3(2P24.1) WILD-TYPE
  R0                          56                           268
  R1                           5                            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  3(2P24.1) MUTATED                                  0    21
  AMP PEAK  3(2P24.1) WILD-TYPE                                2   137
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  3(2P24.1) MUTATED                           4    40
  AMP PEAK  3(2P24.1) WILD-TYPE                        13   143
D3V11, multiclass
                                  clus
vv                                 AMP PEAK  3(2P24.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                     21
  BLACK OR AFRICAN AMERICAN                                  4
  WHITE                                                     40
                                  clus
vv                                 AMP PEAK  3(2P24.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             2
  ASIAN                                                      137
  BLACK OR AFRICAN AMERICAN                                   13
  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"
D3V12, binary
                               cls
clus                              0   1
  AMP PEAK  3(2P24.1) MUTATED     3  61
  AMP PEAK  3(2P24.1) WILD-TYPE  13 274
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(2P24.1) MUTATED      3   61
  AMP PEAK  3(2P24.1) WILD-TYPE   13  274
                        clus
vv                       AMP PEAK  3(2P24.1) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                          61
                        clus
vv                       AMP PEAK  3(2P24.1) WILD-TYPE
  HISPANIC OR LATINO                                13
  NOT HISPANIC OR LATINO                           274
[1] 2 2
[1] FALSE

Clustering(4) Variable = AMP PEAK  4(2Q33.1) MUTATION ANALYSIS
D4V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  4(2Q33.1) MUTATED    32  29
  AMP PEAK  4(2Q33.1) WILD-TYPE 203 100
  AMP PEAK  4(2Q33.1) MUTATED AMP PEAK  4(2Q33.1) WILD-TYPE 
                           61                           303 
  AMP PEAK  4(2Q33.1) MUTATED AMP PEAK  4(2Q33.1) WILD-TYPE 
                           29                           100 
$`AMP PEAK  4(2Q33.1) MUTATED`
TCGA-ES-A2HS TCGA-G3-A25W TCGA-LG-A6GG TCGA-2Y-A9GY TCGA-2Y-A9H0 TCGA-2Y-A9H5 
       22.62        30.74        12.72        24.89       120.82        18.25 
TCGA-5R-AA1C TCGA-BC-4072 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10Y TCGA-BC-A217 
       17.10        48.99        37.32        10.13        23.38        45.93 
TCGA-BC-A8YO TCGA-CC-A7IE TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A8HV TCGA-DD-A113 
       18.48         7.13        12.56         8.61         9.17        79.73 
TCGA-DD-A11C TCGA-DD-A1E9 TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39W TCGA-DD-A39X 
       21.76        90.71        33.04        13.64        27.19        55.69 
TCGA-DD-A3A5 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-AA3A 
      102.74        13.78        30.61        22.78         1.45        13.48 
TCGA-DD-AACB TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACZ TCGA-DD-AAD5 TCGA-DD-AAD6 
       76.41         6.41        53.19         5.62        44.22        22.09 
TCGA-DD-AAD8 TCGA-DD-AADC TCGA-DD-AADF TCGA-DD-AADJ TCGA-DD-AADO TCGA-DD-AADU 
       40.08        13.97         3.78        35.05        14.89        18.21 
TCGA-DD-AADW TCGA-DD-AAE6 TCGA-DD-AAEE TCGA-DD-AAVS TCGA-ED-A7PY TCGA-ED-A82E 
       19.30         4.64        26.63        59.93        12.82        13.41 
TCGA-ED-A8O6 TCGA-EP-A2KA TCGA-FV-A495 TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25Z 
        1.84        20.61         0.03        13.68        51.06        21.53 
TCGA-G3-A5SM TCGA-G3-AAV6 TCGA-RC-A7SK TCGA-UB-A7MA TCGA-XR-A8TE TCGA-YA-A8S7 
       17.10         2.14        15.52        27.88        30.41        13.55 
TCGA-ZS-A9CF 
       79.30 

$`AMP PEAK  4(2Q33.1) WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 
       83.24        11.74        38.40         8.61        69.57         5.03 
TCGA-BC-A5W4 TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV 
       17.98        36.66         0.36        90.28        26.83        18.87 
TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-FV-A3I1 
       21.17        21.83        18.90        23.64         9.96         8.12 
TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A3CG TCGA-G3-A6UC TCGA-G3-A7M9 TCGA-K7-A5RF 
        6.38        81.73        22.13        22.06         1.84        20.75 
TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-MI-A75H TCGA-T1-A6J8 TCGA-UB-A7MF TCGA-UB-AA0V 
        2.14        31.27        24.56         0.76         7.04        10.32 
TCGA-XR-A8TG TCGA-ZP-A9D1 TCGA-ZS-A9CE TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU 
       29.52         0.69        40.80        23.80        53.39        63.75 
TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GZ TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 
       41.79        80.28        27.88        40.41        56.91        49.84 
TCGA-2Y-A9H4 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 
       47.74        20.81        22.92         1.18         8.55        13.02 
TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4073 
       10.78        10.59         0.66        14.76         1.51        27.91 
TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Z 
       46.78        27.52        27.52         2.99        25.32         1.12 
TCGA-BC-A216 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A69I TCGA-BD-A2L6 
       44.42         0.26        22.36        14.60        12.72        44.81 
TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
       13.45         0.66         4.24         2.86         3.19         3.39 
TCGA-CC-5263 TCGA-CC-5264 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB 
        4.24         3.35         3.32         9.86         9.96        10.36 
TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IF TCGA-CC-A7IG 
       11.93        11.41         9.99         8.94        21.34         9.83 
TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IL TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A9FS 
       12.00        13.12         9.14         4.60        11.31         6.94 
TCGA-CC-A9FW TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 
        8.15        37.78        83.57        53.33       113.00         7.33 
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-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-A1EK TCGA-DD-A39V TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 
       18.35        21.14         5.62        19.76        25.81         7.66 
TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A6 TCGA-DD-A4NA TCGA-DD-A4NB 
       70.06        17.59        20.12       107.11        33.14        32.52 
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-A4NV 
       73.81       108.76        12.26         0.30        80.75        78.84 
TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AAC8 
       23.93         9.30        23.05        35.67       114.35         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        71.80        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-AACP TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACU 
       61.68        13.64        14.20        59.31        51.35        51.52 
TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AAD0 TCGA-DD-AAD1 
       50.33        46.82         5.59        47.67         4.50        18.54 
TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADD TCGA-DD-AADE 
       21.63        42.58        40.54        40.83        40.47        39.52 
TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN 
       37.64        35.67        34.49        20.91         0.39        29.52 
TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADY TCGA-DD-AAE0 
       15.06        14.33        66.67        15.58        18.25        18.25 
TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE9 TCGA-DD-AAEB 
       18.15        20.98        18.61        19.99        23.74        15.72 
TCGA-DD-AAED TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ 
       25.08        25.78        50.33        35.08        90.48        89.69 
TCGA-DD-AAVR TCGA-DD-AAVU TCGA-DD-AAVV TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY 
       82.62        72.39        80.71        76.18        56.48        64.77 
TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 
       62.47        66.25        65.39        60.99        53.69        29.92 
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-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A8O5 TCGA-ED-A97K TCGA-EP-A12J 
        0.20        14.04        13.15        13.35         0.20        18.74 
TCGA-EP-A26S TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B 
       19.99        19.59         0.62        11.93        14.40        60.89 
TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A496 TCGA-FV-A4ZQ 
       23.97        19.10        27.88        12.03         0.33         0.39 
TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A3CH TCGA-G3-A3CI 
       53.79        28.27        58.49        14.86        25.64         5.92 
TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A7M5 
       19.53        19.23        25.25        22.95        20.42        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-AAV7 TCGA-GJ-A3OU 
       12.23        13.55         0.89        11.64        11.87        28.90 
TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 
        1.02         2.20         2.99        37.71        17.06        16.83 
TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C 
       11.80        27.25        29.79        13.97        12.03         9.57 
TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 
       16.67        22.95        20.71         7.53        10.85        58.88 
TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A6M4 TCGA-RC-A6M5 
       26.27        17.69        21.01         3.09         0.72         0.49 
TCGA-RC-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RG-A7D4 
        0.30        21.04        19.33        19.04        15.39        36.10 
TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WJ-A86L 
       19.76        16.44         1.71        15.98        10.75        11.34 
TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TD 
        0.99        12.99        20.22        24.85        18.28        33.86 
TCGA-XR-A8TF TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 
       22.78        35.77        25.71        23.21        35.87        25.15 
TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CG 
       12.99        45.57        11.21 

  AMP PEAK  4(2Q33.1) MUTATED AMP PEAK  4(2Q33.1) WILD-TYPE 
                         0.03                          0.20 
  AMP PEAK  4(2Q33.1) MUTATED AMP PEAK  4(2Q33.1) WILD-TYPE 
                       120.82                        114.35 
  AMP PEAK  4(2Q33.1) MUTATED AMP PEAK  4(2Q33.1) WILD-TYPE 
                        20.61                         19.76 
[1] "0.0 - 120.8 (20.6)" "0.2 - 114.3 (19.8)"
[1] "hr=" "1.3"
D4V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IIIA
  AMP PEAK  4(2Q33.1) MUTATED        22       18         2         13
  AMP PEAK  4(2Q33.1) WILD-TYPE     151       69         1         49
                               vv
clus                            STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK  4(2Q33.1) MUTATED            2          2        1         0
  AMP PEAK  4(2Q33.1) WILD-TYPE          7          5        1         1
                               vv
clus                            STAGE IVB
  AMP PEAK  4(2Q33.1) MUTATED           1
  AMP PEAK  4(2Q33.1) WILD-TYPE         1
D4V3, multiclass
            clus
vv           AMP PEAK  4(2Q33.1) MUTATED AMP PEAK  4(2Q33.1) WILD-TYPE
  STAGE I                             22                           151
  STAGE II                            18                            69
  STAGE III                            2                             1
  STAGE IIIA                          13                            49
  STAGE IIIB                           2                             7
  STAGE IIIC                           2                             5
  STAGE IV                             1                             1
  STAGE IVA                            0                             1
  STAGE IVB                            1                             1
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  AMP PEAK  4(2Q33.1) MUTATED    23  20  18   3
  AMP PEAK  4(2Q33.1) WILD-TYPE 160  75  59   9
D4V4, multiclass
    clus
vv   AMP PEAK  4(2Q33.1) MUTATED AMP PEAK  4(2Q33.1) WILD-TYPE
  T1                          23                           160
  T2                          20                            75
  T3                          18                            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"
D4V5, binary
                               cls
clus                              0   1
  AMP PEAK  4(2Q33.1) MUTATED    49   1
  AMP PEAK  4(2Q33.1) WILD-TYPE 205   2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(2Q33.1) MUTATED     49    1
  AMP PEAK  4(2Q33.1) WILD-TYPE  205    2
   clus
vv  AMP PEAK  4(2Q33.1) MUTATED AMP PEAK  4(2Q33.1) WILD-TYPE
  0                          49                           205
  1                           1                             2
[1] 2 2
[1] FALSE
D4V6, binary
                               cls
clus                              0   1
  AMP PEAK  4(2Q33.1) MUTATED    50   2
  AMP PEAK  4(2Q33.1) WILD-TYPE 216   2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(2Q33.1) MUTATED     50    2
  AMP PEAK  4(2Q33.1) WILD-TYPE  216    2
   clus
vv  AMP PEAK  4(2Q33.1) MUTATED AMP PEAK  4(2Q33.1) WILD-TYPE
  0                          50                           216
  1                           2                             2
[1] 2 2
[1] FALSE
D4V7, binary
                               cls
clus                              0   1
  AMP PEAK  4(2Q33.1) MUTATED    34  30
  AMP PEAK  4(2Q33.1) WILD-TYPE  84 222
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(2Q33.1) MUTATED     34   30
  AMP PEAK  4(2Q33.1) WILD-TYPE   84  222
        clus
vv       AMP PEAK  4(2Q33.1) MUTATED AMP PEAK  4(2Q33.1) WILD-TYPE
  FEMALE                          34                            84
  MALE                            30                           222
[1] 2 2
[1] FALSE
D4V8, binary
                               cls
clus                              0   1
  AMP PEAK  4(2Q33.1) MUTATED    58   0
  AMP PEAK  4(2Q33.1) WILD-TYPE 280   9
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(2Q33.1) MUTATED     58    0
  AMP PEAK  4(2Q33.1) WILD-TYPE  280    9
     clus
vv    AMP PEAK  4(2Q33.1) MUTATED AMP PEAK  4(2Q33.1) WILD-TYPE
  NO                           58                           280
  YES                           0                             9
[1] 2 2
[1] FALSE
                               vv
clus                            FIBROLAMELLAR CARCINOMA
  AMP PEAK  4(2Q33.1) MUTATED                         0
  AMP PEAK  4(2Q33.1) WILD-TYPE                       3
                               vv
clus                            HEPATOCELLULAR CARCINOMA
  AMP PEAK  4(2Q33.1) MUTATED                         62
  AMP PEAK  4(2Q33.1) WILD-TYPE                      298
                               vv
clus                            HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK  4(2Q33.1) MUTATED                                  2
  AMP PEAK  4(2Q33.1) WILD-TYPE                                5
D4V9, multiclass
                                  clus
vv                                 AMP PEAK  4(2Q33.1) MUTATED
  FIBROLAMELLAR CARCINOMA                                    0
  HEPATOCELLULAR CARCINOMA                                  62
  HEPATOCHOLANGIOCARCINOMA (MIXED)                           2
                                  clus
vv                                 AMP PEAK  4(2Q33.1) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                      3
  HEPATOCELLULAR CARCINOMA                                   298
  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(2Q33.1) MUTATED    58   4   0   2
  AMP PEAK  4(2Q33.1) WILD-TYPE 266  13   1  19
D4V10, multiclass
    clus
vv   AMP PEAK  4(2Q33.1) MUTATED AMP PEAK  4(2Q33.1) WILD-TYPE
  R0                          58                           266
  R1                           4                            13
  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  4(2Q33.1) MUTATED                                  1    26
  AMP PEAK  4(2Q33.1) WILD-TYPE                                1   132
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  4(2Q33.1) MUTATED                           1    35
  AMP PEAK  4(2Q33.1) WILD-TYPE                        16   148
D4V11, multiclass
                                  clus
vv                                 AMP PEAK  4(2Q33.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                     26
  BLACK OR AFRICAN AMERICAN                                  1
  WHITE                                                     35
                                  clus
vv                                 AMP PEAK  4(2Q33.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                      132
  BLACK OR AFRICAN AMERICAN                                   16
  WHITE                                                      148
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V12, binary
                               cls
clus                              0   1
  AMP PEAK  4(2Q33.1) MUTATED     4  57
  AMP PEAK  4(2Q33.1) WILD-TYPE  12 278
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(2Q33.1) MUTATED      4   57
  AMP PEAK  4(2Q33.1) WILD-TYPE   12  278
                        clus
vv                       AMP PEAK  4(2Q33.1) MUTATED
  HISPANIC OR LATINO                               4
  NOT HISPANIC OR LATINO                          57
                        clus
vv                       AMP PEAK  4(2Q33.1) WILD-TYPE
  HISPANIC OR LATINO                                12
  NOT HISPANIC OR LATINO                           278
[1] 2 2
[1] FALSE

Clustering(5) Variable = AMP PEAK  5(3Q26.31) MUTATION ANALYSIS
D5V1, survival
                                sevent
clus2                              0   1
  AMP PEAK  5(3Q26.31) MUTATED    44  32
  AMP PEAK  5(3Q26.31) WILD-TYPE 191  97
  AMP PEAK  5(3Q26.31) MUTATED AMP PEAK  5(3Q26.31) WILD-TYPE 
                            76                            288 
  AMP PEAK  5(3Q26.31) MUTATED AMP PEAK  5(3Q26.31) WILD-TYPE 
                            32                             97 
$`AMP PEAK  5(3Q26.31) MUTATED`
TCGA-BC-A5W4 TCGA-DD-A4NI TCGA-ES-A2HS TCGA-FV-A3R2 TCGA-G3-A7M9 TCGA-XR-A8TG 
       17.98        26.83        22.62         6.38         1.84        29.52 
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-A69H TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-A3MA 
       45.93        22.36        14.60        13.45         0.66         9.96 
TCGA-CC-A7IE TCGA-CC-A7IG TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-DD-A114 TCGA-DD-A115 
        7.13         9.83        12.56         8.61        37.78        83.57 
TCGA-DD-A11C TCGA-DD-A1EF TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39Y TCGA-DD-A3A5 
       21.76        12.95        33.04        13.64         5.62       102.74 
TCGA-DD-A4NV TCGA-DD-A73E TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AACG TCGA-DD-AACL 
       78.84         1.45       114.35        13.48        15.42         3.52 
TCGA-DD-AACS TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACZ TCGA-DD-AAD5 TCGA-DD-AADC 
       59.31        50.33        46.82         5.62        44.22        13.97 
TCGA-DD-AADD TCGA-DD-AADL TCGA-DD-AADN TCGA-DD-AADR TCGA-DD-AADU TCGA-DD-AAE1 
       40.47        20.91        29.52        66.67        18.21        18.15 
TCGA-DD-AAE6 TCGA-DD-AAE9 TCGA-DD-AAEK TCGA-DD-AAVS TCGA-DD-AAVV TCGA-DD-AAW0 
        4.64        23.74        35.08        59.93        80.71        66.25 
TCGA-ED-A7PX TCGA-ED-A7PZ TCGA-ED-A82E TCGA-EP-A2KA TCGA-FV-A495 TCGA-G3-A25X 
        0.20         0.20        13.41        20.61         0.03        58.49 
TCGA-GJ-A6C0 TCGA-KR-A7K8 TCGA-LG-A9QD TCGA-MI-A75G TCGA-PD-A5DF TCGA-UB-A7MC 
        1.02        29.79        12.03        22.95        21.01        16.44 
TCGA-UB-A7MD TCGA-WJ-A86L TCGA-WX-AA44 TCGA-ZS-A9CF 
        1.71        11.34        20.22        79.30 

$`AMP PEAK  5(3Q26.31) WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 
       83.24        11.74        38.40         8.61        69.57         5.03 
TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-AADV TCGA-DD-AAE7 TCGA-DD-AAE8 
       36.66         0.36        90.28        18.87        21.17        21.83 
TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-FV-A3I1 TCGA-FV-A4ZP TCGA-G3-A25W 
       18.90        23.64         9.96         8.12        81.73        30.74 
TCGA-G3-A3CG TCGA-G3-A6UC TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG 
       22.13        22.06        20.75         2.14        31.27        12.72 
TCGA-MI-A75H TCGA-T1-A6J8 TCGA-UB-A7MF TCGA-UB-AA0V TCGA-ZP-A9D1 TCGA-ZS-A9CE 
       24.56         0.76         7.04        10.32         0.69        40.80 
TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GY TCGA-2Y-A9H1 
       53.39        63.75        41.79        80.28        24.89        40.41 
TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H5 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB 
       56.91        49.84        18.25        22.92         1.18         8.55 
TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-4073 
       10.78        10.59        14.76         1.51        48.99        27.91 
TCGA-BC-A10Q TCGA-BC-A10S TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A216 
       37.32        46.78        27.52         2.99        25.32        44.42 
TCGA-BC-A3KF TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-CC-5258 TCGA-CC-5260 
        0.26        12.72        18.48        44.81         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-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-A7IH TCGA-CC-A7II TCGA-CC-A7IL TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV 
       12.00        13.12         9.14         4.60        11.31         9.17 
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-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB 
        2.60         0.46        51.29        90.71        79.40        66.31 
TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI 
       19.79        75.65        11.47        45.11        49.15         6.02 
TCGA-DD-A1EK TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Z TCGA-DD-A3A0 
       18.35        21.14        27.19        55.69        19.76        25.81 
TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A6 TCGA-DD-A3A7 
        7.66        70.06        17.59        20.12       107.11        13.78 
TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NJ 
       30.61        33.14        32.52        30.97        30.15        30.51 
TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ 
       39.78        56.25        29.56        73.81       108.76        12.26 
TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D 
        0.30        80.75        23.93         9.30        23.05        22.78 
TCGA-DD-A73F TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC 
       35.67         0.53        11.41        75.65        76.41        55.40 
TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ 
       12.53        71.80        12.00         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-AACT TCGA-DD-AACU TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AAD0 TCGA-DD-AAD1 
       51.35        51.52         5.59        47.67         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-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-AADO TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADS TCGA-DD-AADW 
        0.39        14.89        15.06        14.33        15.58        19.30 
TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAEB 
       18.25        18.25        20.98        18.61        19.99        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        90.48        89.69 
TCGA-DD-AAVR TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ 
       82.62        72.39        76.18        56.48        64.77        62.47 
TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG 
       65.39        60.99        53.69        29.92        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-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KB 
       13.35         1.84         0.20        18.74        19.99        19.59 
TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR 
        0.62        11.93        14.40        60.89        23.97        19.10 
TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T 
       27.88        12.03         0.33         0.39        13.68        51.06 
TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI 
       53.79        28.27        14.86        21.53        25.64         5.92 
TCGA-G3-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-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        11.64         2.14 
TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RG 
       11.87        28.90         2.20         2.99        37.71        17.06 
TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-LG-A9QC TCGA-MI-A75C TCGA-MI-A75E 
       16.83        11.80        27.25        13.97         9.57        16.67 
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-A6M4 TCGA-RC-A6M5 TCGA-RC-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SB 
        3.09         0.72         0.49         0.30        21.04        19.33 
TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB 
       19.04        15.39        15.52        36.10        27.88        19.76 
TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA46 TCGA-WX-AA47 
       15.98        10.75         0.99        12.99        24.85        18.28 
TCGA-XR-A8TD TCGA-XR-A8TE TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY 
       33.86        30.41        22.78        13.55        35.77        25.71 
TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CG 
       23.21        35.87        25.15        12.99        45.57        11.21 

  AMP PEAK  5(3Q26.31) MUTATED AMP PEAK  5(3Q26.31) WILD-TYPE 
                          0.03                           0.20 
  AMP PEAK  5(3Q26.31) MUTATED AMP PEAK  5(3Q26.31) WILD-TYPE 
                        120.82                         113.00 
  AMP PEAK  5(3Q26.31) MUTATED AMP PEAK  5(3Q26.31) WILD-TYPE 
                        20.415                         19.760 
[1] "0.0 - 120.8 (20.4)" "0.2 - 113.0 (19.8)"
[1] "hr=" "1.2"
D5V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IIIA
  AMP PEAK  5(3Q26.31) MUTATED        33       22         1         12
  AMP PEAK  5(3Q26.31) WILD-TYPE     140       65         2         50
                                vv
clus                             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK  5(3Q26.31) MUTATED            3          1        0         0
  AMP PEAK  5(3Q26.31) WILD-TYPE          6          6        2         1
                                vv
clus                             STAGE IVB
  AMP PEAK  5(3Q26.31) MUTATED           0
  AMP PEAK  5(3Q26.31) WILD-TYPE         2
D5V3, multiclass
            clus
vv           AMP PEAK  5(3Q26.31) MUTATED AMP PEAK  5(3Q26.31) WILD-TYPE
  STAGE I                              33                            140
  STAGE II                             22                             65
  STAGE III                             1                              2
  STAGE IIIA                           12                             50
  STAGE IIIB                            3                              6
  STAGE IIIC                            1                              6
  STAGE IV                              0                              2
  STAGE IVA                             0                              1
  STAGE IVB                             0                              2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  AMP PEAK  5(3Q26.31) MUTATED    35  23  16   3
  AMP PEAK  5(3Q26.31) WILD-TYPE 148  72  61   9
D5V4, multiclass
    clus
vv   AMP PEAK  5(3Q26.31) MUTATED AMP PEAK  5(3Q26.31) WILD-TYPE
  T1                           35                            148
  T2                           23                             72
  T3                           16                             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"
D5V5, binary
                                cls
clus                               0   1
  AMP PEAK  5(3Q26.31) MUTATED    48   1
  AMP PEAK  5(3Q26.31) WILD-TYPE 206   2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  5(3Q26.31) MUTATED     48    1
  AMP PEAK  5(3Q26.31) WILD-TYPE  206    2
   clus
vv  AMP PEAK  5(3Q26.31) MUTATED AMP PEAK  5(3Q26.31) WILD-TYPE
  0                           48                            206
  1                            1                              2
[1] 2 2
[1] FALSE
D5V6, binary
                                cls
clus                               0   1
  AMP PEAK  5(3Q26.31) MUTATED    54   0
  AMP PEAK  5(3Q26.31) WILD-TYPE 212   4
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  5(3Q26.31) MUTATED     54    0
  AMP PEAK  5(3Q26.31) WILD-TYPE  212    4
   clus
vv  AMP PEAK  5(3Q26.31) MUTATED AMP PEAK  5(3Q26.31) WILD-TYPE
  0                           54                            212
  1                            0                              4
[1] 2 2
[1] FALSE
D5V7, binary
                                cls
clus                               0   1
  AMP PEAK  5(3Q26.31) MUTATED    23  54
  AMP PEAK  5(3Q26.31) WILD-TYPE  95 198
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  5(3Q26.31) MUTATED     23   54
  AMP PEAK  5(3Q26.31) WILD-TYPE   95  198
        clus
vv       AMP PEAK  5(3Q26.31) MUTATED AMP PEAK  5(3Q26.31) WILD-TYPE
  FEMALE                           23                             95
  MALE                             54                            198
[1] 2 2
[1] FALSE
D5V8, binary
                                cls
clus                               0   1
  AMP PEAK  5(3Q26.31) MUTATED    71   2
  AMP PEAK  5(3Q26.31) WILD-TYPE 267   7
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  5(3Q26.31) MUTATED     71    2
  AMP PEAK  5(3Q26.31) WILD-TYPE  267    7
     clus
vv    AMP PEAK  5(3Q26.31) MUTATED AMP PEAK  5(3Q26.31) WILD-TYPE
  NO                            71                            267
  YES                            2                              7
[1] 2 2
[1] FALSE
                                vv
clus                             FIBROLAMELLAR CARCINOMA
  AMP PEAK  5(3Q26.31) MUTATED                         0
  AMP PEAK  5(3Q26.31) WILD-TYPE                       3
                                vv
clus                             HEPATOCELLULAR CARCINOMA
  AMP PEAK  5(3Q26.31) MUTATED                         75
  AMP PEAK  5(3Q26.31) WILD-TYPE                      285
                                vv
clus                             HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK  5(3Q26.31) MUTATED                                  2
  AMP PEAK  5(3Q26.31) WILD-TYPE                                5
D5V9, multiclass
                                  clus
vv                                 AMP PEAK  5(3Q26.31) MUTATED
  FIBROLAMELLAR CARCINOMA                                     0
  HEPATOCELLULAR CARCINOMA                                   75
  HEPATOCHOLANGIOCARCINOMA (MIXED)                            2
                                  clus
vv                                 AMP PEAK  5(3Q26.31) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                       3
  HEPATOCELLULAR CARCINOMA                                    285
  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(3Q26.31) MUTATED    68   2   0   6
  AMP PEAK  5(3Q26.31) WILD-TYPE 256  15   1  15
D5V10, multiclass
    clus
vv   AMP PEAK  5(3Q26.31) MUTATED AMP PEAK  5(3Q26.31) WILD-TYPE
  R0                           68                            256
  R1                            2                             15
  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  5(3Q26.31) MUTATED                                  0    31
  AMP PEAK  5(3Q26.31) WILD-TYPE                                2   127
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  5(3Q26.31) MUTATED                           7    38
  AMP PEAK  5(3Q26.31) WILD-TYPE                        10   145
D5V11, multiclass
                                  clus
vv                                 AMP PEAK  5(3Q26.31) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                      31
  BLACK OR AFRICAN AMERICAN                                   7
  WHITE                                                      38
                                  clus
vv                                 AMP PEAK  5(3Q26.31) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              2
  ASIAN                                                       127
  BLACK OR AFRICAN AMERICAN                                    10
  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"
D5V12, binary
                                cls
clus                               0   1
  AMP PEAK  5(3Q26.31) MUTATED     5  69
  AMP PEAK  5(3Q26.31) WILD-TYPE  11 266
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  5(3Q26.31) MUTATED      5   69
  AMP PEAK  5(3Q26.31) WILD-TYPE   11  266
                        clus
vv                       AMP PEAK  5(3Q26.31) MUTATED
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                           69
                        clus
vv                       AMP PEAK  5(3Q26.31) WILD-TYPE
  HISPANIC OR LATINO                                 11
  NOT HISPANIC OR LATINO                            266
[1] 2 2
[1] FALSE

Clustering(6) Variable = AMP PEAK  6(4P14) MUTATION ANALYSIS
D6V1, survival
                             sevent
clus2                           0   1
  AMP PEAK  6(4P14) MUTATED    38  15
  AMP PEAK  6(4P14) WILD-TYPE 197 114
  AMP PEAK  6(4P14) MUTATED AMP PEAK  6(4P14) WILD-TYPE 
                         53                         311 
  AMP PEAK  6(4P14) MUTATED AMP PEAK  6(4P14) WILD-TYPE 
                         15                         114 
$`AMP PEAK  6(4P14) MUTATED`
TCGA-2Y-A9H6 TCGA-BC-A5W4 TCGA-G3-A3CG TCGA-G3-A7M9 TCGA-LG-A6GG TCGA-T1-A6J8 
       11.74        17.98        22.13         1.84        12.72         0.76 
TCGA-XR-A8TG TCGA-2Y-A9GU TCGA-2Y-A9GY TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H8 
       29.52        63.75        24.89        56.91        49.84        20.81 
TCGA-BC-A10R TCGA-BC-A217 TCGA-BD-A3EP TCGA-CC-5261 TCGA-CC-A3M9 TCGA-CC-A3MB 
       10.13        45.93        13.45         3.19         9.86        10.36 
TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A8HV TCGA-CC-A9FS TCGA-DD-A113 TCGA-DD-A118 
        9.83        12.00         9.17         6.94        79.73       113.00 
TCGA-DD-A11A TCGA-DD-A1EC TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A4NN TCGA-DD-A73G 
        2.60        19.79        49.15         6.02        29.56       114.35 
TCGA-DD-AACG TCGA-DD-AACI TCGA-DD-AACM TCGA-DD-AAD3 TCGA-DD-AADB TCGA-DD-AADO 
       15.42        53.19        58.16        42.58        40.83        14.89 
TCGA-DD-AADP TCGA-DD-AADR TCGA-DD-AAED TCGA-DD-AAVR TCGA-DD-AAVS TCGA-ED-A66X 
       15.06        66.67        25.08        82.62        59.93        13.35 
TCGA-ED-A7PZ TCGA-ED-A82E TCGA-ED-A8O5 TCGA-EP-A2KA TCGA-FV-A2QR TCGA-K7-AAU7 
        0.20        13.41        13.35        20.61        19.10        11.80 
TCGA-QA-A7B7 TCGA-RC-A7SK TCGA-WQ-A9G7 TCGA-XR-A8TD TCGA-ZS-A9CF 
        3.09        15.52         0.99        33.86        79.30 

$`AMP PEAK  6(4P14) WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 TCGA-BD-A3ER 
       83.24        38.40         8.61        69.57         5.03        36.66 
TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV TCGA-DD-AAE7 TCGA-DD-AAE8 
        0.36        90.28        26.83        18.87        21.17        21.83 
TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-ES-A2HS TCGA-FV-A3I1 TCGA-FV-A3R2 
       18.90        23.64         9.96        22.62         8.12         6.38 
TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A6UC TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-KR-A7K7 
       81.73        30.74        22.06        20.75         2.14        31.27 
TCGA-MI-A75H TCGA-UB-A7MF TCGA-UB-AA0V TCGA-ZP-A9D1 TCGA-ZS-A9CE TCGA-2Y-A9GS 
       24.56         7.04        10.32         0.69        40.80        23.80 
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-A9H5 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 
       47.74        18.25        22.92         1.18         8.55        13.02 
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-4073 TCGA-BC-A10Q TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
       48.99        27.91        37.32        46.78        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A3KF 
        2.99        25.32        23.38         1.12        44.42         0.26 
TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BW-A5NO 
       22.36        14.60        12.72        18.48        44.81         0.66 
TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-5264 TCGA-CC-A1HT 
        4.24         2.86         3.39         4.24         3.35         3.32 
TCGA-CC-A3MA TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IE 
        9.96        11.93        11.41         9.99         8.94         7.13 
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-A9FW TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A119 
       11.31         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-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EJ TCGA-DD-A1EK 
       75.65        11.47        12.95        45.11        33.04        18.35 
TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z 
       13.64        21.14        27.19        55.69         5.62        19.76 
TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 
       25.81         7.66        70.06        17.59        20.12       102.74 
TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NF 
      107.11        13.78        30.61        33.14        32.52        30.97 
TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NO TCGA-DD-A4NP 
       30.15        30.51        39.78        56.25        73.81       108.76 
TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B 
       12.26         0.30        80.75        78.84        23.93         9.30 
TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-AA3A TCGA-DD-AAC8 
       23.05        22.78         1.45        35.67        13.48         0.53 
TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE 
       11.41        75.65        76.41        55.40        12.53        71.80 
TCGA-DD-AACF TCGA-DD-AACH TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACN 
       12.00         6.41        69.11         0.30         3.52        42.81 
TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACU 
       61.68        13.64        14.20        59.31        51.35        51.52 
TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD0 
       50.33        46.82         5.59        47.67         5.62         4.50 
TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA 
       18.54        21.63        44.22        22.09        40.08        40.54 
TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI 
       13.97        40.47        39.52         3.78        37.64        35.67 
TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADQ 
       35.05        34.49        20.91         0.39        29.52        14.33 
TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 
       15.58        18.21        19.30        18.25        18.25        18.15 
TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE9 TCGA-DD-AAEB 
       20.98        18.61        19.99         4.64        23.74        15.72 
TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ 
       26.63        25.78        50.33        35.08        90.48        89.69 
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        60.99        53.69        29.92        26.93 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7XO 
       28.08        13.91         9.73         0.20        12.82        14.04 
TCGA-ED-A7XP TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KB 
       13.15         1.84         0.20        18.74        19.99        19.59 
TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A3I0 
        0.62        11.93        14.40        60.89        23.97        27.88 
TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T 
       12.03         0.03         0.33         0.39        13.68        51.06 
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-A5SM TCGA-G3-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ 
       17.10        14.70        20.78        11.87        14.14        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        11.64 
TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ 
        2.14        11.87        28.90         1.02         2.20         2.99 
TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A9QC 
       37.71        17.06        16.83        27.25        29.79        13.97 
TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A520 
       12.03         9.57        16.67        22.95        20.71         7.53 
TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-RC-A6M4 
       10.85        58.88        26.27        17.69        21.01         0.72 
TCGA-RC-A6M5 TCGA-RC-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH 
        0.49         0.30        21.04        19.33        19.04        15.39 
TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME 
       36.10        27.88        19.76        16.44         1.71        15.98 
TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 
       10.75        11.34        12.99        20.22        24.85        18.28 
TCGA-XR-A8TE TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ 
       30.41        22.78        13.55        35.77        25.71        23.21 
TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CG 
       35.87        25.15        12.99        45.57        11.21 

  AMP PEAK  6(4P14) MUTATED AMP PEAK  6(4P14) WILD-TYPE 
                       0.20                        0.03 
  AMP PEAK  6(4P14) MUTATED AMP PEAK  6(4P14) WILD-TYPE 
                     114.35                      120.82 
  AMP PEAK  6(4P14) MUTATED AMP PEAK  6(4P14) WILD-TYPE 
                      17.98                       19.99 
[1] "0.2 - 114.3 (18.0)" "0.0 - 120.8 (20.0)"
[1] "hr=" "1.4"
D6V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  6(4P14) MUTATED        21       17         1          9          2
  AMP PEAK  6(4P14) WILD-TYPE     152       70         2         53          7
                             vv
clus                          STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK  6(4P14) MUTATED            0        0         0         0
  AMP PEAK  6(4P14) WILD-TYPE          7        2         1         2
D6V3, multiclass
            clus
vv           AMP PEAK  6(4P14) MUTATED AMP PEAK  6(4P14) WILD-TYPE
  STAGE I                           21                         152
  STAGE II                          17                          70
  STAGE III                          1                           2
  STAGE IIIA                         9                          53
  STAGE IIIB                         2                           7
  STAGE IIIC                         0                           7
  STAGE IV                           0                           2
  STAGE IVA                          0                           1
  STAGE IVB                          0                           2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           T1  T2  T3  T4
  AMP PEAK  6(4P14) MUTATED    23  17  14   0
  AMP PEAK  6(4P14) WILD-TYPE 160  78  63  12
D6V4, multiclass
    clus
vv   AMP PEAK  6(4P14) MUTATED AMP PEAK  6(4P14) WILD-TYPE
  T1                        23                         160
  T2                        17                          78
  T3                        14                          63
  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"
D6V5, binary
                             cls
clus                            0   1
  AMP PEAK  6(4P14) MUTATED    36   0
  AMP PEAK  6(4P14) WILD-TYPE 218   3
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  6(4P14) MUTATED     36    0
  AMP PEAK  6(4P14) WILD-TYPE  218    3
   clus
vv  AMP PEAK  6(4P14) MUTATED AMP PEAK  6(4P14) WILD-TYPE
  0                        36                         218
  1                         0                           3
[1] 2 2
[1] FALSE
D6V6, binary
                             cls
clus                            0   1
  AMP PEAK  6(4P14) MUTATED    42   0
  AMP PEAK  6(4P14) WILD-TYPE 224   4
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  6(4P14) MUTATED     42    0
  AMP PEAK  6(4P14) WILD-TYPE  224    4
   clus
vv  AMP PEAK  6(4P14) MUTATED AMP PEAK  6(4P14) WILD-TYPE
  0                        42                         224
  1                         0                           4
[1] 2 2
[1] FALSE
D6V7, binary
                             cls
clus                            0   1
  AMP PEAK  6(4P14) MUTATED    21  33
  AMP PEAK  6(4P14) WILD-TYPE  97 219
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  6(4P14) MUTATED     21   33
  AMP PEAK  6(4P14) WILD-TYPE   97  219
        clus
vv       AMP PEAK  6(4P14) MUTATED AMP PEAK  6(4P14) WILD-TYPE
  FEMALE                        21                          97
  MALE                          33                         219
[1] 2 2
[1] FALSE
D6V8, binary
                             cls
clus                            0   1
  AMP PEAK  6(4P14) MUTATED    49   1
  AMP PEAK  6(4P14) WILD-TYPE 289   8
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  6(4P14) MUTATED     49    1
  AMP PEAK  6(4P14) WILD-TYPE  289    8
     clus
vv    AMP PEAK  6(4P14) MUTATED AMP PEAK  6(4P14) WILD-TYPE
  NO                         49                         289
  YES                         1                           8
[1] 2 2
[1] FALSE
                             vv
clus                          FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  AMP PEAK  6(4P14) MUTATED                         0                       53
  AMP PEAK  6(4P14) WILD-TYPE                       3                      307
                             vv
clus                          HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK  6(4P14) MUTATED                                  1
  AMP PEAK  6(4P14) WILD-TYPE                                6
D6V9, multiclass
                                  clus
vv                                 AMP PEAK  6(4P14) MUTATED
  FIBROLAMELLAR CARCINOMA                                  0
  HEPATOCELLULAR CARCINOMA                                53
  HEPATOCHOLANGIOCARCINOMA (MIXED)                         1
                                  clus
vv                                 AMP PEAK  6(4P14) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                    3
  HEPATOCELLULAR CARCINOMA                                 307
  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  6(4P14) MUTATED    47   2   0   5
  AMP PEAK  6(4P14) WILD-TYPE 277  15   1  16
D6V10, multiclass
    clus
vv   AMP PEAK  6(4P14) MUTATED AMP PEAK  6(4P14) WILD-TYPE
  R0                        47                         277
  R1                         2                          15
  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  6(4P14) MUTATED                                  0    25
  AMP PEAK  6(4P14) WILD-TYPE                                2   133
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  6(4P14) MUTATED                           3    26
  AMP PEAK  6(4P14) WILD-TYPE                        14   157
D6V11, multiclass
                                  clus
vv                                 AMP PEAK  6(4P14) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         0
  ASIAN                                                   25
  BLACK OR AFRICAN AMERICAN                                3
  WHITE                                                   26
                                  clus
vv                                 AMP PEAK  6(4P14) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           2
  ASIAN                                                    133
  BLACK OR AFRICAN AMERICAN                                 14
  WHITE                                                    157
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V12, binary
                             cls
clus                            0   1
  AMP PEAK  6(4P14) MUTATED     3  50
  AMP PEAK  6(4P14) WILD-TYPE  13 285
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  6(4P14) MUTATED      3   50
  AMP PEAK  6(4P14) WILD-TYPE   13  285
                        clus
vv                       AMP PEAK  6(4P14) MUTATED AMP PEAK  6(4P14) WILD-TYPE
  HISPANIC OR LATINO                             3                          13
  NOT HISPANIC OR LATINO                        50                         285
[1] 2 2
[1] FALSE

Clustering(7) Variable = AMP PEAK  7(5P15.33) MUTATION ANALYSIS
D7V1, survival
                                sevent
clus2                              0   1
  AMP PEAK  7(5P15.33) MUTATED    93  67
  AMP PEAK  7(5P15.33) WILD-TYPE 142  62
  AMP PEAK  7(5P15.33) MUTATED AMP PEAK  7(5P15.33) WILD-TYPE 
                           160                            204 
  AMP PEAK  7(5P15.33) MUTATED AMP PEAK  7(5P15.33) WILD-TYPE 
                            67                             62 
$`AMP PEAK  7(5P15.33) MUTATED`
TCGA-BC-A112 TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-AADV TCGA-DD-AAEA TCGA-DD-AAEG 
        5.03         0.36        90.28        18.87        18.90        23.64 
TCGA-EP-A3JL TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A7M9 TCGA-LG-A6GG 
        9.96        81.73        30.74        22.13         1.84        12.72 
TCGA-UB-A7MF TCGA-XR-A8TG TCGA-ZP-A9D1 TCGA-ZS-A9CE TCGA-2Y-A9GW TCGA-2Y-A9GY 
        7.04        29.52         0.69        40.80        41.79        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-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-BC-A10Q TCGA-BC-A10R TCGA-BC-A10W TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A217 
       37.32        10.13         2.99         1.12        44.42        45.93 
TCGA-BC-A3KG TCGA-BC-A8YO TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5263 
       22.36        18.48        13.45         0.66         4.24         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-A5UD TCGA-CC-A7IG TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IL TCGA-CC-A8HU 
        9.99         9.83        13.12        12.56         9.14        11.31 
TCGA-CC-A9FW TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A11A TCGA-DD-A11D 
        8.15        83.57        53.33       113.00         2.60        51.29 
TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EI TCGA-DD-A1EL 
       90.71        79.40        11.47        12.95         6.02        13.64 
TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A3A1 TCGA-DD-A3A3 TCGA-DD-A3A5 
       21.14        55.69         5.62         7.66        17.59       102.74 
TCGA-DD-A3A7 TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NO TCGA-DD-A4NV TCGA-DD-A73C 
       13.78        30.51        39.78        73.81        78.84        23.05 
TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AACA TCGA-DD-AACF TCGA-DD-AACG 
      114.35        13.48         0.53        75.65        12.00        15.42 
TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACP TCGA-DD-AACT TCGA-DD-AACV TCGA-DD-AACY 
       53.19        69.11        13.64        51.35        50.33        47.67 
TCGA-DD-AACZ TCGA-DD-AAD2 TCGA-DD-AAD5 TCGA-DD-AAD8 TCGA-DD-AADC TCGA-DD-AADF 
        5.62        21.63        44.22        40.08        13.97         3.78 
TCGA-DD-AADG TCGA-DD-AADN TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADU TCGA-DD-AAE2 
       37.64        29.52        14.33        66.67        18.21        20.98 
TCGA-DD-AAE3 TCGA-DD-AAE6 TCGA-DD-AAEE TCGA-DD-AAEK TCGA-DD-AAVU TCGA-DD-AAVV 
       18.61         4.64        26.63        35.08        72.39        80.71 
TCGA-DD-AAVY TCGA-DD-AAW2 TCGA-ED-A459 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7XO 
       64.77        60.99        29.92        13.35         9.73        14.04 
TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O6 TCGA-EP-A2KB TCGA-EP-A2KC TCGA-ES-A2HT 
       13.15        13.41         1.84        19.59         0.62        14.40 
TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A495 TCGA-FV-A4ZQ 
       60.89        23.97        19.10        27.88         0.03         0.39 
TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25X TCGA-G3-A3CJ TCGA-G3-A5SI TCGA-G3-A5SM 
       13.68        51.06        58.49        19.53        25.25        17.10 
TCGA-G3-A7M5 TCGA-G3-A7M6 TCGA-G3-AAUZ TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV5 
       14.70        20.78        15.78        11.80        12.23        11.64 
TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-KR-A7K2 TCGA-LG-A9QC 
        2.14        11.87         2.20         2.99        27.25        13.97 
TCGA-MI-A75G TCGA-MI-A75I TCGA-NI-A4U2 TCGA-O8-A75V TCGA-PD-A5DF TCGA-RC-A7SF 
       22.95        20.71        58.88        17.69        21.01        19.04 
TCGA-RG-A7D4 TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA47 
       36.10        15.98        10.75         0.99        12.99        18.28 
TCGA-XR-A8TF TCGA-ZP-A9CZ TCGA-ZP-A9D2 TCGA-ZP-A9D4 
       22.78        23.21        25.15        12.99 

$`AMP PEAK  7(5P15.33) WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A5W4 
       83.24        11.74        38.40         8.61        69.57        17.98 
TCGA-BD-A3ER TCGA-DD-A4NI TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-ES-A2HS TCGA-FV-A3I1 
       36.66        26.83        21.17        21.83        22.62         8.12 
TCGA-FV-A3R2 TCGA-G3-A6UC TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-MI-A75H 
        6.38        22.06        20.75         2.14        31.27        24.56 
TCGA-T1-A6J8 TCGA-UB-AA0V TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GX 
        0.76        10.32        23.80        53.39        63.75        80.28 
TCGA-2Y-A9H5 TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM 
       18.25        10.59         0.66        17.10        14.76         1.51 
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10X 
       48.99        27.91        46.78        27.52        27.52        25.32 
TCGA-BC-A10Y TCGA-BC-A3KF TCGA-BC-A69H TCGA-BC-A69I TCGA-BD-A2L6 TCGA-CC-5260 
       23.38         0.26        14.60        12.72        44.81         2.86 
TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-A3MA TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IF 
        3.19         3.39         9.96         8.94         7.13        21.34 
TCGA-CC-A7IH TCGA-CC-A7IK TCGA-CC-A8HT TCGA-CC-A8HV TCGA-CC-A9FS TCGA-DD-A113 
       12.00         8.61         4.60         9.17         6.94        79.73 
TCGA-DD-A114 TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A1EB TCGA-DD-A1EC 
       37.78         7.33         0.46        21.76        66.31        19.79 
TCGA-DD-A1ED TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A39W 
       75.65        45.11        49.15        33.04        18.35        27.19 
TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A2 TCGA-DD-A3A4 TCGA-DD-A3A6 TCGA-DD-A3A9 
       19.76        25.81        70.06        20.12       107.11        30.61 
TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NL TCGA-DD-A4NN 
       33.14        32.52        30.97        30.15        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        71.80         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-AAE9 TCGA-DD-AAEB 
       18.25        18.25        18.15        19.99        23.74        15.72 
TCGA-DD-AAED TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR 
       25.08        25.78        50.33        90.48        89.69        82.62 
TCGA-DD-AAVS TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 
       59.93        76.18        56.48        62.47        66.25        65.39 
TCGA-DD-AAW3 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A7PX TCGA-ED-A7PY 
       53.69        26.93        28.08        13.91         0.20        12.82 
TCGA-ED-A7PZ TCGA-ED-A8O5 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
        0.20        13.35         0.20        18.74        19.99        20.61 
TCGA-EP-A3RK TCGA-FV-A3R3 TCGA-FV-A496 TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25Y 
       11.93        12.03         0.33        53.79        28.27        14.86 
TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CK TCGA-G3-A5SJ TCGA-G3-A5SL 
       21.53        25.64         5.92        19.23        22.95        20.42 
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        28.90 
TCGA-GJ-A6C0 TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K8 
        1.02        37.71        17.06        16.83        11.80        29.79 
TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A8LF 
       12.03         9.57        16.67         7.53        10.85        26.27 
TCGA-QA-A7B7 TCGA-RC-A6M4 TCGA-RC-A6M5 TCGA-RC-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SB 
        3.09         0.72         0.49         0.30        21.04        19.33 
TCGA-RC-A7SH TCGA-RC-A7SK TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD 
       15.39        15.52        27.88        19.76        16.44         1.71 
TCGA-WJ-A86L TCGA-WX-AA44 TCGA-WX-AA46 TCGA-XR-A8TD TCGA-XR-A8TE TCGA-YA-A8S7 
       11.34        20.22        24.85        33.86        30.41        13.55 
TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9D0 TCGA-ZS-A9CD TCGA-ZS-A9CF TCGA-ZS-A9CG 
       35.77        25.71        35.87        45.57        79.30        11.21 

  AMP PEAK  7(5P15.33) MUTATED AMP PEAK  7(5P15.33) WILD-TYPE 
                          0.03                           0.20 
  AMP PEAK  7(5P15.33) MUTATED AMP PEAK  7(5P15.33) WILD-TYPE 
                        120.82                         108.76 
  AMP PEAK  7(5P15.33) MUTATED AMP PEAK  7(5P15.33) WILD-TYPE 
                         18.38                          20.83 
[1] "0.0 - 120.8 (18.4)" "0.2 - 108.8 (20.8)"
[1] "hr=" "1.4"
D7V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IIIA
  AMP PEAK  7(5P15.33) MUTATED        66       42         1         35
  AMP PEAK  7(5P15.33) WILD-TYPE     107       45         2         27
                                vv
clus                             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK  7(5P15.33) MUTATED            5          2        1         0
  AMP PEAK  7(5P15.33) WILD-TYPE          4          5        1         1
                                vv
clus                             STAGE IVB
  AMP PEAK  7(5P15.33) MUTATED           0
  AMP PEAK  7(5P15.33) WILD-TYPE         2
D7V3, multiclass
            clus
vv           AMP PEAK  7(5P15.33) MUTATED AMP PEAK  7(5P15.33) WILD-TYPE
  STAGE I                              66                            107
  STAGE II                             42                             45
  STAGE III                             1                              2
  STAGE IIIA                           35                             27
  STAGE IIIB                            5                              4
  STAGE IIIC                            2                              5
  STAGE IV                              1                              1
  STAGE IVA                             0                              1
  STAGE IVB                             0                              2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  AMP PEAK  7(5P15.33) MUTATED    70  46  43   4
  AMP PEAK  7(5P15.33) WILD-TYPE 113  49  34   8
D7V4, multiclass
    clus
vv   AMP PEAK  7(5P15.33) MUTATED AMP PEAK  7(5P15.33) WILD-TYPE
  T1                           70                            113
  T2                           46                             49
  T3                           43                             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"
D7V5, binary
                                cls
clus                               0   1
  AMP PEAK  7(5P15.33) MUTATED   112   0
  AMP PEAK  7(5P15.33) WILD-TYPE 142   3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  7(5P15.33) MUTATED    112    0
  AMP PEAK  7(5P15.33) WILD-TYPE  142    3
   clus
vv  AMP PEAK  7(5P15.33) MUTATED AMP PEAK  7(5P15.33) WILD-TYPE
  0                          112                            142
  1                            0                              3
[1] 2 2
[1] FALSE
D7V6, binary
                                cls
clus                               0   1
  AMP PEAK  7(5P15.33) MUTATED   119   1
  AMP PEAK  7(5P15.33) WILD-TYPE 147   3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  7(5P15.33) MUTATED    119    1
  AMP PEAK  7(5P15.33) WILD-TYPE  147    3
   clus
vv  AMP PEAK  7(5P15.33) MUTATED AMP PEAK  7(5P15.33) WILD-TYPE
  0                          119                            147
  1                            1                              3
[1] 2 2
[1] FALSE
D7V7, binary
                                cls
clus                               0   1
  AMP PEAK  7(5P15.33) MUTATED    50 113
  AMP PEAK  7(5P15.33) WILD-TYPE  68 139
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  7(5P15.33) MUTATED     50  113
  AMP PEAK  7(5P15.33) WILD-TYPE   68  139
        clus
vv       AMP PEAK  7(5P15.33) MUTATED AMP PEAK  7(5P15.33) WILD-TYPE
  FEMALE                           50                             68
  MALE                            113                            139
[1] 2 2
[1] FALSE
D7V8, binary
                                cls
clus                               0   1
  AMP PEAK  7(5P15.33) MUTATED   148   6
  AMP PEAK  7(5P15.33) WILD-TYPE 190   3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  7(5P15.33) MUTATED    148    6
  AMP PEAK  7(5P15.33) WILD-TYPE  190    3
     clus
vv    AMP PEAK  7(5P15.33) MUTATED AMP PEAK  7(5P15.33) WILD-TYPE
  NO                           148                            190
  YES                            6                              3
[1] 2 2
[1] FALSE
                                vv
clus                             FIBROLAMELLAR CARCINOMA
  AMP PEAK  7(5P15.33) MUTATED                         0
  AMP PEAK  7(5P15.33) WILD-TYPE                       3
                                vv
clus                             HEPATOCELLULAR CARCINOMA
  AMP PEAK  7(5P15.33) MUTATED                        160
  AMP PEAK  7(5P15.33) WILD-TYPE                      200
                                vv
clus                             HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK  7(5P15.33) MUTATED                                  3
  AMP PEAK  7(5P15.33) WILD-TYPE                                4
D7V9, multiclass
                                  clus
vv                                 AMP PEAK  7(5P15.33) MUTATED
  FIBROLAMELLAR CARCINOMA                                     0
  HEPATOCELLULAR CARCINOMA                                  160
  HEPATOCHOLANGIOCARCINOMA (MIXED)                            3
                                  clus
vv                                 AMP PEAK  7(5P15.33) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                       3
  HEPATOCELLULAR CARCINOMA                                    200
  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  7(5P15.33) MUTATED   145   7   0   8
  AMP PEAK  7(5P15.33) WILD-TYPE 179  10   1  13
D7V10, multiclass
    clus
vv   AMP PEAK  7(5P15.33) MUTATED AMP PEAK  7(5P15.33) WILD-TYPE
  R0                          145                            179
  R1                            7                             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
  AMP PEAK  7(5P15.33) MUTATED                                  2    69
  AMP PEAK  7(5P15.33) WILD-TYPE                                0    89
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  7(5P15.33) MUTATED                          10    76
  AMP PEAK  7(5P15.33) WILD-TYPE                         7   107
D7V11, multiclass
                                  clus
vv                                 AMP PEAK  7(5P15.33) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            2
  ASIAN                                                      69
  BLACK OR AFRICAN AMERICAN                                  10
  WHITE                                                      76
                                  clus
vv                                 AMP PEAK  7(5P15.33) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                        89
  BLACK OR AFRICAN AMERICAN                                     7
  WHITE                                                       107
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V12, binary
                                cls
clus                               0   1
  AMP PEAK  7(5P15.33) MUTATED     8 147
  AMP PEAK  7(5P15.33) WILD-TYPE   8 188
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  7(5P15.33) MUTATED      8  147
  AMP PEAK  7(5P15.33) WILD-TYPE    8  188
                        clus
vv                       AMP PEAK  7(5P15.33) MUTATED
  HISPANIC OR LATINO                                8
  NOT HISPANIC OR LATINO                          147
                        clus
vv                       AMP PEAK  7(5P15.33) WILD-TYPE
  HISPANIC OR LATINO                                  8
  NOT HISPANIC OR LATINO                            188
[1] 2 2
[1] FALSE

Clustering(8) Variable = AMP PEAK  8(5Q35.3) MUTATION ANALYSIS
D8V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  8(5Q35.3) MUTATED    78  54
  AMP PEAK  8(5Q35.3) WILD-TYPE 157  75
  AMP PEAK  8(5Q35.3) MUTATED AMP PEAK  8(5Q35.3) WILD-TYPE 
                          132                           232 
  AMP PEAK  8(5Q35.3) MUTATED AMP PEAK  8(5Q35.3) WILD-TYPE 
                           54                            75 
$`AMP PEAK  8(5Q35.3) MUTATED`
TCGA-2Y-A9H6 TCGA-BC-A112 TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-AADV TCGA-DD-AAEG 
       11.74         5.03         0.36        90.28        18.87        23.64 
TCGA-EP-A3JL TCGA-FV-A3R2 TCGA-G3-A25W TCGA-G3-A3CG TCGA-LG-A6GG TCGA-ZP-A9D1 
        9.96         6.38        30.74        22.13        12.72         0.69 
TCGA-ZS-A9CE TCGA-2Y-A9GW TCGA-2Y-A9GZ TCGA-2Y-A9H1 TCGA-2Y-A9H3 TCGA-2Y-A9H4 
       40.80        41.79        27.88        40.41        49.84        47.74 
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-A216 TCGA-BC-A217 TCGA-CC-A1HT TCGA-CC-A3MB 
       27.52         2.99        44.42        45.93         3.32        10.36 
TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A7IG TCGA-CC-A7IL TCGA-CC-A8HU TCGA-CC-A9FW 
       11.93        11.41         9.83         9.14        11.31         8.15 
TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11D TCGA-DD-A1E9 
       83.57        53.33       113.00         7.33        51.29        90.71 
TCGA-DD-A1EA TCGA-DD-A1EE TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Y 
       79.40        11.47        21.14        27.19        55.69         5.62 
TCGA-DD-A3A1 TCGA-DD-A3A3 TCGA-DD-A3A5 TCGA-DD-A3A7 TCGA-DD-A4NK TCGA-DD-A4NO 
        7.66        17.59       102.74        13.78        39.78        73.81 
TCGA-DD-A4NR TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 
        0.30        78.84        23.93       114.35        13.48         0.53 
TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI 
       55.40        12.53        12.00        15.42         6.41        53.19 
TCGA-DD-AACJ TCGA-DD-AACP TCGA-DD-AACT TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD1 
       69.11        13.64        51.35        47.67         5.62        18.54 
TCGA-DD-AAD2 TCGA-DD-AADC TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI 
       21.63        13.97        39.52         3.78        37.64        35.67 
TCGA-DD-AADK TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS 
       34.49         0.39        29.52        14.33        66.67        15.58 
TCGA-DD-AADU TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE3 TCGA-DD-AAEE TCGA-DD-AAEK 
       18.21        18.25        18.15        18.61        26.63        35.08 
TCGA-DD-AAVP TCGA-DD-AAVR TCGA-DD-AAVU TCGA-DD-AAVV TCGA-DD-AAVX TCGA-DD-AAVY 
       90.48        82.62        72.39        80.71        56.48        64.77 
TCGA-DD-AAW0 TCGA-DD-AAW2 TCGA-ED-A66Y TCGA-ED-A7XO TCGA-ED-A7XP TCGA-EP-A2KB 
       66.25        60.99         9.73        14.04        13.15        19.59 
TCGA-EP-A2KC TCGA-ES-A2HT TCGA-FV-A3I0 TCGA-FV-A495 TCGA-FV-A4ZQ TCGA-G3-A25S 
        0.62        14.40        27.88         0.03         0.39        13.68 
TCGA-G3-A25T TCGA-G3-A5SM TCGA-G3-A7M5 TCGA-G3-AAV1 TCGA-G3-AAV5 TCGA-GJ-A9DB 
       51.06        17.10        14.70        11.80        11.64         2.20 
TCGA-HP-A5MZ TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C 
        2.99        11.80        27.25        13.97        12.03         9.57 
TCGA-MI-A75G TCGA-MI-A75I TCGA-NI-A8LF TCGA-O8-A75V TCGA-RC-A7SF TCGA-RG-A7D4 
       22.95        20.71        26.27        17.69        19.04        36.10 
TCGA-UB-A7MA TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA47 TCGA-XR-A8TF TCGA-ZP-A9CZ 
       27.88         0.99        12.99        18.28        22.78        23.21 

$`AMP PEAK  8(5Q35.3) WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A5W4 TCGA-BD-A3ER 
       83.24        38.40         8.61        69.57        17.98        36.66 
TCGA-DD-A4NI TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-ES-A2HS TCGA-FV-A3I1 
       26.83        21.17        21.83        18.90        22.62         8.12 
TCGA-FV-A4ZP TCGA-G3-A6UC TCGA-G3-A7M9 TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-KR-A7K7 
       81.73        22.06         1.84        20.75         2.14        31.27 
TCGA-MI-A75H TCGA-T1-A6J8 TCGA-UB-A7MF TCGA-UB-AA0V TCGA-XR-A8TG TCGA-2Y-A9GS 
       24.56         0.76         7.04        10.32        29.52        23.80 
TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GX TCGA-2Y-A9GY TCGA-2Y-A9H0 TCGA-2Y-A9H2 
       53.39        63.75        80.28        24.89       120.82        56.91 
TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D 
       18.25        20.81        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-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A69H 
       25.32        23.38         1.12         0.26        22.36        14.60 
TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5258 
       12.72        18.48        44.81        13.45         0.66         4.24 
TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-5264 TCGA-CC-A3M9 
        2.86         3.19         3.39         4.24         3.35         9.86 
TCGA-CC-A3MA TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IH 
        9.96         9.99         8.94         7.13        21.34        12.00 
TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A8HT TCGA-CC-A8HV TCGA-CC-A9FS 
       13.12        12.56         8.61         4.60         9.17         6.94 
TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A1EB 
       79.73        37.78         2.60         0.46        21.76        66.31 
TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI 
       19.79        75.65        12.95        45.11        49.15         6.02 
TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A2 
       33.04        18.35        13.64        19.76        25.81        70.06 
TCGA-DD-A3A4 TCGA-DD-A3A6 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NF 
       20.12       107.11        30.61        33.14        32.52        30.97 
TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NP TCGA-DD-A4NQ 
       30.15        30.51        56.25        29.56       108.76        12.26 
TCGA-DD-A4NS TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F 
       80.75         9.30        23.05        22.78         1.45        35.67 
TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACE TCGA-DD-AACK TCGA-DD-AACL 
       11.41        75.65        76.41        71.80         0.30         3.52 
TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACU 
       58.16        42.81        61.68        14.20        59.31        51.52 
TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AAD0 TCGA-DD-AAD3 TCGA-DD-AAD5 
       50.33        46.82         5.59         4.50        42.58        44.22 
TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADD TCGA-DD-AADJ 
       22.09        40.08        40.54        40.83        40.47        35.05 
TCGA-DD-AADL TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE2 
       20.91        14.89        15.06        19.30        18.25        20.98 
TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEH 
       19.99         4.64        23.74        15.72        25.08        25.78 
TCGA-DD-AAEI TCGA-DD-AAVQ TCGA-DD-AAVS TCGA-DD-AAVW TCGA-DD-AAVZ TCGA-DD-AAW1 
       50.33        89.69        59.93        76.18        62.47        65.39 
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-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 
        0.20        12.82         0.20        13.41        13.35         1.84 
TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A3RK TCGA-FV-A23B 
        0.20        18.74        19.99        20.61        11.93        60.89 
TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3R3 TCGA-FV-A496 TCGA-G3-A25U TCGA-G3-A25V 
       23.97        19.10        12.03         0.33        53.79        28.27 
TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ 
       58.49        14.86        21.53        25.64         5.92        19.53 
TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A7M6 TCGA-G3-A7M7 
       19.23        25.25        22.95        20.42        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-AAV6 TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-HP-A5N0 TCGA-K7-A5RG 
        2.14        11.87        28.90         1.02        37.71        17.06 
TCGA-K7-A6G5 TCGA-KR-A7K8 TCGA-MI-A75E TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 
       16.83        29.79        16.67         7.53        10.85        58.88 
TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A6M4 TCGA-RC-A6M5 TCGA-RC-A6M6 TCGA-RC-A7S9 
       21.01         3.09         0.72         0.49         0.30        21.04 
TCGA-RC-A7SB TCGA-RC-A7SH TCGA-RC-A7SK TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD 
       19.33        15.39        15.52        19.76        16.44         1.71 
TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WX-AA44 TCGA-WX-AA46 TCGA-XR-A8TD 
       15.98        10.75        11.34        20.22        24.85        33.86 
TCGA-XR-A8TE TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9D0 TCGA-ZP-A9D2 
       30.41        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  8(5Q35.3) MUTATED AMP PEAK  8(5Q35.3) WILD-TYPE 
                         0.03                          0.20 
  AMP PEAK  8(5Q35.3) MUTATED AMP PEAK  8(5Q35.3) WILD-TYPE 
                       114.35                        120.82 
  AMP PEAK  8(5Q35.3) MUTATED AMP PEAK  8(5Q35.3) WILD-TYPE 
                       18.575                        20.170 
[1] "0.0 - 114.3 (18.6)" "0.2 - 120.8 (20.2)"
[1] "hr=" "1.2"
D8V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IIIA
  AMP PEAK  8(5Q35.3) MUTATED        62       35         2         22
  AMP PEAK  8(5Q35.3) WILD-TYPE     111       52         1         40
                               vv
clus                            STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK  8(5Q35.3) MUTATED            3          1        2         0
  AMP PEAK  8(5Q35.3) WILD-TYPE          6          6        0         1
                               vv
clus                            STAGE IVB
  AMP PEAK  8(5Q35.3) MUTATED           0
  AMP PEAK  8(5Q35.3) WILD-TYPE         2
D8V3, multiclass
            clus
vv           AMP PEAK  8(5Q35.3) MUTATED AMP PEAK  8(5Q35.3) WILD-TYPE
  STAGE I                             62                           111
  STAGE II                            35                            52
  STAGE III                            2                             1
  STAGE IIIA                          22                            40
  STAGE IIIB                           3                             6
  STAGE IIIC                           1                             6
  STAGE IV                             2                             0
  STAGE IVA                            0                             1
  STAGE IVB                            0                             2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  AMP PEAK  8(5Q35.3) MUTATED    64  38  30   3
  AMP PEAK  8(5Q35.3) WILD-TYPE 119  57  47   9
D8V4, multiclass
    clus
vv   AMP PEAK  8(5Q35.3) MUTATED AMP PEAK  8(5Q35.3) WILD-TYPE
  T1                          64                           119
  T2                          38                            57
  T3                          30                            47
  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"
D8V5, binary
                               cls
clus                              0   1
  AMP PEAK  8(5Q35.3) MUTATED    92   0
  AMP PEAK  8(5Q35.3) WILD-TYPE 162   3
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(5Q35.3) MUTATED     92    0
  AMP PEAK  8(5Q35.3) WILD-TYPE  162    3
   clus
vv  AMP PEAK  8(5Q35.3) MUTATED AMP PEAK  8(5Q35.3) WILD-TYPE
  0                          92                           162
  1                           0                             3
[1] 2 2
[1] FALSE
D8V6, binary
                               cls
clus                              0   1
  AMP PEAK  8(5Q35.3) MUTATED    99   2
  AMP PEAK  8(5Q35.3) WILD-TYPE 167   2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(5Q35.3) MUTATED     99    2
  AMP PEAK  8(5Q35.3) WILD-TYPE  167    2
   clus
vv  AMP PEAK  8(5Q35.3) MUTATED AMP PEAK  8(5Q35.3) WILD-TYPE
  0                          99                           167
  1                           2                             2
[1] 2 2
[1] FALSE
D8V7, binary
                               cls
clus                              0   1
  AMP PEAK  8(5Q35.3) MUTATED    38  97
  AMP PEAK  8(5Q35.3) WILD-TYPE  80 155
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(5Q35.3) MUTATED     38   97
  AMP PEAK  8(5Q35.3) WILD-TYPE   80  155
        clus
vv       AMP PEAK  8(5Q35.3) MUTATED AMP PEAK  8(5Q35.3) WILD-TYPE
  FEMALE                          38                            80
  MALE                            97                           155
[1] 2 2
[1] FALSE
D8V8, binary
                               cls
clus                              0   1
  AMP PEAK  8(5Q35.3) MUTATED   123   5
  AMP PEAK  8(5Q35.3) WILD-TYPE 215   4
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(5Q35.3) MUTATED    123    5
  AMP PEAK  8(5Q35.3) WILD-TYPE  215    4
     clus
vv    AMP PEAK  8(5Q35.3) MUTATED AMP PEAK  8(5Q35.3) WILD-TYPE
  NO                          123                           215
  YES                           5                             4
[1] 2 2
[1] FALSE
                               vv
clus                            FIBROLAMELLAR CARCINOMA
  AMP PEAK  8(5Q35.3) MUTATED                         0
  AMP PEAK  8(5Q35.3) WILD-TYPE                       3
                               vv
clus                            HEPATOCELLULAR CARCINOMA
  AMP PEAK  8(5Q35.3) MUTATED                        130
  AMP PEAK  8(5Q35.3) WILD-TYPE                      230
                               vv
clus                            HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK  8(5Q35.3) MUTATED                                  5
  AMP PEAK  8(5Q35.3) WILD-TYPE                                2
D8V9, multiclass
                                  clus
vv                                 AMP PEAK  8(5Q35.3) MUTATED
  FIBROLAMELLAR CARCINOMA                                    0
  HEPATOCELLULAR CARCINOMA                                 130
  HEPATOCHOLANGIOCARCINOMA (MIXED)                           5
                                  clus
vv                                 AMP PEAK  8(5Q35.3) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                      3
  HEPATOCELLULAR CARCINOMA                                   230
  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  8(5Q35.3) MUTATED   120   8   1   4
  AMP PEAK  8(5Q35.3) WILD-TYPE 204   9   0  17
D8V10, multiclass
    clus
vv   AMP PEAK  8(5Q35.3) MUTATED AMP PEAK  8(5Q35.3) WILD-TYPE
  R0                         120                           204
  R1                           8                             9
  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  8(5Q35.3) MUTATED                                  0    63
  AMP PEAK  8(5Q35.3) WILD-TYPE                                2    95
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  8(5Q35.3) MUTATED                           6    61
  AMP PEAK  8(5Q35.3) WILD-TYPE                        11   122
D8V11, multiclass
                                  clus
vv                                 AMP PEAK  8(5Q35.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                     63
  BLACK OR AFRICAN AMERICAN                                  6
  WHITE                                                     61
                                  clus
vv                                 AMP PEAK  8(5Q35.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             2
  ASIAN                                                       95
  BLACK OR AFRICAN AMERICAN                                   11
  WHITE                                                      122
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V12, binary
                               cls
clus                              0   1
  AMP PEAK  8(5Q35.3) MUTATED     6 122
  AMP PEAK  8(5Q35.3) WILD-TYPE  10 213
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(5Q35.3) MUTATED      6  122
  AMP PEAK  8(5Q35.3) WILD-TYPE   10  213
                        clus
vv                       AMP PEAK  8(5Q35.3) MUTATED
  HISPANIC OR LATINO                               6
  NOT HISPANIC OR LATINO                         122
                        clus
vv                       AMP PEAK  8(5Q35.3) WILD-TYPE
  HISPANIC OR LATINO                                10
  NOT HISPANIC OR LATINO                           213
[1] 2 2
[1] FALSE

Clustering(9) Variable = AMP PEAK  9(6P25.2) MUTATION ANALYSIS
D9V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  9(6P25.2) MUTATED    93  61
  AMP PEAK  9(6P25.2) WILD-TYPE 142  68
  AMP PEAK  9(6P25.2) MUTATED AMP PEAK  9(6P25.2) WILD-TYPE 
                          154                           210 
  AMP PEAK  9(6P25.2) MUTATED AMP PEAK  9(6P25.2) WILD-TYPE 
                           61                            68 
$`AMP PEAK  9(6P25.2) MUTATED`
TCGA-2Y-A9GV TCGA-BC-A112 TCGA-DD-A3A8 TCGA-DD-AADV TCGA-DD-AAEG TCGA-ES-A2HS 
       83.24         5.03         0.36        18.87        23.64        22.62 
TCGA-FV-A3R2 TCGA-G3-A3CG TCGA-G3-A6UC TCGA-LG-A6GG TCGA-MI-A75H TCGA-UB-A7MF 
        6.38        22.13        22.06        12.72        24.56         7.04 
TCGA-XR-A8TG TCGA-2Y-A9GS TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H2 TCGA-2Y-A9H3 
       29.52        23.80        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-A216 TCGA-BC-A217 TCGA-BC-A3KG TCGA-BC-A69H 
       10.13        27.52        44.42        45.93        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-DD-A114 TCGA-DD-A118 
       13.12         8.61         9.14        11.31        37.78       113.00 
TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11C TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG 
        7.33         2.60        21.76        11.47        12.95        45.11 
TCGA-DD-A1EH TCGA-DD-A1EJ TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A5 
       49.15        33.04        55.69         5.62        19.76       102.74 
TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NN 
       13.78        30.61        30.15        30.51        39.78        29.56 
TCGA-DD-A4NS TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-AAC8 TCGA-DD-AACA TCGA-DD-AACB 
       80.75        22.78         1.45         0.53        75.65        76.41 
TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ 
       12.53        71.80        12.00         6.41        53.19        69.11 
TCGA-DD-AACN TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACT TCGA-DD-AAD3 TCGA-DD-AADA 
       42.81        13.64        14.20        51.35        42.58        40.54 
TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO 
        3.78        37.64        20.91         0.39        29.52        14.89 
TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADW TCGA-DD-AAE0 TCGA-DD-AAE2 TCGA-DD-AAE3 
       15.06        14.33        19.30        18.25        20.98        18.61 
TCGA-DD-AAE9 TCGA-DD-AAEH TCGA-DD-AAEK TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVV 
       23.74        25.78        35.08        82.62        59.93        80.71 
TCGA-DD-AAVW TCGA-DD-AAVY TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A66X TCGA-ED-A7PY 
       76.18        64.77        60.99        53.69        13.35        12.82 
TCGA-ED-A7PZ TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-EP-A2KA TCGA-EP-A2KB 
        0.20        13.41        13.35         1.84        20.61        19.59 
TCGA-EP-A2KC TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25U 
        0.62        27.88        12.03         0.39        13.68        53.79 
TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SL TCGA-G3-AAV1 
       58.49        14.86        19.23        25.25        20.42        11.80 
TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV6 TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-MI-A75G 
       13.55         0.89         2.14        27.25        29.79        22.95 
TCGA-MI-A75I TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-RC-A6M4 TCGA-RC-A7S9 
       20.71        26.27        17.69        21.01         0.72        21.04 
TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7ME 
       15.52        36.10        27.88        19.76        16.44        15.98 
TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WX-AA44 TCGA-XR-A8TD TCGA-XR-A8TE 
       10.75        11.34         0.99        20.22        33.86        30.41 
TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZS-A9CD TCGA-ZS-A9CF 
       22.78        13.55        45.57        79.30 

$`AMP PEAK  9(6P25.2) WILD-TYPE`
TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A5W4 TCGA-BD-A3ER 
       11.74        38.40         8.61        69.57        17.98        36.66 
TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-EP-A3JL 
       90.28        26.83        21.17        21.83        18.90         9.96 
TCGA-FV-A3I1 TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A7M9 TCGA-K7-A5RF TCGA-KR-A7K0 
        8.12        81.73        30.74         1.84        20.75         2.14 
TCGA-KR-A7K7 TCGA-T1-A6J8 TCGA-UB-AA0V TCGA-ZP-A9D1 TCGA-ZS-A9CE TCGA-2Y-A9GT 
       31.27         0.76        10.32         0.69        40.80        53.39 
TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H4 
       63.75        41.79        80.28       120.82        40.41        47.74 
TCGA-2Y-A9H9 TCGA-2Y-A9HB TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1D 
       22.92         8.55        10.78        10.59         0.66        14.76 
TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-A10Q TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10W 
        1.51        48.99        37.32        46.78        27.52         2.99 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A3KF TCGA-BC-A8YO TCGA-CC-5258 
       25.32        23.38         1.12         0.26        18.48         4.24 
TCGA-CC-5260 TCGA-CC-5262 TCGA-CC-5264 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA 
        2.86         3.39         3.35         3.32         9.86         9.96 
TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A7IF TCGA-CC-A7IJ TCGA-CC-A8HT TCGA-CC-A8HV 
       11.41         9.99        21.34        12.56         4.60         9.17 
TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A11B 
        6.94         8.15        79.73        83.57        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-A1EI TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A3A0 
        6.02        18.35        13.64        21.14        27.19        25.81 
TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A6 TCGA-DD-A4NA 
        7.66        70.06        17.59        20.12       107.11        33.14 
TCGA-DD-A4NB TCGA-DD-A4NF TCGA-DD-A4NL TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ 
       32.52        30.97        56.25        73.81       108.76        12.26 
TCGA-DD-A4NR TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73F 
        0.30        78.84        23.93         9.30        23.05        35.67 
TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC9 TCGA-DD-AACC TCGA-DD-AACG TCGA-DD-AACK 
      114.35        13.48        11.41        55.40        15.42         0.30 
TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACO TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACV 
        3.52        58.16        61.68        59.31        51.52        50.33 
TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 
       46.82         5.59        47.67         5.62         4.50        18.54 
TCGA-DD-AAD2 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADB TCGA-DD-AADC 
       21.63        44.22        22.09        40.08        40.83        13.97 
TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADR 
       40.47        39.52        35.67        35.05        34.49        66.67 
TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADY TCGA-DD-AAE1 TCGA-DD-AAE4 TCGA-DD-AAE6 
       15.58        18.21        18.25        18.15        19.99         4.64 
TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEI TCGA-DD-AAVP TCGA-DD-AAVQ 
       15.72        25.08        26.63        50.33        90.48        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-A3RK TCGA-ES-A2HT 
       13.15         0.20        18.74        19.99        11.93        14.40 
TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A495 TCGA-FV-A496 TCGA-G3-A25T 
       60.89        23.97        19.10         0.03         0.33        51.06 
TCGA-G3-A25V TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A5SJ 
       28.27        21.53        25.64         5.92        19.53        22.95 
TCGA-G3-A5SM TCGA-G3-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ 
       17.10        14.70        20.78        11.87        14.14        15.78 
TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV5 TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 
       15.65        12.23        11.64        11.87        28.90         1.02 
TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 
        2.20         2.99        37.71        17.06        16.83        11.80 
TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MR-A520 TCGA-MR-A8JO 
       13.97        12.03         9.57        16.67         7.53        10.85 
TCGA-NI-A4U2 TCGA-QA-A7B7 TCGA-RC-A6M5 TCGA-RC-A6M6 TCGA-RC-A7SB TCGA-RC-A7SF 
       58.88         3.09         0.49         0.30        19.33        19.04 
TCGA-RC-A7SH TCGA-UB-A7MD TCGA-WQ-AB4B TCGA-WX-AA46 TCGA-WX-AA47 TCGA-ZP-A9CV 
       15.39         1.71        12.99        24.85        18.28        35.77 
TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CG 
       25.71        23.21        35.87        25.15        12.99        11.21 

  AMP PEAK  9(6P25.2) MUTATED AMP PEAK  9(6P25.2) WILD-TYPE 
                         0.20                          0.03 
  AMP PEAK  9(6P25.2) MUTATED AMP PEAK  9(6P25.2) WILD-TYPE 
                       113.00                        120.82 
  AMP PEAK  9(6P25.2) MUTATED AMP PEAK  9(6P25.2) WILD-TYPE 
                        20.32                         19.43 
[1] "0.2 - 113.0 (20.3)" "0.0 - 120.8 (19.4)"
[1] "hr=" "1.3"
D9V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IIIA
  AMP PEAK  9(6P25.2) MUTATED        66       41         2         29
  AMP PEAK  9(6P25.2) WILD-TYPE     107       46         1         33
                               vv
clus                            STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK  9(6P25.2) MUTATED            7          2        2         0
  AMP PEAK  9(6P25.2) WILD-TYPE          2          5        0         1
                               vv
clus                            STAGE IVB
  AMP PEAK  9(6P25.2) MUTATED           1
  AMP PEAK  9(6P25.2) WILD-TYPE         1
D9V3, multiclass
            clus
vv           AMP PEAK  9(6P25.2) MUTATED AMP PEAK  9(6P25.2) WILD-TYPE
  STAGE I                             66                           107
  STAGE II                            41                            46
  STAGE III                            2                             1
  STAGE IIIA                          29                            33
  STAGE IIIB                           7                             2
  STAGE IIIC                           2                             5
  STAGE IV                             2                             0
  STAGE IVA                            0                             1
  STAGE IVB                            1                             1
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  AMP PEAK  9(6P25.2) MUTATED    68  46  40   4
  AMP PEAK  9(6P25.2) WILD-TYPE 115  49  37   8
D9V4, multiclass
    clus
vv   AMP PEAK  9(6P25.2) MUTATED AMP PEAK  9(6P25.2) WILD-TYPE
  T1                          68                           115
  T2                          46                            49
  T3                          40                            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"
D9V5, binary
                               cls
clus                              0   1
  AMP PEAK  9(6P25.2) MUTATED   106   1
  AMP PEAK  9(6P25.2) WILD-TYPE 148   2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  9(6P25.2) MUTATED    106    1
  AMP PEAK  9(6P25.2) WILD-TYPE  148    2
   clus
vv  AMP PEAK  9(6P25.2) MUTATED AMP PEAK  9(6P25.2) WILD-TYPE
  0                         106                           148
  1                           1                             2
[1] 2 2
[1] FALSE
D9V6, binary
                               cls
clus                              0   1
  AMP PEAK  9(6P25.2) MUTATED   113   3
  AMP PEAK  9(6P25.2) WILD-TYPE 153   1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  9(6P25.2) MUTATED    113    3
  AMP PEAK  9(6P25.2) WILD-TYPE  153    1
   clus
vv  AMP PEAK  9(6P25.2) MUTATED AMP PEAK  9(6P25.2) WILD-TYPE
  0                         113                           153
  1                           3                             1
[1] 2 2
[1] FALSE
D9V7, binary
                               cls
clus                              0   1
  AMP PEAK  9(6P25.2) MUTATED    55 104
  AMP PEAK  9(6P25.2) WILD-TYPE  63 148
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  9(6P25.2) MUTATED     55  104
  AMP PEAK  9(6P25.2) WILD-TYPE   63  148
        clus
vv       AMP PEAK  9(6P25.2) MUTATED AMP PEAK  9(6P25.2) WILD-TYPE
  FEMALE                          55                            63
  MALE                           104                           148
[1] 2 2
[1] FALSE
D9V8, binary
                               cls
clus                              0   1
  AMP PEAK  9(6P25.2) MUTATED   146   2
  AMP PEAK  9(6P25.2) WILD-TYPE 192   7
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  9(6P25.2) MUTATED    146    2
  AMP PEAK  9(6P25.2) WILD-TYPE  192    7
     clus
vv    AMP PEAK  9(6P25.2) MUTATED AMP PEAK  9(6P25.2) WILD-TYPE
  NO                          146                           192
  YES                           2                             7
[1] 2 2
[1] FALSE
                               vv
clus                            FIBROLAMELLAR CARCINOMA
  AMP PEAK  9(6P25.2) MUTATED                         0
  AMP PEAK  9(6P25.2) WILD-TYPE                       3
                               vv
clus                            HEPATOCELLULAR CARCINOMA
  AMP PEAK  9(6P25.2) MUTATED                        156
  AMP PEAK  9(6P25.2) WILD-TYPE                      204
                               vv
clus                            HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK  9(6P25.2) MUTATED                                  3
  AMP PEAK  9(6P25.2) WILD-TYPE                                4
D9V9, multiclass
                                  clus
vv                                 AMP PEAK  9(6P25.2) MUTATED
  FIBROLAMELLAR CARCINOMA                                    0
  HEPATOCELLULAR CARCINOMA                                 156
  HEPATOCHOLANGIOCARCINOMA (MIXED)                           3
                                  clus
vv                                 AMP PEAK  9(6P25.2) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                      3
  HEPATOCELLULAR CARCINOMA                                   204
  HEPATOCHOLANGIOCARCINOMA (MIXED)                             4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  9(6P25.2) MUTATED   141   8   1   8
  AMP PEAK  9(6P25.2) WILD-TYPE 183   9   0  13
D9V10, multiclass
    clus
vv   AMP PEAK  9(6P25.2) MUTATED AMP PEAK  9(6P25.2) WILD-TYPE
  R0                         141                           183
  R1                           8                             9
  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  9(6P25.2) MUTATED                                  1    70
  AMP PEAK  9(6P25.2) WILD-TYPE                                1    88
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  9(6P25.2) MUTATED                           8    76
  AMP PEAK  9(6P25.2) WILD-TYPE                         9   107
D9V11, multiclass
                                  clus
vv                                 AMP PEAK  9(6P25.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                     70
  BLACK OR AFRICAN AMERICAN                                  8
  WHITE                                                     76
                                  clus
vv                                 AMP PEAK  9(6P25.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                       88
  BLACK OR AFRICAN AMERICAN                                    9
  WHITE                                                      107
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V12, binary
                               cls
clus                              0   1
  AMP PEAK  9(6P25.2) MUTATED    10 140
  AMP PEAK  9(6P25.2) WILD-TYPE   6 195
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  9(6P25.2) MUTATED     10  140
  AMP PEAK  9(6P25.2) WILD-TYPE    6  195
                        clus
vv                       AMP PEAK  9(6P25.2) MUTATED
  HISPANIC OR LATINO                              10
  NOT HISPANIC OR LATINO                         140
                        clus
vv                       AMP PEAK  9(6P25.2) WILD-TYPE
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                           195
[1] 2 2
[1] FALSE

Clustering(10) Variable = AMP PEAK 10(6P21.1) MUTATION ANALYSIS
D10V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 10(6P21.1) MUTATED    93  61
  AMP PEAK 10(6P21.1) WILD-TYPE 142  68
  AMP PEAK 10(6P21.1) MUTATED AMP PEAK 10(6P21.1) WILD-TYPE 
                          154                           210 
  AMP PEAK 10(6P21.1) MUTATED AMP PEAK 10(6P21.1) WILD-TYPE 
                           61                            68 
$`AMP PEAK 10(6P21.1) MUTATED`
TCGA-2Y-A9GV TCGA-4R-AA8I TCGA-DD-A3A8 TCGA-DD-AADV TCGA-DD-AAE7 TCGA-ES-A2HS 
       83.24         8.61         0.36        18.87        21.17        22.62 
TCGA-FV-A3R2 TCGA-G3-A3CG TCGA-G3-A6UC TCGA-LG-A6GG TCGA-MI-A75H TCGA-UB-A7MF 
        6.38        22.13        22.06        12.72        24.56         7.04 
TCGA-2Y-A9GS TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H5 
       23.80        24.89        27.88        56.91        49.84        18.25 
TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-5R-AA1C 
       20.81        22.92         1.18        13.02        10.78        17.10 
TCGA-5R-AAAM TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A216 
        1.51        27.52        27.52        23.38         1.12        44.42 
TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A69I TCGA-BD-A2L6 
       45.93         0.26        22.36        14.60        12.72        44.81 
TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5261 TCGA-CC-5263 TCGA-CC-A3MB TCGA-CC-A3MC 
       13.45         0.66         3.19         4.24        10.36        11.93 
TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IK 
        8.94         7.13         9.83        12.00        13.12         8.61 
TCGA-CC-A7IL TCGA-CC-A8HU TCGA-CC-A8HV TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A118 
        9.14        11.31         9.17        37.78        83.57       113.00 
TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1EB TCGA-DD-A1EE 
        7.33         2.60        21.76        51.29        66.31        11.47 
TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z 
       12.95        45.11        49.15        55.69         5.62        19.76 
TCGA-DD-A3A5 TCGA-DD-A3A9 TCGA-DD-A4NH TCGA-DD-A4NK TCGA-DD-A4NN TCGA-DD-A4NS 
      102.74        30.61        30.15        39.78        29.56        80.75 
TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 
       22.78         1.45        35.67       114.35        13.48         0.53 
TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACI 
       75.65        76.41        12.53        71.80        12.00        53.19 
TCGA-DD-AACJ TCGA-DD-AACN TCGA-DD-AACP TCGA-DD-AACT TCGA-DD-AACZ TCGA-DD-AAD3 
       69.11        42.81        13.64        51.35         5.62        42.58 
TCGA-DD-AADA TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADL TCGA-DD-AADN TCGA-DD-AADO 
       40.54         3.78        37.64        20.91        29.52        14.89 
TCGA-DD-AADQ TCGA-DD-AAE0 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE9 TCGA-DD-AAEH 
       14.33        18.25        18.61        19.99        23.74        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-A7PZ TCGA-ED-A7XO TCGA-ED-A82E 
       60.99        53.69        13.35         0.20        14.04        13.41 
TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-FV-A23B 
       13.35         1.84        20.61        19.59         0.62        60.89 
TCGA-FV-A3I0 TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25X TCGA-G3-A3CK 
       27.88         0.39        13.68        53.79        58.49        19.23 
TCGA-G3-A5SL TCGA-G3-AAV1 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-HP-A5N0 TCGA-KR-A7K2 
       20.42        11.80        13.55         0.89        37.71        27.25 
TCGA-KR-A7K8 TCGA-MI-A75G TCGA-MI-A75I TCGA-NI-A8LF TCGA-O8-A75V TCGA-RC-A6M4 
       29.79        22.95        20.71        26.27        17.69         0.72 
TCGA-RC-A7S9 TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC 
       21.04        15.52        36.10        27.88        19.76        16.44 
TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WQ-A9G7 TCGA-WX-AA44 TCGA-XR-A8TD TCGA-XR-A8TE 
       15.98        10.75         0.99        20.22        33.86        30.41 
TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZS-A9CD TCGA-ZS-A9CF 
       22.78        13.55        45.57        79.30 

$`AMP PEAK 10(6P21.1) WILD-TYPE`
TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A5W4 TCGA-BD-A3ER 
       11.74        38.40        69.57         5.03        17.98        36.66 
TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL 
       90.28        26.83        21.83        18.90        23.64         9.96 
TCGA-FV-A3I1 TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A7M9 TCGA-K7-A5RF TCGA-KR-A7K0 
        8.12        81.73        30.74         1.84        20.75         2.14 
TCGA-KR-A7K7 TCGA-T1-A6J8 TCGA-UB-AA0V TCGA-XR-A8TG TCGA-ZP-A9D1 TCGA-ZS-A9CE 
       31.27         0.76        10.32        29.52         0.69        40.80 
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-A9HB TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1D TCGA-BC-4072 
       47.74         8.55        10.59         0.66        14.76        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-A8YO TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5262 TCGA-CC-5264 TCGA-CC-A1HT 
       18.48         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-A4NF TCGA-DD-A4NJ TCGA-DD-A4NL TCGA-DD-A4NO TCGA-DD-A4NP 
       32.52        30.97        30.51        56.25        73.81       108.76 
TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C 
       12.26         0.30        78.84        23.93         9.30        23.05 
TCGA-DD-AAC9 TCGA-DD-AACC TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACK TCGA-DD-AACL 
       11.41        55.40        15.42         6.41         0.30         3.52 
TCGA-DD-AACM TCGA-DD-AACO TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACV 
       58.16        61.68        14.20        59.31        51.52        50.33 
TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 
       46.82         5.59        47.67         4.50        18.54        21.63 
TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD 
       44.22        22.09        40.08        40.83        13.97        40.47 
TCGA-DD-AADE TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADM TCGA-DD-AADP 
       39.52        35.67        35.05        34.49         0.39        15.06 
TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE1 
       66.67        15.58        18.21        19.30        18.25        18.15 
TCGA-DD-AAE2 TCGA-DD-AAE6 TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEI 
       20.98         4.64        15.72        25.08        26.63        50.33 
TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVU TCGA-DD-AAVX TCGA-DD-AAVZ TCGA-DD-AAW0 
       90.48        89.69        72.39        56.48        62.47        66.25 
TCGA-DD-AAW1 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66Y 
       65.39        29.92        26.93        28.08        13.91         9.73 
TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7XP TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S 
        0.20        12.82        13.15         0.20        18.74        19.99 
TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3R3 TCGA-FV-A495 
       11.93        14.40        23.97        19.10        12.03         0.03 
TCGA-FV-A496 TCGA-G3-A25T TCGA-G3-A25V TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH 
        0.33        51.06        28.27        14.86        21.53        25.64 
TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SM TCGA-G3-A7M5 
        5.92        19.53        25.25        22.95        17.10        14.70 
TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV2 
       20.78        11.87        14.14        15.78        15.65        12.23 
TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB 
       11.64         2.14        11.87        28.90         1.02         2.20 
TCGA-HP-A5MZ TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-LG-A9QC TCGA-LG-A9QD 
        2.99        17.06        16.83        11.80        13.97        12.03 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-PD-A5DF 
        9.57        16.67         7.53        10.85        58.88        21.01 
TCGA-QA-A7B7 TCGA-RC-A6M5 TCGA-RC-A6M6 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH 
        3.09         0.49         0.30        19.33        19.04        15.39 
TCGA-UB-A7MD TCGA-WJ-A86L TCGA-WQ-AB4B TCGA-WX-AA46 TCGA-WX-AA47 TCGA-ZP-A9CV 
        1.71        11.34        12.99        24.85        18.28        35.77 
TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CG 
       25.71        23.21        35.87        25.15        12.99        11.21 

  AMP PEAK 10(6P21.1) MUTATED AMP PEAK 10(6P21.1) WILD-TYPE 
                         0.20                          0.03 
  AMP PEAK 10(6P21.1) MUTATED AMP PEAK 10(6P21.1) WILD-TYPE 
                       114.35                        120.82 
  AMP PEAK 10(6P21.1) MUTATED AMP PEAK 10(6P21.1) WILD-TYPE 
                        20.76                         18.97 
[1] "0.2 - 114.3 (20.8)" "0.0 - 120.8 (19.0)"
[1] "hr=" "1.2"
D10V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IIIA
  AMP PEAK 10(6P21.1) MUTATED        69       39         2         29
  AMP PEAK 10(6P21.1) WILD-TYPE     104       48         1         33
                               vv
clus                            STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 10(6P21.1) MUTATED            5          1        2         0
  AMP PEAK 10(6P21.1) WILD-TYPE          4          6        0         1
                               vv
clus                            STAGE IVB
  AMP PEAK 10(6P21.1) MUTATED           1
  AMP PEAK 10(6P21.1) WILD-TYPE         1
D10V3, multiclass
            clus
vv           AMP PEAK 10(6P21.1) MUTATED AMP PEAK 10(6P21.1) WILD-TYPE
  STAGE I                             69                           104
  STAGE II                            39                            48
  STAGE III                            2                             1
  STAGE IIIA                          29                            33
  STAGE IIIB                           5                             4
  STAGE IIIC                           1                             6
  STAGE IV                             2                             0
  STAGE IVA                            0                             1
  STAGE IVB                            1                             1
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  AMP PEAK 10(6P21.1) MUTATED    70  44  37   5
  AMP PEAK 10(6P21.1) WILD-TYPE 113  51  40   7
D10V4, multiclass
    clus
vv   AMP PEAK 10(6P21.1) MUTATED AMP PEAK 10(6P21.1) WILD-TYPE
  T1                          70                           113
  T2                          44                            51
  T3                          37                            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"
D10V5, binary
                               cls
clus                              0   1
  AMP PEAK 10(6P21.1) MUTATED   108   0
  AMP PEAK 10(6P21.1) WILD-TYPE 146   3
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(6P21.1) MUTATED    108    0
  AMP PEAK 10(6P21.1) WILD-TYPE  146    3
   clus
vv  AMP PEAK 10(6P21.1) MUTATED AMP PEAK 10(6P21.1) WILD-TYPE
  0                         108                           146
  1                           0                             3
[1] 2 2
[1] FALSE
D10V6, binary
                               cls
clus                              0   1
  AMP PEAK 10(6P21.1) MUTATED   112   3
  AMP PEAK 10(6P21.1) WILD-TYPE 154   1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(6P21.1) MUTATED    112    3
  AMP PEAK 10(6P21.1) WILD-TYPE  154    1
   clus
vv  AMP PEAK 10(6P21.1) MUTATED AMP PEAK 10(6P21.1) WILD-TYPE
  0                         112                           154
  1                           3                             1
[1] 2 2
[1] FALSE
D10V7, binary
                               cls
clus                              0   1
  AMP PEAK 10(6P21.1) MUTATED    58 100
  AMP PEAK 10(6P21.1) WILD-TYPE  60 152
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(6P21.1) MUTATED     58  100
  AMP PEAK 10(6P21.1) WILD-TYPE   60  152
        clus
vv       AMP PEAK 10(6P21.1) MUTATED AMP PEAK 10(6P21.1) WILD-TYPE
  FEMALE                          58                            60
  MALE                           100                           152
[1] 2 2
[1] FALSE
D10V8, binary
                               cls
clus                              0   1
  AMP PEAK 10(6P21.1) MUTATED   145   1
  AMP PEAK 10(6P21.1) WILD-TYPE 193   8
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(6P21.1) MUTATED    145    1
  AMP PEAK 10(6P21.1) WILD-TYPE  193    8
     clus
vv    AMP PEAK 10(6P21.1) MUTATED AMP PEAK 10(6P21.1) WILD-TYPE
  NO                          145                           193
  YES                           1                             8
[1] 2 2
[1] FALSE
                               vv
clus                            FIBROLAMELLAR CARCINOMA
  AMP PEAK 10(6P21.1) MUTATED                         0
  AMP PEAK 10(6P21.1) WILD-TYPE                       3
                               vv
clus                            HEPATOCELLULAR CARCINOMA
  AMP PEAK 10(6P21.1) MUTATED                        154
  AMP PEAK 10(6P21.1) WILD-TYPE                      206
                               vv
clus                            HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK 10(6P21.1) MUTATED                                  4
  AMP PEAK 10(6P21.1) WILD-TYPE                                3
D10V9, multiclass
                                  clus
vv                                 AMP PEAK 10(6P21.1) MUTATED
  FIBROLAMELLAR CARCINOMA                                    0
  HEPATOCELLULAR CARCINOMA                                 154
  HEPATOCHOLANGIOCARCINOMA (MIXED)                           4
                                  clus
vv                                 AMP PEAK 10(6P21.1) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                      3
  HEPATOCELLULAR CARCINOMA                                   206
  HEPATOCHOLANGIOCARCINOMA (MIXED)                             3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK 10(6P21.1) MUTATED   141   8   1   8
  AMP PEAK 10(6P21.1) WILD-TYPE 183   9   0  13
D10V10, multiclass
    clus
vv   AMP PEAK 10(6P21.1) MUTATED AMP PEAK 10(6P21.1) WILD-TYPE
  R0                         141                           183
  R1                           8                             9
  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(6P21.1) MUTATED                                  1    64
  AMP PEAK 10(6P21.1) WILD-TYPE                                1    94
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 10(6P21.1) MUTATED                           8    80
  AMP PEAK 10(6P21.1) WILD-TYPE                         9   103
D10V11, multiclass
                                  clus
vv                                 AMP PEAK 10(6P21.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                     64
  BLACK OR AFRICAN AMERICAN                                  8
  WHITE                                                     80
                                  clus
vv                                 AMP PEAK 10(6P21.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                       94
  BLACK OR AFRICAN AMERICAN                                    9
  WHITE                                                      103
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V12, binary
                               cls
clus                              0   1
  AMP PEAK 10(6P21.1) MUTATED     9 137
  AMP PEAK 10(6P21.1) WILD-TYPE   7 198
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(6P21.1) MUTATED      9  137
  AMP PEAK 10(6P21.1) WILD-TYPE    7  198
                        clus
vv                       AMP PEAK 10(6P21.1) MUTATED
  HISPANIC OR LATINO                               9
  NOT HISPANIC OR LATINO                         137
                        clus
vv                       AMP PEAK 10(6P21.1) WILD-TYPE
  HISPANIC OR LATINO                                 7
  NOT HISPANIC OR LATINO                           198
[1] 2 2
[1] FALSE

Clustering(11) Variable = AMP PEAK 11(6Q12) MUTATION ANALYSIS
D11V1, survival
                             sevent
clus2                           0   1
  AMP PEAK 11(6Q12) MUTATED    63  42
  AMP PEAK 11(6Q12) WILD-TYPE 172  87
  AMP PEAK 11(6Q12) MUTATED AMP PEAK 11(6Q12) WILD-TYPE 
                        105                         259 
  AMP PEAK 11(6Q12) MUTATED AMP PEAK 11(6Q12) WILD-TYPE 
                         42                          87 
$`AMP PEAK 11(6Q12) MUTATED`
TCGA-DD-A3A8 TCGA-DD-AADV TCGA-DD-AAEG TCGA-ES-A2HS TCGA-G3-A3CG TCGA-G3-A6UC 
        0.36        18.87        23.64        22.62        22.13        22.06 
TCGA-LG-A6GG TCGA-T1-A6J8 TCGA-UB-A7MF TCGA-2Y-A9GS TCGA-2Y-A9GY TCGA-2Y-A9GZ 
       12.72         0.76         7.04        23.80        24.89        27.88 
TCGA-2Y-A9H3 TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-2Y-A9HA TCGA-3K-AAZ8 TCGA-5C-A9VG 
       49.84        18.25        20.81         1.18        13.02        10.78 
TCGA-BC-A10Q TCGA-BC-A10T TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A69H 
       37.32        27.52        45.93         0.26        22.36        14.60 
TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5263 TCGA-CC-A3MB 
       18.48        44.81        13.45         0.66         4.24        10.36 
TCGA-CC-A3MC TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IG TCGA-CC-A7II TCGA-CC-A7IJ 
       11.93         8.94         7.13         9.83        13.12        12.56 
TCGA-CC-A7IK TCGA-CC-A8HU TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A118 TCGA-DD-A119 
        8.61        11.31        37.78        83.57       113.00         7.33 
TCGA-DD-A11A TCGA-DD-A11C TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EJ 
        2.60        21.76        11.47        12.95        49.15        33.04 
TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A5 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NA 
        5.62        19.76       102.74        13.78        30.61        33.14 
TCGA-DD-A4NH TCGA-DD-A4NK TCGA-DD-A4NN TCGA-DD-A4NS TCGA-DD-A73E TCGA-DD-A73G 
       30.15        39.78        29.56        80.75         1.45       114.35 
TCGA-DD-AA3A TCGA-DD-AACB TCGA-DD-AACD TCGA-DD-AACJ TCGA-DD-AACN TCGA-DD-AACT 
       13.48        76.41        12.53        69.11        42.81        51.35 
TCGA-DD-AAD3 TCGA-DD-AADF TCGA-DD-AADL TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADQ 
       42.58         3.78        20.91        29.52        14.89        14.33 
TCGA-DD-AAE0 TCGA-DD-AAE3 TCGA-DD-AAEK TCGA-DD-AAVS TCGA-DD-AAVV TCGA-DD-AAVW 
       18.25        18.61        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 
       60.99        53.69        13.35         0.20        13.35        19.59 
TCGA-EP-A2KC TCGA-FV-A3I0 TCGA-G3-A25U TCGA-G3-A3CK TCGA-G3-AAV1 TCGA-KR-A7K2 
        0.62        27.88        53.79        19.23        11.80        27.25 
TCGA-O8-A75V TCGA-RC-A6M4 TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MC 
       17.69         0.72        15.52        36.10        27.88        16.44 
TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WQ-A9G7 TCGA-XR-A8TD TCGA-XR-A8TE TCGA-XR-A8TF 
       15.98        10.75         0.99        33.86        30.41        22.78 
TCGA-YA-A8S7 TCGA-ZS-A9CD TCGA-ZS-A9CF 
       13.55        45.57        79.30 

$`AMP PEAK 11(6Q12) WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 
       83.24        11.74        38.40         8.61        69.57         5.03 
TCGA-BC-A5W4 TCGA-BD-A3ER TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AAE7 TCGA-DD-AAE8 
       17.98        36.66        90.28        26.83        21.17        21.83 
TCGA-DD-AAEA TCGA-EP-A3JL TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25W 
       18.90         9.96         8.12         6.38        81.73        30.74 
TCGA-G3-A7M9 TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-MI-A75H TCGA-UB-AA0V 
        1.84        20.75         2.14        31.27        24.56        10.32 
TCGA-XR-A8TG TCGA-ZP-A9D1 TCGA-ZS-A9CE TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW 
       29.52         0.69        40.80        53.39        63.75        41.79 
TCGA-2Y-A9GX TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H4 TCGA-2Y-A9H9 
       80.28       120.82        40.41        56.91        47.74        22.92 
TCGA-2Y-A9HB TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM 
        8.55        10.59         0.66        17.10        14.76         1.51 
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10U TCGA-BC-A10W 
       48.99        27.91        10.13        46.78        27.52         2.99 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A69I TCGA-CC-5258 
       25.32        23.38         1.12        44.42        12.72         4.24 
TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5264 TCGA-CC-A1HT TCGA-CC-A3M9 
        2.86         3.19         3.39         3.35         3.32         9.86 
TCGA-CC-A3MA TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A7IF TCGA-CC-A7IH TCGA-CC-A7IL 
        9.96        11.41         9.99        21.34        12.00         9.14 
TCGA-CC-A8HT TCGA-CC-A8HV TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A116 
        4.60         9.17         6.94         8.15        79.73        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-A1EG TCGA-DD-A1EI TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V 
       75.65        45.11         6.02        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-A3A6 TCGA-DD-A4NB TCGA-DD-A4NF TCGA-DD-A4NJ TCGA-DD-A4NL 
       20.12       107.11        32.52        30.97        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-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-AACC TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH 
       75.65        55.40        71.80        12.00        15.42         6.41 
TCGA-DD-AACI TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACO TCGA-DD-AACP 
       53.19         0.30         3.52        58.16        61.68        13.64 
TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX 
       14.20        59.31        51.52        50.33        46.82         5.59 
TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD5 
       47.67         5.62         4.50        18.54        21.63        44.22 
TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD 
       22.09        40.08        40.54        40.83        13.97        40.47 
TCGA-DD-AADE TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADM 
       39.52        37.64        35.67        35.05        34.49         0.39 
TCGA-DD-AADP TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY 
       15.06        66.67        15.58        18.21        19.30        18.25 
TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE9 TCGA-DD-AAEB 
       18.15        20.98        19.99         4.64        23.74        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        90.48        89.69 
TCGA-DD-AAVR TCGA-DD-AAVU TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 
       82.62        72.39        56.48        64.77        62.47        66.25 
TCGA-DD-AAW1 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66Y 
       65.39        29.92        26.93        28.08        13.91         9.73 
TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O6 
        0.20        12.82        14.04        13.15        13.41         1.84 
TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A3RK TCGA-ES-A2HT 
        0.20        18.74        19.99        20.61        11.93        14.40 
TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 
       60.89        23.97        19.10        12.03         0.03         0.33 
TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25V TCGA-G3-A25X TCGA-G3-A25Y 
        0.39        13.68        51.06        28.27        58.49        14.86 
TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A5SI TCGA-G3-A5SJ 
       21.53        25.64         5.92        19.53        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-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        11.64 
TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ 
        2.14        11.87        28.90         1.02         2.20         2.99 
TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K8 TCGA-LG-A9QC 
       37.71        17.06        16.83        11.80        29.79        13.97 
TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A520 
       12.03         9.57        16.67        22.95        20.71         7.53 
TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A6M5 
       10.85        58.88        26.27        21.01         3.09         0.49 
TCGA-RC-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH TCGA-UB-A7MB 
        0.30        21.04        19.33        19.04        15.39        19.76 
TCGA-UB-A7MD TCGA-WJ-A86L TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 
        1.71        11.34        12.99        20.22        24.85        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-A9CG 
       11.21 

  AMP PEAK 11(6Q12) MUTATED AMP PEAK 11(6Q12) WILD-TYPE 
                       0.20                        0.03 
  AMP PEAK 11(6Q12) MUTATED AMP PEAK 11(6Q12) WILD-TYPE 
                     114.35                      120.82 
  AMP PEAK 11(6Q12) MUTATED AMP PEAK 11(6Q12) WILD-TYPE 
                      19.59                       19.99 
[1] "0.2 - 114.3 (19.6)" "0.0 - 120.8 (20.0)"
[1] "hr=" "1.2"
D11V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 11(6Q12) MUTATED        40       28         2         20          6
  AMP PEAK 11(6Q12) WILD-TYPE     133       59         1         42          3
                             vv
clus                          STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 11(6Q12) MUTATED            4        1         0         1
  AMP PEAK 11(6Q12) WILD-TYPE          3        1         1         1
D11V3, multiclass
            clus
vv           AMP PEAK 11(6Q12) MUTATED AMP PEAK 11(6Q12) WILD-TYPE
  STAGE I                           40                         133
  STAGE II                          28                          59
  STAGE III                          2                           1
  STAGE IIIA                        20                          42
  STAGE IIIB                         6                           3
  STAGE IIIC                         4                           3
  STAGE IV                           1                           1
  STAGE IVA                          0                           1
  STAGE IVB                          1                           1
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           T1  T2  T3  T4
  AMP PEAK 11(6Q12) MUTATED    43  32  29   5
  AMP PEAK 11(6Q12) WILD-TYPE 140  63  48   7
D11V4, multiclass
    clus
vv   AMP PEAK 11(6Q12) MUTATED AMP PEAK 11(6Q12) WILD-TYPE
  T1                        43                         140
  T2                        32                          63
  T3                        29                          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"
D11V5, binary
                             cls
clus                            0   1
  AMP PEAK 11(6Q12) MUTATED    71   2
  AMP PEAK 11(6Q12) WILD-TYPE 183   1
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 11(6Q12) MUTATED     71    2
  AMP PEAK 11(6Q12) WILD-TYPE  183    1
   clus
vv  AMP PEAK 11(6Q12) MUTATED AMP PEAK 11(6Q12) WILD-TYPE
  0                        71                         183
  1                         2                           1
[1] 2 2
[1] FALSE
D11V6, binary
                             cls
clus                            0   1
  AMP PEAK 11(6Q12) MUTATED    77   2
  AMP PEAK 11(6Q12) WILD-TYPE 189   2
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 11(6Q12) MUTATED     77    2
  AMP PEAK 11(6Q12) WILD-TYPE  189    2
   clus
vv  AMP PEAK 11(6Q12) MUTATED AMP PEAK 11(6Q12) WILD-TYPE
  0                        77                         189
  1                         2                           2
[1] 2 2
[1] FALSE
D11V7, binary
                             cls
clus                            0   1
  AMP PEAK 11(6Q12) MUTATED    39  70
  AMP PEAK 11(6Q12) WILD-TYPE  79 182
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 11(6Q12) MUTATED     39   70
  AMP PEAK 11(6Q12) WILD-TYPE   79  182
        clus
vv       AMP PEAK 11(6Q12) MUTATED AMP PEAK 11(6Q12) WILD-TYPE
  FEMALE                        39                          79
  MALE                          70                         182
[1] 2 2
[1] FALSE
D11V8, binary
                             cls
clus                            0   1
  AMP PEAK 11(6Q12) MUTATED    97   0
  AMP PEAK 11(6Q12) WILD-TYPE 241   9
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 11(6Q12) MUTATED     97    0
  AMP PEAK 11(6Q12) WILD-TYPE  241    9
     clus
vv    AMP PEAK 11(6Q12) MUTATED AMP PEAK 11(6Q12) WILD-TYPE
  NO                         97                         241
  YES                         0                           9
[1] 2 2
[1] FALSE
                             vv
clus                          FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  AMP PEAK 11(6Q12) MUTATED                         0                      105
  AMP PEAK 11(6Q12) WILD-TYPE                       3                      255
                             vv
clus                          HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK 11(6Q12) MUTATED                                  4
  AMP PEAK 11(6Q12) WILD-TYPE                                3
D11V9, multiclass
                                  clus
vv                                 AMP PEAK 11(6Q12) MUTATED
  FIBROLAMELLAR CARCINOMA                                  0
  HEPATOCELLULAR CARCINOMA                               105
  HEPATOCHOLANGIOCARCINOMA (MIXED)                         4
                                  clus
vv                                 AMP PEAK 11(6Q12) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                    3
  HEPATOCELLULAR CARCINOMA                                 255
  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(6Q12) MUTATED    95   7   1   6
  AMP PEAK 11(6Q12) WILD-TYPE 229  10   0  15
D11V10, multiclass
    clus
vv   AMP PEAK 11(6Q12) MUTATED AMP PEAK 11(6Q12) WILD-TYPE
  R0                        95                         229
  R1                         7                          10
  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 11(6Q12) MUTATED                                  1    43
  AMP PEAK 11(6Q12) WILD-TYPE                                1   115
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 11(6Q12) MUTATED                           7    55
  AMP PEAK 11(6Q12) WILD-TYPE                        10   128
D11V11, multiclass
                                  clus
vv                                 AMP PEAK 11(6Q12) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         1
  ASIAN                                                   43
  BLACK OR AFRICAN AMERICAN                                7
  WHITE                                                   55
                                  clus
vv                                 AMP PEAK 11(6Q12) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                    115
  BLACK OR AFRICAN AMERICAN                                 10
  WHITE                                                    128
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V12, binary
                             cls
clus                            0   1
  AMP PEAK 11(6Q12) MUTATED     7  94
  AMP PEAK 11(6Q12) WILD-TYPE   9 241
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 11(6Q12) MUTATED      7   94
  AMP PEAK 11(6Q12) WILD-TYPE    9  241
                        clus
vv                       AMP PEAK 11(6Q12) MUTATED AMP PEAK 11(6Q12) WILD-TYPE
  HISPANIC OR LATINO                             7                           9
  NOT HISPANIC OR LATINO                        94                         241
[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    48  32
  AMP PEAK 12(6Q12) WILD-TYPE 187  97
  AMP PEAK 12(6Q12) MUTATED AMP PEAK 12(6Q12) WILD-TYPE 
                         80                         284 
  AMP PEAK 12(6Q12) MUTATED AMP PEAK 12(6Q12) WILD-TYPE 
                         32                          97 
$`AMP PEAK 12(6Q12) MUTATED`
TCGA-2Y-A9H7 TCGA-DD-A3A8 TCGA-DD-AAEG TCGA-ES-A2HS TCGA-LG-A6GG TCGA-UB-A7MF 
       38.40         0.36        23.64        22.62        12.72         7.04 
TCGA-2Y-A9GS TCGA-2Y-A9GY TCGA-2Y-A9H3 TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-2Y-A9HA 
       23.80        24.89        49.84        18.25        20.81         1.18 
TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A69H 
       13.02        10.78        45.93         0.26        22.36        14.60 
TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-CC-5260 TCGA-CC-5263 TCGA-CC-A3MB TCGA-CC-A3MC 
       44.81        13.45         2.86         4.24        10.36        11.93 
TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IG TCGA-CC-A7II TCGA-CC-A7IK TCGA-CC-A8HU 
        8.94         7.13         9.83        13.12         8.61        11.31 
TCGA-CC-A8HV TCGA-DD-A115 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11D 
        9.17        83.57       113.00         7.33         2.60        51.29 
TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A39Y TCGA-DD-A3A9 TCGA-DD-A73G TCGA-DD-AACJ 
       12.95        49.15         5.62        30.61       114.35        69.11 
TCGA-DD-AACN TCGA-DD-AACT TCGA-DD-AADF TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP 
       42.81        51.35         3.78        29.52        14.89        15.06 
TCGA-DD-AAE0 TCGA-DD-AAE3 TCGA-DD-AAE9 TCGA-DD-AAEK TCGA-DD-AAVV TCGA-DD-AAVW 
       18.25        18.61        23.74        35.08        80.71        76.18 
TCGA-DD-AAW2 TCGA-ED-A66X TCGA-ED-A7PZ TCGA-ED-A8O5 TCGA-EP-A12J TCGA-EP-A2KA 
       60.99        13.35         0.20        13.35        18.74        20.61 
TCGA-EP-A2KB TCGA-EP-A2KC TCGA-FV-A3I0 TCGA-G3-A25U TCGA-G3-A3CK TCGA-G3-AAV1 
       19.59         0.62        27.88        53.79        19.23        11.80 
TCGA-KR-A7K2 TCGA-O8-A75V TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MC 
       27.25        17.69        15.52        36.10        27.88        16.44 
TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WQ-A9G7 TCGA-XR-A8TD TCGA-XR-A8TE TCGA-XR-A8TF 
       15.98        10.75         0.99        33.86        30.41        22.78 
TCGA-YA-A8S7 TCGA-ZS-A9CD 
       13.55        45.57 

$`AMP PEAK 12(6Q12) WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A5W4 
       83.24        11.74         8.61        69.57         5.03        17.98 
TCGA-BD-A3ER TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV TCGA-DD-AAE7 TCGA-DD-AAE8 
       36.66        90.28        26.83        18.87        21.17        21.83 
TCGA-DD-AAEA TCGA-EP-A3JL TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25W 
       18.90         9.96         8.12         6.38        81.73        30.74 
TCGA-G3-A3CG TCGA-G3-A6UC TCGA-G3-A7M9 TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-KR-A7K7 
       22.13        22.06         1.84        20.75         2.14        31.27 
TCGA-MI-A75H TCGA-T1-A6J8 TCGA-UB-AA0V TCGA-XR-A8TG TCGA-ZP-A9D1 TCGA-ZS-A9CE 
       24.56         0.76        10.32        29.52         0.69        40.80 
TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GZ TCGA-2Y-A9H0 
       53.39        63.75        41.79        80.28        27.88       120.82 
TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H4 TCGA-2Y-A9H9 TCGA-2Y-A9HB TCGA-5C-A9VH 
       40.41        56.91        47.74        22.92         8.55        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-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W 
       37.32        10.13        46.78        27.52        27.52         2.99 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A69I TCGA-BC-A8YO 
       25.32        23.38         1.12        44.42        12.72        18.48 
TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5264 TCGA-CC-A1HT 
        0.66         4.24         3.19         3.39         3.35         3.32 
TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A7IF TCGA-CC-A7IH 
        9.86         9.96        11.41         9.99        21.34        12.00 
TCGA-CC-A7IJ TCGA-CC-A7IL TCGA-CC-A8HT TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A113 
       12.56         9.14         4.60         6.94         8.15        79.73 
TCGA-DD-A114 TCGA-DD-A116 TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A1E9 TCGA-DD-A1EA 
       37.78        53.33         0.46        21.76        90.71        79.40 
TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EG TCGA-DD-A1EI 
       66.31        19.79        75.65        11.47        45.11         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-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-A4NA TCGA-DD-A4NB TCGA-DD-A4NF 
      102.74       107.11        13.78        33.14        32.52        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-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-AACK 
       71.80        12.00        15.42         6.41        53.19         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-AACU TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AACZ 
       51.52        50.33        46.82         5.59        47.67         5.62 
TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 
        4.50        18.54        21.63        42.58        44.22        22.09 
TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE 
       40.08        40.54        40.83        13.97        40.47        39.52 
TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM 
       37.64        35.67        35.05        34.49        20.91         0.39 
TCGA-DD-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-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAEB TCGA-DD-AAED 
       18.15        20.98        19.99         4.64        15.72        25.08 
TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR 
       26.63        25.78        50.33        90.48        89.69        82.62 
TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 
       59.93        72.39        56.48        64.77        62.47        66.25 
TCGA-DD-AAW1 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 
       65.39        53.69        29.92        26.93        28.08        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-A8O6 TCGA-ED-A97K TCGA-EP-A26S TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B 
        1.84         0.20        19.99        11.93        14.40        60.89 
TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ 
       23.97        19.10        12.03         0.03         0.33         0.39 
TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25V TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z 
       13.68        51.06        28.27        58.49        14.86        21.53 
TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL 
       25.64         5.92        19.53        25.25        22.95        20.42 
TCGA-G3-A5SM TCGA-G3-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ 
       17.10        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        11.64         2.14 
TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 
       11.87        28.90         1.02         2.20         2.99        37.71 
TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD 
       17.06        16.83        11.80        29.79        13.97        12.03 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO 
        9.57        16.67        22.95        20.71         7.53        10.85 
TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A6M4 TCGA-RC-A6M5 
       58.88        26.27        21.01         3.09         0.72         0.49 
TCGA-RC-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH TCGA-UB-A7MB 
        0.30        21.04        19.33        19.04        15.39        19.76 
TCGA-UB-A7MD TCGA-WJ-A86L TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 
        1.71        11.34        12.99        20.22        24.85        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-A9CF TCGA-ZS-A9CG 
       79.30        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 
                      18.25                       20.32 
[1] "0.2 - 114.3 (18.2)" "0.0 - 120.8 (20.3)"
[1] "hr=" "1.2"
D12V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 12(6Q12) MUTATED        32       22         1         17          3
  AMP PEAK 12(6Q12) WILD-TYPE     141       65         2         45          6
                             vv
clus                          STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 12(6Q12) MUTATED            2        1         0         1
  AMP PEAK 12(6Q12) WILD-TYPE          5        1         1         1
D12V3, multiclass
            clus
vv           AMP PEAK 12(6Q12) MUTATED AMP PEAK 12(6Q12) WILD-TYPE
  STAGE I                           32                         141
  STAGE II                          22                          65
  STAGE III                          1                           2
  STAGE IIIA                        17                          45
  STAGE IIIB                         3                           6
  STAGE IIIC                         2                           5
  STAGE IV                           1                           1
  STAGE IVA                          0                           1
  STAGE IVB                          1                           1
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           T1  T2  T3  T4
  AMP PEAK 12(6Q12) MUTATED    33  24  22   4
  AMP PEAK 12(6Q12) WILD-TYPE 150  71  55   8
D12V4, multiclass
    clus
vv   AMP PEAK 12(6Q12) MUTATED AMP PEAK 12(6Q12) WILD-TYPE
  T1                        33                         150
  T2                        24                          71
  T3                        22                          55
  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"
D12V5, binary
                             cls
clus                            0   1
  AMP PEAK 12(6Q12) MUTATED    55   0
  AMP PEAK 12(6Q12) WILD-TYPE 199   3
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 12(6Q12) MUTATED     55    0
  AMP PEAK 12(6Q12) WILD-TYPE  199    3
   clus
vv  AMP PEAK 12(6Q12) MUTATED AMP PEAK 12(6Q12) WILD-TYPE
  0                        55                         199
  1                         0                           3
[1] 2 2
[1] FALSE
D12V6, binary
                             cls
clus                            0   1
  AMP PEAK 12(6Q12) MUTATED    56   2
  AMP PEAK 12(6Q12) WILD-TYPE 210   2
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 12(6Q12) MUTATED     56    2
  AMP PEAK 12(6Q12) WILD-TYPE  210    2
   clus
vv  AMP PEAK 12(6Q12) MUTATED AMP PEAK 12(6Q12) WILD-TYPE
  0                        56                         210
  1                         2                           2
[1] 2 2
[1] FALSE
D12V7, binary
                             cls
clus                            0   1
  AMP PEAK 12(6Q12) MUTATED    30  53
  AMP PEAK 12(6Q12) WILD-TYPE  88 199
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 12(6Q12) MUTATED     30   53
  AMP PEAK 12(6Q12) WILD-TYPE   88  199
        clus
vv       AMP PEAK 12(6Q12) MUTATED AMP PEAK 12(6Q12) WILD-TYPE
  FEMALE                        30                          88
  MALE                          53                         199
[1] 2 2
[1] FALSE
D12V8, binary
                             cls
clus                            0   1
  AMP PEAK 12(6Q12) MUTATED    74   0
  AMP PEAK 12(6Q12) WILD-TYPE 264   9
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 12(6Q12) MUTATED     74    0
  AMP PEAK 12(6Q12) WILD-TYPE  264    9
     clus
vv    AMP PEAK 12(6Q12) MUTATED AMP PEAK 12(6Q12) WILD-TYPE
  NO                         74                         264
  YES                         0                           9
[1] 2 2
[1] FALSE
                             vv
clus                          FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  AMP PEAK 12(6Q12) MUTATED                         0                       80
  AMP PEAK 12(6Q12) WILD-TYPE                       3                      280
                             vv
clus                          HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK 12(6Q12) MUTATED                                  3
  AMP PEAK 12(6Q12) WILD-TYPE                                4
D12V9, multiclass
                                  clus
vv                                 AMP PEAK 12(6Q12) MUTATED
  FIBROLAMELLAR CARCINOMA                                  0
  HEPATOCELLULAR CARCINOMA                                80
  HEPATOCHOLANGIOCARCINOMA (MIXED)                         3
                                  clus
vv                                 AMP PEAK 12(6Q12) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                    3
  HEPATOCELLULAR CARCINOMA                                 280
  HEPATOCHOLANGIOCARCINOMA (MIXED)                           4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           R0  R1  R2  RX
  AMP PEAK 12(6Q12) MUTATED    75   3   1   4
  AMP PEAK 12(6Q12) WILD-TYPE 249  14   0  17
D12V10, multiclass
    clus
vv   AMP PEAK 12(6Q12) MUTATED AMP PEAK 12(6Q12) WILD-TYPE
  R0                        75                         249
  R1                         3                          14
  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 12(6Q12) MUTATED                                  1    37
  AMP PEAK 12(6Q12) WILD-TYPE                                1   121
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 12(6Q12) MUTATED                           6    38
  AMP PEAK 12(6Q12) WILD-TYPE                        11   145
D12V11, multiclass
                                  clus
vv                                 AMP PEAK 12(6Q12) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         1
  ASIAN                                                   37
  BLACK OR AFRICAN AMERICAN                                6
  WHITE                                                   38
                                  clus
vv                                 AMP PEAK 12(6Q12) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                    121
  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"
D12V12, binary
                             cls
clus                            0   1
  AMP PEAK 12(6Q12) MUTATED     7  70
  AMP PEAK 12(6Q12) WILD-TYPE   9 265
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 12(6Q12) MUTATED      7   70
  AMP PEAK 12(6Q12) WILD-TYPE    9  265
                        clus
vv                       AMP PEAK 12(6Q12) MUTATED AMP PEAK 12(6Q12) WILD-TYPE
  HISPANIC OR LATINO                             7                           9
  NOT HISPANIC OR LATINO                        70                         265
[1] 2 2
[1] FALSE

Clustering(13) Variable = AMP PEAK 13(7Q31.2) MUTATION ANALYSIS
D13V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 13(7Q31.2) MUTATED    75  41
  AMP PEAK 13(7Q31.2) WILD-TYPE 160  88
  AMP PEAK 13(7Q31.2) MUTATED AMP PEAK 13(7Q31.2) WILD-TYPE 
                          116                           248 
  AMP PEAK 13(7Q31.2) MUTATED AMP PEAK 13(7Q31.2) WILD-TYPE 
                           41                            88 
$`AMP PEAK 13(7Q31.2) MUTATED`
TCGA-BC-A5W4 TCGA-BD-A3ER TCGA-DD-A4NI TCGA-DD-AADV TCGA-DD-AAEA TCGA-EP-A3JL 
       17.98        36.66        26.83        18.87        18.90         9.96 
TCGA-ES-A2HS TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A3CG TCGA-G3-A6UC 
       22.62         8.12         6.38        81.73        22.13        22.06 
TCGA-LG-A6GG TCGA-ZP-A9D1 TCGA-2Y-A9GS TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GY 
       12.72         0.69        23.80        63.75        41.79        24.89 
TCGA-2Y-A9GZ TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H9 TCGA-3K-AAZ8 TCGA-5C-A9VG 
       27.88        56.91        49.84        22.92        13.02        10.78 
TCGA-5C-A9VH TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10U TCGA-BC-A3KF TCGA-BC-A69H 
       10.59        37.32        10.13        27.52         0.26        14.60 
TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5260 TCGA-CC-5264 TCGA-CC-A3M9 TCGA-CC-A3MB 
       13.45         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-A4NK TCGA-DD-A4NQ 
        5.62        19.76        70.06        33.14        39.78        12.26 
TCGA-DD-A4NV TCGA-DD-A73C TCGA-DD-A73E TCGA-DD-A73G TCGA-DD-AAC9 TCGA-DD-AACA 
       78.84        23.05         1.45       114.35        11.41        75.65 
TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACI TCGA-DD-AACP TCGA-DD-AACS 
       12.53        71.80        12.00        53.19        13.64        59.31 
TCGA-DD-AACT TCGA-DD-AADD TCGA-DD-AADG TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADS 
       51.35        40.47        37.64        20.91         0.39        15.58 
TCGA-DD-AADW TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE6 TCGA-DD-AAE9 TCGA-DD-AAEB 
       19.30        20.98        18.61         4.64        23.74        15.72 
TCGA-DD-AAEI TCGA-DD-AAVV TCGA-DD-AAVX TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 
       50.33        80.71        56.48        60.99        53.69        29.92 
TCGA-ED-A66Y TCGA-ED-A7PY TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC TCGA-G3-A25T 
        9.73        12.82        19.99        20.61         0.62        51.06 
TCGA-G3-A25V TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A3CJ TCGA-G3-A5SL TCGA-G3-A5SM 
       28.27        58.49        14.86        19.53        20.42        17.10 
TCGA-G3-A7M5 TCGA-G3-AAV1 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-KR-A7K2 TCGA-KR-A7K8 
       14.70        11.80        11.64         2.14        27.25        29.79 
TCGA-MI-A75E TCGA-MI-A75G TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-RC-A6M6 TCGA-RC-A7S9 
       16.67        22.95        58.88        26.27         0.30        21.04 
TCGA-UB-A7MD TCGA-UB-AA0U TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA46 TCGA-XR-A8TE 
        1.71        10.75         0.99        12.99        24.85        30.41 
TCGA-XR-A8TF TCGA-YA-A8S7 
       22.78        13.55 

$`AMP PEAK 13(7Q31.2) WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 
       83.24        11.74        38.40         8.61        69.57         5.03 
TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEG TCGA-G3-A25W 
        0.36        90.28        21.17        21.83        23.64        30.74 
TCGA-G3-A7M9 TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-MI-A75H TCGA-T1-A6J8 
        1.84        20.75         2.14        31.27        24.56         0.76 
TCGA-UB-A7MF TCGA-UB-AA0V TCGA-XR-A8TG TCGA-ZS-A9CE TCGA-2Y-A9GT TCGA-2Y-A9GX 
        7.04        10.32        29.52        40.80        53.39        80.28 
TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-2Y-A9HA 
      120.82        40.41        47.74        18.25        20.81         1.18 
TCGA-2Y-A9HB TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4072 
        8.55         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-A216 TCGA-BC-A217 TCGA-BC-A3KG TCGA-BC-A69I TCGA-BC-A8YO 
        1.12        44.42        45.93        22.36        12.72        18.48 
TCGA-BD-A2L6 TCGA-CC-5258 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT 
       44.81         4.24         3.19         3.39         4.24         3.32 
TCGA-CC-A3MA TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A7IE TCGA-CC-A7IF 
        9.96        11.93        11.41         9.99         7.13        21.34 
TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7IK TCGA-CC-A7IL TCGA-CC-A8HT TCGA-CC-A8HV 
        9.83        12.00         8.61         9.14         4.60         9.17 
TCGA-CC-A9FS TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A119 
        6.94        79.73        37.78        83.57        53.33         7.33 
TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1ED 
        2.60         0.46        21.76        79.40        66.31        75.65 
TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EK TCGA-DD-A1EL 
       12.95        45.11        49.15         6.02        18.35        13.64 
TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A3 TCGA-DD-A3A4 
       27.19        55.69        25.81         7.66        17.59        20.12 
TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NB TCGA-DD-A4NF 
      102.74       107.11        13.78        30.61        32.52        30.97 
TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP 
       30.15        30.51        56.25        29.56        73.81       108.76 
TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73D TCGA-DD-A73F 
        0.30        80.75        23.93         9.30        22.78        35.67 
TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACG TCGA-DD-AACH 
       13.48         0.53        76.41        55.40        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-AACQ TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY 
       14.20        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-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADE 
       22.09        40.08        40.54        40.83        13.97        39.52 
TCGA-DD-AADF TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADN TCGA-DD-AADO 
        3.78        35.67        35.05        34.49        29.52        14.89 
TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADU TCGA-DD-AADY TCGA-DD-AAE0 
       15.06        14.33        66.67        18.21        18.25        18.25 
TCGA-DD-AAE1 TCGA-DD-AAE4 TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAEK 
       18.15        19.99        25.08        26.63        25.78        35.08 
TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW 
       90.48        89.69        82.62        59.93        72.39        76.18 
TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-ED-A4XI TCGA-ED-A5KG 
       64.77        62.47        66.25        65.39        26.93        28.08 
TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A7PX TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP 
       13.91        13.35         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-A2KB 
       13.41        13.35         1.84         0.20        18.74        19.59 
TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 
       11.93        14.40        60.89        23.97        19.10        27.88 
TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25U 
       12.03         0.03         0.33         0.39        13.68        53.79 
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-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV2 
       20.78        11.87        14.14        15.78        15.65        12.23 
TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB 
       13.55         0.89        11.87        28.90         1.02         2.20 
TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-LG-A9QC 
        2.99        37.71        17.06        16.83        11.80        13.97 
TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-O8-A75V 
       12.03         9.57        20.71         7.53        10.85        17.69 
TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A6M4 TCGA-RC-A6M5 TCGA-RC-A7SB TCGA-RC-A7SF 
       21.01         3.09         0.72         0.49        19.33        19.04 
TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC 
       15.39        15.52        36.10        27.88        19.76        16.44 
TCGA-UB-A7ME TCGA-WJ-A86L TCGA-WX-AA44 TCGA-WX-AA47 TCGA-XR-A8TD TCGA-ZP-A9CV 
       15.98        11.34        20.22        18.28        33.86        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-A9CF TCGA-ZS-A9CG 
       79.30        11.21 

  AMP PEAK 13(7Q31.2) MUTATED AMP PEAK 13(7Q31.2) WILD-TYPE 
                         0.26                          0.03 
  AMP PEAK 13(7Q31.2) MUTATED AMP PEAK 13(7Q31.2) WILD-TYPE 
                       114.35                        120.82 
  AMP PEAK 13(7Q31.2) MUTATED AMP PEAK 13(7Q31.2) WILD-TYPE 
                       19.890                        19.675 
[1] "0.3 - 114.3 (19.9)" "0.0 - 120.8 (19.7)"
[1] "hr=" "1"  
D13V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IIIA
  AMP PEAK 13(7Q31.2) MUTATED        52       31         0         22
  AMP PEAK 13(7Q31.2) WILD-TYPE     121       56         3         40
                               vv
clus                            STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 13(7Q31.2) MUTATED            3          5        1         0
  AMP PEAK 13(7Q31.2) WILD-TYPE          6          2        1         1
                               vv
clus                            STAGE IVB
  AMP PEAK 13(7Q31.2) MUTATED           0
  AMP PEAK 13(7Q31.2) WILD-TYPE         2
D13V3, multiclass
            clus
vv           AMP PEAK 13(7Q31.2) MUTATED AMP PEAK 13(7Q31.2) WILD-TYPE
  STAGE I                             52                           121
  STAGE II                            31                            56
  STAGE III                            0                             3
  STAGE IIIA                          22                            40
  STAGE IIIB                           3                             6
  STAGE IIIC                           5                             2
  STAGE IV                             1                             1
  STAGE IVA                            0                             1
  STAGE IVB                            0                             2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  AMP PEAK 13(7Q31.2) MUTATED    54  36  26   4
  AMP PEAK 13(7Q31.2) WILD-TYPE 129  59  51   8
D13V4, multiclass
    clus
vv   AMP PEAK 13(7Q31.2) MUTATED AMP PEAK 13(7Q31.2) WILD-TYPE
  T1                          54                           129
  T2                          36                            59
  T3                          26                            51
  T4                           4                             8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V5, binary
                               cls
clus                              0   1
  AMP PEAK 13(7Q31.2) MUTATED    79   2
  AMP PEAK 13(7Q31.2) WILD-TYPE 175   1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 13(7Q31.2) MUTATED     79    2
  AMP PEAK 13(7Q31.2) WILD-TYPE  175    1
   clus
vv  AMP PEAK 13(7Q31.2) MUTATED AMP PEAK 13(7Q31.2) WILD-TYPE
  0                          79                           175
  1                           2                             1
[1] 2 2
[1] FALSE
D13V6, binary
                               cls
clus                              0   1
  AMP PEAK 13(7Q31.2) MUTATED    87   1
  AMP PEAK 13(7Q31.2) WILD-TYPE 179   3
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 13(7Q31.2) MUTATED     87    1
  AMP PEAK 13(7Q31.2) WILD-TYPE  179    3
   clus
vv  AMP PEAK 13(7Q31.2) MUTATED AMP PEAK 13(7Q31.2) WILD-TYPE
  0                          87                           179
  1                           1                             3
[1] 2 2
[1] FALSE
D13V7, binary
                               cls
clus                              0   1
  AMP PEAK 13(7Q31.2) MUTATED    35  85
  AMP PEAK 13(7Q31.2) WILD-TYPE  83 167
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 13(7Q31.2) MUTATED     35   85
  AMP PEAK 13(7Q31.2) WILD-TYPE   83  167
        clus
vv       AMP PEAK 13(7Q31.2) MUTATED AMP PEAK 13(7Q31.2) WILD-TYPE
  FEMALE                          35                            83
  MALE                            85                           167
[1] 2 2
[1] FALSE
D13V8, binary
                               cls
clus                              0   1
  AMP PEAK 13(7Q31.2) MUTATED   109   4
  AMP PEAK 13(7Q31.2) WILD-TYPE 229   5
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 13(7Q31.2) MUTATED    109    4
  AMP PEAK 13(7Q31.2) WILD-TYPE  229    5
     clus
vv    AMP PEAK 13(7Q31.2) MUTATED AMP PEAK 13(7Q31.2) WILD-TYPE
  NO                          109                           229
  YES                           4                             5
[1] 2 2
[1] FALSE
                               vv
clus                            FIBROLAMELLAR CARCINOMA
  AMP PEAK 13(7Q31.2) MUTATED                         0
  AMP PEAK 13(7Q31.2) WILD-TYPE                       3
                               vv
clus                            HEPATOCELLULAR CARCINOMA
  AMP PEAK 13(7Q31.2) MUTATED                        119
  AMP PEAK 13(7Q31.2) WILD-TYPE                      241
                               vv
clus                            HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK 13(7Q31.2) MUTATED                                  1
  AMP PEAK 13(7Q31.2) WILD-TYPE                                6
D13V9, multiclass
                                  clus
vv                                 AMP PEAK 13(7Q31.2) MUTATED
  FIBROLAMELLAR CARCINOMA                                    0
  HEPATOCELLULAR CARCINOMA                                 119
  HEPATOCHOLANGIOCARCINOMA (MIXED)                           1
                                  clus
vv                                 AMP PEAK 13(7Q31.2) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                      3
  HEPATOCELLULAR CARCINOMA                                   241
  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 13(7Q31.2) MUTATED   105   7   0   6
  AMP PEAK 13(7Q31.2) WILD-TYPE 219  10   1  15
D13V10, multiclass
    clus
vv   AMP PEAK 13(7Q31.2) MUTATED AMP PEAK 13(7Q31.2) WILD-TYPE
  R0                         105                           219
  R1                           7                            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
  AMP PEAK 13(7Q31.2) MUTATED                                  2    46
  AMP PEAK 13(7Q31.2) WILD-TYPE                                0   112
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 13(7Q31.2) MUTATED                           5    65
  AMP PEAK 13(7Q31.2) WILD-TYPE                        12   118
D13V11, multiclass
                                  clus
vv                                 AMP PEAK 13(7Q31.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           2
  ASIAN                                                     46
  BLACK OR AFRICAN AMERICAN                                  5
  WHITE                                                     65
                                  clus
vv                                 AMP PEAK 13(7Q31.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                      112
  BLACK OR AFRICAN AMERICAN                                   12
  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"
D13V12, binary
                               cls
clus                              0   1
  AMP PEAK 13(7Q31.2) MUTATED     7 108
  AMP PEAK 13(7Q31.2) WILD-TYPE   9 227
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 13(7Q31.2) MUTATED      7  108
  AMP PEAK 13(7Q31.2) WILD-TYPE    9  227
                        clus
vv                       AMP PEAK 13(7Q31.2) MUTATED
  HISPANIC OR LATINO                               7
  NOT HISPANIC OR LATINO                         108
                        clus
vv                       AMP PEAK 13(7Q31.2) WILD-TYPE
  HISPANIC OR LATINO                                 9
  NOT HISPANIC OR LATINO                           227
[1] 2 2
[1] FALSE

Clustering(14) Variable = AMP PEAK 14(8Q24.21) MUTATION ANALYSIS
D14V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 14(8Q24.21) MUTATED   151  75
  AMP PEAK 14(8Q24.21) WILD-TYPE  84  54
  AMP PEAK 14(8Q24.21) MUTATED AMP PEAK 14(8Q24.21) WILD-TYPE 
                           226                            138 
  AMP PEAK 14(8Q24.21) MUTATED AMP PEAK 14(8Q24.21) WILD-TYPE 
                            75                             54 
$`AMP PEAK 14(8Q24.21) MUTATED`
TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV TCGA-DD-AAE7 
       36.66         0.36        90.28        26.83        18.87        21.17 
TCGA-DD-AAE8 TCGA-DD-AAEG TCGA-EP-A3JL TCGA-ES-A2HS TCGA-FV-A3I1 TCGA-FV-A3R2 
       21.83        23.64         9.96        22.62         8.12         6.38 
TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A3CG TCGA-KR-A7K7 TCGA-MI-A75H TCGA-2Y-A9GW 
       81.73        30.74        22.13        31.27        24.56        41.79 
TCGA-2Y-A9GX TCGA-2Y-A9GY TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H4 TCGA-2Y-A9H5 
       80.28        24.89        40.41        56.91        47.74        18.25 
TCGA-2Y-A9HA TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5R-AA1C TCGA-5R-AA1D 
        1.18        13.02        10.78        10.59        17.10        14.76 
TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W 
        1.51        48.99        46.78        27.52        27.52         2.99 
TCGA-BC-A3KF TCGA-BC-A69H TCGA-BD-A3EP TCGA-CC-5258 TCGA-CC-5261 TCGA-CC-5262 
        0.26        14.60        13.45         4.24         3.19         3.39 
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-A7IE TCGA-CC-A7IF TCGA-CC-A7IG 
       11.41         9.99         8.94         7.13        21.34         9.83 
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-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-A11C TCGA-DD-A1E9 TCGA-DD-A1EC TCGA-DD-A1EE 
        7.33         2.60        21.76        90.71        19.79        11.47 
TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EI TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X 
       12.95        45.11         6.02        13.64        21.14        55.69 
TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A1 TCGA-DD-A3A3 TCGA-DD-A3A7 TCGA-DD-A4NF 
        5.62        19.76         7.66        17.59        13.78        30.97 
TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NQ TCGA-DD-A4NR 
       30.51        39.78        29.56        73.81        12.26         0.30 
TCGA-DD-A4NS TCGA-DD-A73A TCGA-DD-A73D TCGA-DD-A73G TCGA-DD-AAC8 TCGA-DD-AAC9 
       80.75        23.93        22.78       114.35         0.53        11.41 
TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACD TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH 
       75.65        76.41        12.53        12.00        15.42         6.41 
TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP 
       53.19        69.11        58.16        42.81        61.68        13.64 
TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACW TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD0 
       59.31        51.35        46.82        47.67         5.62         4.50 
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-AAE9 
       18.21        18.25        18.15        18.61         4.64        23.74 
TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAEK 
       15.72        25.08        26.63        25.78        50.33        35.08 
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        60.99 
TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PY TCGA-ED-A7PZ 
       53.69        29.92        13.35         9.73        12.82         0.20 
TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A2KA 
       13.15        13.41         1.84         0.20        18.74        20.61 
TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A2QQ TCGA-FV-A3I0 
       19.59         0.62        11.93        14.40        23.97        27.88 
TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25X TCGA-G3-A25Z 
        0.39        51.06        53.79        28.27        58.49        21.53 
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-AAUZ TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV5 
       11.87        15.78        11.80        12.23        13.55        11.64 
TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-K7-AAU7 
        2.14        11.87        28.90         2.99        16.83        11.80 
TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75I 
       27.25        29.79        12.03         9.57        16.67        20.71 
TCGA-MR-A8JO TCGA-NI-A8LF TCGA-O8-A75V TCGA-RC-A6M4 TCGA-RC-A6M6 TCGA-RC-A7SF 
       10.85        26.27        17.69         0.72         0.30        19.04 
TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MC TCGA-UB-A7MD 
       15.39        15.52        36.10        27.88        16.44         1.71 
TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-YA-A8S7 
       15.98        10.75         0.99        12.99        20.22        13.55 
TCGA-ZP-A9CV TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CG 
       35.77        12.99        45.57        11.21 

$`AMP PEAK 14(8Q24.21) WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 
       83.24        11.74        38.40         8.61        69.57         5.03 
TCGA-BC-A5W4 TCGA-DD-AAEA TCGA-G3-A6UC TCGA-G3-A7M9 TCGA-K7-A5RF TCGA-KR-A7K0 
       17.98        18.90        22.06         1.84        20.75         2.14 
TCGA-LG-A6GG TCGA-T1-A6J8 TCGA-UB-A7MF TCGA-UB-AA0V TCGA-XR-A8TG TCGA-ZP-A9D1 
       12.72         0.76         7.04        10.32        29.52         0.69 
TCGA-ZS-A9CE TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GZ TCGA-2Y-A9H0 
       40.80        23.80        53.39        63.75        27.88       120.82 
TCGA-2Y-A9H3 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HB TCGA-5C-AAPD TCGA-BC-4073 
       49.84        20.81        22.92         8.55         0.66        27.91 
TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A216 
       37.32        10.13        25.32        23.38         1.12        44.42 
TCGA-BC-A217 TCGA-BC-A3KG TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BW-A5NO 
       45.93        22.36        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        71.80         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-AAVP TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A7PX 
       19.99        90.48        26.93        28.08        13.91         0.20 
TCGA-ED-A7XO TCGA-ED-A8O5 TCGA-EP-A26S TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3R3 
       14.04        13.35        19.99        60.89        19.10        12.03 
TCGA-FV-A495 TCGA-FV-A496 TCGA-G3-A25S TCGA-G3-A25Y TCGA-G3-A3CI TCGA-G3-A3CK 
        0.03         0.33        13.68        14.86         5.92        19.23 
TCGA-G3-A5SM TCGA-G3-A7M5 TCGA-G3-A7M8 TCGA-G3-AAV0 TCGA-G3-AAV4 TCGA-GJ-A6C0 
       17.10        14.70        14.14        15.65         0.89         1.02 
TCGA-GJ-A9DB TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-LG-A9QC TCGA-MI-A75G TCGA-MR-A520 
        2.20        37.71        17.06        13.97        22.95         7.53 
TCGA-NI-A4U2 TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A6M5 TCGA-RC-A7S9 TCGA-RC-A7SB 
       58.88        21.01         3.09         0.49        21.04        19.33 
TCGA-UB-A7MB TCGA-WJ-A86L TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TD TCGA-XR-A8TE 
       19.76        11.34        24.85        18.28        33.86        30.41 
TCGA-XR-A8TF TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZS-A9CF 
       22.78        25.71        23.21        35.87        25.15        79.30 

  AMP PEAK 14(8Q24.21) MUTATED AMP PEAK 14(8Q24.21) WILD-TYPE 
                          0.20                           0.03 
  AMP PEAK 14(8Q24.21) MUTATED AMP PEAK 14(8Q24.21) WILD-TYPE 
                        114.35                         120.82 
  AMP PEAK 14(8Q24.21) MUTATED AMP PEAK 14(8Q24.21) WILD-TYPE 
                        18.675                         20.995 
[1] "0.2 - 114.3 (18.7)" "0.0 - 120.8 (21.0)"
[1] "hr=" "1.1"
D14V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IIIA
  AMP PEAK 14(8Q24.21) MUTATED       110       61         0         42
  AMP PEAK 14(8Q24.21) WILD-TYPE      63       26         3         20
                                vv
clus                             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 14(8Q24.21) MUTATED            4          3        2         0
  AMP PEAK 14(8Q24.21) WILD-TYPE          5          4        0         1
                                vv
clus                             STAGE IVB
  AMP PEAK 14(8Q24.21) MUTATED           0
  AMP PEAK 14(8Q24.21) WILD-TYPE         2
D14V3, multiclass
            clus
vv           AMP PEAK 14(8Q24.21) MUTATED AMP PEAK 14(8Q24.21) WILD-TYPE
  STAGE I                             110                             63
  STAGE II                             61                             26
  STAGE III                             0                              3
  STAGE IIIA                           42                             20
  STAGE IIIB                            4                              5
  STAGE IIIC                            3                              4
  STAGE IV                              2                              0
  STAGE IVA                             0                              1
  STAGE IVB                             0                              2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  AMP PEAK 14(8Q24.21) MUTATED   112  64  48   6
  AMP PEAK 14(8Q24.21) WILD-TYPE  71  31  29   6
D14V4, multiclass
    clus
vv   AMP PEAK 14(8Q24.21) MUTATED AMP PEAK 14(8Q24.21) WILD-TYPE
  T1                          112                             71
  T2                           64                             31
  T3                           48                             29
  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"
D14V5, binary
                                cls
clus                               0   1
  AMP PEAK 14(8Q24.21) MUTATED   174   0
  AMP PEAK 14(8Q24.21) WILD-TYPE  80   3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 14(8Q24.21) MUTATED    174    0
  AMP PEAK 14(8Q24.21) WILD-TYPE   80    3
   clus
vv  AMP PEAK 14(8Q24.21) MUTATED AMP PEAK 14(8Q24.21) WILD-TYPE
  0                          174                             80
  1                            0                              3
[1] 2 2
[1] FALSE
D14V6, binary
                                cls
clus                               0   1
  AMP PEAK 14(8Q24.21) MUTATED   179   2
  AMP PEAK 14(8Q24.21) WILD-TYPE  87   2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 14(8Q24.21) MUTATED    179    2
  AMP PEAK 14(8Q24.21) WILD-TYPE   87    2
   clus
vv  AMP PEAK 14(8Q24.21) MUTATED AMP PEAK 14(8Q24.21) WILD-TYPE
  0                          179                             87
  1                            2                              2
[1] 2 2
[1] FALSE
D14V7, binary
                                cls
clus                               0   1
  AMP PEAK 14(8Q24.21) MUTATED    57 174
  AMP PEAK 14(8Q24.21) WILD-TYPE  61  78
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 14(8Q24.21) MUTATED     57  174
  AMP PEAK 14(8Q24.21) WILD-TYPE   61   78
        clus
vv       AMP PEAK 14(8Q24.21) MUTATED AMP PEAK 14(8Q24.21) WILD-TYPE
  FEMALE                           57                             61
  MALE                            174                             78
[1] 2 2
[1] FALSE
D14V8, binary
                                cls
clus                               0   1
  AMP PEAK 14(8Q24.21) MUTATED   209   7
  AMP PEAK 14(8Q24.21) WILD-TYPE 129   2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 14(8Q24.21) MUTATED    209    7
  AMP PEAK 14(8Q24.21) WILD-TYPE  129    2
     clus
vv    AMP PEAK 14(8Q24.21) MUTATED AMP PEAK 14(8Q24.21) WILD-TYPE
  NO                           209                            129
  YES                            7                              2
[1] 2 2
[1] FALSE
                                vv
clus                             FIBROLAMELLAR CARCINOMA
  AMP PEAK 14(8Q24.21) MUTATED                         1
  AMP PEAK 14(8Q24.21) WILD-TYPE                       2
                                vv
clus                             HEPATOCELLULAR CARCINOMA
  AMP PEAK 14(8Q24.21) MUTATED                        225
  AMP PEAK 14(8Q24.21) WILD-TYPE                      135
                                vv
clus                             HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK 14(8Q24.21) MUTATED                                  5
  AMP PEAK 14(8Q24.21) WILD-TYPE                                2
D14V9, multiclass
                                  clus
vv                                 AMP PEAK 14(8Q24.21) MUTATED
  FIBROLAMELLAR CARCINOMA                                     1
  HEPATOCELLULAR CARCINOMA                                  225
  HEPATOCHOLANGIOCARCINOMA (MIXED)                            5
                                  clus
vv                                 AMP PEAK 14(8Q24.21) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                       2
  HEPATOCELLULAR CARCINOMA                                    135
  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 14(8Q24.21) MUTATED   201  13   1  12
  AMP PEAK 14(8Q24.21) WILD-TYPE 123   4   0   9
D14V10, multiclass
    clus
vv   AMP PEAK 14(8Q24.21) MUTATED AMP PEAK 14(8Q24.21) WILD-TYPE
  R0                          201                            123
  R1                           13                              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 14(8Q24.21) MUTATED                                  2   119
  AMP PEAK 14(8Q24.21) WILD-TYPE                                0    39
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 14(8Q24.21) MUTATED                          11    92
  AMP PEAK 14(8Q24.21) WILD-TYPE                         6    91
D14V11, multiclass
                                  clus
vv                                 AMP PEAK 14(8Q24.21) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            2
  ASIAN                                                     119
  BLACK OR AFRICAN AMERICAN                                  11
  WHITE                                                      92
                                  clus
vv                                 AMP PEAK 14(8Q24.21) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                        39
  BLACK OR AFRICAN AMERICAN                                     6
  WHITE                                                        91
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V12, binary
                                cls
clus                               0   1
  AMP PEAK 14(8Q24.21) MUTATED     7 214
  AMP PEAK 14(8Q24.21) WILD-TYPE   9 121
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 14(8Q24.21) MUTATED      7  214
  AMP PEAK 14(8Q24.21) WILD-TYPE    9  121
                        clus
vv                       AMP PEAK 14(8Q24.21) MUTATED
  HISPANIC OR LATINO                                7
  NOT HISPANIC OR LATINO                          214
                        clus
vv                       AMP PEAK 14(8Q24.21) WILD-TYPE
  HISPANIC OR LATINO                                  9
  NOT HISPANIC OR LATINO                            121
[1] 2 2
[1] FALSE

Clustering(15) Variable = AMP PEAK 15(9Q34.2) MUTATION ANALYSIS
D15V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 15(9Q34.2) MUTATED    27  18
  AMP PEAK 15(9Q34.2) WILD-TYPE 208 111
  AMP PEAK 15(9Q34.2) MUTATED AMP PEAK 15(9Q34.2) WILD-TYPE 
                           45                           319 
  AMP PEAK 15(9Q34.2) MUTATED AMP PEAK 15(9Q34.2) WILD-TYPE 
                           18                           111 
$`AMP PEAK 15(9Q34.2) MUTATED`
TCGA-ES-A2HS TCGA-FV-A4ZP TCGA-G3-A3CG TCGA-G3-A7M9 TCGA-XR-A8TG TCGA-2Y-A9GY 
       22.62        81.73        22.13         1.84        29.52        24.89 
TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H9 TCGA-5R-AA1C TCGA-BC-A10T TCGA-BC-A10Y 
       27.88       120.82        22.92        17.10        27.52        23.38 
TCGA-BC-A8YO TCGA-BW-A5NO TCGA-CC-5261 TCGA-CC-5263 TCGA-CC-5264 TCGA-CC-A7IG 
       18.48         0.66         3.19         4.24         3.35         9.83 
TCGA-CC-A7II TCGA-CC-A7IK TCGA-DD-A1EG TCGA-DD-A3A0 TCGA-DD-A3A5 TCGA-DD-A3A6 
       13.12         8.61        45.11        25.81       102.74       107.11 
TCGA-DD-A4NV TCGA-DD-A73G TCGA-DD-AACY TCGA-DD-AAD6 TCGA-DD-AADJ TCGA-DD-AADO 
       78.84       114.35        47.67        22.09        35.05        14.89 
TCGA-DD-AAE0 TCGA-DD-AAE2 TCGA-DD-AAVV TCGA-DD-AAVZ TCGA-ED-A66Y TCGA-ED-A82E 
       18.25        20.98        80.71        62.47         9.73        13.41 
TCGA-EP-A2KB TCGA-FV-A2QQ TCGA-FV-A495 TCGA-G3-A25U TCGA-KR-A7K2 TCGA-KR-A7K8 
       19.59        23.97         0.03        53.79        27.25        29.79 
TCGA-RC-A6M6 TCGA-WQ-A9G7 TCGA-ZS-A9CF 
        0.30         0.99        79.30 

$`AMP PEAK 15(9Q34.2) WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 
       83.24        11.74        38.40         8.61        69.57         5.03 
TCGA-BC-A5W4 TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV 
       17.98        36.66         0.36        90.28        26.83        18.87 
TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-FV-A3I1 
       21.17        21.83        18.90        23.64         9.96         8.12 
TCGA-FV-A3R2 TCGA-G3-A25W TCGA-G3-A6UC TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-KR-A7K7 
        6.38        30.74        22.06        20.75         2.14        31.27 
TCGA-LG-A6GG TCGA-MI-A75H TCGA-T1-A6J8 TCGA-UB-A7MF TCGA-UB-AA0V TCGA-ZP-A9D1 
       12.72        24.56         0.76         7.04        10.32         0.69 
TCGA-ZS-A9CE TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX 
       40.80        23.80        53.39        63.75        41.79        80.28 
TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H8 
       40.41        56.91        49.84        47.74        18.25        20.81 
TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD 
        1.18         8.55        13.02        10.78        10.59         0.66 
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-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Z TCGA-BC-A216 
       46.78        27.52         2.99        25.32         1.12        44.42 
TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A69I TCGA-BD-A2L6 
       45.93         0.26        22.36        14.60        12.72        44.81 
TCGA-BD-A3EP TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5262 TCGA-CC-A1HT TCGA-CC-A3M9 
       13.45         4.24         2.86         3.39         3.32         9.86 
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-A7IH TCGA-CC-A7IJ TCGA-CC-A7IL TCGA-CC-A8HT 
        7.13        21.34        12.00        12.56         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-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B 
       83.57        53.33       113.00         7.33         2.60         0.46 
TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC 
       21.76        51.29        90.71        79.40        66.31        19.79 
TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ 
       75.65        11.47        12.95        49.15         6.02        33.04 
TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Y 
       18.35        13.64        21.14        27.19        55.69         5.62 
TCGA-DD-A39Z TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A7 
       19.76         7.66        70.06        17.59        20.12        13.78 
TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NJ 
       30.61        33.14        32.52        30.97        30.15        30.51 
TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ 
       39.78        56.25        29.56        73.81       108.76        12.26 
TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D 
        0.30        80.75        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        71.80        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-AACZ TCGA-DD-AAD0 
       51.52        50.33        46.82         5.59         5.62         4.50 
TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD8 TCGA-DD-AADA 
       18.54        21.63        42.58        44.22        40.08        40.54 
TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG 
       40.83        13.97        40.47        39.52         3.78        37.64 
TCGA-DD-AADI TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADP 
       35.67        34.49        20.91         0.39        29.52        15.06 
TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY 
       14.33        66.67        15.58        18.21        19.30        18.25 
TCGA-DD-AAE1 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE9 TCGA-DD-AAEB 
       18.15        18.61        19.99         4.64        23.74        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        90.48 
TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVX 
       89.69        82.62        59.93        72.39        76.18        56.48 
TCGA-DD-AAVY TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 
       64.77        66.25        65.39        60.99        53.69        29.92 
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-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K 
        0.20        14.04        13.15        13.35         1.84         0.20 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HT 
       18.74        19.99        20.61         0.62        11.93        14.40 
TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A496 TCGA-FV-A4ZQ 
       60.89        19.10        27.88        12.03         0.33         0.39 
TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25V TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z 
       13.68        51.06        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-A5SJ 
       25.64         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-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 
       11.64         2.14        11.87        28.90         1.02         2.20 
TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-LG-A9QC 
        2.99        37.71        17.06        16.83        11.80        13.97 
TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A520 
       12.03         9.57        16.67        22.95        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-A6M4 TCGA-RC-A6M5 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH 
        0.72         0.49        21.04        19.33        19.04        15.39 
TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD 
       15.52        36.10        27.88        19.76        16.44         1.71 
TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-WX-AA46 
       15.98        10.75        11.34        12.99        20.22        24.85 
TCGA-WX-AA47 TCGA-XR-A8TD TCGA-XR-A8TE TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CV 
       18.28        33.86        30.41        22.78        13.55        35.77 
TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD 
       25.71        23.21        35.87        25.15        12.99        45.57 
TCGA-ZS-A9CG 
       11.21 

  AMP PEAK 15(9Q34.2) MUTATED AMP PEAK 15(9Q34.2) WILD-TYPE 
                         0.03                          0.20 
  AMP PEAK 15(9Q34.2) MUTATED AMP PEAK 15(9Q34.2) WILD-TYPE 
                       120.82                        113.00 
  AMP PEAK 15(9Q34.2) MUTATED AMP PEAK 15(9Q34.2) WILD-TYPE 
                        22.92                         19.30 
[1] "0.0 - 120.8 (22.9)" "0.2 - 113.0 (19.3)"
[1] "hr=" "1.1"
D15V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IIIA
  AMP PEAK 15(9Q34.2) MUTATED        17       10         1         13
  AMP PEAK 15(9Q34.2) WILD-TYPE     156       77         2         49
                               vv
clus                            STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 15(9Q34.2) MUTATED            1          1        1         0
  AMP PEAK 15(9Q34.2) WILD-TYPE          8          6        1         1
                               vv
clus                            STAGE IVB
  AMP PEAK 15(9Q34.2) MUTATED           0
  AMP PEAK 15(9Q34.2) WILD-TYPE         2
D15V3, multiclass
            clus
vv           AMP PEAK 15(9Q34.2) MUTATED AMP PEAK 15(9Q34.2) WILD-TYPE
  STAGE I                             17                           156
  STAGE II                            10                            77
  STAGE III                            1                             2
  STAGE IIIA                          13                            49
  STAGE IIIB                           1                             8
  STAGE IIIC                           1                             6
  STAGE IV                             1                             1
  STAGE IVA                            0                             1
  STAGE IVB                            0                             2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  AMP PEAK 15(9Q34.2) MUTATED    17  11  16   3
  AMP PEAK 15(9Q34.2) WILD-TYPE 166  84  61   9
D15V4, multiclass
    clus
vv   AMP PEAK 15(9Q34.2) MUTATED AMP PEAK 15(9Q34.2) WILD-TYPE
  T1                          17                           166
  T2                          11                            84
  T3                          16                            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"
D15V5, binary
                               cls
clus                              0   1
  AMP PEAK 15(9Q34.2) MUTATED    32   0
  AMP PEAK 15(9Q34.2) WILD-TYPE 222   3
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 15(9Q34.2) MUTATED     32    0
  AMP PEAK 15(9Q34.2) WILD-TYPE  222    3
   clus
vv  AMP PEAK 15(9Q34.2) MUTATED AMP PEAK 15(9Q34.2) WILD-TYPE
  0                          32                           222
  1                           0                             3
[1] 2 2
[1] FALSE
D15V6, binary
                               cls
clus                              0   1
  AMP PEAK 15(9Q34.2) MUTATED    35   1
  AMP PEAK 15(9Q34.2) WILD-TYPE 231   3
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 15(9Q34.2) MUTATED     35    1
  AMP PEAK 15(9Q34.2) WILD-TYPE  231    3
   clus
vv  AMP PEAK 15(9Q34.2) MUTATED AMP PEAK 15(9Q34.2) WILD-TYPE
  0                          35                           231
  1                           1                             3
[1] 2 2
[1] FALSE
D15V7, binary
                               cls
clus                              0   1
  AMP PEAK 15(9Q34.2) MUTATED    16  31
  AMP PEAK 15(9Q34.2) WILD-TYPE 102 221
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 15(9Q34.2) MUTATED     16   31
  AMP PEAK 15(9Q34.2) WILD-TYPE  102  221
        clus
vv       AMP PEAK 15(9Q34.2) MUTATED AMP PEAK 15(9Q34.2) WILD-TYPE
  FEMALE                          16                           102
  MALE                            31                           221
[1] 2 2
[1] FALSE
D15V8, binary
                               cls
clus                              0   1
  AMP PEAK 15(9Q34.2) MUTATED    42   1
  AMP PEAK 15(9Q34.2) WILD-TYPE 296   8
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 15(9Q34.2) MUTATED     42    1
  AMP PEAK 15(9Q34.2) WILD-TYPE  296    8
     clus
vv    AMP PEAK 15(9Q34.2) MUTATED AMP PEAK 15(9Q34.2) WILD-TYPE
  NO                           42                           296
  YES                           1                             8
[1] 2 2
[1] FALSE
                               vv
clus                            FIBROLAMELLAR CARCINOMA
  AMP PEAK 15(9Q34.2) MUTATED                         0
  AMP PEAK 15(9Q34.2) WILD-TYPE                       3
                               vv
clus                            HEPATOCELLULAR CARCINOMA
  AMP PEAK 15(9Q34.2) MUTATED                         46
  AMP PEAK 15(9Q34.2) WILD-TYPE                      314
                               vv
clus                            HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK 15(9Q34.2) MUTATED                                  1
  AMP PEAK 15(9Q34.2) WILD-TYPE                                6
D15V9, multiclass
                                  clus
vv                                 AMP PEAK 15(9Q34.2) MUTATED
  FIBROLAMELLAR CARCINOMA                                    0
  HEPATOCELLULAR CARCINOMA                                  46
  HEPATOCHOLANGIOCARCINOMA (MIXED)                           1
                                  clus
vv                                 AMP PEAK 15(9Q34.2) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                      3
  HEPATOCELLULAR CARCINOMA                                   314
  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 15(9Q34.2) MUTATED    38   4   0   5
  AMP PEAK 15(9Q34.2) WILD-TYPE 286  13   1  16
D15V10, multiclass
    clus
vv   AMP PEAK 15(9Q34.2) MUTATED AMP PEAK 15(9Q34.2) WILD-TYPE
  R0                          38                           286
  R1                           4                            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 15(9Q34.2) MUTATED                                  0    18
  AMP PEAK 15(9Q34.2) WILD-TYPE                                2   140
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 15(9Q34.2) MUTATED                           1    27
  AMP PEAK 15(9Q34.2) WILD-TYPE                        16   156
D15V11, multiclass
                                  clus
vv                                 AMP PEAK 15(9Q34.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                     18
  BLACK OR AFRICAN AMERICAN                                  1
  WHITE                                                     27
                                  clus
vv                                 AMP PEAK 15(9Q34.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             2
  ASIAN                                                      140
  BLACK OR AFRICAN AMERICAN                                   16
  WHITE                                                      156
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V12, binary
                               cls
clus                              0   1
  AMP PEAK 15(9Q34.2) MUTATED     3  42
  AMP PEAK 15(9Q34.2) WILD-TYPE  13 293
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 15(9Q34.2) MUTATED      3   42
  AMP PEAK 15(9Q34.2) WILD-TYPE   13  293
                        clus
vv                       AMP PEAK 15(9Q34.2) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                          42
                        clus
vv                       AMP PEAK 15(9Q34.2) WILD-TYPE
  HISPANIC OR LATINO                                13
  NOT HISPANIC OR LATINO                           293
[1] 2 2
[1] FALSE

Clustering(16) Variable = AMP PEAK 16(10P15.1) MUTATION ANALYSIS
D16V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 16(10P15.1) MUTATED    39  32
  AMP PEAK 16(10P15.1) WILD-TYPE 196  97
  AMP PEAK 16(10P15.1) MUTATED AMP PEAK 16(10P15.1) WILD-TYPE 
                            71                            293 
  AMP PEAK 16(10P15.1) MUTATED AMP PEAK 16(10P15.1) WILD-TYPE 
                            32                             97 
$`AMP PEAK 16(10P15.1) MUTATED`
TCGA-BD-A3ER TCGA-DD-AAE8 TCGA-DD-AAEG TCGA-ES-A2HS TCGA-2Y-A9GS TCGA-2Y-A9HA 
       36.66        21.83        23.64        22.62        23.80         1.18 
TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A217 
       13.02        10.78        37.32        10.13        27.52        45.93 
TCGA-BD-A3EP TCGA-CC-5264 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A5UC TCGA-CC-A5UD 
       13.45         3.35         9.96        10.36        11.41         9.99 
TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7IJ TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV 
        9.83        12.00        12.56         4.60        11.31         9.17 
TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A3A7 
        8.15        79.73        37.78        18.35        13.64        13.78 
TCGA-DD-A3A9 TCGA-DD-A4NQ TCGA-DD-A4NV TCGA-DD-A73D TCGA-DD-A73G TCGA-DD-AACB 
       30.61        12.26        78.84        22.78       114.35        76.41 
TCGA-DD-AACV TCGA-DD-AACZ TCGA-DD-AAD5 TCGA-DD-AADD TCGA-DD-AADF TCGA-DD-AADN 
       50.33         5.62        44.22        40.47         3.78        29.52 
TCGA-DD-AADW TCGA-DD-AAE3 TCGA-DD-AAE9 TCGA-DD-AAEK TCGA-DD-AAVR TCGA-ED-A459 
       19.30        18.61        23.74        35.08        82.62        29.92 
TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7XO TCGA-ED-A82E TCGA-ED-A8O6 TCGA-EP-A2KA 
       13.35         9.73        14.04        13.41         1.84        20.61 
TCGA-EP-A2KB TCGA-FV-A4ZQ TCGA-G3-A25X TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM 
       19.59         0.39        58.49        22.95        20.42        17.10 
TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-GJ-A6C0 TCGA-MR-A8JO TCGA-RC-A6M6 TCGA-RC-A7SK 
       11.64         2.14         1.02        10.85         0.30        15.52 
TCGA-UB-A7MA TCGA-UB-A7ME TCGA-UB-AA0U TCGA-XR-A8TF TCGA-YA-A8S7 
       27.88        15.98        10.75        22.78        13.55 

$`AMP PEAK 16(10P15.1) WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 
       83.24        11.74        38.40         8.61        69.57         5.03 
TCGA-BC-A5W4 TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV TCGA-DD-AAE7 
       17.98         0.36        90.28        26.83        18.87        21.17 
TCGA-DD-AAEA TCGA-EP-A3JL TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25W 
       18.90         9.96         8.12         6.38        81.73        30.74 
TCGA-G3-A3CG TCGA-G3-A6UC TCGA-G3-A7M9 TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-KR-A7K7 
       22.13        22.06         1.84        20.75         2.14        31.27 
TCGA-LG-A6GG TCGA-MI-A75H TCGA-T1-A6J8 TCGA-UB-A7MF TCGA-UB-AA0V TCGA-XR-A8TG 
       12.72        24.56         0.76         7.04        10.32        29.52 
TCGA-ZP-A9D1 TCGA-ZS-A9CE TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX 
        0.69        40.80        53.39        63.75        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-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HB TCGA-5C-A9VH 
       47.74        18.25        20.81        22.92         8.55        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-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-BW-A5NO TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
       44.81         0.66         4.24         2.86         3.19         3.39 
TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MC TCGA-CC-A5UE TCGA-CC-A7IE 
        4.24         3.32         9.86        11.93         8.94         7.13 
TCGA-CC-A7IF TCGA-CC-A7II TCGA-CC-A7IK TCGA-CC-A7IL TCGA-CC-A9FS TCGA-DD-A115 
       21.34        13.12         8.61         9.14         6.94        83.57 
TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C 
       53.33       113.00         7.33         2.60         0.46        21.76 
TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED 
       51.29        90.71        79.40        66.31        19.79        75.65 
TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ 
       11.47        12.95        45.11        49.15         6.02        33.04 
TCGA-DD-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-A4NA TCGA-DD-A4NB TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK 
       33.14        32.52        30.97        30.15        30.51        39.78 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NR TCGA-DD-A4NS 
       56.25        29.56        73.81       108.76         0.30        80.75 
TCGA-DD-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-AACC TCGA-DD-AACD TCGA-DD-AACE 
        0.53        11.41        75.65        55.40        12.53        71.80 
TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK 
       12.00        15.42         6.41        53.19        69.11         0.30 
TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ 
        3.52        58.16        42.81        61.68        13.64        14.20 
TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY 
       59.31        51.35        51.52        46.82         5.59        47.67 
TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD6 TCGA-DD-AAD8 
        4.50        18.54        21.63        42.58        22.09        40.08 
TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADE TCGA-DD-AADG TCGA-DD-AADI 
       40.54        40.83        13.97        39.52        37.64        35.67 
TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADO TCGA-DD-AADP 
       35.05        34.49        20.91         0.39        14.89        15.06 
TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADY TCGA-DD-AAE0 
       14.33        66.67        15.58        18.21        18.25        18.25 
TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAEB TCGA-DD-AAED 
       18.15        20.98        19.99         4.64        15.72        25.08 
TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVS 
       26.63        25.78        50.33        90.48        89.69        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        60.99        53.69        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-A2KC TCGA-EP-A3RK TCGA-ES-A2HT 
        0.20        18.74        19.99         0.62        11.93        14.40 
TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A495 
       60.89        23.97        19.10        27.88        12.03         0.03 
TCGA-FV-A496 TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25Y 
        0.33        13.68        51.06        53.79        28.27        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-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-AAV7 TCGA-GJ-A3OU 
       11.80        12.23        13.55         0.89        11.87        28.90 
TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 
        2.20         2.99        37.71        17.06        16.83        11.80 
TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E 
       27.25        29.79        13.97        12.03         9.57        16.67 
TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A520 TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V 
       22.95        20.71         7.53        58.88        26.27        17.69 
TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A6M4 TCGA-RC-A6M5 TCGA-RC-A7S9 TCGA-RC-A7SB 
       21.01         3.09         0.72         0.49        21.04        19.33 
TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RG-A7D4 TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD 
       19.04        15.39        36.10        19.76        16.44         1.71 
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-A8TD TCGA-XR-A8TE TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 
       33.86        30.41        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 

  AMP PEAK 16(10P15.1) MUTATED AMP PEAK 16(10P15.1) WILD-TYPE 
                          0.30                           0.03 
  AMP PEAK 16(10P15.1) MUTATED AMP PEAK 16(10P15.1) WILD-TYPE 
                        114.35                         120.82 
  AMP PEAK 16(10P15.1) MUTATED AMP PEAK 16(10P15.1) WILD-TYPE 
                         15.52                          20.75 
[1] "0.3 - 114.3 (15.5)" "0.0 - 120.8 (20.8)"
[1] "hr=" "1.6"
D16V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IIIA
  AMP PEAK 16(10P15.1) MUTATED        23       22         0         19
  AMP PEAK 16(10P15.1) WILD-TYPE     150       65         3         43
                                vv
clus                             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 16(10P15.1) MUTATED            2          0        0         0
  AMP PEAK 16(10P15.1) WILD-TYPE          7          7        2         1
                                vv
clus                             STAGE IVB
  AMP PEAK 16(10P15.1) MUTATED           2
  AMP PEAK 16(10P15.1) WILD-TYPE         0
D16V3, multiclass
            clus
vv           AMP PEAK 16(10P15.1) MUTATED AMP PEAK 16(10P15.1) WILD-TYPE
  STAGE I                              23                            150
  STAGE II                             22                             65
  STAGE III                             0                              3
  STAGE IIIA                           19                             43
  STAGE IIIB                            2                              7
  STAGE IIIC                            0                              7
  STAGE IV                              0                              2
  STAGE IVA                             0                              1
  STAGE IVB                             2                              0
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  AMP PEAK 16(10P15.1) MUTATED    23  24  22   3
  AMP PEAK 16(10P15.1) WILD-TYPE 160  71  55   9
D16V4, multiclass
    clus
vv   AMP PEAK 16(10P15.1) MUTATED AMP PEAK 16(10P15.1) WILD-TYPE
  T1                           23                            160
  T2                           24                             71
  T3                           22                             55
  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"
D16V5, binary
                                cls
clus                               0   1
  AMP PEAK 16(10P15.1) MUTATED    49   0
  AMP PEAK 16(10P15.1) WILD-TYPE 205   3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(10P15.1) MUTATED     49    0
  AMP PEAK 16(10P15.1) WILD-TYPE  205    3
   clus
vv  AMP PEAK 16(10P15.1) MUTATED AMP PEAK 16(10P15.1) WILD-TYPE
  0                           49                            205
  1                            0                              3
[1] 2 2
[1] FALSE
D16V6, binary
                                cls
clus                               0   1
  AMP PEAK 16(10P15.1) MUTATED    52   2
  AMP PEAK 16(10P15.1) WILD-TYPE 214   2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(10P15.1) MUTATED     52    2
  AMP PEAK 16(10P15.1) WILD-TYPE  214    2
   clus
vv  AMP PEAK 16(10P15.1) MUTATED AMP PEAK 16(10P15.1) WILD-TYPE
  0                           52                            214
  1                            2                              2
[1] 2 2
[1] FALSE
D16V7, binary
                                cls
clus                               0   1
  AMP PEAK 16(10P15.1) MUTATED    24  48
  AMP PEAK 16(10P15.1) WILD-TYPE  94 204
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(10P15.1) MUTATED     24   48
  AMP PEAK 16(10P15.1) WILD-TYPE   94  204
        clus
vv       AMP PEAK 16(10P15.1) MUTATED AMP PEAK 16(10P15.1) WILD-TYPE
  FEMALE                           24                             94
  MALE                             48                            204
[1] 2 2
[1] FALSE
D16V8, binary
                                cls
clus                               0   1
  AMP PEAK 16(10P15.1) MUTATED    65   2
  AMP PEAK 16(10P15.1) WILD-TYPE 273   7
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(10P15.1) MUTATED     65    2
  AMP PEAK 16(10P15.1) WILD-TYPE  273    7
     clus
vv    AMP PEAK 16(10P15.1) MUTATED AMP PEAK 16(10P15.1) WILD-TYPE
  NO                            65                            273
  YES                            2                              7
[1] 2 2
[1] FALSE
                                vv
clus                             FIBROLAMELLAR CARCINOMA
  AMP PEAK 16(10P15.1) MUTATED                         1
  AMP PEAK 16(10P15.1) WILD-TYPE                       2
                                vv
clus                             HEPATOCELLULAR CARCINOMA
  AMP PEAK 16(10P15.1) MUTATED                         70
  AMP PEAK 16(10P15.1) WILD-TYPE                      290
                                vv
clus                             HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK 16(10P15.1) MUTATED                                  1
  AMP PEAK 16(10P15.1) WILD-TYPE                                6
D16V9, multiclass
                                  clus
vv                                 AMP PEAK 16(10P15.1) MUTATED
  FIBROLAMELLAR CARCINOMA                                     1
  HEPATOCELLULAR CARCINOMA                                   70
  HEPATOCHOLANGIOCARCINOMA (MIXED)                            1
                                  clus
vv                                 AMP PEAK 16(10P15.1) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                       2
  HEPATOCELLULAR CARCINOMA                                    290
  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 16(10P15.1) MUTATED    63   5   0   4
  AMP PEAK 16(10P15.1) WILD-TYPE 261  12   1  17
D16V10, multiclass
    clus
vv   AMP PEAK 16(10P15.1) MUTATED AMP PEAK 16(10P15.1) WILD-TYPE
  R0                           63                            261
  R1                            5                             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 16(10P15.1) MUTATED                                  0    36
  AMP PEAK 16(10P15.1) WILD-TYPE                                2   122
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 16(10P15.1) MUTATED                           4    31
  AMP PEAK 16(10P15.1) WILD-TYPE                        13   152
D16V11, multiclass
                                  clus
vv                                 AMP PEAK 16(10P15.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                      36
  BLACK OR AFRICAN AMERICAN                                   4
  WHITE                                                      31
                                  clus
vv                                 AMP PEAK 16(10P15.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              2
  ASIAN                                                       122
  BLACK OR AFRICAN AMERICAN                                    13
  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"
D16V12, binary
                                cls
clus                               0   1
  AMP PEAK 16(10P15.1) MUTATED     4  65
  AMP PEAK 16(10P15.1) WILD-TYPE  12 270
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(10P15.1) MUTATED      4   65
  AMP PEAK 16(10P15.1) WILD-TYPE   12  270
                        clus
vv                       AMP PEAK 16(10P15.1) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                           65
                        clus
vv                       AMP PEAK 16(10P15.1) WILD-TYPE
  HISPANIC OR LATINO                                 12
  NOT HISPANIC OR LATINO                            270
[1] 2 2
[1] FALSE

Clustering(17) Variable = AMP PEAK 17(11Q13.3) MUTATION ANALYSIS
D17V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 17(11Q13.3) MUTATED    38  17
  AMP PEAK 17(11Q13.3) WILD-TYPE 197 112
  AMP PEAK 17(11Q13.3) MUTATED AMP PEAK 17(11Q13.3) WILD-TYPE 
                            55                            309 
  AMP PEAK 17(11Q13.3) MUTATED AMP PEAK 17(11Q13.3) WILD-TYPE 
                            17                            112 
$`AMP PEAK 17(11Q13.3) MUTATED`
TCGA-BD-A3ER TCGA-DD-A4ND TCGA-DD-AADV TCGA-G3-A25W TCGA-G3-A3CG TCGA-LG-A6GG 
       36.66        90.28        18.87        30.74        22.13        12.72 
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-CC-5264 TCGA-CC-A3M9 TCGA-CC-A3MB 
       22.36        12.72        13.45         3.35         9.86        10.36 
TCGA-CC-A7IE TCGA-CC-A7II TCGA-CC-A7IJ TCGA-DD-A115 TCGA-DD-A119 TCGA-DD-A11A 
        7.13        13.12        12.56        83.57         7.33         2.60 
TCGA-DD-A1EB TCGA-DD-A39Y TCGA-DD-A3A0 TCGA-DD-A4NN TCGA-DD-A4NV TCGA-DD-A73E 
       66.31         5.62        25.81        29.56        78.84         1.45 
TCGA-DD-A73G TCGA-DD-AACB TCGA-DD-AAD1 TCGA-DD-AAD8 TCGA-DD-AADL TCGA-DD-AADP 
      114.35        76.41        18.54        40.08        20.91        15.06 
TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE6 TCGA-DD-AAED TCGA-ED-A66Y TCGA-ED-A82E 
       18.25        18.25         4.64        25.08         9.73        13.41 
TCGA-EP-A2KA TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A5SJ TCGA-G3-AAV0 
       20.61         0.33         0.39        13.68        22.95        15.65 
TCGA-GJ-A9DB TCGA-K7-A5RG TCGA-KR-A7K8 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-UB-A7ME 
        2.20        17.06        29.79        19.33        19.04        15.98 
TCGA-WQ-A9G7 
        0.99 

$`AMP PEAK 17(11Q13.3) WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 
       83.24        11.74        38.40         8.61        69.57         5.03 
TCGA-BC-A5W4 TCGA-DD-A3A8 TCGA-DD-A4NI TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEA 
       17.98         0.36        26.83        21.17        21.83        18.90 
TCGA-DD-AAEG TCGA-EP-A3JL TCGA-ES-A2HS TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A4ZP 
       23.64         9.96        22.62         8.12         6.38        81.73 
TCGA-G3-A6UC TCGA-G3-A7M9 TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-MI-A75H 
       22.06         1.84        20.75         2.14        31.27        24.56 
TCGA-T1-A6J8 TCGA-UB-A7MF TCGA-UB-AA0V TCGA-XR-A8TG TCGA-ZP-A9D1 TCGA-ZS-A9CE 
        0.76         7.04        10.32        29.52         0.69        40.80 
TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GY TCGA-2Y-A9H0 TCGA-2Y-A9H1 
       63.75        41.79        80.28        24.89       120.82        40.41 
TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-2Y-A9HA 
       56.91        49.84        47.74        18.25        20.81         1.18 
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-A10Q TCGA-BC-A10R TCGA-BC-A10S 
       14.76         1.51        48.99        37.32        10.13        46.78 
TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A216 
       27.52         2.99        25.32        23.38         1.12        44.42 
TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A69H TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BW-A5NO 
       45.93         0.26        14.60        18.48        44.81         0.66 
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-A3MC TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IF 
        9.96        11.93        11.41         9.99         8.94        21.34 
TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7IK TCGA-CC-A7IL TCGA-CC-A8HT TCGA-CC-A8HU 
        9.83        12.00         8.61         9.14         4.60        11.31 
TCGA-CC-A8HV TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A116 
        9.17         6.94         8.15        79.73        37.78        53.33 
TCGA-DD-A118 TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA 
      113.00         0.46        21.76        51.29        90.71        79.40 
TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH 
       19.79        75.65        11.47        12.95        45.11        49.15 
TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W 
        6.02        33.04        18.35        13.64        21.14        27.19 
TCGA-DD-A39X TCGA-DD-A39Z TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 
       55.69        19.76         7.66        70.06        17.59        20.12 
TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB 
      102.74       107.11        13.78        30.61        33.14        32.52 
TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NO 
       30.97        30.15        30.51        39.78        56.25        73.81 
TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A73A TCGA-DD-A73B 
      108.76        12.26         0.30        80.75        23.93         9.30 
TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73F TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 
       23.05        22.78        35.67        13.48         0.53        11.41 
TCGA-DD-AACA TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG 
       75.65        55.40        12.53        71.80        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-AACZ 
       51.52        50.33        46.82         5.59        47.67         5.62 
TCGA-DD-AAD0 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AADA 
        4.50        21.63        42.58        44.22        22.09        40.54 
TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG 
       40.83        13.97        40.47        39.52         3.78        37.64 
TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO 
       35.67        35.05        34.49         0.39        29.52        14.89 
TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AAE1 
       14.33        66.67        15.58        18.21        19.30        18.15 
TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAEE 
       20.98        18.61        19.99        23.74        15.72        26.63 
TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR 
       25.78        50.33        35.08        90.48        89.69        82.62 
TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVV TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY 
       59.93        72.39        80.71        76.18        56.48        64.77 
TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 
       62.47        66.25        65.39        60.99        53.69        29.92 
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-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K 
        0.20        14.04        13.15        13.35         1.84         0.20 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HT 
       18.74        19.99        19.59         0.62        11.93        14.40 
TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A495 
       60.89        23.97        19.10        27.88        12.03         0.03 
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-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ 
       17.10        14.70        20.78        11.87        14.14        15.78 
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        11.64         2.14 
TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A6G5 
       11.87        28.90         1.02         2.99        37.71        16.83 
TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E 
       11.80        27.25        13.97        12.03         9.57        16.67 
TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF 
       22.95        20.71         7.53        10.85        58.88        26.27 
TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A6M4 TCGA-RC-A6M5 TCGA-RC-A6M6 
       17.69        21.01         3.09         0.72         0.49         0.30 
TCGA-RC-A7S9 TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB 
       21.04        15.39        15.52        36.10        27.88        19.76 
TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-AB4B TCGA-WX-AA44 
       16.44         1.71        10.75        11.34        12.99        20.22 
TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TD TCGA-XR-A8TE TCGA-XR-A8TF TCGA-YA-A8S7 
       24.85        18.28        33.86        30.41        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-A9CF TCGA-ZS-A9CG 
       45.57        79.30        11.21 

  AMP PEAK 17(11Q13.3) MUTATED AMP PEAK 17(11Q13.3) WILD-TYPE 
                          0.33                           0.03 
  AMP PEAK 17(11Q13.3) MUTATED AMP PEAK 17(11Q13.3) WILD-TYPE 
                        114.35                         120.82 
  AMP PEAK 17(11Q13.3) MUTATED AMP PEAK 17(11Q13.3) WILD-TYPE 
                         18.54                          20.12 
[1] "0.3 - 114.3 (18.5)" "0.0 - 120.8 (20.1)"
[1] "hr=" "1.1"
D17V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IIIA
  AMP PEAK 17(11Q13.3) MUTATED        33        7         0         12
  AMP PEAK 17(11Q13.3) WILD-TYPE     140       80         3         50
                                vv
clus                             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 17(11Q13.3) MUTATED            1          0        1         0
  AMP PEAK 17(11Q13.3) WILD-TYPE          8          7        1         1
                                vv
clus                             STAGE IVB
  AMP PEAK 17(11Q13.3) MUTATED           0
  AMP PEAK 17(11Q13.3) WILD-TYPE         2
D17V3, multiclass
            clus
vv           AMP PEAK 17(11Q13.3) MUTATED AMP PEAK 17(11Q13.3) WILD-TYPE
  STAGE I                              33                            140
  STAGE II                              7                             80
  STAGE III                             0                              3
  STAGE IIIA                           12                             50
  STAGE IIIB                            1                              8
  STAGE IIIC                            0                              7
  STAGE IV                              1                              1
  STAGE IVA                             0                              1
  STAGE IVB                             0                              2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  AMP PEAK 17(11Q13.3) MUTATED    33   8  15   1
  AMP PEAK 17(11Q13.3) WILD-TYPE 150  87  62  11
D17V4, multiclass
    clus
vv   AMP PEAK 17(11Q13.3) MUTATED AMP PEAK 17(11Q13.3) WILD-TYPE
  T1                           33                            150
  T2                            8                             87
  T3                           15                             62
  T4                            1                             11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V5, binary
                                cls
clus                               0   1
  AMP PEAK 17(11Q13.3) MUTATED    40   0
  AMP PEAK 17(11Q13.3) WILD-TYPE 214   3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(11Q13.3) MUTATED     40    0
  AMP PEAK 17(11Q13.3) WILD-TYPE  214    3
   clus
vv  AMP PEAK 17(11Q13.3) MUTATED AMP PEAK 17(11Q13.3) WILD-TYPE
  0                           40                            214
  1                            0                              3
[1] 2 2
[1] FALSE
D17V6, binary
                                cls
clus                               0   1
  AMP PEAK 17(11Q13.3) MUTATED    43   1
  AMP PEAK 17(11Q13.3) WILD-TYPE 223   3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(11Q13.3) MUTATED     43    1
  AMP PEAK 17(11Q13.3) WILD-TYPE  223    3
   clus
vv  AMP PEAK 17(11Q13.3) MUTATED AMP PEAK 17(11Q13.3) WILD-TYPE
  0                           43                            223
  1                            1                              3
[1] 2 2
[1] FALSE
D17V7, binary
                                cls
clus                               0   1
  AMP PEAK 17(11Q13.3) MUTATED    20  37
  AMP PEAK 17(11Q13.3) WILD-TYPE  98 215
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(11Q13.3) MUTATED     20   37
  AMP PEAK 17(11Q13.3) WILD-TYPE   98  215
        clus
vv       AMP PEAK 17(11Q13.3) MUTATED AMP PEAK 17(11Q13.3) WILD-TYPE
  FEMALE                           20                             98
  MALE                             37                            215
[1] 2 2
[1] FALSE
D17V8, binary
                                cls
clus                               0   1
  AMP PEAK 17(11Q13.3) MUTATED    52   0
  AMP PEAK 17(11Q13.3) WILD-TYPE 286   9
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(11Q13.3) MUTATED     52    0
  AMP PEAK 17(11Q13.3) WILD-TYPE  286    9
     clus
vv    AMP PEAK 17(11Q13.3) MUTATED AMP PEAK 17(11Q13.3) WILD-TYPE
  NO                            52                            286
  YES                            0                              9
[1] 2 2
[1] FALSE
                                vv
clus                             FIBROLAMELLAR CARCINOMA
  AMP PEAK 17(11Q13.3) MUTATED                         0
  AMP PEAK 17(11Q13.3) WILD-TYPE                       3
                                vv
clus                             HEPATOCELLULAR CARCINOMA
  AMP PEAK 17(11Q13.3) MUTATED                         57
  AMP PEAK 17(11Q13.3) WILD-TYPE                      303
                                vv
clus                             HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK 17(11Q13.3) MUTATED                                  0
  AMP PEAK 17(11Q13.3) WILD-TYPE                                7
D17V9, multiclass
                                  clus
vv                                 AMP PEAK 17(11Q13.3) MUTATED
  FIBROLAMELLAR CARCINOMA                                     0
  HEPATOCELLULAR CARCINOMA                                   57
  HEPATOCHOLANGIOCARCINOMA (MIXED)                            0
                                  clus
vv                                 AMP PEAK 17(11Q13.3) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                       3
  HEPATOCELLULAR CARCINOMA                                    303
  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 17(11Q13.3) MUTATED    49   5   1   2
  AMP PEAK 17(11Q13.3) WILD-TYPE 275  12   0  19
D17V10, multiclass
    clus
vv   AMP PEAK 17(11Q13.3) MUTATED AMP PEAK 17(11Q13.3) WILD-TYPE
  R0                           49                            275
  R1                            5                             12
  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 17(11Q13.3) MUTATED                                  0    25
  AMP PEAK 17(11Q13.3) WILD-TYPE                                2   133
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 17(11Q13.3) MUTATED                           3    27
  AMP PEAK 17(11Q13.3) WILD-TYPE                        14   156
D17V11, multiclass
                                  clus
vv                                 AMP PEAK 17(11Q13.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                      25
  BLACK OR AFRICAN AMERICAN                                   3
  WHITE                                                      27
                                  clus
vv                                 AMP PEAK 17(11Q13.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              2
  ASIAN                                                       133
  BLACK OR AFRICAN AMERICAN                                    14
  WHITE                                                       156
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V12, binary
                                cls
clus                               0   1
  AMP PEAK 17(11Q13.3) MUTATED     1  52
  AMP PEAK 17(11Q13.3) WILD-TYPE  15 283
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(11Q13.3) MUTATED      1   52
  AMP PEAK 17(11Q13.3) WILD-TYPE   15  283
                        clus
vv                       AMP PEAK 17(11Q13.3) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           52
                        clus
vv                       AMP PEAK 17(11Q13.3) WILD-TYPE
  HISPANIC OR LATINO                                 15
  NOT HISPANIC OR LATINO                            283
[1] 2 2
[1] FALSE

Clustering(18) Variable = AMP PEAK 18(13Q32.3) MUTATION ANALYSIS
D18V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 18(13Q32.3) MUTATED    38  27
  AMP PEAK 18(13Q32.3) WILD-TYPE 197 102
  AMP PEAK 18(13Q32.3) MUTATED AMP PEAK 18(13Q32.3) WILD-TYPE 
                            65                            299 
  AMP PEAK 18(13Q32.3) MUTATED AMP PEAK 18(13Q32.3) WILD-TYPE 
                            27                            102 
$`AMP PEAK 18(13Q32.3) MUTATED`
TCGA-DD-AADV TCGA-DD-AAE8 TCGA-EP-A3JL TCGA-UB-A7MF TCGA-XR-A8TG TCGA-2Y-A9GW 
       18.87        21.83         9.96         7.04        29.52        41.79 
TCGA-2Y-A9GZ TCGA-2Y-A9H8 TCGA-BC-A10W TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A3KF 
       27.88        20.81         2.99         1.12        44.42         0.26 
TCGA-BC-A8YO TCGA-BD-A3EP TCGA-CC-5258 TCGA-CC-5261 TCGA-CC-5263 TCGA-CC-A3MA 
       18.48        13.45         4.24         3.19         4.24         9.96 
TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A8HU TCGA-DD-A113 TCGA-DD-A11A 
        7.13        21.34         9.83        11.31        79.73         2.60 
TCGA-DD-A11C TCGA-DD-A1EG TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39X TCGA-DD-A39Y 
       21.76        45.11        33.04        13.64        55.69         5.62 
TCGA-DD-A3A7 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACE TCGA-DD-AACO TCGA-DD-AAD5 
       13.78        75.65        76.41        71.80        61.68        44.22 
TCGA-DD-AADD TCGA-DD-AADF TCGA-DD-AADW TCGA-DD-AAE0 TCGA-DD-AAE3 TCGA-DD-AAE6 
       40.47         3.78        19.30        18.25        18.61         4.64 
TCGA-DD-AAEK TCGA-DD-AAVW TCGA-ED-A7PY TCGA-EP-A2KA TCGA-FV-A23B TCGA-FV-A3I0 
       35.08        76.18        12.82        20.61        60.89        27.88 
TCGA-FV-A496 TCGA-G3-A7M6 TCGA-G3-AAV1 TCGA-G3-AAV6 TCGA-KR-A7K2 TCGA-KR-A7K8 
        0.33        20.78        11.80         2.14        27.25        29.79 
TCGA-NI-A8LF TCGA-PD-A5DF TCGA-RC-A6M6 TCGA-RC-A7S9 TCGA-RG-A7D4 TCGA-UB-A7MA 
       26.27        21.01         0.30        21.04        36.10        27.88 
TCGA-UB-A7MC TCGA-UB-AA0U TCGA-WX-AA44 TCGA-WX-AA47 TCGA-ZP-A9CZ 
       16.44        10.75        20.22        18.28        23.21 

$`AMP PEAK 18(13Q32.3) WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 
       83.24        11.74        38.40         8.61        69.57         5.03 
TCGA-BC-A5W4 TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AAE7 
       17.98        36.66         0.36        90.28        26.83        21.17 
TCGA-DD-AAEA TCGA-DD-AAEG TCGA-ES-A2HS TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A4ZP 
       18.90        23.64        22.62         8.12         6.38        81.73 
TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC TCGA-G3-A7M9 TCGA-K7-A5RF TCGA-KR-A7K0 
       30.74        22.13        22.06         1.84        20.75         2.14 
TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H TCGA-T1-A6J8 TCGA-UB-AA0V TCGA-ZP-A9D1 
       31.27        12.72        24.56         0.76        10.32         0.69 
TCGA-ZS-A9CE TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GX TCGA-2Y-A9GY 
       40.80        23.80        53.39        63.75        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-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-5C-A9VH 
       22.92         1.18         8.55        13.02        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-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10X 
       37.32        10.13        46.78        27.52        27.52        25.32 
TCGA-BC-A10Y TCGA-BC-A217 TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A69I TCGA-BD-A2L6 
       23.38        45.93        22.36        14.60        12.72        44.81 
TCGA-BW-A5NO TCGA-CC-5260 TCGA-CC-5262 TCGA-CC-5264 TCGA-CC-A1HT TCGA-CC-A3M9 
        0.66         2.86         3.39         3.35         3.32         9.86 
TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IH 
       10.36        11.93        11.41         9.99         8.94        12.00 
TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A7IL TCGA-CC-A8HT TCGA-CC-A8HV 
       13.12        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-A118 
        6.94         8.15        37.78        83.57        53.33       113.00 
TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB 
        7.33         0.46        51.29        90.71        79.40        66.31 
TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EI 
       19.79        75.65        11.47        12.95        49.15         6.02 
TCGA-DD-A1EK TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 
       18.35        21.14        27.19        19.76        25.81         7.66 
TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A9 
       70.06        17.59        20.12       102.74       107.11        30.61 
TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK 
       33.14        32.52        30.97        30.15        30.51        39.78 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR 
       56.25        29.56        73.81       108.76        12.26         0.30 
TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D 
       80.75        78.84        23.93         9.30        23.05        22.78 
TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 
        1.45        35.67       114.35        13.48         0.53        11.41 
TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI 
       55.40        12.53        12.00        15.42         6.41        53.19 
TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACP 
       69.11         0.30         3.52        58.16        42.81        13.64 
TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW 
       14.20        59.31        51.35        51.52        50.33        46.82 
TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 
        5.59        47.67         5.62         4.50        18.54        21.63 
TCGA-DD-AAD3 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC 
       42.58        22.09        40.08        40.54        40.83        13.97 
TCGA-DD-AADE TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL 
       39.52        37.64        35.67        35.05        34.49        20.91 
TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR 
        0.39        29.52        14.89        15.06        14.33        66.67 
TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADY TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE4 
       15.58        18.21        18.25        18.15        20.98        19.99 
TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAEI 
       23.74        15.72        25.08        26.63        25.78        50.33 
TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVV 
       90.48        89.69        82.62        59.93        72.39        80.71 
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        60.99 
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-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E 
        9.73         0.20         0.20        14.04        13.15        13.41 
TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KB 
       13.35         1.84         0.20        18.74        19.99        19.59 
TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3R3 
        0.62        11.93        14.40        23.97        19.10        12.03 
TCGA-FV-A495 TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V 
        0.03         0.39        13.68        51.06        53.79        28.27 
TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ 
       58.49        14.86        21.53        25.64         5.92        19.53 
TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A7M5 
       19.23        25.25        22.95        20.42        17.10        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        11.64        11.87        28.90         1.02         2.20 
TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-LG-A9QC 
        2.99        37.71        17.06        16.83        11.80        13.97 
TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A520 
       12.03         9.57        16.67        22.95        20.71         7.53 
TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-O8-A75V TCGA-QA-A7B7 TCGA-RC-A6M4 TCGA-RC-A6M5 
       10.85        58.88        17.69         3.09         0.72         0.49 
TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-UB-A7MB TCGA-UB-A7MD 
       19.33        19.04        15.39        15.52        19.76         1.71 
TCGA-UB-A7ME TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA46 TCGA-XR-A8TD 
       15.98        11.34         0.99        12.99        24.85        33.86 
TCGA-XR-A8TE TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9D0 
       30.41        22.78        13.55        35.77        25.71        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 

  AMP PEAK 18(13Q32.3) MUTATED AMP PEAK 18(13Q32.3) WILD-TYPE 
                          0.26                           0.03 
  AMP PEAK 18(13Q32.3) MUTATED AMP PEAK 18(13Q32.3) WILD-TYPE 
                         79.73                         120.82 
  AMP PEAK 18(13Q32.3) MUTATED AMP PEAK 18(13Q32.3) WILD-TYPE 
                         20.22                          19.76 
[1] "0.3 - 79.7 (20.2)"  "0.0 - 120.8 (19.8)"
[1] "hr=" "1.4"
D18V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IIIA
  AMP PEAK 18(13Q32.3) MUTATED        31       14         0         13
  AMP PEAK 18(13Q32.3) WILD-TYPE     142       73         3         49
                                vv
clus                             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 18(13Q32.3) MUTATED            2          3        1         0
  AMP PEAK 18(13Q32.3) WILD-TYPE          7          4        1         1
                                vv
clus                             STAGE IVB
  AMP PEAK 18(13Q32.3) MUTATED           0
  AMP PEAK 18(13Q32.3) WILD-TYPE         2
D18V3, multiclass
            clus
vv           AMP PEAK 18(13Q32.3) MUTATED AMP PEAK 18(13Q32.3) WILD-TYPE
  STAGE I                              31                            142
  STAGE II                             14                             73
  STAGE III                             0                              3
  STAGE IIIA                           13                             49
  STAGE IIIB                            2                              7
  STAGE IIIC                            3                              4
  STAGE IV                              1                              1
  STAGE IVA                             0                              1
  STAGE IVB                             0                              2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  AMP PEAK 18(13Q32.3) MUTATED    34  15  14   4
  AMP PEAK 18(13Q32.3) WILD-TYPE 149  80  63   8
D18V4, multiclass
    clus
vv   AMP PEAK 18(13Q32.3) MUTATED AMP PEAK 18(13Q32.3) WILD-TYPE
  T1                           34                            149
  T2                           15                             80
  T3                           14                             63
  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"
D18V5, binary
                                cls
clus                               0   1
  AMP PEAK 18(13Q32.3) MUTATED    45   1
  AMP PEAK 18(13Q32.3) WILD-TYPE 209   2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 18(13Q32.3) MUTATED     45    1
  AMP PEAK 18(13Q32.3) WILD-TYPE  209    2
   clus
vv  AMP PEAK 18(13Q32.3) MUTATED AMP PEAK 18(13Q32.3) WILD-TYPE
  0                           45                            209
  1                            1                              2
[1] 2 2
[1] FALSE
D18V6, binary
                                cls
clus                               0   1
  AMP PEAK 18(13Q32.3) MUTATED    51   1
  AMP PEAK 18(13Q32.3) WILD-TYPE 215   3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 18(13Q32.3) MUTATED     51    1
  AMP PEAK 18(13Q32.3) WILD-TYPE  215    3
   clus
vv  AMP PEAK 18(13Q32.3) MUTATED AMP PEAK 18(13Q32.3) WILD-TYPE
  0                           51                            215
  1                            1                              3
[1] 2 2
[1] FALSE
D18V7, binary
                                cls
clus                               0   1
  AMP PEAK 18(13Q32.3) MUTATED    29  38
  AMP PEAK 18(13Q32.3) WILD-TYPE  89 214
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 18(13Q32.3) MUTATED     29   38
  AMP PEAK 18(13Q32.3) WILD-TYPE   89  214
        clus
vv       AMP PEAK 18(13Q32.3) MUTATED AMP PEAK 18(13Q32.3) WILD-TYPE
  FEMALE                           29                             89
  MALE                             38                            214
[1] 2 2
[1] FALSE
D18V8, binary
                                cls
clus                               0   1
  AMP PEAK 18(13Q32.3) MUTATED    59   3
  AMP PEAK 18(13Q32.3) WILD-TYPE 279   6
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 18(13Q32.3) MUTATED     59    3
  AMP PEAK 18(13Q32.3) WILD-TYPE  279    6
     clus
vv    AMP PEAK 18(13Q32.3) MUTATED AMP PEAK 18(13Q32.3) WILD-TYPE
  NO                            59                            279
  YES                            3                              6
[1] 2 2
[1] FALSE
                                vv
clus                             FIBROLAMELLAR CARCINOMA
  AMP PEAK 18(13Q32.3) MUTATED                         0
  AMP PEAK 18(13Q32.3) WILD-TYPE                       3
                                vv
clus                             HEPATOCELLULAR CARCINOMA
  AMP PEAK 18(13Q32.3) MUTATED                         64
  AMP PEAK 18(13Q32.3) WILD-TYPE                      296
                                vv
clus                             HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK 18(13Q32.3) MUTATED                                  3
  AMP PEAK 18(13Q32.3) WILD-TYPE                                4
D18V9, multiclass
                                  clus
vv                                 AMP PEAK 18(13Q32.3) MUTATED
  FIBROLAMELLAR CARCINOMA                                     0
  HEPATOCELLULAR CARCINOMA                                   64
  HEPATOCHOLANGIOCARCINOMA (MIXED)                            3
                                  clus
vv                                 AMP PEAK 18(13Q32.3) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                       3
  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
  AMP PEAK 18(13Q32.3) MUTATED    55   4   0   6
  AMP PEAK 18(13Q32.3) WILD-TYPE 269  13   1  15
D18V10, multiclass
    clus
vv   AMP PEAK 18(13Q32.3) MUTATED AMP PEAK 18(13Q32.3) WILD-TYPE
  R0                           55                            269
  R1                            4                             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 18(13Q32.3) MUTATED                                  0    30
  AMP PEAK 18(13Q32.3) WILD-TYPE                                2   128
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 18(13Q32.3) MUTATED                           4    31
  AMP PEAK 18(13Q32.3) WILD-TYPE                        13   152
D18V11, multiclass
                                  clus
vv                                 AMP PEAK 18(13Q32.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                      30
  BLACK OR AFRICAN AMERICAN                                   4
  WHITE                                                      31
                                  clus
vv                                 AMP PEAK 18(13Q32.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              2
  ASIAN                                                       128
  BLACK OR AFRICAN AMERICAN                                    13
  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"
D18V12, binary
                                cls
clus                               0   1
  AMP PEAK 18(13Q32.3) MUTATED     3  59
  AMP PEAK 18(13Q32.3) WILD-TYPE  13 276
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 18(13Q32.3) MUTATED      3   59
  AMP PEAK 18(13Q32.3) WILD-TYPE   13  276
                        clus
vv                       AMP PEAK 18(13Q32.3) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           59
                        clus
vv                       AMP PEAK 18(13Q32.3) WILD-TYPE
  HISPANIC OR LATINO                                 13
  NOT HISPANIC OR LATINO                            276
[1] 2 2
[1] FALSE

Clustering(19) Variable = AMP PEAK 19(13Q33.3) MUTATION ANALYSIS
D19V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 19(13Q33.3) MUTATED    38  27
  AMP PEAK 19(13Q33.3) WILD-TYPE 197 102
  AMP PEAK 19(13Q33.3) MUTATED AMP PEAK 19(13Q33.3) WILD-TYPE 
                            65                            299 
  AMP PEAK 19(13Q33.3) MUTATED AMP PEAK 19(13Q33.3) WILD-TYPE 
                            27                            102 
$`AMP PEAK 19(13Q33.3) MUTATED`
TCGA-DD-AAE8 TCGA-EP-A3JL TCGA-UB-A7MF TCGA-XR-A8TG TCGA-2Y-A9GW TCGA-2Y-A9GZ 
       21.83         9.96         7.04        29.52        41.79        27.88 
TCGA-2Y-A9H8 TCGA-BC-A10W TCGA-BC-A217 TCGA-BC-A3KF TCGA-BD-A3EP TCGA-CC-5258 
       20.81         2.99        45.93         0.26        13.45         4.24 
TCGA-CC-5261 TCGA-CC-5263 TCGA-CC-A3MA TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IG 
        3.19         4.24         9.96         7.13        21.34         9.83 
TCGA-CC-A8HU TCGA-DD-A113 TCGA-DD-A11A TCGA-DD-A1EG TCGA-DD-A1EJ TCGA-DD-A1EL 
       11.31        79.73         2.60        45.11        33.04        13.64 
TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A3A7 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACE 
       55.69         5.62        13.78        75.65        76.41        71.80 
TCGA-DD-AACO TCGA-DD-AAD5 TCGA-DD-AADD TCGA-DD-AADF TCGA-DD-AADQ TCGA-DD-AADW 
       61.68        44.22        40.47         3.78        14.33        19.30 
TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE3 TCGA-DD-AAE6 TCGA-DD-AAEK TCGA-DD-AAVW 
       18.25        18.15        18.61         4.64        35.08        76.18 
TCGA-ED-A66Y TCGA-ED-A7PY TCGA-EP-A26S TCGA-EP-A2KC TCGA-FV-A23B TCGA-FV-A3I0 
        9.73        12.82        19.99         0.62        60.89        27.88 
TCGA-FV-A496 TCGA-G3-A7M6 TCGA-G3-AAV1 TCGA-G3-AAV6 TCGA-KR-A7K2 TCGA-KR-A7K8 
        0.33        20.78        11.80         2.14        27.25        29.79 
TCGA-NI-A8LF TCGA-RC-A7S9 TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MC 
       26.27        21.04        15.52        36.10        27.88        16.44 
TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WX-AA44 TCGA-WX-AA47 TCGA-ZP-A9CZ 
       10.75        11.34        20.22        18.28        23.21 

$`AMP PEAK 19(13Q33.3) WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 
       83.24        11.74        38.40         8.61        69.57         5.03 
TCGA-BC-A5W4 TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV 
       17.98        36.66         0.36        90.28        26.83        18.87 
TCGA-DD-AAE7 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-ES-A2HS TCGA-FV-A3I1 TCGA-FV-A3R2 
       21.17        18.90        23.64        22.62         8.12         6.38 
TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC TCGA-G3-A7M9 TCGA-K7-A5RF 
       81.73        30.74        22.13        22.06         1.84        20.75 
TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H TCGA-T1-A6J8 TCGA-UB-AA0V 
        2.14        31.27        12.72        24.56         0.76        10.32 
TCGA-ZP-A9D1 TCGA-ZS-A9CE TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GX 
        0.69        40.80        23.80        53.39        63.75        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-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-5C-A9VG 
       18.25        22.92         1.18         8.55        13.02        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-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A3KG TCGA-BC-A69H 
       25.32        23.38         1.12        44.42        22.36        14.60 
TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BW-A5NO TCGA-CC-5260 TCGA-CC-5262 
       12.72        18.48        44.81         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-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB 
       20.12       102.74       107.11        30.61        33.14        32.52 
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-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-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADY 
       14.89        15.06        66.67        15.58        18.21        18.25 
TCGA-DD-AAE2 TCGA-DD-AAE4 TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE 
       20.98        19.99        23.74        15.72        25.08        26.63 
TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS 
       25.78        50.33        90.48        89.69        82.62        59.93 
TCGA-DD-AAVU TCGA-DD-AAVV TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 
       72.39        80.71        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        60.99        53.69        29.92        26.93        28.08 
TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A7PX TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP 
       13.91        13.35         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-A2KA 
       13.41        13.35         1.84         0.20        18.74        20.61 
TCGA-EP-A2KB TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3R3 
       19.59        11.93        14.40        23.97        19.10        12.03 
TCGA-FV-A495 TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V 
        0.03         0.39        13.68        51.06        53.79        28.27 
TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ 
       58.49        14.86        21.53        25.64         5.92        19.53 
TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A7M5 
       19.23        25.25        22.95        20.42        17.10        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        11.64        11.87        28.90         1.02         2.20 
TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-LG-A9QC 
        2.99        37.71        17.06        16.83        11.80        13.97 
TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A520 
       12.03         9.57        16.67        22.95        20.71         7.53 
TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A6M4 
       10.85        58.88        17.69        21.01         3.09         0.72 
TCGA-RC-A6M5 TCGA-RC-A6M6 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH TCGA-UB-A7MB 
        0.49         0.30        19.33        19.04        15.39        19.76 
TCGA-UB-A7MD TCGA-UB-A7ME TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA46 TCGA-XR-A8TD 
        1.71        15.98         0.99        12.99        24.85        33.86 
TCGA-XR-A8TE TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9D0 
       30.41        22.78        13.55        35.77        25.71        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 

  AMP PEAK 19(13Q33.3) MUTATED AMP PEAK 19(13Q33.3) WILD-TYPE 
                          0.26                           0.03 
  AMP PEAK 19(13Q33.3) MUTATED AMP PEAK 19(13Q33.3) WILD-TYPE 
                         79.73                         120.82 
  AMP PEAK 19(13Q33.3) MUTATED AMP PEAK 19(13Q33.3) WILD-TYPE 
                         18.61                          19.99 
[1] "0.3 - 79.7 (18.6)"  "0.0 - 120.8 (20.0)"
[1] "hr=" "1.4"
D19V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IIIA
  AMP PEAK 19(13Q33.3) MUTATED        33       15         0         12
  AMP PEAK 19(13Q33.3) WILD-TYPE     140       72         3         50
                                vv
clus                             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 19(13Q33.3) MUTATED            1          2        1         0
  AMP PEAK 19(13Q33.3) WILD-TYPE          8          5        1         1
                                vv
clus                             STAGE IVB
  AMP PEAK 19(13Q33.3) MUTATED           0
  AMP PEAK 19(13Q33.3) WILD-TYPE         2
D19V3, multiclass
            clus
vv           AMP PEAK 19(13Q33.3) MUTATED AMP PEAK 19(13Q33.3) WILD-TYPE
  STAGE I                              33                            140
  STAGE II                             15                             72
  STAGE III                             0                              3
  STAGE IIIA                           12                             50
  STAGE IIIB                            1                              8
  STAGE IIIC                            2                              5
  STAGE IV                              1                              1
  STAGE IVA                             0                              1
  STAGE IVB                             0                              2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  AMP PEAK 19(13Q33.3) MUTATED    36  16  13   2
  AMP PEAK 19(13Q33.3) WILD-TYPE 147  79  64  10
D19V4, multiclass
    clus
vv   AMP PEAK 19(13Q33.3) MUTATED AMP PEAK 19(13Q33.3) WILD-TYPE
  T1                           36                            147
  T2                           16                             79
  T3                           13                             64
  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"
D19V5, binary
                                cls
clus                               0   1
  AMP PEAK 19(13Q33.3) MUTATED    45   1
  AMP PEAK 19(13Q33.3) WILD-TYPE 209   2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 19(13Q33.3) MUTATED     45    1
  AMP PEAK 19(13Q33.3) WILD-TYPE  209    2
   clus
vv  AMP PEAK 19(13Q33.3) MUTATED AMP PEAK 19(13Q33.3) WILD-TYPE
  0                           45                            209
  1                            1                              2
[1] 2 2
[1] FALSE
D19V6, binary
                                cls
clus                               0   1
  AMP PEAK 19(13Q33.3) MUTATED    50   1
  AMP PEAK 19(13Q33.3) WILD-TYPE 216   3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 19(13Q33.3) MUTATED     50    1
  AMP PEAK 19(13Q33.3) WILD-TYPE  216    3
   clus
vv  AMP PEAK 19(13Q33.3) MUTATED AMP PEAK 19(13Q33.3) WILD-TYPE
  0                           50                            216
  1                            1                              3
[1] 2 2
[1] FALSE
D19V7, binary
                                cls
clus                               0   1
  AMP PEAK 19(13Q33.3) MUTATED    27  40
  AMP PEAK 19(13Q33.3) WILD-TYPE  91 212
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 19(13Q33.3) MUTATED     27   40
  AMP PEAK 19(13Q33.3) WILD-TYPE   91  212
        clus
vv       AMP PEAK 19(13Q33.3) MUTATED AMP PEAK 19(13Q33.3) WILD-TYPE
  FEMALE                           27                             91
  MALE                             40                            212
[1] 2 2
[1] FALSE
D19V8, binary
                                cls
clus                               0   1
  AMP PEAK 19(13Q33.3) MUTATED    60   3
  AMP PEAK 19(13Q33.3) WILD-TYPE 278   6
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 19(13Q33.3) MUTATED     60    3
  AMP PEAK 19(13Q33.3) WILD-TYPE  278    6
     clus
vv    AMP PEAK 19(13Q33.3) MUTATED AMP PEAK 19(13Q33.3) WILD-TYPE
  NO                            60                            278
  YES                            3                              6
[1] 2 2
[1] FALSE
                                vv
clus                             FIBROLAMELLAR CARCINOMA
  AMP PEAK 19(13Q33.3) MUTATED                         0
  AMP PEAK 19(13Q33.3) WILD-TYPE                       3
                                vv
clus                             HEPATOCELLULAR CARCINOMA
  AMP PEAK 19(13Q33.3) MUTATED                         64
  AMP PEAK 19(13Q33.3) WILD-TYPE                      296
                                vv
clus                             HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK 19(13Q33.3) MUTATED                                  3
  AMP PEAK 19(13Q33.3) WILD-TYPE                                4
D19V9, multiclass
                                  clus
vv                                 AMP PEAK 19(13Q33.3) MUTATED
  FIBROLAMELLAR CARCINOMA                                     0
  HEPATOCELLULAR CARCINOMA                                   64
  HEPATOCHOLANGIOCARCINOMA (MIXED)                            3
                                  clus
vv                                 AMP PEAK 19(13Q33.3) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                       3
  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
  AMP PEAK 19(13Q33.3) MUTATED    57   3   0   5
  AMP PEAK 19(13Q33.3) WILD-TYPE 267  14   1  16
D19V10, multiclass
    clus
vv   AMP PEAK 19(13Q33.3) MUTATED AMP PEAK 19(13Q33.3) WILD-TYPE
  R0                           57                            267
  R1                            3                             14
  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 19(13Q33.3) MUTATED                                  0    33
  AMP PEAK 19(13Q33.3) WILD-TYPE                                2   125
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 19(13Q33.3) MUTATED                           5    27
  AMP PEAK 19(13Q33.3) WILD-TYPE                        12   156
D19V11, multiclass
                                  clus
vv                                 AMP PEAK 19(13Q33.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                      33
  BLACK OR AFRICAN AMERICAN                                   5
  WHITE                                                      27
                                  clus
vv                                 AMP PEAK 19(13Q33.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              2
  ASIAN                                                       125
  BLACK OR AFRICAN AMERICAN                                    12
  WHITE                                                       156
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V12, binary
                                cls
clus                               0   1
  AMP PEAK 19(13Q33.3) MUTATED     3  59
  AMP PEAK 19(13Q33.3) WILD-TYPE  13 276
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 19(13Q33.3) MUTATED      3   59
  AMP PEAK 19(13Q33.3) WILD-TYPE   13  276
                        clus
vv                       AMP PEAK 19(13Q33.3) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           59
                        clus
vv                       AMP PEAK 19(13Q33.3) WILD-TYPE
  HISPANIC OR LATINO                                 13
  NOT HISPANIC OR LATINO                            276
[1] 2 2
[1] FALSE

Clustering(20) Variable = AMP PEAK 20(15Q26.3) MUTATION ANALYSIS
D20V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 20(15Q26.3) MUTATED    36  17
  AMP PEAK 20(15Q26.3) WILD-TYPE 199 112
  AMP PEAK 20(15Q26.3) MUTATED AMP PEAK 20(15Q26.3) WILD-TYPE 
                            53                            311 
  AMP PEAK 20(15Q26.3) MUTATED AMP PEAK 20(15Q26.3) WILD-TYPE 
                            17                            112 
$`AMP PEAK 20(15Q26.3) MUTATED`
TCGA-DD-A4NI TCGA-DD-AADV TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-ES-A2HS TCGA-G3-A6UC 
       26.83        18.87        21.83        18.90        22.62        22.06 
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-A4NJ TCGA-DD-A4NV TCGA-DD-A73G TCGA-DD-AACB TCGA-DD-AACP TCGA-DD-AACV 
       30.51        78.84       114.35        76.41        13.64        50.33 
TCGA-DD-AACZ TCGA-DD-AADO TCGA-DD-AADU TCGA-DD-AAE0 TCGA-DD-AAE3 TCGA-DD-AAE6 
        5.62        14.89        18.21        18.25        18.61         4.64 
TCGA-ED-A5KG TCGA-ED-A66X TCGA-ED-A7PZ TCGA-ED-A8O6 TCGA-EP-A2KA TCGA-FV-A23B 
       28.08        13.35         0.20         1.84        20.61        60.89 
TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25Y TCGA-G3-A3CH TCGA-MI-A75G TCGA-MR-A8JO 
        0.39        51.06        14.86        25.64        22.95        10.85 
TCGA-O8-A75V TCGA-RC-A7SK TCGA-UB-A7MA TCGA-WQ-AB4B TCGA-WX-AA47 
       17.69        15.52        27.88        12.99        18.28 

$`AMP PEAK 20(15Q26.3) WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 
       83.24        11.74        38.40         8.61        69.57         5.03 
TCGA-BC-A5W4 TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-AAE7 TCGA-DD-AAEG 
       17.98        36.66         0.36        90.28        21.17        23.64 
TCGA-EP-A3JL TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A3CG 
        9.96         8.12         6.38        81.73        30.74        22.13 
TCGA-G3-A7M9 TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H 
        1.84        20.75         2.14        31.27        12.72        24.56 
TCGA-T1-A6J8 TCGA-UB-A7MF TCGA-UB-AA0V TCGA-XR-A8TG TCGA-ZP-A9D1 TCGA-ZS-A9CE 
        0.76         7.04        10.32        29.52         0.69        40.80 
TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GY TCGA-2Y-A9GZ 
       53.39        63.75        41.79        80.28        24.89        27.88 
TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-2Y-A9H9 
      120.82        40.41        47.74        18.25        20.81        22.92 
TCGA-2Y-A9HA TCGA-3K-AAZ8 TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D 
        1.18        13.02        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-A10T 
        1.51        48.99        27.91        10.13        46.78        27.52 
TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A3KG 
       27.52         2.99        25.32         1.12        44.42        22.36 
TCGA-BC-A69H TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-CC-5258 
       14.60        12.72        18.48        44.81        13.45         4.24 
TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5264 TCGA-CC-A1HT TCGA-CC-A3MA TCGA-CC-A3MB 
        2.86         3.19         3.35         3.32         9.96        10.36 
TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A7IE TCGA-CC-A7IG TCGA-CC-A7IH 
       11.93        11.41         9.99         7.13         9.83        12.00 
TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A7IL TCGA-CC-A8HT TCGA-CC-A8HU 
       13.12        12.56         8.61         9.14         4.60        11.31 
TCGA-CC-A8HV TCGA-CC-A9FS TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 
        9.17         6.94        79.73        37.78        83.57        53.33 
TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 
      113.00         7.33         0.46        21.76        51.29        90.71 
TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF 
       79.40        66.31        19.79        75.65        11.47        12.95 
TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL 
       45.11        49.15         6.02        33.04        18.35        13.64 
TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A3A0 TCGA-DD-A3A1 
       21.14        27.19        55.69         5.62        25.81         7.66 
TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 
       70.06        17.59        20.12       102.74       107.11        13.78 
TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NK 
       30.61        33.14        32.52        30.97        30.15        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-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-AACC 
       35.67        13.48         0.53        11.41        75.65        55.40 
TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI 
       12.53        71.80        12.00        15.42         6.41        53.19 
TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO 
       69.11         0.30         3.52        58.16        42.81        61.68 
TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACW TCGA-DD-AACX 
       14.20        59.31        51.35        51.52        46.82         5.59 
TCGA-DD-AACY TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 
       47.67         4.50        18.54        21.63        42.58        44.22 
TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD 
       22.09        40.08        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-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-AADW TCGA-DD-AADY TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE4 
       15.58        19.30        18.25        18.15        20.98        19.99 
TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAEI 
       23.74        15.72        25.08        26.63        25.78        50.33 
TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU 
       35.08        90.48        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        60.99        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-A3RK TCGA-ES-A2HT TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R3 
       11.93        14.40        23.97        19.10        27.88        12.03 
TCGA-FV-A495 TCGA-FV-A496 TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25X 
        0.03         0.33        13.68        53.79        28.27        58.49 
TCGA-G3-A25Z TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ 
       21.53         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-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 
       11.64         2.14        11.87        28.90         1.02         2.20 
TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K2 
        2.99        37.71        17.06        16.83        11.80        27.25 
TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75I 
       29.79        13.97        12.03         9.57        16.67        20.71 
TCGA-MR-A520 TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A6M4 
        7.53        58.88        26.27        21.01         3.09         0.72 
TCGA-RC-A6M5 TCGA-RC-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH 
        0.49         0.30        21.04        19.33        19.04        15.39 
TCGA-RG-A7D4 TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0U 
       36.10        19.76        16.44         1.71        15.98        10.75 
TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WX-AA44 TCGA-WX-AA46 TCGA-XR-A8TD TCGA-XR-A8TE 
       11.34         0.99        20.22        24.85        33.86        30.41 
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-A9CF TCGA-ZS-A9CG 
       25.15        12.99        45.57        79.30        11.21 

  AMP PEAK 20(15Q26.3) MUTATED AMP PEAK 20(15Q26.3) WILD-TYPE 
                          0.20                           0.03 
  AMP PEAK 20(15Q26.3) MUTATED AMP PEAK 20(15Q26.3) WILD-TYPE 
                        114.35                         120.82 
  AMP PEAK 20(15Q26.3) MUTATED AMP PEAK 20(15Q26.3) WILD-TYPE 
                         18.61                          20.12 
[1] "0.2 - 114.3 (18.6)" "0.0 - 120.8 (20.1)"
[1] "hr=" "1"  
D20V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IIIA
  AMP PEAK 20(15Q26.3) MUTATED        21       13         0         13
  AMP PEAK 20(15Q26.3) WILD-TYPE     152       74         3         49
                                vv
clus                             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 20(15Q26.3) MUTATED            2          1        1         0
  AMP PEAK 20(15Q26.3) WILD-TYPE          7          6        1         1
                                vv
clus                             STAGE IVB
  AMP PEAK 20(15Q26.3) MUTATED           0
  AMP PEAK 20(15Q26.3) WILD-TYPE         2
D20V3, multiclass
            clus
vv           AMP PEAK 20(15Q26.3) MUTATED AMP PEAK 20(15Q26.3) WILD-TYPE
  STAGE I                              21                            152
  STAGE II                             13                             74
  STAGE III                             0                              3
  STAGE IIIA                           13                             49
  STAGE IIIB                            2                              7
  STAGE IIIC                            1                              6
  STAGE IV                              1                              1
  STAGE IVA                             0                              1
  STAGE IVB                             0                              2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  AMP PEAK 20(15Q26.3) MUTATED    21  16  14   3
  AMP PEAK 20(15Q26.3) WILD-TYPE 162  79  63   9
D20V4, multiclass
    clus
vv   AMP PEAK 20(15Q26.3) MUTATED AMP PEAK 20(15Q26.3) WILD-TYPE
  T1                           21                            162
  T2                           16                             79
  T3                           14                             63
  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"
D20V5, binary
                                cls
clus                               0   1
  AMP PEAK 20(15Q26.3) MUTATED    37   0
  AMP PEAK 20(15Q26.3) WILD-TYPE 217   3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(15Q26.3) MUTATED     37    0
  AMP PEAK 20(15Q26.3) WILD-TYPE  217    3
   clus
vv  AMP PEAK 20(15Q26.3) MUTATED AMP PEAK 20(15Q26.3) WILD-TYPE
  0                           37                            217
  1                            0                              3
[1] 2 2
[1] FALSE
D20V6, binary
                                cls
clus                               0   1
  AMP PEAK 20(15Q26.3) MUTATED    41   1
  AMP PEAK 20(15Q26.3) WILD-TYPE 225   3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(15Q26.3) MUTATED     41    1
  AMP PEAK 20(15Q26.3) WILD-TYPE  225    3
   clus
vv  AMP PEAK 20(15Q26.3) MUTATED AMP PEAK 20(15Q26.3) WILD-TYPE
  0                           41                            225
  1                            1                              3
[1] 2 2
[1] FALSE
D20V7, binary
                                cls
clus                               0   1
  AMP PEAK 20(15Q26.3) MUTATED    20  34
  AMP PEAK 20(15Q26.3) WILD-TYPE  98 218
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(15Q26.3) MUTATED     20   34
  AMP PEAK 20(15Q26.3) WILD-TYPE   98  218
        clus
vv       AMP PEAK 20(15Q26.3) MUTATED AMP PEAK 20(15Q26.3) WILD-TYPE
  FEMALE                           20                             98
  MALE                             34                            218
[1] 2 2
[1] FALSE
D20V8, binary
                                cls
clus                               0   1
  AMP PEAK 20(15Q26.3) MUTATED    48   1
  AMP PEAK 20(15Q26.3) WILD-TYPE 290   8
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(15Q26.3) MUTATED     48    1
  AMP PEAK 20(15Q26.3) WILD-TYPE  290    8
     clus
vv    AMP PEAK 20(15Q26.3) MUTATED AMP PEAK 20(15Q26.3) WILD-TYPE
  NO                            48                            290
  YES                            1                              8
[1] 2 2
[1] FALSE
                                vv
clus                             FIBROLAMELLAR CARCINOMA
  AMP PEAK 20(15Q26.3) MUTATED                         1
  AMP PEAK 20(15Q26.3) WILD-TYPE                       2
                                vv
clus                             HEPATOCELLULAR CARCINOMA
  AMP PEAK 20(15Q26.3) MUTATED                         52
  AMP PEAK 20(15Q26.3) WILD-TYPE                      308
                                vv
clus                             HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK 20(15Q26.3) MUTATED                                  1
  AMP PEAK 20(15Q26.3) WILD-TYPE                                6
D20V9, multiclass
                                  clus
vv                                 AMP PEAK 20(15Q26.3) MUTATED
  FIBROLAMELLAR CARCINOMA                                     1
  HEPATOCELLULAR CARCINOMA                                   52
  HEPATOCHOLANGIOCARCINOMA (MIXED)                            1
                                  clus
vv                                 AMP PEAK 20(15Q26.3) 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 20(15Q26.3) MUTATED    46   3   0   4
  AMP PEAK 20(15Q26.3) WILD-TYPE 278  14   1  17
D20V10, multiclass
    clus
vv   AMP PEAK 20(15Q26.3) MUTATED AMP PEAK 20(15Q26.3) WILD-TYPE
  R0                           46                            278
  R1                            3                             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
  AMP PEAK 20(15Q26.3) MUTATED                                  0    25
  AMP PEAK 20(15Q26.3) WILD-TYPE                                2   133
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 20(15Q26.3) MUTATED                           2    24
  AMP PEAK 20(15Q26.3) WILD-TYPE                        15   159
D20V11, multiclass
                                  clus
vv                                 AMP PEAK 20(15Q26.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                      25
  BLACK OR AFRICAN AMERICAN                                   2
  WHITE                                                      24
                                  clus
vv                                 AMP PEAK 20(15Q26.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              2
  ASIAN                                                       133
  BLACK OR AFRICAN AMERICAN                                    15
  WHITE                                                       159
[1] 4 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(15Q26.3) MUTATED     5  45
  AMP PEAK 20(15Q26.3) WILD-TYPE  11 290
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(15Q26.3) MUTATED      5   45
  AMP PEAK 20(15Q26.3) WILD-TYPE   11  290
                        clus
vv                       AMP PEAK 20(15Q26.3) MUTATED
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                           45
                        clus
vv                       AMP PEAK 20(15Q26.3) WILD-TYPE
  HISPANIC OR LATINO                                 11
  NOT HISPANIC OR LATINO                            290
[1] 2 2
[1] FALSE

Clustering(21) Variable = AMP PEAK 21(17P11.2) MUTATION ANALYSIS
D21V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 21(17P11.2) MUTATED    25  21
  AMP PEAK 21(17P11.2) WILD-TYPE 210 108
  AMP PEAK 21(17P11.2) MUTATED AMP PEAK 21(17P11.2) WILD-TYPE 
                            46                            318 
  AMP PEAK 21(17P11.2) MUTATED AMP PEAK 21(17P11.2) WILD-TYPE 
                            21                            108 
$`AMP PEAK 21(17P11.2) MUTATED`
TCGA-ES-A2HS TCGA-FV-A4ZP TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-3K-AAZ8 TCGA-BC-4073 
       22.62        81.73        27.88       120.82        13.02        27.91 
TCGA-BC-A10Q TCGA-BC-A217 TCGA-BC-A3KF TCGA-CC-5260 TCGA-CC-5264 TCGA-CC-A3M9 
       37.32        45.93         0.26         2.86         3.35         9.86 
TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IK TCGA-CC-A9FW TCGA-DD-A115 TCGA-DD-A119 
        8.94         7.13         8.61         8.15        83.57         7.33 
TCGA-DD-A11A TCGA-DD-A3A3 TCGA-DD-A3A5 TCGA-DD-A3A7 TCGA-DD-A4NO TCGA-DD-A4NP 
        2.60        17.59       102.74        13.78        73.81       108.76 
TCGA-DD-A73E TCGA-DD-AACB TCGA-DD-AACI TCGA-DD-AAD0 TCGA-DD-AADD TCGA-DD-AADE 
        1.45        76.41        53.19         4.50        40.47        39.52 
TCGA-DD-AADO TCGA-DD-AADR TCGA-DD-AAVR TCGA-DD-AAW1 TCGA-ED-A66X TCGA-ED-A66Y 
       14.89        66.67        82.62        65.39        13.35         9.73 
TCGA-ED-A7PZ TCGA-ED-A8O6 TCGA-EP-A2KA TCGA-EP-A2KB TCGA-G3-AAUZ TCGA-G3-AAV6 
        0.20         1.84        20.61        19.59        15.78         2.14 
TCGA-MI-A75G TCGA-O8-A75V TCGA-UB-A7MA TCGA-UB-A7MB 
       22.95        17.69        27.88        19.76 

$`AMP PEAK 21(17P11.2) WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 
       83.24        11.74        38.40         8.61        69.57         5.03 
TCGA-BC-A5W4 TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV 
       17.98        36.66         0.36        90.28        26.83        18.87 
TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-FV-A3I1 
       21.17        21.83        18.90        23.64         9.96         8.12 
TCGA-FV-A3R2 TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC TCGA-G3-A7M9 TCGA-K7-A5RF 
        6.38        30.74        22.13        22.06         1.84        20.75 
TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H TCGA-T1-A6J8 TCGA-UB-A7MF 
        2.14        31.27        12.72        24.56         0.76         7.04 
TCGA-UB-AA0V TCGA-XR-A8TG TCGA-ZP-A9D1 TCGA-ZS-A9CE TCGA-2Y-A9GS TCGA-2Y-A9GT 
       10.32        29.52         0.69        40.80        23.80        53.39 
TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GY TCGA-2Y-A9H1 TCGA-2Y-A9H2 
       63.75        41.79        80.28        24.89        40.41        56.91 
TCGA-2Y-A9H3 TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA 
       49.84        47.74        18.25        20.81        22.92         1.18 
TCGA-2Y-A9HB TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D 
        8.55        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-A216 TCGA-BC-A3KG 
        2.99        25.32        23.38         1.12        44.42        22.36 
TCGA-BC-A69H TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BW-A5NO 
       14.60        12.72        18.48        44.81        13.45         0.66 
TCGA-CC-5258 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3MA 
        4.24         3.19         3.39         4.24         3.32         9.96 
TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A7IF TCGA-CC-A7IG 
       10.36        11.93        11.41         9.99        21.34         9.83 
TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IL TCGA-CC-A8HT TCGA-CC-A8HU 
       12.00        13.12        12.56         9.14         4.60        11.31 
TCGA-CC-A8HV TCGA-CC-A9FS TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A116 TCGA-DD-A118 
        9.17         6.94        79.73        37.78        53.33       113.00 
TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB 
        0.46        21.76        51.29        90.71        79.40        66.31 
TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH 
       19.79        75.65        11.47        12.95        45.11        49.15 
TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W 
        6.02        33.04        18.35        13.64        21.14        27.19 
TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 
       55.69         5.62        19.76        25.81         7.66        70.06 
TCGA-DD-A3A4 TCGA-DD-A3A6 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NF 
       20.12       107.11        30.61        33.14        32.52        30.97 
TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NQ 
       30.15        30.51        39.78        56.25        29.56        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-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 
       22.78        35.67       114.35        13.48         0.53        11.41 
TCGA-DD-AACA TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG 
       75.65        55.40        12.53        71.80        12.00        15.42 
TCGA-DD-AACH TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN 
        6.41        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-AACU 
       61.68        13.64        14.20        59.31        51.35        51.52 
TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD1 
       50.33        46.82         5.59        47.67         5.62        18.54 
TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA 
       21.63        42.58        44.22        22.09        40.08        40.54 
TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ 
       40.83        13.97         3.78        37.64        35.67        35.05 
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-AADS TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 
       15.58        18.21        19.30        18.25        18.25        18.15 
TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE9 TCGA-DD-AAEB 
       20.98        18.61        19.99         4.64        23.74        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        90.48 
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        60.99        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-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR 
        0.62        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-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-A5SJ 
       25.64         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-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        11.64 
TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 
       11.87        28.90         1.02         2.20         2.99        37.71 
TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A9QC 
       17.06        16.83        11.80        27.25        29.79        13.97 
TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO 
       12.03         9.57        16.67        20.71         7.53        10.85 
TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A6M4 TCGA-RC-A6M5 
       58.88        26.27        21.01         3.09         0.72         0.49 
TCGA-RC-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK 
        0.30        21.04        19.33        19.04        15.39        15.52 
TCGA-RG-A7D4 TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WJ-A86L 
       36.10        16.44         1.71        15.98        10.75        11.34 
TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TD 
        0.99        12.99        20.22        24.85        18.28        33.86 
TCGA-XR-A8TE TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ 
       30.41        22.78        13.55        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 

  AMP PEAK 21(17P11.2) MUTATED AMP PEAK 21(17P11.2) WILD-TYPE 
                          0.20                           0.03 
  AMP PEAK 21(17P11.2) MUTATED AMP PEAK 21(17P11.2) WILD-TYPE 
                        120.82                         114.35 
  AMP PEAK 21(17P11.2) MUTATED AMP PEAK 21(17P11.2) WILD-TYPE 
                         18.64                          19.99 
[1] "0.2 - 120.8 (18.6)" "0.0 - 114.3 (20.0)"
[1] "hr=" "1.1"
D21V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IIIA
  AMP PEAK 21(17P11.2) MUTATED        17        7         1         15
  AMP PEAK 21(17P11.2) WILD-TYPE     156       80         2         47
                                vv
clus                             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 21(17P11.2) MUTATED            3          1        1         0
  AMP PEAK 21(17P11.2) WILD-TYPE          6          6        1         1
                                vv
clus                             STAGE IVB
  AMP PEAK 21(17P11.2) MUTATED           0
  AMP PEAK 21(17P11.2) WILD-TYPE         2
D21V3, multiclass
            clus
vv           AMP PEAK 21(17P11.2) MUTATED AMP PEAK 21(17P11.2) WILD-TYPE
  STAGE I                              17                            156
  STAGE II                              7                             80
  STAGE III                             1                              2
  STAGE IIIA                           15                             47
  STAGE IIIB                            3                              6
  STAGE IIIC                            1                              6
  STAGE IV                              1                              1
  STAGE IVA                             0                              1
  STAGE IVB                             0                              2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  AMP PEAK 21(17P11.2) MUTATED    17   8  19   2
  AMP PEAK 21(17P11.2) WILD-TYPE 166  87  58  10
D21V4, multiclass
    clus
vv   AMP PEAK 21(17P11.2) MUTATED AMP PEAK 21(17P11.2) WILD-TYPE
  T1                           17                            166
  T2                            8                             87
  T3                           19                             58
  T4                            2                             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V5, binary
                                cls
clus                               0   1
  AMP PEAK 21(17P11.2) MUTATED    34   0
  AMP PEAK 21(17P11.2) WILD-TYPE 220   3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 21(17P11.2) MUTATED     34    0
  AMP PEAK 21(17P11.2) WILD-TYPE  220    3
   clus
vv  AMP PEAK 21(17P11.2) MUTATED AMP PEAK 21(17P11.2) WILD-TYPE
  0                           34                            220
  1                            0                              3
[1] 2 2
[1] FALSE
D21V6, binary
                                cls
clus                               0   1
  AMP PEAK 21(17P11.2) MUTATED    36   1
  AMP PEAK 21(17P11.2) WILD-TYPE 230   3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 21(17P11.2) MUTATED     36    1
  AMP PEAK 21(17P11.2) WILD-TYPE  230    3
   clus
vv  AMP PEAK 21(17P11.2) MUTATED AMP PEAK 21(17P11.2) WILD-TYPE
  0                           36                            230
  1                            1                              3
[1] 2 2
[1] FALSE
D21V7, binary
                                cls
clus                               0   1
  AMP PEAK 21(17P11.2) MUTATED    14  32
  AMP PEAK 21(17P11.2) WILD-TYPE 104 220
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 21(17P11.2) MUTATED     14   32
  AMP PEAK 21(17P11.2) WILD-TYPE  104  220
        clus
vv       AMP PEAK 21(17P11.2) MUTATED AMP PEAK 21(17P11.2) WILD-TYPE
  FEMALE                           14                            104
  MALE                             32                            220
[1] 2 2
[1] FALSE
D21V8, binary
                                cls
clus                               0   1
  AMP PEAK 21(17P11.2) MUTATED    41   0
  AMP PEAK 21(17P11.2) WILD-TYPE 297   9
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 21(17P11.2) MUTATED     41    0
  AMP PEAK 21(17P11.2) WILD-TYPE  297    9
     clus
vv    AMP PEAK 21(17P11.2) MUTATED AMP PEAK 21(17P11.2) WILD-TYPE
  NO                            41                            297
  YES                            0                              9
[1] 2 2
[1] FALSE
                                vv
clus                             FIBROLAMELLAR CARCINOMA
  AMP PEAK 21(17P11.2) MUTATED                         0
  AMP PEAK 21(17P11.2) WILD-TYPE                       3
                                vv
clus                             HEPATOCELLULAR CARCINOMA
  AMP PEAK 21(17P11.2) MUTATED                         45
  AMP PEAK 21(17P11.2) WILD-TYPE                      315
                                vv
clus                             HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK 21(17P11.2) MUTATED                                  1
  AMP PEAK 21(17P11.2) WILD-TYPE                                6
D21V9, multiclass
                                  clus
vv                                 AMP PEAK 21(17P11.2) MUTATED
  FIBROLAMELLAR CARCINOMA                                     0
  HEPATOCELLULAR CARCINOMA                                   45
  HEPATOCHOLANGIOCARCINOMA (MIXED)                            1
                                  clus
vv                                 AMP PEAK 21(17P11.2) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                       3
  HEPATOCELLULAR CARCINOMA                                    315
  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(17P11.2) MUTATED    37   5   1   3
  AMP PEAK 21(17P11.2) WILD-TYPE 287  12   0  18
D21V10, multiclass
    clus
vv   AMP PEAK 21(17P11.2) MUTATED AMP PEAK 21(17P11.2) WILD-TYPE
  R0                           37                            287
  R1                            5                             12
  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 21(17P11.2) MUTATED                                  0    22
  AMP PEAK 21(17P11.2) WILD-TYPE                                2   136
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 21(17P11.2) MUTATED                           2    19
  AMP PEAK 21(17P11.2) WILD-TYPE                        15   164
D21V11, multiclass
                                  clus
vv                                 AMP PEAK 21(17P11.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                      22
  BLACK OR AFRICAN AMERICAN                                   2
  WHITE                                                      19
                                  clus
vv                                 AMP PEAK 21(17P11.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              2
  ASIAN                                                       136
  BLACK OR AFRICAN AMERICAN                                    15
  WHITE                                                       164
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V12, binary
                                cls
clus                               0   1
  AMP PEAK 21(17P11.2) MUTATED     3  39
  AMP PEAK 21(17P11.2) WILD-TYPE  13 296
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 21(17P11.2) MUTATED      3   39
  AMP PEAK 21(17P11.2) WILD-TYPE   13  296
                        clus
vv                       AMP PEAK 21(17P11.2) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           39
                        clus
vv                       AMP PEAK 21(17P11.2) WILD-TYPE
  HISPANIC OR LATINO                                 13
  NOT HISPANIC OR LATINO                            296
[1] 2 2
[1] FALSE

Clustering(22) Variable = AMP PEAK 22(17Q25.3) MUTATION ANALYSIS
D22V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 22(17Q25.3) MUTATED    86  56
  AMP PEAK 22(17Q25.3) WILD-TYPE 149  73
  AMP PEAK 22(17Q25.3) MUTATED AMP PEAK 22(17Q25.3) WILD-TYPE 
                           142                            222 
  AMP PEAK 22(17Q25.3) MUTATED AMP PEAK 22(17Q25.3) WILD-TYPE 
                            56                             73 
$`AMP PEAK 22(17Q25.3) MUTATED`
TCGA-BC-A112 TCGA-DD-A4NI TCGA-DD-AAEA TCGA-ES-A2HS TCGA-FV-A4ZP TCGA-G3-A25W 
        5.03        26.83        18.90        22.62        81.73        30.74 
TCGA-LG-A6GG TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 
       12.72        24.89        27.88       120.82        40.41        56.91 
TCGA-2Y-A9H9 TCGA-3K-AAZ8 TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-A10Q TCGA-BC-A10T 
       22.92        13.02         1.51        48.99        37.32        27.52 
TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A217 
       27.52         2.99        23.38         1.12        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-A4NJ TCGA-DD-A4NO TCGA-DD-A4NP 
       13.78        30.61        30.15        30.51        73.81       108.76 
TCGA-DD-A73A TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-AAC8 TCGA-DD-AAC9 
       23.93        22.78         1.45        35.67         0.53        11.41 
TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACE TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACS 
       75.65        76.41        71.80        53.19        69.11        59.31 
TCGA-DD-AACX TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE 
        5.59        44.22        22.09        13.97        40.47        39.52 
TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADR TCGA-DD-AADU 
        3.78        37.64        29.52        14.89        66.67        18.21 
TCGA-DD-AADW TCGA-DD-AAE0 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAEE TCGA-DD-AAEK 
       19.30        18.25        20.98        18.61        26.63        35.08 
TCGA-DD-AAVR TCGA-DD-AAVV TCGA-DD-AAW1 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PZ 
       82.62        80.71        65.39        13.35         9.73         0.20 
TCGA-ED-A7XP TCGA-ED-A8O6 TCGA-EP-A2KB TCGA-EP-A2KC TCGA-FV-A2QR TCGA-FV-A495 
       13.15         1.84        19.59         0.62        19.10         0.03 
TCGA-FV-A496 TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25X TCGA-G3-A25Z TCGA-G3-A3CJ 
        0.33        13.68        53.79        58.49        21.53        19.53 
TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A7M6 TCGA-G3-AAUZ 
       19.23        25.25        22.95        20.42        20.78        15.78 
TCGA-G3-AAV1 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-K7-AAU7 TCGA-KR-A7K8 TCGA-LG-A9QC 
       11.80        11.64         2.14        11.80        29.79        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-RC-A6M6 TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MC TCGA-UB-AA0U TCGA-XR-A8TD 
        0.30        36.10        27.88        16.44        10.75        33.86 
TCGA-ZP-A9CZ TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CF 
       23.21        25.15        12.99        79.30 

$`AMP PEAK 22(17Q25.3) WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A5W4 
       83.24        11.74        38.40         8.61        69.57        17.98 
TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-AADV TCGA-DD-AAE7 TCGA-DD-AAE8 
       36.66         0.36        90.28        18.87        21.17        21.83 
TCGA-DD-AAEG TCGA-EP-A3JL TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-G3-A3CG TCGA-G3-A6UC 
       23.64         9.96         8.12         6.38        22.13        22.06 
TCGA-G3-A7M9 TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-MI-A75H TCGA-T1-A6J8 
        1.84        20.75         2.14        31.27        24.56         0.76 
TCGA-UB-A7MF TCGA-UB-AA0V TCGA-XR-A8TG TCGA-ZP-A9D1 TCGA-ZS-A9CE TCGA-2Y-A9GS 
        7.04        10.32        29.52         0.69        40.80        23.80 
TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9H3 TCGA-2Y-A9H4 
       53.39        63.75        41.79        80.28        49.84        47.74 
TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-5C-A9VG TCGA-5C-A9VH 
       18.25        20.81         1.18         8.55        10.78        10.59 
TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D TCGA-BC-4073 TCGA-BC-A10R TCGA-BC-A10S 
        0.66        17.10        14.76        27.91        10.13        46.78 
TCGA-BC-A10X TCGA-BC-A3KF TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-CC-5258 
       25.32         0.26        12.72        18.48        44.81         4.24 
TCGA-CC-5262 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A5UD TCGA-CC-A7IH 
        3.39         3.32         9.86         9.96         9.99        12.00 
TCGA-CC-A7II TCGA-CC-A8HV TCGA-CC-A9FS TCGA-DD-A113 TCGA-DD-A118 TCGA-DD-A11B 
       13.12         9.17         6.94        79.73       113.00         0.46 
TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF 
       51.29        90.71        19.79        75.65        11.47        12.95 
TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W 
       45.11        49.15        18.35        13.64        21.14        27.19 
TCGA-DD-A39X TCGA-DD-A39Z TCGA-DD-A3A2 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A4NA 
       55.69        19.76        70.06       102.74       107.11        33.14 
TCGA-DD-A4NB TCGA-DD-A4NF TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NQ 
       32.52        30.97        39.78        56.25        29.56        12.26 
TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73G 
        0.30        80.75        78.84         9.30        23.05       114.35 
TCGA-DD-AA3A TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH 
       13.48        55.40        12.53        12.00        15.42         6.41 
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-AACT TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACY 
       14.20        51.35        51.52        50.33        46.82        47.67 
TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD8 
        5.62         4.50        18.54        21.63        42.58        40.08 
TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL 
       40.54        40.83        35.67        35.05        34.49        20.91 
TCGA-DD-AADM TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADS TCGA-DD-AADY TCGA-DD-AAE1 
        0.39        15.06        14.33        15.58        18.25        18.15 
TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEH 
       19.99         4.64        23.74        15.72        25.08        25.78 
TCGA-DD-AAEI TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW 
       50.33        90.48        89.69        59.93        72.39        76.18 
TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW2 TCGA-DD-AAW3 
       56.48        64.77        62.47        66.25        60.99        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-A7XO TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S 
       14.04        13.41        13.35         0.20        18.74        19.99 
TCGA-EP-A2KA TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A3I0 
       20.61        11.93        14.40        60.89        23.97        27.88 
TCGA-FV-A3R3 TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25V TCGA-G3-A25Y TCGA-G3-A3CH 
       12.03         0.39        51.06        28.27        14.86        25.64 
TCGA-G3-A3CI TCGA-G3-A5SM TCGA-G3-A7M5 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAV0 
        5.92        17.10        14.70        11.87        14.14        15.65 
TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 
       12.23        13.55         0.89        11.87        28.90         1.02 
TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-KR-A7K2 
        2.20         2.99        37.71        17.06        16.83        27.25 
TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MR-A520 TCGA-MR-A8JO TCGA-QA-A7B7 
       12.03         9.57        16.67         7.53        10.85         3.09 
TCGA-RC-A6M4 TCGA-RC-A6M5 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH 
        0.72         0.49        21.04        19.33        19.04        15.39 
TCGA-RC-A7SK TCGA-UB-A7MB TCGA-UB-A7MD TCGA-UB-A7ME TCGA-WJ-A86L TCGA-WQ-A9G7 
       15.52        19.76         1.71        15.98        11.34         0.99 
TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TE TCGA-XR-A8TF 
       12.99        20.22        24.85        18.28        30.41        22.78 
TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9D0 TCGA-ZS-A9CD TCGA-ZS-A9CG 
       13.55        35.77        25.71        35.87        45.57        11.21 

  AMP PEAK 22(17Q25.3) MUTATED AMP PEAK 22(17Q25.3) WILD-TYPE 
                          0.03                           0.20 
  AMP PEAK 22(17Q25.3) MUTATED AMP PEAK 22(17Q25.3) WILD-TYPE 
                        120.82                         114.35 
  AMP PEAK 22(17Q25.3) MUTATED AMP PEAK 22(17Q25.3) WILD-TYPE 
                        20.745                         19.185 
[1] "0.0 - 120.8 (20.7)" "0.2 - 114.3 (19.2)"
[1] "hr=" "1.2"
D22V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IIIA
  AMP PEAK 22(17Q25.3) MUTATED        54       37         0         32
  AMP PEAK 22(17Q25.3) WILD-TYPE     119       50         3         30
                                vv
clus                             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 22(17Q25.3) MUTATED            7          3        1         0
  AMP PEAK 22(17Q25.3) WILD-TYPE          2          4        1         1
                                vv
clus                             STAGE IVB
  AMP PEAK 22(17Q25.3) MUTATED           1
  AMP PEAK 22(17Q25.3) WILD-TYPE         1
D22V3, multiclass
            clus
vv           AMP PEAK 22(17Q25.3) MUTATED AMP PEAK 22(17Q25.3) WILD-TYPE
  STAGE I                              54                            119
  STAGE II                             37                             50
  STAGE III                             0                              3
  STAGE IIIA                           32                             30
  STAGE IIIB                            7                              2
  STAGE IIIC                            3                              4
  STAGE IV                              1                              1
  STAGE IVA                             0                              1
  STAGE IVB                             1                              1
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  AMP PEAK 22(17Q25.3) MUTATED    57  41  39   8
  AMP PEAK 22(17Q25.3) WILD-TYPE 126  54  38   4
D22V4, multiclass
    clus
vv   AMP PEAK 22(17Q25.3) MUTATED AMP PEAK 22(17Q25.3) WILD-TYPE
  T1                           57                            126
  T2                           41                             54
  T3                           39                             38
  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"
D22V5, binary
                                cls
clus                               0   1
  AMP PEAK 22(17Q25.3) MUTATED    99   1
  AMP PEAK 22(17Q25.3) WILD-TYPE 155   2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 22(17Q25.3) MUTATED     99    1
  AMP PEAK 22(17Q25.3) WILD-TYPE  155    2
   clus
vv  AMP PEAK 22(17Q25.3) MUTATED AMP PEAK 22(17Q25.3) WILD-TYPE
  0                           99                            155
  1                            1                              2
[1] 2 2
[1] FALSE
D22V6, binary
                                cls
clus                               0   1
  AMP PEAK 22(17Q25.3) MUTATED   110   2
  AMP PEAK 22(17Q25.3) WILD-TYPE 156   2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 22(17Q25.3) MUTATED    110    2
  AMP PEAK 22(17Q25.3) WILD-TYPE  156    2
   clus
vv  AMP PEAK 22(17Q25.3) MUTATED AMP PEAK 22(17Q25.3) WILD-TYPE
  0                          110                            156
  1                            2                              2
[1] 2 2
[1] FALSE
D22V7, binary
                                cls
clus                               0   1
  AMP PEAK 22(17Q25.3) MUTATED    39 106
  AMP PEAK 22(17Q25.3) WILD-TYPE  79 146
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 22(17Q25.3) MUTATED     39  106
  AMP PEAK 22(17Q25.3) WILD-TYPE   79  146
        clus
vv       AMP PEAK 22(17Q25.3) MUTATED AMP PEAK 22(17Q25.3) WILD-TYPE
  FEMALE                           39                             79
  MALE                            106                            146
[1] 2 2
[1] FALSE
D22V8, binary
                                cls
clus                               0   1
  AMP PEAK 22(17Q25.3) MUTATED   132   2
  AMP PEAK 22(17Q25.3) WILD-TYPE 206   7
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 22(17Q25.3) MUTATED    132    2
  AMP PEAK 22(17Q25.3) WILD-TYPE  206    7
     clus
vv    AMP PEAK 22(17Q25.3) MUTATED AMP PEAK 22(17Q25.3) WILD-TYPE
  NO                           132                            206
  YES                            2                              7
[1] 2 2
[1] FALSE
                                vv
clus                             FIBROLAMELLAR CARCINOMA
  AMP PEAK 22(17Q25.3) MUTATED                         0
  AMP PEAK 22(17Q25.3) WILD-TYPE                       3
                                vv
clus                             HEPATOCELLULAR CARCINOMA
  AMP PEAK 22(17Q25.3) MUTATED                        143
  AMP PEAK 22(17Q25.3) WILD-TYPE                      217
                                vv
clus                             HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK 22(17Q25.3) MUTATED                                  2
  AMP PEAK 22(17Q25.3) WILD-TYPE                                5
D22V9, multiclass
                                  clus
vv                                 AMP PEAK 22(17Q25.3) MUTATED
  FIBROLAMELLAR CARCINOMA                                     0
  HEPATOCELLULAR CARCINOMA                                  143
  HEPATOCHOLANGIOCARCINOMA (MIXED)                            2
                                  clus
vv                                 AMP PEAK 22(17Q25.3) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                       3
  HEPATOCELLULAR CARCINOMA                                    217
  HEPATOCHOLANGIOCARCINOMA (MIXED)                              5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 22(17Q25.3) MUTATED   122  11   1  10
  AMP PEAK 22(17Q25.3) WILD-TYPE 202   6   0  11
D22V10, multiclass
    clus
vv   AMP PEAK 22(17Q25.3) MUTATED AMP PEAK 22(17Q25.3) WILD-TYPE
  R0                          122                            202
  R1                           11                              6
  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 22(17Q25.3) MUTATED                                  1    68
  AMP PEAK 22(17Q25.3) WILD-TYPE                                1    90
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 22(17Q25.3) MUTATED                           8    62
  AMP PEAK 22(17Q25.3) WILD-TYPE                         9   121
D22V11, multiclass
                                  clus
vv                                 AMP PEAK 22(17Q25.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                      68
  BLACK OR AFRICAN AMERICAN                                   8
  WHITE                                                      62
                                  clus
vv                                 AMP PEAK 22(17Q25.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        90
  BLACK OR AFRICAN AMERICAN                                     9
  WHITE                                                       121
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V12, binary
                                cls
clus                               0   1
  AMP PEAK 22(17Q25.3) MUTATED     4 134
  AMP PEAK 22(17Q25.3) WILD-TYPE  12 201
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 22(17Q25.3) MUTATED      4  134
  AMP PEAK 22(17Q25.3) WILD-TYPE   12  201
                        clus
vv                       AMP PEAK 22(17Q25.3) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                          134
                        clus
vv                       AMP PEAK 22(17Q25.3) WILD-TYPE
  HISPANIC OR LATINO                                 12
  NOT HISPANIC OR LATINO                            201
[1] 2 2
[1] FALSE

Clustering(23) Variable = AMP PEAK 23(19P13.12) MUTATION ANALYSIS
D23V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 23(19P13.12) MUTATED    44  23
  AMP PEAK 23(19P13.12) WILD-TYPE 191 106
  AMP PEAK 23(19P13.12) MUTATED AMP PEAK 23(19P13.12) WILD-TYPE 
                             67                             297 
  AMP PEAK 23(19P13.12) MUTATED AMP PEAK 23(19P13.12) WILD-TYPE 
                             23                             106 
$`AMP PEAK 23(19P13.12) MUTATED`
TCGA-2Y-A9H6 TCGA-BC-A112 TCGA-DD-A4ND TCGA-DD-AAEG TCGA-ES-A2HS TCGA-FV-A3I1 
       11.74         5.03        90.28        23.64        22.62         8.12 
TCGA-FV-A4ZP TCGA-ZP-A9D1 TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9H3 TCGA-3K-AAZ8 
       81.73         0.69        63.75        41.79        49.84        13.02 
TCGA-BC-A10Q TCGA-BC-A10R TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5261 TCGA-CC-A7II 
       37.32        10.13        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-A4NN 
       12.95        21.14        55.69        13.78        30.61        29.56 
TCGA-DD-A4NO TCGA-DD-A4NV TCGA-DD-A73G TCGA-DD-AACL TCGA-DD-AACT TCGA-DD-AACY 
       73.81        78.84       114.35         3.52        51.35        47.67 
TCGA-DD-AAD5 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADF TCGA-DD-AAE0 TCGA-DD-AAE3 
       44.22        40.54        40.83         3.78        18.25        18.61 
TCGA-DD-AAE6 TCGA-DD-AAE9 TCGA-DD-AAEK TCGA-DD-AAVR TCGA-ED-A66X TCGA-ED-A66Y 
        4.64        23.74        35.08        82.62        13.35         9.73 
TCGA-ED-A82E TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-FV-A2QQ TCGA-FV-A3I0 
       13.41        20.61        19.59         0.62        23.97        27.88 
TCGA-G3-A25T TCGA-G3-A25X TCGA-G3-A5SM TCGA-G3-A7M7 TCGA-G3-AAUZ TCGA-G3-AAV0 
       51.06        58.49        17.10        11.87        15.78        15.65 
TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-KR-A7K2 TCGA-RC-A6M6 TCGA-RC-A7S9 TCGA-UB-A7MA 
       11.87        28.90        27.25         0.30        21.04        27.88 
TCGA-YA-A8S7 
       13.55 

$`AMP PEAK 23(19P13.12) WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A5W4 TCGA-BD-A3ER 
       83.24        38.40         8.61        69.57        17.98        36.66 
TCGA-DD-A3A8 TCGA-DD-A4NI TCGA-DD-AADV TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEA 
        0.36        26.83        18.87        21.17        21.83        18.90 
TCGA-EP-A3JL TCGA-FV-A3R2 TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC TCGA-G3-A7M9 
        9.96         6.38        30.74        22.13        22.06         1.84 
TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H TCGA-T1-A6J8 
       20.75         2.14        31.27        12.72        24.56         0.76 
TCGA-UB-A7MF TCGA-UB-AA0V TCGA-XR-A8TG TCGA-ZS-A9CE TCGA-2Y-A9GS TCGA-2Y-A9GT 
        7.04        10.32        29.52        40.80        23.80        53.39 
TCGA-2Y-A9GX TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 
       80.28        24.89        27.88       120.82        40.41        56.91 
TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB 
       47.74        18.25        20.81        22.92         1.18         8.55 
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-4073 TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W 
       48.99        27.91        46.78        27.52        27.52         2.99 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF 
       25.32        23.38         1.12        44.42        45.93         0.26 
TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-CC-5258 
       22.36        14.60        12.72        18.48        44.81         4.24 
TCGA-CC-5260 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-5264 TCGA-CC-A1HT TCGA-CC-A3M9 
        2.86         3.39         4.24         3.35         3.32         9.86 
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-A7IL TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FW TCGA-DD-A114 
        9.14         4.60        11.31         9.17         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-A1EG TCGA-DD-A1EH 
       79.40        66.31        75.65        11.47        45.11        49.15 
TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39W TCGA-DD-A39Y 
        6.02        33.04        18.35        13.64        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-A4NA TCGA-DD-A4NB TCGA-DD-A4NF TCGA-DD-A4NH 
      102.74       107.11        33.14        32.52        30.97        30.15 
TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR 
       30.51        39.78        56.25       108.76        12.26         0.30 
TCGA-DD-A4NS TCGA-DD-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-AACG TCGA-DD-AACH 
       55.40        12.53        71.80        12.00        15.42         6.41 
TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO 
       53.19        69.11         0.30        58.16        42.81        61.68 
TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-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-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 
        5.59         5.62         4.50        18.54        21.63        42.58 
TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADG 
       22.09        40.08        13.97        40.47        39.52        37.64 
TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-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-AADW TCGA-DD-AADY TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE4 TCGA-DD-AAEB 
       19.30        18.25        18.15        20.98        19.99        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        90.48        89.69 
TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVV TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY 
       59.93        72.39        80.71        76.18        56.48        64.77 
TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 
       62.47        66.25        65.39        60.99        53.69        29.92 
TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ 
       26.93        28.08        13.91         0.20        12.82         0.20 
TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J 
       14.04        13.15        13.35         1.84         0.20        18.74 
TCGA-EP-A26S TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3R3 
       19.99        11.93        14.40        60.89        19.10        12.03 
TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25V 
        0.03         0.33         0.39        13.68        53.79        28.27 
TCGA-G3-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-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M8 
       25.25        22.95        20.42        14.70        20.78        14.14 
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        11.64         2.14 
TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 
        1.02         2.20         2.99        37.71        17.06        16.83 
TCGA-K7-AAU7 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E 
       11.80        29.79        13.97        12.03         9.57        16.67 
TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF 
       22.95        20.71         7.53        10.85        58.88        26.27 
TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A6M4 TCGA-RC-A6M5 TCGA-RC-A7SB 
       17.69        21.01         3.09         0.72         0.49        19.33 
TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MB TCGA-UB-A7MC 
       19.04        15.39        15.52        36.10        19.76        16.44 
TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B 
        1.71        15.98        10.75        11.34         0.99        12.99 
TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TD TCGA-XR-A8TE TCGA-XR-A8TF 
       20.22        24.85        18.28        33.86        30.41        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-A9CF TCGA-ZS-A9CG 
       45.57        79.30        11.21 

  AMP PEAK 23(19P13.12) MUTATED AMP PEAK 23(19P13.12) WILD-TYPE 
                           0.30                            0.03 
  AMP PEAK 23(19P13.12) MUTATED AMP PEAK 23(19P13.12) WILD-TYPE 
                         114.35                          120.82 
  AMP PEAK 23(19P13.12) MUTATED AMP PEAK 23(19P13.12) WILD-TYPE 
                          21.04                           19.53 
[1] "0.3 - 114.3 (21.0)" "0.0 - 120.8 (19.5)"
[1] "hr=" "1.2"
D23V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE III STAGE IIIA
  AMP PEAK 23(19P13.12) MUTATED        34       15         0         11
  AMP PEAK 23(19P13.12) WILD-TYPE     139       72         3         51
                                 vv
clus                              STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 23(19P13.12) MUTATED            2          0        2         0
  AMP PEAK 23(19P13.12) WILD-TYPE          7          7        0         1
                                 vv
clus                              STAGE IVB
  AMP PEAK 23(19P13.12) MUTATED           1
  AMP PEAK 23(19P13.12) WILD-TYPE         1
D23V3, multiclass
            clus
vv           AMP PEAK 23(19P13.12) MUTATED AMP PEAK 23(19P13.12) WILD-TYPE
  STAGE I                               34                             139
  STAGE II                              15                              72
  STAGE III                              0                               3
  STAGE IIIA                            11                              51
  STAGE IIIB                             2                               7
  STAGE IIIC                             0                               7
  STAGE IV                               2                               0
  STAGE IVA                              0                               1
  STAGE IVB                              1                               1
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               T1  T2  T3  T4
  AMP PEAK 23(19P13.12) MUTATED    35  17  16   1
  AMP PEAK 23(19P13.12) WILD-TYPE 148  78  61  11
D23V4, multiclass
    clus
vv   AMP PEAK 23(19P13.12) MUTATED AMP PEAK 23(19P13.12) WILD-TYPE
  T1                            35                             148
  T2                            17                              78
  T3                            16                              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"
D23V5, binary
                                 cls
clus                                0   1
  AMP PEAK 23(19P13.12) MUTATED    48   0
  AMP PEAK 23(19P13.12) WILD-TYPE 206   3
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 23(19P13.12) MUTATED     48    0
  AMP PEAK 23(19P13.12) WILD-TYPE  206    3
   clus
vv  AMP PEAK 23(19P13.12) MUTATED AMP PEAK 23(19P13.12) WILD-TYPE
  0                            48                             206
  1                             0                               3
[1] 2 2
[1] FALSE
D23V6, binary
                                 cls
clus                                0   1
  AMP PEAK 23(19P13.12) MUTATED    47   3
  AMP PEAK 23(19P13.12) WILD-TYPE 219   1
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 23(19P13.12) MUTATED     47    3
  AMP PEAK 23(19P13.12) WILD-TYPE  219    1
   clus
vv  AMP PEAK 23(19P13.12) MUTATED AMP PEAK 23(19P13.12) WILD-TYPE
  0                            47                             219
  1                             3                               1
[1] 2 2
[1] FALSE
D23V7, binary
                                 cls
clus                                0   1
  AMP PEAK 23(19P13.12) MUTATED    32  37
  AMP PEAK 23(19P13.12) WILD-TYPE  86 215
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 23(19P13.12) MUTATED     32   37
  AMP PEAK 23(19P13.12) WILD-TYPE   86  215
        clus
vv       AMP PEAK 23(19P13.12) MUTATED AMP PEAK 23(19P13.12) WILD-TYPE
  FEMALE                            32                              86
  MALE                              37                             215
[1] 2 2
[1] FALSE
D23V8, binary
                                 cls
clus                                0   1
  AMP PEAK 23(19P13.12) MUTATED    62   1
  AMP PEAK 23(19P13.12) WILD-TYPE 276   8
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 23(19P13.12) MUTATED     62    1
  AMP PEAK 23(19P13.12) WILD-TYPE  276    8
     clus
vv    AMP PEAK 23(19P13.12) MUTATED AMP PEAK 23(19P13.12) WILD-TYPE
  NO                             62                             276
  YES                             1                               8
[1] 2 2
[1] FALSE
                                 vv
clus                              FIBROLAMELLAR CARCINOMA
  AMP PEAK 23(19P13.12) MUTATED                         0
  AMP PEAK 23(19P13.12) WILD-TYPE                       3
                                 vv
clus                              HEPATOCELLULAR CARCINOMA
  AMP PEAK 23(19P13.12) MUTATED                         66
  AMP PEAK 23(19P13.12) WILD-TYPE                      294
                                 vv
clus                              HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK 23(19P13.12) MUTATED                                  3
  AMP PEAK 23(19P13.12) WILD-TYPE                                4
D23V9, multiclass
                                  clus
vv                                 AMP PEAK 23(19P13.12) MUTATED
  FIBROLAMELLAR CARCINOMA                                      0
  HEPATOCELLULAR CARCINOMA                                    66
  HEPATOCHOLANGIOCARCINOMA (MIXED)                             3
                                  clus
vv                                 AMP PEAK 23(19P13.12) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                        3
  HEPATOCELLULAR CARCINOMA                                     294
  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 23(19P13.12) MUTATED    59   4   1   5
  AMP PEAK 23(19P13.12) WILD-TYPE 265  13   0  16
D23V10, multiclass
    clus
vv   AMP PEAK 23(19P13.12) MUTATED AMP PEAK 23(19P13.12) WILD-TYPE
  R0                            59                             265
  R1                             4                              13
  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 23(19P13.12) MUTATED                                  1    25
  AMP PEAK 23(19P13.12) WILD-TYPE                                1   133
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 23(19P13.12) MUTATED                           4    37
  AMP PEAK 23(19P13.12) WILD-TYPE                        13   146
D23V11, multiclass
                                  clus
vv                                 AMP PEAK 23(19P13.12) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                       25
  BLACK OR AFRICAN AMERICAN                                    4
  WHITE                                                       37
                                  clus
vv                                 AMP PEAK 23(19P13.12) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               1
  ASIAN                                                        133
  BLACK OR AFRICAN AMERICAN                                     13
  WHITE                                                        146
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V12, binary
                                 cls
clus                                0   1
  AMP PEAK 23(19P13.12) MUTATED     4  62
  AMP PEAK 23(19P13.12) WILD-TYPE  12 273
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 23(19P13.12) MUTATED      4   62
  AMP PEAK 23(19P13.12) WILD-TYPE   12  273
                        clus
vv                       AMP PEAK 23(19P13.12) MUTATED
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                            62
                        clus
vv                       AMP PEAK 23(19P13.12) WILD-TYPE
  HISPANIC OR LATINO                                  12
  NOT HISPANIC OR LATINO                             273
[1] 2 2
[1] FALSE

Clustering(24) Variable = AMP PEAK 24(19Q13.11) MUTATION ANALYSIS
D24V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 24(19Q13.11) MUTATED    53  34
  AMP PEAK 24(19Q13.11) WILD-TYPE 182  95
  AMP PEAK 24(19Q13.11) MUTATED AMP PEAK 24(19Q13.11) WILD-TYPE 
                             87                             277 
  AMP PEAK 24(19Q13.11) MUTATED AMP PEAK 24(19Q13.11) WILD-TYPE 
                             34                              95 
$`AMP PEAK 24(19Q13.11) MUTATED`
TCGA-BC-A112 TCGA-DD-A4ND TCGA-DD-AAE7 TCGA-DD-AAEA TCGA-ES-A2HS TCGA-G3-A7M9 
        5.03        90.28        21.17        18.90        22.62         1.84 
TCGA-XR-A8TG TCGA-ZP-A9D1 TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GY TCGA-2Y-A9H3 
       29.52         0.69        63.75        41.79        24.89        49.84 
TCGA-3K-AAZ8 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10Y TCGA-BC-A217 
       13.02        37.32        10.13        27.52        23.38        45.93 
TCGA-BC-A3KG TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5261 TCGA-CC-A3M9 TCGA-CC-A7II 
       22.36        13.45         0.66         3.19         9.86        13.12 
TCGA-CC-A8HU TCGA-DD-A113 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A1E9 TCGA-DD-A1EC 
       11.31        79.73       113.00         7.33        90.71        19.79 
TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EI TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A3A7 
       12.95        45.11         6.02        13.64        21.14        13.78 
TCGA-DD-A3A9 TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NQ TCGA-DD-A4NV TCGA-DD-A73F 
       30.61        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-AAEK TCGA-DD-AAVV TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PZ TCGA-ED-A7XO 
       35.08        80.71        13.35         9.73         0.20        14.04 
TCGA-ED-A82E TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-FV-A2QQ TCGA-FV-A3I0 
       13.41        20.61        19.59         0.62        23.97        27.88 
TCGA-FV-A495 TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25X TCGA-G3-A5SM TCGA-G3-A7M6 
        0.03         0.39        51.06        58.49        17.10        20.78 
TCGA-G3-A7M7 TCGA-G3-AAV0 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-K7-AAU7 TCGA-KR-A7K2 
       11.87        15.65        28.90         1.02        11.80        27.25 
TCGA-MI-A75G TCGA-NI-A8LF TCGA-PD-A5DF TCGA-RC-A7S9 TCGA-RC-A7SH TCGA-UB-A7ME 
       22.95        26.27        21.01        21.04        15.39        15.98 
TCGA-WQ-AB4B TCGA-YA-A8S7 TCGA-ZS-A9CF 
       12.99        13.55        79.30 

$`AMP PEAK 24(19Q13.11) WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A5W4 
       83.24        11.74        38.40         8.61        69.57        17.98 
TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4NI TCGA-DD-AADV TCGA-DD-AAE8 TCGA-DD-AAEG 
       36.66         0.36        26.83        18.87        21.83        23.64 
TCGA-EP-A3JL TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A3CG 
        9.96         8.12         6.38        81.73        30.74        22.13 
TCGA-G3-A6UC TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H 
       22.06        20.75         2.14        31.27        12.72        24.56 
TCGA-T1-A6J8 TCGA-UB-A7MF TCGA-UB-AA0V TCGA-ZS-A9CE TCGA-2Y-A9GS TCGA-2Y-A9GT 
        0.76         7.04        10.32        40.80        23.80        53.39 
TCGA-2Y-A9GX TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H4 
       80.28        27.88       120.82        40.41        56.91        47.74 
TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-5C-A9VG 
       18.25        20.81        22.92         1.18         8.55        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-A216 TCGA-BC-A3KF TCGA-BC-A69H TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A2L6 
       44.42         0.26        14.60        12.72        18.48        44.81 
TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-5264 TCGA-CC-A1HT 
        4.24         2.86         3.39         4.24         3.35         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-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-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D 
       83.57        53.33         2.60         0.46        21.76        51.29 
TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EH TCGA-DD-A1EJ 
       79.40        66.31        75.65        11.47        49.15        33.04 
TCGA-DD-A1EK TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 
       18.35        27.19        55.69         5.62        19.76        25.81 
TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 
        7.66        70.06        17.59        20.12       102.74       107.11 
TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK 
       33.14        32.52        30.97        30.15        30.51        39.78 
TCGA-DD-A4NL TCGA-DD-A4NP TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A73A TCGA-DD-A73B 
       56.25       108.76         0.30        80.75        23.93         9.30 
TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 
       23.05        22.78         1.45        13.48         0.53        11.41 
TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF 
       75.65        76.41        55.40        12.53        71.80        12.00 
TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM 
        6.41        53.19        69.11         0.30         3.52        58.16 
TCGA-DD-AACN TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACX 
       42.81        14.20        59.31        51.52        50.33         5.59 
TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 
       47.67         5.62         4.50        18.54        21.63        42.58 
TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADE TCGA-DD-AADG 
       44.22        22.09        40.08        40.54        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-AAE4 TCGA-DD-AAE6 
       18.25        18.15        20.98        18.61        19.99         4.64 
TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAEI 
       23.74        15.72        25.08        26.63        25.78        50.33 
TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW 
       90.48        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        60.99 
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-A7XP TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J 
       12.82        13.15        13.35         1.84         0.20        18.74 
TCGA-EP-A26S TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3R3 
       19.99        11.93        14.40        60.89        19.10        12.03 
TCGA-FV-A496 TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25Y TCGA-G3-A25Z 
        0.33        13.68        53.79        28.27        14.86        21.53 
TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ 
       25.64         5.92        19.53        19.23        25.25        22.95 
TCGA-G3-A5SL TCGA-G3-A7M5 TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV1 TCGA-G3-AAV2 
       20.42        14.70        14.14        15.78        11.80        12.23 
TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A9DB 
       13.55         0.89        11.64         2.14        11.87         2.20 
TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-KR-A7K8 TCGA-LG-A9QC 
        2.99        37.71        17.06        16.83        29.79        13.97 
TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO 
       12.03         9.57        16.67        20.71         7.53        10.85 
TCGA-NI-A4U2 TCGA-O8-A75V TCGA-QA-A7B7 TCGA-RC-A6M4 TCGA-RC-A6M5 TCGA-RC-A6M6 
       58.88        17.69         3.09         0.72         0.49         0.30 
TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB 
       19.33        19.04        15.52        36.10        27.88        19.76 
TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WX-AA44 
       16.44         1.71        10.75        11.34         0.99        20.22 
TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TD TCGA-XR-A8TE TCGA-XR-A8TF TCGA-ZP-A9CV 
       24.85        18.28        33.86        30.41        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-A9CG 
       11.21 

  AMP PEAK 24(19Q13.11) MUTATED AMP PEAK 24(19Q13.11) WILD-TYPE 
                           0.03                            0.20 
  AMP PEAK 24(19Q13.11) MUTATED AMP PEAK 24(19Q13.11) WILD-TYPE 
                         114.35                          120.82 
  AMP PEAK 24(19Q13.11) MUTATED AMP PEAK 24(19Q13.11) WILD-TYPE 
                          20.61                           19.76 
[1] "0.0 - 114.3 (20.6)" "0.2 - 120.8 (19.8)"
[1] "hr=" "1.1"
D24V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE III STAGE IIIA
  AMP PEAK 24(19Q13.11) MUTATED        38       26         0         14
  AMP PEAK 24(19Q13.11) WILD-TYPE     135       61         3         48
                                 vv
clus                              STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 24(19Q13.11) MUTATED            4          0        2         0
  AMP PEAK 24(19Q13.11) WILD-TYPE          5          7        0         1
                                 vv
clus                              STAGE IVB
  AMP PEAK 24(19Q13.11) MUTATED           1
  AMP PEAK 24(19Q13.11) WILD-TYPE         1
D24V3, multiclass
            clus
vv           AMP PEAK 24(19Q13.11) MUTATED AMP PEAK 24(19Q13.11) WILD-TYPE
  STAGE I                               38                             135
  STAGE II                              26                              61
  STAGE III                              0                               3
  STAGE IIIA                            14                              48
  STAGE IIIB                             4                               5
  STAGE IIIC                             0                               7
  STAGE IV                               2                               0
  STAGE IVA                              0                               1
  STAGE IVB                              1                               1
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               T1  T2  T3  T4
  AMP PEAK 24(19Q13.11) MUTATED    39  28  20   4
  AMP PEAK 24(19Q13.11) WILD-TYPE 144  67  57   8
D24V4, multiclass
    clus
vv   AMP PEAK 24(19Q13.11) MUTATED AMP PEAK 24(19Q13.11) WILD-TYPE
  T1                            39                             144
  T2                            28                              67
  T3                            20                              57
  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"
D24V5, binary
                                 cls
clus                                0   1
  AMP PEAK 24(19Q13.11) MUTATED    57   0
  AMP PEAK 24(19Q13.11) WILD-TYPE 197   3
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 24(19Q13.11) MUTATED     57    0
  AMP PEAK 24(19Q13.11) WILD-TYPE  197    3
   clus
vv  AMP PEAK 24(19Q13.11) MUTATED AMP PEAK 24(19Q13.11) WILD-TYPE
  0                            57                             197
  1                             0                               3
[1] 2 2
[1] FALSE
D24V6, binary
                                 cls
clus                                0   1
  AMP PEAK 24(19Q13.11) MUTATED    60   3
  AMP PEAK 24(19Q13.11) WILD-TYPE 206   1
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 24(19Q13.11) MUTATED     60    3
  AMP PEAK 24(19Q13.11) WILD-TYPE  206    1
   clus
vv  AMP PEAK 24(19Q13.11) MUTATED AMP PEAK 24(19Q13.11) WILD-TYPE
  0                            60                             206
  1                             3                               1
[1] 2 2
[1] FALSE
D24V7, binary
                                 cls
clus                                0   1
  AMP PEAK 24(19Q13.11) MUTATED    34  57
  AMP PEAK 24(19Q13.11) WILD-TYPE  84 195
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 24(19Q13.11) MUTATED     34   57
  AMP PEAK 24(19Q13.11) WILD-TYPE   84  195
        clus
vv       AMP PEAK 24(19Q13.11) MUTATED AMP PEAK 24(19Q13.11) WILD-TYPE
  FEMALE                            34                              84
  MALE                              57                             195
[1] 2 2
[1] FALSE
D24V8, binary
                                 cls
clus                                0   1
  AMP PEAK 24(19Q13.11) MUTATED    79   2
  AMP PEAK 24(19Q13.11) WILD-TYPE 259   7
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 24(19Q13.11) MUTATED     79    2
  AMP PEAK 24(19Q13.11) WILD-TYPE  259    7
     clus
vv    AMP PEAK 24(19Q13.11) MUTATED AMP PEAK 24(19Q13.11) WILD-TYPE
  NO                             79                             259
  YES                             2                               7
[1] 2 2
[1] FALSE
                                 vv
clus                              FIBROLAMELLAR CARCINOMA
  AMP PEAK 24(19Q13.11) MUTATED                         0
  AMP PEAK 24(19Q13.11) WILD-TYPE                       3
                                 vv
clus                              HEPATOCELLULAR CARCINOMA
  AMP PEAK 24(19Q13.11) MUTATED                         88
  AMP PEAK 24(19Q13.11) WILD-TYPE                      272
                                 vv
clus                              HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK 24(19Q13.11) MUTATED                                  3
  AMP PEAK 24(19Q13.11) WILD-TYPE                                4
D24V9, multiclass
                                  clus
vv                                 AMP PEAK 24(19Q13.11) MUTATED
  FIBROLAMELLAR CARCINOMA                                      0
  HEPATOCELLULAR CARCINOMA                                    88
  HEPATOCHOLANGIOCARCINOMA (MIXED)                             3
                                  clus
vv                                 AMP PEAK 24(19Q13.11) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                        3
  HEPATOCELLULAR CARCINOMA                                     272
  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(19Q13.11) MUTATED    79   2   1   8
  AMP PEAK 24(19Q13.11) WILD-TYPE 245  15   0  13
D24V10, multiclass
    clus
vv   AMP PEAK 24(19Q13.11) MUTATED AMP PEAK 24(19Q13.11) WILD-TYPE
  R0                            79                             245
  R1                             2                              15
  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 24(19Q13.11) MUTATED                                  1    32
  AMP PEAK 24(19Q13.11) WILD-TYPE                                1   126
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 24(19Q13.11) MUTATED                           5    52
  AMP PEAK 24(19Q13.11) WILD-TYPE                        12   131
D24V11, multiclass
                                  clus
vv                                 AMP PEAK 24(19Q13.11) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                       32
  BLACK OR AFRICAN AMERICAN                                    5
  WHITE                                                       52
                                  clus
vv                                 AMP PEAK 24(19Q13.11) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               1
  ASIAN                                                        126
  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"
D24V12, binary
                                 cls
clus                                0   1
  AMP PEAK 24(19Q13.11) MUTATED     5  82
  AMP PEAK 24(19Q13.11) WILD-TYPE  11 253
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 24(19Q13.11) MUTATED      5   82
  AMP PEAK 24(19Q13.11) WILD-TYPE   11  253
                        clus
vv                       AMP PEAK 24(19Q13.11) MUTATED
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                            82
                        clus
vv                       AMP PEAK 24(19Q13.11) WILD-TYPE
  HISPANIC OR LATINO                                  11
  NOT HISPANIC OR LATINO                             253
[1] 2 2
[1] FALSE

Clustering(25) Variable = AMP PEAK 25(20Q13.13) MUTATION ANALYSIS
D25V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 25(20Q13.13) MUTATED    71  52
  AMP PEAK 25(20Q13.13) WILD-TYPE 164  77
  AMP PEAK 25(20Q13.13) MUTATED AMP PEAK 25(20Q13.13) WILD-TYPE 
                            123                             241 
  AMP PEAK 25(20Q13.13) MUTATED AMP PEAK 25(20Q13.13) WILD-TYPE 
                             52                              77 
$`AMP PEAK 25(20Q13.13) MUTATED`
TCGA-DD-A4ND TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-ES-A2HS TCGA-FV-A3R2 
       90.28        18.90        23.64         9.96        22.62         6.38 
TCGA-G3-A25W TCGA-G3-A7M9 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-XR-A8TG TCGA-2Y-A9GS 
       30.74         1.84        31.27        12.72        29.52        23.80 
TCGA-2Y-A9GX TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H8 TCGA-2Y-A9H9 
       80.28        24.89        27.88       120.82        20.81        22.92 
TCGA-2Y-A9HA TCGA-5C-A9VH TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-A10Q TCGA-BC-A10R 
        1.18        10.59         1.51        48.99        37.32        10.13 
TCGA-BC-A10T TCGA-BC-A10Y TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A69H TCGA-BD-A2L6 
       27.52        23.38        45.93         0.26        14.60        44.81 
TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5261 TCGA-CC-5264 TCGA-CC-A1HT TCGA-CC-A3M9 
       13.45         0.66         3.19         3.35         3.32         9.86 
TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7II 
       10.36        11.93        11.41         8.94         7.13        13.12 
TCGA-CC-A7IL TCGA-CC-A8HU TCGA-CC-A9FW TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A 
        9.14        11.31         8.15       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-A4NN TCGA-DD-A4NO 
       21.14       102.74        13.78        30.61        29.56        73.81 
TCGA-DD-A4NR TCGA-DD-A4NV TCGA-DD-A73G TCGA-DD-AAC8 TCGA-DD-AACB TCGA-DD-AACC 
        0.30        78.84       114.35         0.53        76.41        55.40 
TCGA-DD-AACI TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACV 
       53.19        61.68        13.64        59.31        51.35        50.33 
TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD6 TCGA-DD-AADA TCGA-DD-AADD TCGA-DD-AADF 
        5.62         4.50        22.09        40.54        40.47         3.78 
TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AAE0 
       29.52        14.89        15.58        18.21        19.30        18.25 
TCGA-DD-AAE3 TCGA-DD-AAE6 TCGA-DD-AAE9 TCGA-DD-AAEH TCGA-DD-AAEK TCGA-DD-AAVV 
       18.61         4.64        23.74        25.78        35.08        80.71 
TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7XO TCGA-ED-A82E TCGA-ED-A8O6 TCGA-EP-A2KB 
       13.35         9.73        14.04        13.41         1.84        19.59 
TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A495 TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A5SM 
       60.89        23.97         0.03         0.39        13.68        17.10 
TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-AAV1 TCGA-G3-AAV6 TCGA-HP-A5MZ TCGA-KR-A7K2 
       20.78        11.87        11.80         2.14         2.99        27.25 
TCGA-MI-A75G TCGA-PD-A5DF TCGA-RC-A6M5 TCGA-RC-A6M6 TCGA-RG-A7D4 TCGA-UB-A7MA 
       22.95        21.01         0.49         0.30        36.10        27.88 
TCGA-UB-A7MB TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-XR-A8TD 
       19.76        15.98        10.75         0.99        12.99        33.86 
TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZS-A9CD 
       22.78        13.55        45.57 

$`AMP PEAK 25(20Q13.13) WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 
       83.24        11.74        38.40         8.61        69.57         5.03 
TCGA-BC-A5W4 TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4NI TCGA-DD-AADV TCGA-DD-AAE7 
       17.98        36.66         0.36        26.83        18.87        21.17 
TCGA-DD-AAE8 TCGA-FV-A3I1 TCGA-FV-A4ZP TCGA-G3-A3CG TCGA-G3-A6UC TCGA-K7-A5RF 
       21.83         8.12        81.73        22.13        22.06        20.75 
TCGA-KR-A7K0 TCGA-MI-A75H TCGA-T1-A6J8 TCGA-UB-A7MF TCGA-UB-AA0V TCGA-ZP-A9D1 
        2.14        24.56         0.76         7.04        10.32         0.69 
TCGA-ZS-A9CE TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9H1 TCGA-2Y-A9H2 
       40.80        53.39        63.75        41.79        40.41        56.91 
TCGA-2Y-A9H3 TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-5C-A9VG 
       49.84        47.74        18.25         8.55        13.02        10.78 
TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D TCGA-BC-4073 TCGA-BC-A10S TCGA-BC-A10U 
        0.66        17.10        14.76        27.91        46.78        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A3KG TCGA-BC-A69I 
        2.99        25.32         1.12        44.42        22.36        12.72 
TCGA-BC-A8YO TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A3MA 
       18.48         4.24         2.86         3.39         4.24         9.96 
TCGA-CC-A5UD TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7IJ TCGA-CC-A7IK 
        9.99        21.34         9.83        12.00        12.56         8.61 
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-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC 
       53.33        51.29        90.71        79.40        66.31        19.79 
TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EI TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39W 
       75.65        11.47         6.02        18.35        13.64        27.19 
TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 
       55.69         5.62        19.76        25.81         7.66        70.06 
TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A6 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NF 
       17.59        20.12       107.11        33.14        32.52        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-A4NS TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E 
       80.75        23.93         9.30        23.05        22.78         1.45 
TCGA-DD-A73F TCGA-DD-AA3A TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACD TCGA-DD-AACE 
       35.67        13.48        11.41        75.65        12.53        71.80 
TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL 
       12.00        15.42         6.41        69.11         0.30         3.52 
TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACQ TCGA-DD-AACU TCGA-DD-AACW TCGA-DD-AACX 
       58.16        42.81        14.20        51.52        46.82         5.59 
TCGA-DD-AACY TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD8 
       47.67        18.54        21.63        42.58        44.22        40.08 
TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADE TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ 
       40.83        13.97        39.52        37.64        35.67        35.05 
TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR 
       34.49        20.91         0.39        15.06        14.33        66.67 
TCGA-DD-AADY TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE4 TCGA-DD-AAEB TCGA-DD-AAED 
       18.25        18.15        20.98        19.99        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        90.48        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        60.99        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-A3R3 TCGA-FV-A496 TCGA-G3-A25T 
       14.40        19.10        27.88        12.03         0.33        51.06 
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-A7M5 TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV3 
       14.70        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        11.64        11.87        28.90         1.02         2.20 
TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K8 TCGA-LG-A9QC 
       37.71        17.06        16.83        11.80        29.79        13.97 
TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO 
       12.03         9.57        16.67        20.71         7.53        10.85 
TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-QA-A7B7 TCGA-RC-A6M4 TCGA-RC-A7S9 
       58.88        26.27        17.69         3.09         0.72        21.04 
TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-UB-A7MC TCGA-UB-A7MD 
       19.33        19.04        15.39        15.52        16.44         1.71 
TCGA-WJ-A86L TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TE TCGA-ZP-A9CV 
       11.34        20.22        24.85        18.28        30.41        35.77 
TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CF 
       25.71        23.21        35.87        25.15        12.99        79.30 
TCGA-ZS-A9CG 
       11.21 

  AMP PEAK 25(20Q13.13) MUTATED AMP PEAK 25(20Q13.13) WILD-TYPE 
                           0.03                            0.20 
  AMP PEAK 25(20Q13.13) MUTATED AMP PEAK 25(20Q13.13) WILD-TYPE 
                         120.82                          108.76 
  AMP PEAK 25(20Q13.13) MUTATED AMP PEAK 25(20Q13.13) WILD-TYPE 
                          18.61                           20.22 
[1] "0.0 - 120.8 (18.6)" "0.2 - 108.8 (20.2)"
[1] "hr=" "1.4"
D25V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE III STAGE IIIA
  AMP PEAK 25(20Q13.13) MUTATED        52       26         2         25
  AMP PEAK 25(20Q13.13) WILD-TYPE     121       61         1         37
                                 vv
clus                              STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 25(20Q13.13) MUTATED            6          2        1         1
  AMP PEAK 25(20Q13.13) WILD-TYPE          3          5        1         0
                                 vv
clus                              STAGE IVB
  AMP PEAK 25(20Q13.13) MUTATED           1
  AMP PEAK 25(20Q13.13) WILD-TYPE         1
D25V3, multiclass
            clus
vv           AMP PEAK 25(20Q13.13) MUTATED AMP PEAK 25(20Q13.13) WILD-TYPE
  STAGE I                               52                             121
  STAGE II                              26                              61
  STAGE III                              2                               1
  STAGE IIIA                            25                              37
  STAGE IIIB                             6                               3
  STAGE IIIC                             2                               5
  STAGE IV                               1                               1
  STAGE IVA                              1                               0
  STAGE IVB                              1                               1
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               T1  T2  T3  T4
  AMP PEAK 25(20Q13.13) MUTATED    55  29  34   6
  AMP PEAK 25(20Q13.13) WILD-TYPE 128  66  43   6
D25V4, multiclass
    clus
vv   AMP PEAK 25(20Q13.13) MUTATED AMP PEAK 25(20Q13.13) WILD-TYPE
  T1                            55                             128
  T2                            29                              66
  T3                            34                              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"
D25V5, binary
                                 cls
clus                                0   1
  AMP PEAK 25(20Q13.13) MUTATED    84   2
  AMP PEAK 25(20Q13.13) WILD-TYPE 170   1
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 25(20Q13.13) MUTATED     84    2
  AMP PEAK 25(20Q13.13) WILD-TYPE  170    1
   clus
vv  AMP PEAK 25(20Q13.13) MUTATED AMP PEAK 25(20Q13.13) WILD-TYPE
  0                            84                             170
  1                             2                               1
[1] 2 2
[1] FALSE
D25V6, binary
                                 cls
clus                                0   1
  AMP PEAK 25(20Q13.13) MUTATED    94   2
  AMP PEAK 25(20Q13.13) WILD-TYPE 172   2
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 25(20Q13.13) MUTATED     94    2
  AMP PEAK 25(20Q13.13) WILD-TYPE  172    2
   clus
vv  AMP PEAK 25(20Q13.13) MUTATED AMP PEAK 25(20Q13.13) WILD-TYPE
  0                            94                             172
  1                             2                               2
[1] 2 2
[1] FALSE
D25V7, binary
                                 cls
clus                                0   1
  AMP PEAK 25(20Q13.13) MUTATED    46  78
  AMP PEAK 25(20Q13.13) WILD-TYPE  72 174
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 25(20Q13.13) MUTATED     46   78
  AMP PEAK 25(20Q13.13) WILD-TYPE   72  174
        clus
vv       AMP PEAK 25(20Q13.13) MUTATED AMP PEAK 25(20Q13.13) WILD-TYPE
  FEMALE                            46                              72
  MALE                              78                             174
[1] 2 2
[1] FALSE
D25V8, binary
                                 cls
clus                                0   1
  AMP PEAK 25(20Q13.13) MUTATED   111   2
  AMP PEAK 25(20Q13.13) WILD-TYPE 227   7
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 25(20Q13.13) MUTATED    111    2
  AMP PEAK 25(20Q13.13) WILD-TYPE  227    7
     clus
vv    AMP PEAK 25(20Q13.13) MUTATED AMP PEAK 25(20Q13.13) WILD-TYPE
  NO                            111                             227
  YES                             2                               7
[1] 2 2
[1] FALSE
                                 vv
clus                              FIBROLAMELLAR CARCINOMA
  AMP PEAK 25(20Q13.13) MUTATED                         1
  AMP PEAK 25(20Q13.13) WILD-TYPE                       2
                                 vv
clus                              HEPATOCELLULAR CARCINOMA
  AMP PEAK 25(20Q13.13) MUTATED                        121
  AMP PEAK 25(20Q13.13) WILD-TYPE                      239
                                 vv
clus                              HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK 25(20Q13.13) MUTATED                                  2
  AMP PEAK 25(20Q13.13) WILD-TYPE                                5
D25V9, multiclass
                                  clus
vv                                 AMP PEAK 25(20Q13.13) MUTATED
  FIBROLAMELLAR CARCINOMA                                      1
  HEPATOCELLULAR CARCINOMA                                   121
  HEPATOCHOLANGIOCARCINOMA (MIXED)                             2
                                  clus
vv                                 AMP PEAK 25(20Q13.13) 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
  AMP PEAK 25(20Q13.13) MUTATED   107   8   1   5
  AMP PEAK 25(20Q13.13) WILD-TYPE 217   9   0  16
D25V10, multiclass
    clus
vv   AMP PEAK 25(20Q13.13) MUTATED AMP PEAK 25(20Q13.13) WILD-TYPE
  R0                           107                             217
  R1                             8                               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
  AMP PEAK 25(20Q13.13) MUTATED                                  0    51
  AMP PEAK 25(20Q13.13) WILD-TYPE                                2   107
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 25(20Q13.13) MUTATED                           4    67
  AMP PEAK 25(20Q13.13) WILD-TYPE                        13   116
D25V11, multiclass
                                  clus
vv                                 AMP PEAK 25(20Q13.13) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                       51
  BLACK OR AFRICAN AMERICAN                                    4
  WHITE                                                       67
                                  clus
vv                                 AMP PEAK 25(20Q13.13) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               2
  ASIAN                                                        107
  BLACK OR AFRICAN AMERICAN                                     13
  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"
D25V12, binary
                                 cls
clus                                0   1
  AMP PEAK 25(20Q13.13) MUTATED     6 110
  AMP PEAK 25(20Q13.13) WILD-TYPE  10 225
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 25(20Q13.13) MUTATED      6  110
  AMP PEAK 25(20Q13.13) WILD-TYPE   10  225
                        clus
vv                       AMP PEAK 25(20Q13.13) MUTATED
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                           110
                        clus
vv                       AMP PEAK 25(20Q13.13) WILD-TYPE
  HISPANIC OR LATINO                                  10
  NOT HISPANIC OR LATINO                             225
[1] 2 2
[1] FALSE

Clustering(26) Variable = AMP PEAK 26(20Q13.33) MUTATION ANALYSIS
D26V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 26(20Q13.33) MUTATED    74  52
  AMP PEAK 26(20Q13.33) WILD-TYPE 161  77
  AMP PEAK 26(20Q13.33) MUTATED AMP PEAK 26(20Q13.33) WILD-TYPE 
                            126                             238 
  AMP PEAK 26(20Q13.33) MUTATED AMP PEAK 26(20Q13.33) WILD-TYPE 
                             52                              77 
$`AMP PEAK 26(20Q13.33) MUTATED`
TCGA-DD-A4ND TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-ES-A2HS TCGA-FV-A3R2 
       90.28        18.90        23.64         9.96        22.62         6.38 
TCGA-G3-A25W TCGA-G3-A7M9 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-XR-A8TG TCGA-2Y-A9GS 
       30.74         1.84        31.27        12.72        29.52        23.80 
TCGA-2Y-A9GX TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-5C-A9VG 
       80.28        24.89        27.88        22.92         1.18        10.78 
TCGA-5C-A9VH TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10Y 
       10.59         1.51        48.99        37.32        10.13        23.38 
TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A69H TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BW-A5NO 
       45.93         0.26        14.60        44.81        13.45         0.66 
TCGA-CC-5261 TCGA-CC-5264 TCGA-CC-A3M9 TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UC 
        3.19         3.35         9.86        10.36        11.93        11.41 
TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7II TCGA-CC-A7IL TCGA-CC-A8HU TCGA-CC-A8HV 
        8.94         7.13        13.12         9.14        11.31         9.17 
TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B 
        8.15        79.73       113.00         7.33         2.60         0.46 
TCGA-DD-A11C TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EJ TCGA-DD-A39V 
       21.76        12.95        45.11        49.15        33.04        21.14 
TCGA-DD-A3A5 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NR 
      102.74        13.78        30.61        29.56        73.81         0.30 
TCGA-DD-A4NV TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AAC8 TCGA-DD-AACB TCGA-DD-AACC 
       78.84        35.67       114.35         0.53        76.41        55.40 
TCGA-DD-AACI TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT 
       53.19        61.68        13.64        14.20        59.31        51.35 
TCGA-DD-AACV TCGA-DD-AACX TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD6 TCGA-DD-AADA 
       50.33         5.59         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-AAEH 
       19.30        18.25        18.61         4.64        23.74        25.78 
TCGA-DD-AAEK TCGA-DD-AAVR TCGA-DD-AAVV TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7XO 
       35.08        82.62        80.71        13.35         9.73        14.04 
TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-EP-A2KA TCGA-EP-A2KB TCGA-FV-A23B 
       13.41        13.35         1.84        20.61        19.59        60.89 
TCGA-FV-A2QQ TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25X TCGA-G3-A5SM TCGA-G3-A7M6 
       23.97         0.39        13.68        58.49        17.10        20.78 
TCGA-G3-AAV1 TCGA-G3-AAV6 TCGA-HP-A5MZ TCGA-KR-A7K2 TCGA-MI-A75G TCGA-PD-A5DF 
       11.80         2.14         2.99        27.25        22.95        21.01 
TCGA-RC-A6M6 TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7ME TCGA-UB-AA0U 
        0.30        36.10        27.88        19.76        15.98        10.75 
TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-XR-A8TD TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZS-A9CD 
        0.99        12.99        33.86        22.78        13.55        45.57 

$`AMP PEAK 26(20Q13.33) WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 
       83.24        11.74        38.40         8.61        69.57         5.03 
TCGA-BC-A5W4 TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4NI TCGA-DD-AADV TCGA-DD-AAE7 
       17.98        36.66         0.36        26.83        18.87        21.17 
TCGA-DD-AAE8 TCGA-FV-A3I1 TCGA-FV-A4ZP TCGA-G3-A3CG TCGA-G3-A6UC TCGA-K7-A5RF 
       21.83         8.12        81.73        22.13        22.06        20.75 
TCGA-KR-A7K0 TCGA-MI-A75H TCGA-T1-A6J8 TCGA-UB-A7MF TCGA-UB-AA0V TCGA-ZP-A9D1 
        2.14        24.56         0.76         7.04        10.32         0.69 
TCGA-ZS-A9CE TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9H0 TCGA-2Y-A9H1 
       40.80        53.39        63.75        41.79       120.82        40.41 
TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-2Y-A9HB 
       56.91        49.84        47.74        18.25        20.81         8.55 
TCGA-3K-AAZ8 TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D TCGA-BC-4073 TCGA-BC-A10S 
       13.02         0.66        17.10        14.76        27.91        46.78 
TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Z TCGA-BC-A216 
       27.52        27.52         2.99        25.32         1.12        44.42 
TCGA-BC-A3KG TCGA-BC-A69I TCGA-BC-A8YO TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5262 
       22.36        12.72        18.48         4.24         2.86         3.39 
TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3MA TCGA-CC-A5UD TCGA-CC-A7IF TCGA-CC-A7IG 
        4.24         3.32         9.96         9.99        21.34         9.83 
TCGA-CC-A7IH TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A8HT TCGA-CC-A9FS TCGA-DD-A114 
       12.00        12.56         8.61         4.60         6.94        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-A4NA TCGA-DD-A4NB 
       70.06        17.59        20.12       107.11        33.14        32.52 
TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NP 
       30.97        30.15        30.51        39.78        56.25       108.76 
TCGA-DD-A4NQ TCGA-DD-A4NS TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D 
       12.26        80.75        23.93         9.30        23.05        22.78 
TCGA-DD-A73E TCGA-DD-AA3A TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACD TCGA-DD-AACE 
        1.45        13.48        11.41        75.65        12.53        71.80 
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-AACU TCGA-DD-AACW TCGA-DD-AACY TCGA-DD-AAD1 
       58.16        42.81        51.52        46.82        47.67        18.54 
TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD8 TCGA-DD-AADB TCGA-DD-AADC 
       21.63        42.58        44.22        40.08        40.83        13.97 
TCGA-DD-AADE TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL 
       39.52        37.64        35.67        35.05        34.49        20.91 
TCGA-DD-AADM TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADY TCGA-DD-AAE1 
        0.39        15.06        14.33        66.67        18.25        18.15 
TCGA-DD-AAE2 TCGA-DD-AAE4 TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEI 
       20.98        19.99        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 
       90.48        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        60.99        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-A3R3 TCGA-FV-A495 
       11.93        14.40        19.10        27.88        12.03         0.03 
TCGA-FV-A496 TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25Y TCGA-G3-A25Z 
        0.33        51.06        53.79        28.27        14.86        21.53 
TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ 
       25.64         5.92        19.53        19.23        25.25        22.95 
TCGA-G3-A5SL TCGA-G3-A7M5 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV0 
       20.42        14.70        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-A3OU 
       12.23        13.55         0.89        11.64        11.87        28.90 
TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 
        1.02         2.20        37.71        17.06        16.83        11.80 
TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75I 
       29.79        13.97        12.03         9.57        16.67        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-A6M4 TCGA-RC-A6M5 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH 
        0.72         0.49        21.04        19.33        19.04        15.39 
TCGA-RC-A7SK TCGA-UB-A7MC TCGA-UB-A7MD TCGA-WJ-A86L TCGA-WX-AA44 TCGA-WX-AA46 
       15.52        16.44         1.71        11.34        20.22        24.85 
TCGA-WX-AA47 TCGA-XR-A8TE TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 
       18.28        30.41        35.77        25.71        23.21        35.87 
TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CF TCGA-ZS-A9CG 
       25.15        12.99        79.30        11.21 

  AMP PEAK 26(20Q13.33) MUTATED AMP PEAK 26(20Q13.33) WILD-TYPE 
                           0.26                            0.03 
  AMP PEAK 26(20Q13.33) MUTATED AMP PEAK 26(20Q13.33) WILD-TYPE 
                         114.35                          120.82 
  AMP PEAK 26(20Q13.33) MUTATED AMP PEAK 26(20Q13.33) WILD-TYPE 
                         18.755                          20.170 
[1] "0.3 - 114.3 (18.8)" "0.0 - 120.8 (20.2)"
[1] "hr=" "1.4"
D26V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE III STAGE IIIA
  AMP PEAK 26(20Q13.33) MUTATED        53       31         2         25
  AMP PEAK 26(20Q13.33) WILD-TYPE     120       56         1         37
                                 vv
clus                              STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 26(20Q13.33) MUTATED            6          2        2         0
  AMP PEAK 26(20Q13.33) WILD-TYPE          3          5        0         1
                                 vv
clus                              STAGE IVB
  AMP PEAK 26(20Q13.33) MUTATED           1
  AMP PEAK 26(20Q13.33) WILD-TYPE         1
D26V3, multiclass
            clus
vv           AMP PEAK 26(20Q13.33) MUTATED AMP PEAK 26(20Q13.33) WILD-TYPE
  STAGE I                               53                             120
  STAGE II                              31                              56
  STAGE III                              2                               1
  STAGE IIIA                            25                              37
  STAGE IIIB                             6                               3
  STAGE IIIC                             2                               5
  STAGE IV                               2                               0
  STAGE IVA                              0                               1
  STAGE IVB                              1                               1
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               T1  T2  T3  T4
  AMP PEAK 26(20Q13.33) MUTATED    54  35  34   5
  AMP PEAK 26(20Q13.33) WILD-TYPE 129  60  43   7
D26V4, multiclass
    clus
vv   AMP PEAK 26(20Q13.33) MUTATED AMP PEAK 26(20Q13.33) WILD-TYPE
  T1                            54                             129
  T2                            35                              60
  T3                            34                              43
  T4                             5                               7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V5, binary
                                 cls
clus                                0   1
  AMP PEAK 26(20Q13.33) MUTATED    92   1
  AMP PEAK 26(20Q13.33) WILD-TYPE 162   2
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 26(20Q13.33) MUTATED     92    1
  AMP PEAK 26(20Q13.33) WILD-TYPE  162    2
   clus
vv  AMP PEAK 26(20Q13.33) MUTATED AMP PEAK 26(20Q13.33) WILD-TYPE
  0                            92                             162
  1                             1                               2
[1] 2 2
[1] FALSE
D26V6, binary
                                 cls
clus                                0   1
  AMP PEAK 26(20Q13.33) MUTATED    99   3
  AMP PEAK 26(20Q13.33) WILD-TYPE 167   1
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 26(20Q13.33) MUTATED     99    3
  AMP PEAK 26(20Q13.33) WILD-TYPE  167    1
   clus
vv  AMP PEAK 26(20Q13.33) MUTATED AMP PEAK 26(20Q13.33) WILD-TYPE
  0                            99                             167
  1                             3                               1
[1] 2 2
[1] FALSE
D26V7, binary
                                 cls
clus                                0   1
  AMP PEAK 26(20Q13.33) MUTATED    49  79
  AMP PEAK 26(20Q13.33) WILD-TYPE  69 173
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 26(20Q13.33) MUTATED     49   79
  AMP PEAK 26(20Q13.33) WILD-TYPE   69  173
        clus
vv       AMP PEAK 26(20Q13.33) MUTATED AMP PEAK 26(20Q13.33) WILD-TYPE
  FEMALE                            49                              69
  MALE                              79                             173
[1] 2 2
[1] FALSE
D26V8, binary
                                 cls
clus                                0   1
  AMP PEAK 26(20Q13.33) MUTATED   117   2
  AMP PEAK 26(20Q13.33) WILD-TYPE 221   7
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 26(20Q13.33) MUTATED    117    2
  AMP PEAK 26(20Q13.33) WILD-TYPE  221    7
     clus
vv    AMP PEAK 26(20Q13.33) MUTATED AMP PEAK 26(20Q13.33) WILD-TYPE
  NO                            117                             221
  YES                             2                               7
[1] 2 2
[1] FALSE
                                 vv
clus                              FIBROLAMELLAR CARCINOMA
  AMP PEAK 26(20Q13.33) MUTATED                         0
  AMP PEAK 26(20Q13.33) WILD-TYPE                       3
                                 vv
clus                              HEPATOCELLULAR CARCINOMA
  AMP PEAK 26(20Q13.33) MUTATED                        126
  AMP PEAK 26(20Q13.33) WILD-TYPE                      234
                                 vv
clus                              HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK 26(20Q13.33) MUTATED                                  2
  AMP PEAK 26(20Q13.33) WILD-TYPE                                5
D26V9, multiclass
                                  clus
vv                                 AMP PEAK 26(20Q13.33) MUTATED
  FIBROLAMELLAR CARCINOMA                                      0
  HEPATOCELLULAR CARCINOMA                                   126
  HEPATOCHOLANGIOCARCINOMA (MIXED)                             2
                                  clus
vv                                 AMP PEAK 26(20Q13.33) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                        3
  HEPATOCELLULAR CARCINOMA                                     234
  HEPATOCHOLANGIOCARCINOMA (MIXED)                               5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               R0  R1  R2  RX
  AMP PEAK 26(20Q13.33) MUTATED   112   7   1   6
  AMP PEAK 26(20Q13.33) WILD-TYPE 212  10   0  15
D26V10, multiclass
    clus
vv   AMP PEAK 26(20Q13.33) MUTATED AMP PEAK 26(20Q13.33) WILD-TYPE
  R0                           112                             212
  R1                             7                              10
  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 26(20Q13.33) MUTATED                                  0    56
  AMP PEAK 26(20Q13.33) WILD-TYPE                                2   102
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 26(20Q13.33) MUTATED                           4    66
  AMP PEAK 26(20Q13.33) WILD-TYPE                        13   117
D26V11, multiclass
                                  clus
vv                                 AMP PEAK 26(20Q13.33) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                       56
  BLACK OR AFRICAN AMERICAN                                    4
  WHITE                                                       66
                                  clus
vv                                 AMP PEAK 26(20Q13.33) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               2
  ASIAN                                                        102
  BLACK OR AFRICAN AMERICAN                                     13
  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"
D26V12, binary
                                 cls
clus                                0   1
  AMP PEAK 26(20Q13.33) MUTATED     6 115
  AMP PEAK 26(20Q13.33) WILD-TYPE  10 220
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 26(20Q13.33) MUTATED      6  115
  AMP PEAK 26(20Q13.33) WILD-TYPE   10  220
                        clus
vv                       AMP PEAK 26(20Q13.33) MUTATED
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                           115
                        clus
vv                       AMP PEAK 26(20Q13.33) WILD-TYPE
  HISPANIC OR LATINO                                  10
  NOT HISPANIC OR LATINO                             220
[1] 2 2
[1] FALSE

Clustering(27) Variable = AMP PEAK 27(XQ28) MUTATION ANALYSIS
D27V1, survival
                             sevent
clus2                           0   1
  AMP PEAK 27(XQ28) MUTATED    59  27
  AMP PEAK 27(XQ28) WILD-TYPE 176 102
  AMP PEAK 27(XQ28) MUTATED AMP PEAK 27(XQ28) WILD-TYPE 
                         86                         278 
  AMP PEAK 27(XQ28) MUTATED AMP PEAK 27(XQ28) WILD-TYPE 
                         27                         102 
$`AMP PEAK 27(XQ28) MUTATED`
TCGA-EP-A3JL TCGA-ES-A2HS TCGA-G3-A3CG TCGA-G3-A6UC TCGA-LG-A6GG TCGA-2Y-A9GT 
        9.96        22.62        22.13        22.06        12.72        53.39 
TCGA-2Y-A9GW TCGA-2Y-A9GZ TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H4 TCGA-5R-AA1C 
       41.79        27.88        40.41        56.91        47.74        17.10 
TCGA-BC-A10U TCGA-BC-A69I TCGA-BW-A5NO TCGA-CC-5264 TCGA-CC-A3MA TCGA-CC-A5UE 
       27.52        12.72         0.66         3.35         9.96         8.94 
TCGA-CC-A7IE TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A9FS TCGA-DD-A114 TCGA-DD-A11A 
        7.13         9.83        12.00         6.94        37.78         2.60 
TCGA-DD-A1E9 TCGA-DD-A39V TCGA-DD-A39Y TCGA-DD-A3A3 TCGA-DD-A3A7 TCGA-DD-A4NF 
       90.71        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-AAE9 TCGA-DD-AAEH TCGA-DD-AAVP 
       18.21        19.30        18.61        23.74        25.78        90.48 
TCGA-DD-AAVQ TCGA-DD-AAVY TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-ED-A66Y TCGA-ED-A7PZ 
       89.69        64.77        65.39        60.99         9.73         0.20 
TCGA-EP-A12J TCGA-EP-A2KA TCGA-FV-A2QR TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25U 
       18.74        20.61        19.10         0.33         0.39        53.79 
TCGA-G3-A3CJ TCGA-G3-A5SI TCGA-G3-A5SL TCGA-G3-A7M5 TCGA-G3-AAV0 TCGA-G3-AAV2 
       19.53        25.25        20.42        14.70        15.65        12.23 
TCGA-G3-AAV3 TCGA-G3-AAV5 TCGA-G3-AAV7 TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A6G5 
       13.55        11.64        11.87         2.99        37.71        16.83 
TCGA-K7-AAU7 TCGA-KR-A7K8 TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-NI-A4U2 
       11.80        29.79         9.57        16.67        22.95        58.88 
TCGA-O8-A75V TCGA-RC-A6M4 TCGA-UB-A7ME TCGA-WQ-A9G7 TCGA-XR-A8TE TCGA-ZP-A9CV 
       17.69         0.72        15.98         0.99        30.41        35.77 
TCGA-ZS-A9CD TCGA-ZS-A9CG 
       45.57        11.21 

$`AMP PEAK 27(XQ28) WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 
       83.24        11.74        38.40         8.61        69.57         5.03 
TCGA-BC-A5W4 TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV 
       17.98        36.66         0.36        90.28        26.83        18.87 
TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-FV-A3I1 TCGA-FV-A3R2 
       21.17        21.83        18.90        23.64         8.12         6.38 
TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A7M9 TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-KR-A7K7 
       81.73        30.74         1.84        20.75         2.14        31.27 
TCGA-MI-A75H TCGA-T1-A6J8 TCGA-UB-A7MF TCGA-UB-AA0V TCGA-XR-A8TG TCGA-ZP-A9D1 
       24.56         0.76         7.04        10.32        29.52         0.69 
TCGA-ZS-A9CE TCGA-2Y-A9GS TCGA-2Y-A9GU TCGA-2Y-A9GX TCGA-2Y-A9GY TCGA-2Y-A9H0 
       40.80        23.80        63.75        80.28        24.89       120.82 
TCGA-2Y-A9H3 TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB 
       49.84        18.25        20.81        22.92         1.18         8.55 
TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1D TCGA-5R-AAAM 
       13.02        10.78        10.59         0.66        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-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A217 
        2.99        25.32        23.38         1.12        44.42        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-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-A3M9 TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A7IF 
        9.86        10.36        11.93        11.41         9.99        21.34 
TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A7IL TCGA-CC-A8HT TCGA-CC-A8HU 
       13.12        12.56         8.61         9.14         4.60        11.31 
TCGA-CC-A8HV TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 
        9.17         8.15        79.73        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-A1EF TCGA-DD-A1EG TCGA-DD-A1EH 
       19.79        75.65        11.47        12.95        45.11        49.15 
TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39W TCGA-DD-A39X 
        6.02        33.04        18.35        13.64        27.19        55.69 
TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A4 TCGA-DD-A3A5 
       19.76        25.81         7.66        70.06        20.12       102.74 
TCGA-DD-A3A6 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NH TCGA-DD-A4NJ 
      107.11        30.61        33.14        32.52        30.15        30.51 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR 
       56.25        29.56        73.81       108.76        12.26         0.30 
TCGA-DD-A4NS TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73E TCGA-DD-A73F 
       80.75        23.93         9.30        23.05         1.45        35.67 
TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC 
       13.48         0.53        11.41        75.65        76.41        55.40 
TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACK 
       12.53        71.80        12.00        15.42         6.41         0.30 
TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ 
        3.52        58.16        42.81        61.68        13.64        14.20 
TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACZ TCGA-DD-AAD0 
       51.52        50.33        46.82         5.59         5.62         4.50 
TCGA-DD-AAD1 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA 
       18.54        42.58        44.22        22.09        40.08        40.54 
TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG 
       40.83        13.97        40.47        39.52         3.78        37.64 
TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADP 
       35.67        35.05        34.49        20.91         0.39        15.06 
TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 
       14.33        66.67        15.58        18.25        18.25        18.15 
TCGA-DD-AAE2 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE 
       20.98        19.99         4.64        15.72        25.08        26.63 
TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVV 
       50.33        35.08        82.62        59.93        72.39        80.71 
TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW3 TCGA-ED-A459 
       76.18        56.48        62.47        66.25        53.69        29.92 
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-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K 
       14.04        13.15        13.41        13.35         1.84         0.20 
TCGA-EP-A26S TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B 
       19.99        19.59         0.62        11.93        14.40        60.89 
TCGA-FV-A2QQ TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-G3-A25S TCGA-G3-A25T 
       23.97        27.88        12.03         0.03        13.68        51.06 
TCGA-G3-A25V TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI 
       28.27        58.49        14.86        21.53        25.64         5.92 
TCGA-G3-A3CK TCGA-G3-A5SJ TCGA-G3-A5SM TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 
       19.23        22.95        17.10        20.78        11.87        14.14 
TCGA-G3-AAUZ TCGA-G3-AAV1 TCGA-G3-AAV4 TCGA-G3-AAV6 TCGA-GJ-A3OU TCGA-GJ-A6C0 
       15.78        11.80         0.89         2.14        28.90         1.02 
TCGA-GJ-A9DB TCGA-K7-A5RG TCGA-KR-A7K2 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75I 
        2.20        17.06        27.25        13.97        12.03        20.71 
TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A8LF TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A6M5 
        7.53        10.85        26.27        21.01         3.09         0.49 
TCGA-RC-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK 
        0.30        21.04        19.33        19.04        15.39        15.52 
TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-AA0U 
       36.10        27.88        19.76        16.44         1.71        10.75 
TCGA-WJ-A86L TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TD 
       11.34        12.99        20.22        24.85        18.28        33.86 
TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 
       22.78        13.55        25.71        23.21        35.87        25.15 
TCGA-ZP-A9D4 TCGA-ZS-A9CF 
       12.99        79.30 

  AMP PEAK 27(XQ28) MUTATED AMP PEAK 27(XQ28) WILD-TYPE 
                       0.20                        0.03 
  AMP PEAK 27(XQ28) MUTATED AMP PEAK 27(XQ28) WILD-TYPE 
                     114.35                      120.82 
  AMP PEAK 27(XQ28) MUTATED AMP PEAK 27(XQ28) WILD-TYPE 
                     19.975                      19.775 
[1] "0.2 - 114.3 (20.0)" "0.0 - 120.8 (19.8)"
[1] "hr=" "1.2"
D27V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 27(XQ28) MUTATED        42       23         0         14          3
  AMP PEAK 27(XQ28) WILD-TYPE     131       64         3         48          6
                             vv
clus                          STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 27(XQ28) MUTATED            1        0         0         0
  AMP PEAK 27(XQ28) WILD-TYPE          6        2         1         2
D27V3, multiclass
            clus
vv           AMP PEAK 27(XQ28) MUTATED AMP PEAK 27(XQ28) WILD-TYPE
  STAGE I                           42                         131
  STAGE II                          23                          64
  STAGE III                          0                           3
  STAGE IIIA                        14                          48
  STAGE IIIB                         3                           6
  STAGE IIIC                         1                           6
  STAGE IV                           0                           2
  STAGE IVA                          0                           1
  STAGE IVB                          0                           2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           T1  T2  T3  T4
  AMP PEAK 27(XQ28) MUTATED    43  24  17   2
  AMP PEAK 27(XQ28) WILD-TYPE 140  71  60  10
D27V4, multiclass
    clus
vv   AMP PEAK 27(XQ28) MUTATED AMP PEAK 27(XQ28) WILD-TYPE
  T1                        43                         140
  T2                        24                          71
  T3                        17                          60
  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"
D27V5, binary
                             cls
clus                            0   1
  AMP PEAK 27(XQ28) MUTATED    55   0
  AMP PEAK 27(XQ28) WILD-TYPE 199   3
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 27(XQ28) MUTATED     55    0
  AMP PEAK 27(XQ28) WILD-TYPE  199    3
   clus
vv  AMP PEAK 27(XQ28) MUTATED AMP PEAK 27(XQ28) WILD-TYPE
  0                        55                         199
  1                         0                           3
[1] 2 2
[1] FALSE
D27V6, binary
                             cls
clus                            0   1
  AMP PEAK 27(XQ28) MUTATED    61   0
  AMP PEAK 27(XQ28) WILD-TYPE 205   4
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 27(XQ28) MUTATED     61    0
  AMP PEAK 27(XQ28) WILD-TYPE  205    4
   clus
vv  AMP PEAK 27(XQ28) MUTATED AMP PEAK 27(XQ28) WILD-TYPE
  0                        61                         205
  1                         0                           4
[1] 2 2
[1] FALSE
D27V7, binary
                             cls
clus                            0   1
  AMP PEAK 27(XQ28) MUTATED    15  72
  AMP PEAK 27(XQ28) WILD-TYPE 103 180
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 27(XQ28) MUTATED     15   72
  AMP PEAK 27(XQ28) WILD-TYPE  103  180
        clus
vv       AMP PEAK 27(XQ28) MUTATED AMP PEAK 27(XQ28) WILD-TYPE
  FEMALE                        15                         103
  MALE                          72                         180
[1] 2 2
[1] FALSE
D27V8, binary
                             cls
clus                            0   1
  AMP PEAK 27(XQ28) MUTATED    79   2
  AMP PEAK 27(XQ28) WILD-TYPE 259   7
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 27(XQ28) MUTATED     79    2
  AMP PEAK 27(XQ28) WILD-TYPE  259    7
     clus
vv    AMP PEAK 27(XQ28) MUTATED AMP PEAK 27(XQ28) WILD-TYPE
  NO                         79                         259
  YES                         2                           7
[1] 2 2
[1] FALSE
                             vv
clus                          FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  AMP PEAK 27(XQ28) MUTATED                         0                       86
  AMP PEAK 27(XQ28) WILD-TYPE                       3                      274
                             vv
clus                          HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK 27(XQ28) MUTATED                                  1
  AMP PEAK 27(XQ28) WILD-TYPE                                6
D27V9, multiclass
                                  clus
vv                                 AMP PEAK 27(XQ28) MUTATED
  FIBROLAMELLAR CARCINOMA                                  0
  HEPATOCELLULAR CARCINOMA                                86
  HEPATOCHOLANGIOCARCINOMA (MIXED)                         1
                                  clus
vv                                 AMP PEAK 27(XQ28) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                    3
  HEPATOCELLULAR CARCINOMA                                 274
  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 27(XQ28) MUTATED    77   4   0   5
  AMP PEAK 27(XQ28) WILD-TYPE 247  13   1  16
D27V10, multiclass
    clus
vv   AMP PEAK 27(XQ28) MUTATED AMP PEAK 27(XQ28) WILD-TYPE
  R0                        77                         247
  R1                         4                          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 27(XQ28) MUTATED                                  1    36
  AMP PEAK 27(XQ28) WILD-TYPE                                1   122
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 27(XQ28) MUTATED                           5    40
  AMP PEAK 27(XQ28) WILD-TYPE                        12   143
D27V11, multiclass
                                  clus
vv                                 AMP PEAK 27(XQ28) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         1
  ASIAN                                                   36
  BLACK OR AFRICAN AMERICAN                                5
  WHITE                                                   40
                                  clus
vv                                 AMP PEAK 27(XQ28) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                    122
  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"
D27V12, binary
                             cls
clus                            0   1
  AMP PEAK 27(XQ28) MUTATED     2  80
  AMP PEAK 27(XQ28) WILD-TYPE  14 255
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 27(XQ28) MUTATED      2   80
  AMP PEAK 27(XQ28) WILD-TYPE   14  255
                        clus
vv                       AMP PEAK 27(XQ28) MUTATED AMP PEAK 27(XQ28) WILD-TYPE
  HISPANIC OR LATINO                             2                          14
  NOT HISPANIC OR LATINO                        80                         255
[1] 2 2
[1] FALSE

Clustering(28) Variable = DEL PEAK  1(1P36.31) MUTATION ANALYSIS
D28V1, survival
                                sevent
clus2                              0   1
  DEL PEAK  1(1P36.31) MUTATED   101  59
  DEL PEAK  1(1P36.31) WILD-TYPE 134  70
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                           160                            204 
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                            59                             70 
$`DEL PEAK  1(1P36.31) MUTATED`
TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-BD-A3ER TCGA-DD-A4NI TCGA-ES-A2HS TCGA-FV-A4ZP 
       11.74        38.40        36.66        26.83        22.62        81.73 
TCGA-G3-A25W TCGA-G3-A7M9 TCGA-KR-A7K7 TCGA-MI-A75H TCGA-T1-A6J8 TCGA-UB-A7MF 
       30.74         1.84        31.27        24.56         0.76         7.04 
TCGA-ZP-A9D1 TCGA-ZS-A9CE TCGA-2Y-A9GX TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H5 
        0.69        40.80        80.28        56.91        49.84        18.25 
TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-5C-A9VH TCGA-BC-A10Q TCGA-BC-A10S TCGA-BC-A10T 
       13.02        10.78        10.59        37.32        46.78        27.52 
TCGA-BC-A10W TCGA-BC-A10Y TCGA-BC-A217 TCGA-BC-A69H TCGA-CC-5260 TCGA-CC-5261 
        2.99        23.38        45.93        14.60         2.86         3.19 
TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A5UC TCGA-CC-A5UD 
        3.39         4.24         9.96        10.36        11.41         9.99 
TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7IJ TCGA-CC-A7IL TCGA-CC-A9FS 
        7.13        21.34         9.83        12.56         9.14         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-A11D TCGA-DD-A1E9 TCGA-DD-A1EB TCGA-DD-A1EF 
        0.46        21.76        51.29        90.71        66.31        12.95 
TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EJ TCGA-DD-A39X TCGA-DD-A39Z TCGA-DD-A3A0 
       45.11        49.15        33.04        55.69        19.76        25.81 
TCGA-DD-A3A1 TCGA-DD-A3A9 TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NN TCGA-DD-A4NO 
        7.66        30.61        30.15        30.51        29.56        73.81 
TCGA-DD-A4NR TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A 
        0.30        23.93         9.30        35.67       114.35        13.48 
TCGA-DD-AAC8 TCGA-DD-AACA TCGA-DD-AACC TCGA-DD-AACH TCGA-DD-AACJ TCGA-DD-AACK 
        0.53        75.65        55.40         6.41        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-AADD 
       44.22        22.09        40.54        40.83        13.97        40.47 
TCGA-DD-AADF TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADM TCGA-DD-AADN 
        3.78        35.67        35.05        34.49         0.39        29.52 
TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADR TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 
       14.89        15.06        66.67        19.30        18.25        18.25 
TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAEH TCGA-DD-AAEK TCGA-DD-AAVQ 
       18.15        20.98        18.61        25.78        35.08        89.69 
TCGA-DD-AAVS TCGA-DD-AAVW TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-ED-A4XI TCGA-ED-A66X 
       59.93        76.18        62.47        66.25        26.93        13.35 
TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 
        9.73         0.20        12.82        13.41        13.35         1.84 
TCGA-ED-A97K TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK TCGA-FV-A23B TCGA-FV-A2QQ 
        0.20        19.59         0.62        11.93        60.89        23.97 
TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-G3-A25S 
       19.10        27.88        12.03         0.03         0.33        13.68 
TCGA-G3-A25V TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A5SI TCGA-G3-A5SL TCGA-G3-A5SM 
       28.27        58.49        14.86        25.25        20.42        17.10 
TCGA-G3-A7M5 TCGA-G3-AAV1 TCGA-G3-AAV6 TCGA-GJ-A3OU TCGA-KR-A7K2 TCGA-LG-A9QC 
       14.70        11.80         2.14        28.90        27.25        13.97 
TCGA-MI-A75G TCGA-O8-A75V TCGA-RC-A6M4 TCGA-RC-A7S9 TCGA-RC-A7SH TCGA-RC-A7SK 
       22.95        17.69         0.72        21.04        15.39        15.52 
TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MC TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WQ-A9G7 
       36.10        27.88        16.44        15.98        10.75         0.99 
TCGA-WQ-AB4B TCGA-XR-A8TF TCGA-ZP-A9CY TCGA-ZP-A9CZ 
       12.99        22.78        25.71        23.21 

$`DEL PEAK  1(1P36.31) WILD-TYPE`
TCGA-2Y-A9GV TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A5W4 TCGA-DD-A3A8 
       83.24         8.61        69.57         5.03        17.98         0.36 
TCGA-DD-A4ND TCGA-DD-AADV TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG 
       90.28        18.87        21.17        21.83        18.90        23.64 
TCGA-EP-A3JL TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-G3-A3CG TCGA-G3-A6UC TCGA-K7-A5RF 
        9.96         8.12         6.38        22.13        22.06        20.75 
TCGA-KR-A7K0 TCGA-LG-A6GG TCGA-UB-AA0V TCGA-XR-A8TG TCGA-2Y-A9GS TCGA-2Y-A9GT 
        2.14        12.72        10.32        29.52        23.80        53.39 
TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 
       63.75        41.79        24.89        27.88       120.82        40.41 
TCGA-2Y-A9H4 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-5C-AAPD 
       47.74        20.81        22.92         1.18         8.55         0.66 
TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10R 
       17.10        14.76         1.51        48.99        27.91        10.13 
TCGA-BC-A10U TCGA-BC-A10X TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A3KF TCGA-BC-A3KG 
       27.52        25.32         1.12        44.42         0.26        22.36 
TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5258 
       12.72        18.48        44.81        13.45         0.66         4.24 
TCGA-CC-5264 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MC TCGA-CC-A5UE TCGA-CC-A7IH 
        3.35         3.32         9.86        11.93         8.94        12.00 
TCGA-CC-A7II TCGA-CC-A7IK TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV TCGA-DD-A114 
       13.12         8.61         4.60        11.31         9.17        37.78 
TCGA-DD-A115 TCGA-DD-A1EA TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EI 
       83.57        79.40        19.79        75.65        11.47         6.02 
TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39Y TCGA-DD-A3A2 
       18.35        13.64        21.14        27.19         5.62        70.06 
TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A4NA 
       17.59        20.12       102.74       107.11        13.78        33.14 
TCGA-DD-A4NB TCGA-DD-A4NF TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NP TCGA-DD-A4NQ 
       32.52        30.97        39.78        56.25       108.76        12.26 
TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-AAC9 
       80.75        78.84        23.05        22.78         1.45        11.41 
TCGA-DD-AACB TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACI 
       76.41        12.53        71.80        12.00        15.42        53.19 
TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACU 
        3.52        58.16        14.20        59.31        51.35        51.52 
TCGA-DD-AACV TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD2 TCGA-DD-AAD3 
       50.33         5.59        47.67         5.62        21.63        42.58 
TCGA-DD-AAD8 TCGA-DD-AADE TCGA-DD-AADG TCGA-DD-AADL TCGA-DD-AADQ TCGA-DD-AADS 
       40.08        39.52        37.64        20.91        14.33        15.58 
TCGA-DD-AADU TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAED 
       18.21        19.99         4.64        23.74        15.72        25.08 
TCGA-DD-AAEE TCGA-DD-AAEI TCGA-DD-AAVP TCGA-DD-AAVR TCGA-DD-AAVU TCGA-DD-AAVV 
       26.63        50.33        90.48        82.62        72.39        80.71 
TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 
       56.48        64.77        65.39        60.99        53.69        29.92 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-EP-A12J 
       28.08        13.91         0.20        14.04        13.15        18.74 
TCGA-EP-A26S TCGA-EP-A2KA TCGA-ES-A2HT TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25U 
       19.99        20.61        14.40         0.39        51.06        53.79 
TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SJ 
       21.53        25.64         5.92        19.53        19.23        22.95 
TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV2 
       20.78        11.87        14.14        15.78        15.65        12.23 
TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB 
       13.55         0.89        11.64        11.87         1.02         2.20 
TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K8 
        2.99        37.71        17.06        16.83        11.80        29.79 
TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO 
       12.03         9.57        16.67        20.71         7.53        10.85 
TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A6M5 TCGA-RC-A6M6 
       58.88        26.27        21.01         3.09         0.49         0.30 
TCGA-RC-A7SB TCGA-RC-A7SF TCGA-UB-A7MB TCGA-UB-A7MD TCGA-WJ-A86L TCGA-WX-AA44 
       19.33        19.04        19.76         1.71        11.34        20.22 
TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TD TCGA-XR-A8TE TCGA-YA-A8S7 TCGA-ZP-A9CV 
       24.85        18.28        33.86        30.41        13.55        35.77 
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  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 
                        19.675                         19.890 
[1] "0.0 - 114.3 (19.7)" "0.2 - 120.8 (19.9)"
[1] "hr=" "1.1"
D28V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IIIA
  DEL PEAK  1(1P36.31) MUTATED        76       37         1         26
  DEL PEAK  1(1P36.31) WILD-TYPE      97       50         2         36
                                vv
clus                             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK  1(1P36.31) MUTATED            4          4        2         0
  DEL PEAK  1(1P36.31) WILD-TYPE          5          3        0         1
                                vv
clus                             STAGE IVB
  DEL PEAK  1(1P36.31) MUTATED           1
  DEL PEAK  1(1P36.31) WILD-TYPE         1
D28V3, multiclass
            clus
vv           DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE
  STAGE I                              76                             97
  STAGE II                             37                             50
  STAGE III                             1                              2
  STAGE IIIA                           26                             36
  STAGE IIIB                            4                              5
  STAGE IIIC                            4                              3
  STAGE IV                              2                              0
  STAGE IVA                             0                              1
  STAGE IVB                             1                              1
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK  1(1P36.31) MUTATED    81  39  34   7
  DEL PEAK  1(1P36.31) WILD-TYPE 102  56  43   5
D28V4, multiclass
    clus
vv   DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE
  T1                           81                            102
  T2                           39                             56
  T3                           34                             43
  T4                            7                              5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V5, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.31) MUTATED   113   1
  DEL PEAK  1(1P36.31) WILD-TYPE 141   2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.31) MUTATED    113    1
  DEL PEAK  1(1P36.31) WILD-TYPE  141    2
   clus
vv  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE
  0                          113                            141
  1                            1                              2
[1] 2 2
[1] FALSE
D28V6, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.31) MUTATED   123   3
  DEL PEAK  1(1P36.31) WILD-TYPE 143   1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.31) MUTATED    123    3
  DEL PEAK  1(1P36.31) WILD-TYPE  143    1
   clus
vv  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE
  0                          123                            143
  1                            3                              1
[1] 2 2
[1] FALSE
D28V7, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.31) MUTATED    58 104
  DEL PEAK  1(1P36.31) WILD-TYPE  60 148
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.31) MUTATED     58  104
  DEL PEAK  1(1P36.31) WILD-TYPE   60  148
        clus
vv       DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE
  FEMALE                           58                             60
  MALE                            104                            148
[1] 2 2
[1] FALSE
D28V8, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.31) MUTATED   150   1
  DEL PEAK  1(1P36.31) WILD-TYPE 188   8
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.31) MUTATED    150    1
  DEL PEAK  1(1P36.31) WILD-TYPE  188    8
     clus
vv    DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE
  NO                           150                            188
  YES                            1                              8
[1] 2 2
[1] FALSE
                                vv
clus                             FIBROLAMELLAR CARCINOMA
  DEL PEAK  1(1P36.31) MUTATED                         0
  DEL PEAK  1(1P36.31) WILD-TYPE                       3
                                vv
clus                             HEPATOCELLULAR CARCINOMA
  DEL PEAK  1(1P36.31) MUTATED                        157
  DEL PEAK  1(1P36.31) WILD-TYPE                      203
                                vv
clus                             HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK  1(1P36.31) MUTATED                                  5
  DEL PEAK  1(1P36.31) WILD-TYPE                                2
D28V9, multiclass
                                  clus
vv                                 DEL PEAK  1(1P36.31) MUTATED
  FIBROLAMELLAR CARCINOMA                                     0
  HEPATOCELLULAR CARCINOMA                                  157
  HEPATOCHOLANGIOCARCINOMA (MIXED)                            5
                                  clus
vv                                 DEL PEAK  1(1P36.31) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                       3
  HEPATOCELLULAR CARCINOMA                                    203
  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  11   1  10
  DEL PEAK  1(1P36.31) WILD-TYPE 186   6   0  11
D28V10, multiclass
    clus
vv   DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE
  R0                          138                            186
  R1                           11                              6
  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                                2    80
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  1(1P36.31) MUTATED                           4    76
  DEL PEAK  1(1P36.31) WILD-TYPE                        13   107
D28V11, multiclass
                                  clus
vv                                 DEL PEAK  1(1P36.31) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                      78
  BLACK OR AFRICAN AMERICAN                                   4
  WHITE                                                      76
                                  clus
vv                                 DEL PEAK  1(1P36.31) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              2
  ASIAN                                                        80
  BLACK OR AFRICAN AMERICAN                                    13
  WHITE                                                       107
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V12, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.31) MUTATED     5 151
  DEL PEAK  1(1P36.31) WILD-TYPE  11 184
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.31) MUTATED      5  151
  DEL PEAK  1(1P36.31) WILD-TYPE   11  184
                        clus
vv                       DEL PEAK  1(1P36.31) MUTATED
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                          151
                        clus
vv                       DEL PEAK  1(1P36.31) WILD-TYPE
  HISPANIC OR LATINO                                 11
  NOT HISPANIC OR LATINO                            184
[1] 2 2
[1] FALSE

Clustering(29) Variable = DEL PEAK  2(1P36.11) MUTATION ANALYSIS
D29V1, survival
                                sevent
clus2                              0   1
  DEL PEAK  2(1P36.11) MUTATED    90  50
  DEL PEAK  2(1P36.11) WILD-TYPE 145  79
  DEL PEAK  2(1P36.11) MUTATED DEL PEAK  2(1P36.11) WILD-TYPE 
                           140                            224 
  DEL PEAK  2(1P36.11) MUTATED DEL PEAK  2(1P36.11) WILD-TYPE 
                            50                             79 
$`DEL PEAK  2(1P36.11) MUTATED`
TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-BC-A112 TCGA-BD-A3ER TCGA-DD-A4NI TCGA-ES-A2HS 
       11.74        38.40         5.03        36.66        26.83        22.62 
TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A7M9 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-T1-A6J8 
       81.73        30.74         1.84        31.27        12.72         0.76 
TCGA-UB-A7MF TCGA-ZP-A9D1 TCGA-2Y-A9GX TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H5 
        7.04         0.69        80.28        56.91        49.84        18.25 
TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-5C-A9VH TCGA-BC-A10Q TCGA-BC-A10S TCGA-BC-A10T 
       13.02        10.78        10.59        37.32        46.78        27.52 
TCGA-BC-A10W TCGA-BC-A69H TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-A3MA 
        2.99        14.60         4.24         2.86         3.19         9.96 
TCGA-CC-A3MB TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IG 
       10.36        11.41         9.99         7.13        21.34         9.83 
TCGA-CC-A7IJ TCGA-CC-A7IL TCGA-CC-A8HV TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A113 
       12.56         9.14         9.17         6.94         8.15        79.73 
TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C 
       53.33       113.00         7.33         2.60         0.46        21.76 
TCGA-DD-A1E9 TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EJ TCGA-DD-A39V TCGA-DD-A39X 
       90.71        45.11        49.15        33.04        21.14        55.69 
TCGA-DD-A3A1 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NN 
        7.66        30.61        33.14        30.15        30.51        29.56 
TCGA-DD-A4NO TCGA-DD-A73B TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AAC8 TCGA-DD-AACA 
       73.81         9.30        35.67       114.35         0.53        75.65 
TCGA-DD-AACC TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP 
       55.40        69.11         0.30        42.81        61.68        13.64 
TCGA-DD-AACW TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AADA 
       46.82         4.50        18.54        44.22        22.09        40.54 
TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADM 
       40.83        13.97        35.67        35.05        34.49         0.39 
TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADR TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 
       14.89        15.06        66.67        19.30        18.25        18.25 
TCGA-DD-AAE1 TCGA-DD-AAE3 TCGA-DD-AAEE TCGA-DD-AAEK TCGA-DD-AAVQ TCGA-DD-AAVS 
       18.15        18.61        26.63        35.08        89.69        59.93 
TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-ED-A459 TCGA-ED-A66X 
       72.39        76.18        62.47        66.25        29.92        13.35 
TCGA-ED-A66Y TCGA-ED-A7PY TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K 
        9.73        12.82        13.41        13.35         1.84         0.20 
TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A3I0 
       19.59         0.62        11.93        60.89        23.97        27.88 
TCGA-FV-A3R3 TCGA-FV-A496 TCGA-G3-A25S TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A5SI 
       12.03         0.33        13.68        58.49        14.86        25.25 
TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A7M5 TCGA-G3-AAV1 TCGA-G3-AAV6 TCGA-GJ-A3OU 
       20.42        17.10        14.70        11.80         2.14        28.90 
TCGA-KR-A7K2 TCGA-LG-A9QC TCGA-MI-A75G TCGA-RC-A6M6 TCGA-RC-A7SH TCGA-RC-A7SK 
       27.25        13.97        22.95         0.30        15.39        15.52 
TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MC TCGA-UB-AA0U TCGA-WQ-A9G7 TCGA-WQ-AB4B 
       36.10        27.88        16.44        10.75         0.99        12.99 
TCGA-XR-A8TF TCGA-ZP-A9CZ 
       22.78        23.21 

$`DEL PEAK  2(1P36.11) WILD-TYPE`
TCGA-2Y-A9GV TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A5W4 TCGA-DD-A3A8 TCGA-DD-A4ND 
       83.24         8.61        69.57        17.98         0.36        90.28 
TCGA-DD-AADV TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL 
       18.87        21.17        21.83        18.90        23.64         9.96 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-G3-A3CG TCGA-G3-A6UC TCGA-K7-A5RF TCGA-KR-A7K0 
        8.12         6.38        22.13        22.06        20.75         2.14 
TCGA-MI-A75H TCGA-UB-AA0V TCGA-XR-A8TG TCGA-ZS-A9CE TCGA-2Y-A9GS TCGA-2Y-A9GT 
       24.56        10.32        29.52        40.80        23.80        53.39 
TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 
       63.75        41.79        24.89        27.88       120.82        40.41 
TCGA-2Y-A9H4 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-5C-AAPD 
       47.74        20.81        22.92         1.18         8.55         0.66 
TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10R 
       17.10        14.76         1.51        48.99        27.91        10.13 
TCGA-BC-A10U TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A217 
       27.52        25.32        23.38         1.12        44.42        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-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-A4NB 
       17.59        20.12       102.74       107.11        13.78        32.52 
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-AA3A TCGA-DD-AAC9 TCGA-DD-AACB TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF 
       13.48        11.41        76.41        12.53        71.80        12.00 
TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACQ 
       15.42         6.41        53.19         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-AADD TCGA-DD-AADE 
        5.62        21.63        42.58        40.08        40.47        39.52 
TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADL TCGA-DD-AADN TCGA-DD-AADQ TCGA-DD-AADS 
        3.78        37.64        20.91        29.52        14.33        15.58 
TCGA-DD-AADU TCGA-DD-AAE2 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE9 TCGA-DD-AAEB 
       18.21        20.98        19.99         4.64        23.74        15.72 
TCGA-DD-AAED TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAVP TCGA-DD-AAVR TCGA-DD-AAVV 
       25.08        25.78        50.33        90.48        82.62        80.71 
TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A4XI 
       56.48        64.77        65.39        60.99        53.69        26.93 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A7PX TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP 
       28.08        13.91         0.20         0.20        14.04        13.15 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-ES-A2HT TCGA-FV-A2QR TCGA-FV-A495 
       18.74        19.99        20.61        14.40        19.10         0.03 
TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25Z TCGA-G3-A3CH 
        0.39        51.06        53.79        28.27        21.53        25.64 
TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SJ TCGA-G3-A7M6 TCGA-G3-A7M7 
        5.92        19.53        19.23        22.95        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 
       11.64        11.87         1.02         2.20         2.99        37.71 
TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K8 TCGA-LG-A9QD TCGA-MI-A75C 
       17.06        16.83        11.80        29.79        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-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A6M4 TCGA-RC-A6M5 TCGA-RC-A7S9 
       17.69        21.01         3.09         0.72         0.49        21.04 
TCGA-RC-A7SB TCGA-RC-A7SF TCGA-UB-A7MB TCGA-UB-A7MD TCGA-UB-A7ME TCGA-WJ-A86L 
       19.33        19.04        19.76         1.71        15.98        11.34 
TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TD TCGA-XR-A8TE TCGA-YA-A8S7 
       20.22        24.85        18.28        33.86        30.41        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-A9CF TCGA-ZS-A9CG 
       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 
                        18.955                         19.990 
[1] "0.2 - 114.3 (19.0)" "0.0 - 120.8 (20.0)"
[1] "hr=" "1"  
D29V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IIIA
  DEL PEAK  2(1P36.11) MUTATED        60       37         1         24
  DEL PEAK  2(1P36.11) WILD-TYPE     113       50         2         38
                                vv
clus                             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK  2(1P36.11) MUTATED            4          4        2         0
  DEL PEAK  2(1P36.11) WILD-TYPE          5          3        0         1
                                vv
clus                             STAGE IVB
  DEL PEAK  2(1P36.11) MUTATED           1
  DEL PEAK  2(1P36.11) WILD-TYPE         1
D29V3, multiclass
            clus
vv           DEL PEAK  2(1P36.11) MUTATED DEL PEAK  2(1P36.11) WILD-TYPE
  STAGE I                              60                            113
  STAGE II                             37                             50
  STAGE III                             1                              2
  STAGE IIIA                           24                             38
  STAGE IIIB                            4                              5
  STAGE IIIC                            4                              3
  STAGE IV                              2                              0
  STAGE IVA                             0                              1
  STAGE IVB                             1                              1
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK  2(1P36.11) MUTATED    64  40  33   5
  DEL PEAK  2(1P36.11) WILD-TYPE 119  55  44   7
D29V4, multiclass
    clus
vv   DEL PEAK  2(1P36.11) MUTATED DEL PEAK  2(1P36.11) WILD-TYPE
  T1                           64                            119
  T2                           40                             55
  T3                           33                             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"
D29V5, binary
                                cls
clus                               0   1
  DEL PEAK  2(1P36.11) MUTATED   101   2
  DEL PEAK  2(1P36.11) WILD-TYPE 153   1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  2(1P36.11) MUTATED    101    2
  DEL PEAK  2(1P36.11) WILD-TYPE  153    1
   clus
vv  DEL PEAK  2(1P36.11) MUTATED DEL PEAK  2(1P36.11) WILD-TYPE
  0                          101                            153
  1                            2                              1
[1] 2 2
[1] FALSE
D29V6, binary
                                cls
clus                               0   1
  DEL PEAK  2(1P36.11) MUTATED   111   3
  DEL PEAK  2(1P36.11) WILD-TYPE 155   1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  2(1P36.11) MUTATED    111    3
  DEL PEAK  2(1P36.11) WILD-TYPE  155    1
   clus
vv  DEL PEAK  2(1P36.11) MUTATED DEL PEAK  2(1P36.11) WILD-TYPE
  0                          111                            155
  1                            3                              1
[1] 2 2
[1] FALSE
D29V7, binary
                                cls
clus                               0   1
  DEL PEAK  2(1P36.11) MUTATED    47  95
  DEL PEAK  2(1P36.11) WILD-TYPE  71 157
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  2(1P36.11) MUTATED     47   95
  DEL PEAK  2(1P36.11) WILD-TYPE   71  157
        clus
vv       DEL PEAK  2(1P36.11) MUTATED DEL PEAK  2(1P36.11) WILD-TYPE
  FEMALE                           47                             71
  MALE                             95                            157
[1] 2 2
[1] FALSE
D29V8, binary
                                cls
clus                               0   1
  DEL PEAK  2(1P36.11) MUTATED   131   3
  DEL PEAK  2(1P36.11) WILD-TYPE 207   6
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  2(1P36.11) MUTATED    131    3
  DEL PEAK  2(1P36.11) WILD-TYPE  207    6
     clus
vv    DEL PEAK  2(1P36.11) MUTATED DEL PEAK  2(1P36.11) WILD-TYPE
  NO                           131                            207
  YES                            3                              6
[1] 2 2
[1] FALSE
                                vv
clus                             FIBROLAMELLAR CARCINOMA
  DEL PEAK  2(1P36.11) MUTATED                         0
  DEL PEAK  2(1P36.11) WILD-TYPE                       3
                                vv
clus                             HEPATOCELLULAR CARCINOMA
  DEL PEAK  2(1P36.11) MUTATED                        138
  DEL PEAK  2(1P36.11) WILD-TYPE                      222
                                vv
clus                             HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK  2(1P36.11) MUTATED                                  4
  DEL PEAK  2(1P36.11) WILD-TYPE                                3
D29V9, multiclass
                                  clus
vv                                 DEL PEAK  2(1P36.11) MUTATED
  FIBROLAMELLAR CARCINOMA                                     0
  HEPATOCELLULAR CARCINOMA                                  138
  HEPATOCHOLANGIOCARCINOMA (MIXED)                            4
                                  clus
vv                                 DEL PEAK  2(1P36.11) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                       3
  HEPATOCELLULAR CARCINOMA                                    222
  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  10   1   9
  DEL PEAK  2(1P36.11) WILD-TYPE 203   7   0  12
D29V10, multiclass
    clus
vv   DEL PEAK  2(1P36.11) MUTATED DEL PEAK  2(1P36.11) WILD-TYPE
  R0                          121                            203
  R1                           10                              7
  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                                2    87
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  2(1P36.11) MUTATED                           4    66
  DEL PEAK  2(1P36.11) WILD-TYPE                        13   117
D29V11, multiclass
                                  clus
vv                                 DEL PEAK  2(1P36.11) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                      71
  BLACK OR AFRICAN AMERICAN                                   4
  WHITE                                                      66
                                  clus
vv                                 DEL PEAK  2(1P36.11) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              2
  ASIAN                                                        87
  BLACK OR AFRICAN AMERICAN                                    13
  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"
D29V12, binary
                                cls
clus                               0   1
  DEL PEAK  2(1P36.11) MUTATED     4 135
  DEL PEAK  2(1P36.11) WILD-TYPE  12 200
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  2(1P36.11) MUTATED      4  135
  DEL PEAK  2(1P36.11) WILD-TYPE   12  200
                        clus
vv                       DEL PEAK  2(1P36.11) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                          135
                        clus
vv                       DEL PEAK  2(1P36.11) WILD-TYPE
  HISPANIC OR LATINO                                 12
  NOT HISPANIC OR LATINO                            200
[1] 2 2
[1] FALSE

Clustering(30) Variable = DEL PEAK  3(2Q22.1) MUTATION ANALYSIS
D30V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  3(2Q22.1) MUTATED    31  20
  DEL PEAK  3(2Q22.1) WILD-TYPE 204 109
  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                           51                           313 
  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                           20                           109 
$`DEL PEAK  3(2Q22.1) MUTATED`
TCGA-2Y-A9H6 TCGA-4R-AA8I TCGA-DD-AADV TCGA-FV-A3I1 TCGA-T1-A6J8 TCGA-UB-A7MF 
       11.74         8.61        18.87         8.12         0.76         7.04 
TCGA-2Y-A9GU TCGA-2Y-A9H0 TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-3K-AAZ8 
       63.75       120.82        47.74        18.25        20.81        13.02 
TCGA-5C-A9VG TCGA-BC-A10R TCGA-BC-A10Y TCGA-BC-A3KF TCGA-BD-A3EP TCGA-CC-5264 
       10.78        10.13        23.38         0.26        13.45         3.35 
TCGA-CC-A7IG TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IL TCGA-DD-A115 TCGA-DD-A1EL 
        9.83        13.12        12.56         9.14        83.57        13.64 
TCGA-DD-A39V TCGA-DD-A39Y TCGA-DD-A3A1 TCGA-DD-A4NJ TCGA-DD-A73B TCGA-DD-AACE 
       21.14         5.62         7.66        30.51         9.30        71.80 
TCGA-DD-AACU TCGA-DD-AACZ TCGA-DD-AADI TCGA-DD-AADL TCGA-DD-AADN TCGA-DD-AADW 
       51.52         5.62        35.67        20.91        29.52        19.30 
TCGA-DD-AAE2 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAED TCGA-ED-A459 TCGA-ED-A66Y 
       20.98        19.99         4.64        25.08        29.92         9.73 
TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-G3-AAV7 TCGA-GJ-A9DB TCGA-KR-A7K2 TCGA-RC-A6M5 
        0.20        14.04        11.87         2.20        27.25         0.49 
TCGA-RC-A7SH TCGA-WQ-AB4B TCGA-ZP-A9D2 
       15.39        12.99        25.15 

$`DEL PEAK  3(2Q22.1) WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H7 TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A5W4 TCGA-BD-A3ER 
       83.24        38.40        69.57         5.03        17.98        36.66 
TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEA 
        0.36        90.28        26.83        21.17        21.83        18.90 
TCGA-DD-AAEG TCGA-EP-A3JL TCGA-ES-A2HS TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25W 
       23.64         9.96        22.62         6.38        81.73        30.74 
TCGA-G3-A3CG TCGA-G3-A6UC TCGA-G3-A7M9 TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-KR-A7K7 
       22.13        22.06         1.84        20.75         2.14        31.27 
TCGA-LG-A6GG TCGA-MI-A75H TCGA-UB-AA0V TCGA-XR-A8TG TCGA-ZP-A9D1 TCGA-ZS-A9CE 
       12.72        24.56        10.32        29.52         0.69        40.80 
TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GY TCGA-2Y-A9GZ 
       23.80        53.39        41.79        80.28        24.89        27.88 
TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB 
       40.41        56.91        49.84        22.92         1.18         8.55 
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-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W 
       27.91        37.32        46.78        27.52        27.52         2.99 
TCGA-BC-A10X TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KG TCGA-BC-A69H 
       25.32         1.12        44.42        45.93        22.36        14.60 
TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5260 
       12.72        18.48        44.81         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-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB 
      102.74       107.11        13.78        30.61        33.14        32.52 
TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO 
       30.97        30.15        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-AACB TCGA-DD-AACC TCGA-DD-AACD 
        0.53        11.41        75.65        76.41        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-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-AACV TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY 
       59.31        51.35        50.33        46.82         5.59        47.67 
TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 
        4.50        18.54        21.63        42.58        44.22        22.09 
TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE 
       40.08        40.54        40.83        13.97        40.47        39.52 
TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADM TCGA-DD-AADO 
        3.78        37.64        35.05        34.49         0.39        14.89 
TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADY 
       15.06        14.33        66.67        15.58        18.21        18.25 
TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE3 TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAEE 
       18.25        18.15        18.61        23.74        15.72        26.63 
TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR 
       25.78        50.33        35.08        90.48        89.69        82.62 
TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVV TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY 
       59.93        72.39        80.71        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        60.99        53.69        26.93 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7XP 
       28.08        13.91        13.35         0.20        12.82        13.15 
TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S 
       13.41        13.35         1.84         0.20        18.74        19.99 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B 
       20.61        19.59         0.62        11.93        14.40        60.89 
TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 
       23.97        19.10        27.88        12.03         0.03         0.33 
TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25X 
        0.39        13.68        51.06        53.79        28.27        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-A7M5 TCGA-G3-A7M6 
       25.25        22.95        20.42        17.10        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-GJ-A3OU TCGA-GJ-A6C0 
       13.55         0.89        11.64         2.14        28.90         1.02 
TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K8 
        2.99        37.71        17.06        16.83        11.80        29.79 
TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I 
       13.97        12.03         9.57        16.67        22.95        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-A6M4 TCGA-RC-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF 
        3.09         0.72         0.30        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        27.88        19.76        16.44         1.71 
TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WX-AA44 TCGA-WX-AA46 
       15.98        10.75        11.34         0.99        20.22        24.85 
TCGA-WX-AA47 TCGA-XR-A8TD TCGA-XR-A8TE TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CV 
       18.28        33.86        30.41        22.78        13.55        35.77 
TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CF 
       25.71        23.21        35.87        12.99        45.57        79.30 
TCGA-ZS-A9CG 
       11.21 

  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                         0.20                          0.03 
  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                       120.82                        114.35 
  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                        13.45                         20.71 
[1] "0.2 - 120.8 (13.4)" "0.0 - 114.3 (20.7)"
[1] "hr=" "1.4"
D30V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IIIA
  DEL PEAK  3(2Q22.1) MUTATED        23       13         0          9
  DEL PEAK  3(2Q22.1) WILD-TYPE     150       74         3         53
                               vv
clus                            STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK  3(2Q22.1) MUTATED            1          0        0         1
  DEL PEAK  3(2Q22.1) WILD-TYPE          8          7        2         0
                               vv
clus                            STAGE IVB
  DEL PEAK  3(2Q22.1) MUTATED           0
  DEL PEAK  3(2Q22.1) WILD-TYPE         2
D30V3, multiclass
            clus
vv           DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  STAGE I                             23                           150
  STAGE II                            13                            74
  STAGE III                            0                             3
  STAGE IIIA                           9                            53
  STAGE IIIB                           1                             8
  STAGE IIIC                           0                             7
  STAGE IV                             0                             2
  STAGE IVA                            1                             0
  STAGE IVB                            0                             2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  DEL PEAK  3(2Q22.1) MUTATED    26  14  11   1
  DEL PEAK  3(2Q22.1) WILD-TYPE 157  81  66  11
D30V4, multiclass
    clus
vv   DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  T1                          26                           157
  T2                          14                            81
  T3                          11                            66
  T4                           1                            11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V5, binary
                               cls
clus                              0   1
  DEL PEAK  3(2Q22.1) MUTATED    34   1
  DEL PEAK  3(2Q22.1) WILD-TYPE 220   2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2Q22.1) MUTATED     34    1
  DEL PEAK  3(2Q22.1) WILD-TYPE  220    2
   clus
vv  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  0                          34                           220
  1                           1                             2
[1] 2 2
[1] FALSE
D30V6, binary
                               cls
clus                              0   1
  DEL PEAK  3(2Q22.1) MUTATED    37   0
  DEL PEAK  3(2Q22.1) WILD-TYPE 229   4
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2Q22.1) MUTATED     37    0
  DEL PEAK  3(2Q22.1) WILD-TYPE  229    4
   clus
vv  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  0                          37                           229
  1                           0                             4
[1] 2 2
[1] FALSE
D30V7, binary
                               cls
clus                              0   1
  DEL PEAK  3(2Q22.1) MUTATED    16  36
  DEL PEAK  3(2Q22.1) WILD-TYPE 102 216
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2Q22.1) MUTATED     16   36
  DEL PEAK  3(2Q22.1) WILD-TYPE  102  216
        clus
vv       DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  FEMALE                          16                           102
  MALE                            36                           216
[1] 2 2
[1] FALSE
D30V8, binary
                               cls
clus                              0   1
  DEL PEAK  3(2Q22.1) MUTATED    46   2
  DEL PEAK  3(2Q22.1) WILD-TYPE 292   7
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2Q22.1) MUTATED     46    2
  DEL PEAK  3(2Q22.1) WILD-TYPE  292    7
     clus
vv    DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  NO                           46                           292
  YES                           2                             7
[1] 2 2
[1] FALSE
                               vv
clus                            FIBROLAMELLAR CARCINOMA
  DEL PEAK  3(2Q22.1) MUTATED                         1
  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                      310
                               vv
clus                            HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK  3(2Q22.1) MUTATED                                  1
  DEL PEAK  3(2Q22.1) WILD-TYPE                                6
D30V9, multiclass
                                  clus
vv                                 DEL PEAK  3(2Q22.1) MUTATED
  FIBROLAMELLAR CARCINOMA                                    1
  HEPATOCELLULAR CARCINOMA                                  50
  HEPATOCHOLANGIOCARCINOMA (MIXED)                           1
                                  clus
vv                                 DEL PEAK  3(2Q22.1) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                      2
  HEPATOCELLULAR CARCINOMA                                   310
  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    48   0   0   4
  DEL PEAK  3(2Q22.1) WILD-TYPE 276  17   1  17
D30V10, multiclass
    clus
vv   DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  R0                          48                           276
  R1                           0                            17
  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                                2   134
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  3(2Q22.1) MUTATED                           4    23
  DEL PEAK  3(2Q22.1) WILD-TYPE                        13   160
D30V11, multiclass
                                  clus
vv                                 DEL PEAK  3(2Q22.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                     24
  BLACK OR AFRICAN AMERICAN                                  4
  WHITE                                                     23
                                  clus
vv                                 DEL PEAK  3(2Q22.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             2
  ASIAN                                                      134
  BLACK OR AFRICAN AMERICAN                                   13
  WHITE                                                      160
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V12, binary
                               cls
clus                              0   1
  DEL PEAK  3(2Q22.1) MUTATED     2  45
  DEL PEAK  3(2Q22.1) WILD-TYPE  14 290
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2Q22.1) MUTATED      2   45
  DEL PEAK  3(2Q22.1) WILD-TYPE   14  290
                        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                                14
  NOT HISPANIC OR LATINO                           290
[1] 2 2
[1] FALSE

Clustering(31) Variable = DEL PEAK  4(2Q37.3) MUTATION ANALYSIS
D31V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  4(2Q37.3) MUTATED    40  20
  DEL PEAK  4(2Q37.3) WILD-TYPE 195 109
  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                           60                           304 
  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                           20                           109 
$`DEL PEAK  4(2Q37.3) MUTATED`
TCGA-BC-A5W4 TCGA-DD-AAEG TCGA-FV-A3I1 TCGA-G3-A7M9 TCGA-T1-A6J8 TCGA-UB-A7MF 
       17.98        23.64         8.12         1.84         0.76         7.04 
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-BD-A3EP TCGA-BW-A5NO TCGA-CC-5264 TCGA-CC-A3M9 
       44.42         0.26        13.45         0.66         3.35         9.86 
TCGA-CC-A7II TCGA-CC-A7IL TCGA-DD-A113 TCGA-DD-A115 TCGA-DD-A11A TCGA-DD-A11C 
       13.12         9.14        79.73        83.57         2.60        21.76 
TCGA-DD-A1EB TCGA-DD-A1EL TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A4NA TCGA-DD-A4NJ 
       66.31        13.64         5.62        19.76        33.14        30.51 
TCGA-DD-A4NQ TCGA-DD-A73B TCGA-DD-AACE TCGA-DD-AACO TCGA-DD-AACU TCGA-DD-AAD5 
       12.26         9.30        71.80        61.68        51.52        44.22 
TCGA-DD-AADC TCGA-DD-AADF TCGA-DD-AADI TCGA-DD-AADL TCGA-DD-AADN TCGA-DD-AADP 
       13.97         3.78        35.67        20.91        29.52        15.06 
TCGA-DD-AAED TCGA-ED-A459 TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PZ TCGA-ED-A7XO 
       25.08        29.92         9.73         0.20         0.20        14.04 
TCGA-FV-A3I0 TCGA-FV-A496 TCGA-G3-A5SI TCGA-G3-AAV7 TCGA-GJ-A9DB TCGA-KR-A7K2 
       27.88         0.33        25.25        11.87         2.20        27.25 
TCGA-RC-A6M5 TCGA-RC-A7SH TCGA-RC-A7SK TCGA-UB-A7MA TCGA-UB-A7MB TCGA-WQ-AB4B 
        0.49        15.39        15.52        27.88        19.76        12.99 

$`DEL PEAK  4(2Q37.3) WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 
       83.24        11.74        38.40         8.61        69.57         5.03 
TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV TCGA-DD-AAE7 
       36.66         0.36        90.28        26.83        18.87        21.17 
TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-EP-A3JL TCGA-ES-A2HS TCGA-FV-A3R2 TCGA-FV-A4ZP 
       21.83        18.90         9.96        22.62         6.38        81.73 
TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-KR-A7K7 
       30.74        22.13        22.06        20.75         2.14        31.27 
TCGA-LG-A6GG TCGA-MI-A75H TCGA-UB-AA0V TCGA-XR-A8TG TCGA-ZP-A9D1 TCGA-ZS-A9CE 
       12.72        24.56        10.32        29.52         0.69        40.80 
TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GY TCGA-2Y-A9H0 
       23.80        53.39        41.79        80.28        24.89       120.82 
TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-2Y-A9H9 
       40.41        56.91        47.74        18.25        20.81        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-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-A10Z TCGA-BC-A217 
       27.52        27.52         2.99        25.32         1.12        45.93 
TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-CC-5258 
       22.36        14.60        12.72        18.48        44.81         4.24 
TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3MA 
        2.86         3.19         3.39         4.24         3.32         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-A8HT 
       21.34         9.83        12.00        12.56         8.61         4.60 
TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A114 TCGA-DD-A116 
       11.31         9.17         6.94         8.15        37.78        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-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH 
       19.79        75.65        11.47        12.95        45.11        49.15 
TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39X 
        6.02        33.04        18.35        21.14        27.19        55.69 
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-A3A9 TCGA-DD-A4NB TCGA-DD-A4NF TCGA-DD-A4NH 
      107.11        13.78        30.61        32.52        30.97        30.15 
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-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-AACP TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACV TCGA-DD-AACW 
       13.64        14.20        59.31        51.35        50.33        46.82 
TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 
        5.59        47.67         5.62         4.50        18.54        21.63 
TCGA-DD-AAD3 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADD 
       42.58        22.09        40.08        40.54        40.83        40.47 
TCGA-DD-AADE TCGA-DD-AADG TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADM TCGA-DD-AADO 
       39.52        37.64        35.05        34.49         0.39        14.89 
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-AAE9 TCGA-DD-AAEB TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAEK 
       23.74        15.72        26.63        25.78        50.33        35.08 
TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVV 
       90.48        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 
       60.99        53.69        26.93        28.08        13.91        13.35 
TCGA-ED-A7PY TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K 
       12.82        13.15        13.41        13.35         1.84         0.20 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK 
       18.74        19.99        20.61        19.59         0.62        11.93 
TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3R3 TCGA-FV-A495 
       14.40        60.89        23.97        19.10        12.03         0.03 
TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25X 
        0.39        13.68        51.06        53.79        28.27        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-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M7 
       22.95        20.42        17.10        14.70        20.78        11.87 
TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 
       14.14        15.78        15.65        11.80        12.23        13.55 
TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-HP-A5MZ 
        0.89        11.64         2.14        28.90         1.02         2.99 
TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K8 TCGA-LG-A9QC 
       37.71        17.06        16.83        11.80        29.79        13.97 
TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A520 
       12.03         9.57        16.67        22.95        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-A6M4 TCGA-RC-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RG-A7D4 
        0.72         0.30        21.04        19.33        19.04        36.10 
TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-A9G7 
       16.44         1.71        15.98        10.75        11.34         0.99 
TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TD TCGA-XR-A8TE TCGA-XR-A8TF 
       20.22        24.85        18.28        33.86        30.41        22.78 
TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 
       13.55        35.77        25.71        23.21        35.87        25.15 
TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CF TCGA-ZS-A9CG 
       12.99        45.57        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 
                       15.225                        20.320 
[1] "0.2 - 83.6 (15.2)"  "0.0 - 120.8 (20.3)"
[1] "hr=" "1.2"
D31V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IIIA
  DEL PEAK  4(2Q37.3) MUTATED        25       20         0         11
  DEL PEAK  4(2Q37.3) WILD-TYPE     148       67         3         51
                               vv
clus                            STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK  4(2Q37.3) MUTATED            2          1        0         1
  DEL PEAK  4(2Q37.3) WILD-TYPE          7          6        2         0
                               vv
clus                            STAGE IVB
  DEL PEAK  4(2Q37.3) MUTATED           0
  DEL PEAK  4(2Q37.3) WILD-TYPE         2
D31V3, multiclass
            clus
vv           DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE
  STAGE I                             25                           148
  STAGE II                            20                            67
  STAGE III                            0                             3
  STAGE IIIA                          11                            51
  STAGE IIIB                           2                             7
  STAGE IIIC                           1                             6
  STAGE IV                             0                             2
  STAGE IVA                            1                             0
  STAGE IVB                            0                             2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  DEL PEAK  4(2Q37.3) MUTATED    27  21  13   1
  DEL PEAK  4(2Q37.3) WILD-TYPE 156  74  64  11
D31V4, multiclass
    clus
vv   DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE
  T1                          27                           156
  T2                          21                            74
  T3                          13                            64
  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"
D31V5, binary
                               cls
clus                              0   1
  DEL PEAK  4(2Q37.3) MUTATED    38   2
  DEL PEAK  4(2Q37.3) WILD-TYPE 216   1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q37.3) MUTATED     38    2
  DEL PEAK  4(2Q37.3) WILD-TYPE  216    1
   clus
vv  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE
  0                          38                           216
  1                           2                             1
[1] 2 2
[1] FALSE
D31V6, binary
                               cls
clus                              0   1
  DEL PEAK  4(2Q37.3) MUTATED    49   0
  DEL PEAK  4(2Q37.3) WILD-TYPE 217   4
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q37.3) MUTATED     49    0
  DEL PEAK  4(2Q37.3) WILD-TYPE  217    4
   clus
vv  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE
  0                          49                           217
  1                           0                             4
[1] 2 2
[1] FALSE
D31V7, binary
                               cls
clus                              0   1
  DEL PEAK  4(2Q37.3) MUTATED    21  41
  DEL PEAK  4(2Q37.3) WILD-TYPE  97 211
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q37.3) MUTATED     21   41
  DEL PEAK  4(2Q37.3) WILD-TYPE   97  211
        clus
vv       DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE
  FEMALE                          21                            97
  MALE                            41                           211
[1] 2 2
[1] FALSE
D31V8, binary
                               cls
clus                              0   1
  DEL PEAK  4(2Q37.3) MUTATED    53   1
  DEL PEAK  4(2Q37.3) WILD-TYPE 285   8
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q37.3) MUTATED     53    1
  DEL PEAK  4(2Q37.3) WILD-TYPE  285    8
     clus
vv    DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE
  NO                           53                           285
  YES                           1                             8
[1] 2 2
[1] FALSE
                               vv
clus                            FIBROLAMELLAR CARCINOMA
  DEL PEAK  4(2Q37.3) MUTATED                         1
  DEL PEAK  4(2Q37.3) WILD-TYPE                       2
                               vv
clus                            HEPATOCELLULAR CARCINOMA
  DEL PEAK  4(2Q37.3) MUTATED                         58
  DEL PEAK  4(2Q37.3) WILD-TYPE                      302
                               vv
clus                            HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK  4(2Q37.3) MUTATED                                  3
  DEL PEAK  4(2Q37.3) WILD-TYPE                                4
D31V9, multiclass
                                  clus
vv                                 DEL PEAK  4(2Q37.3) MUTATED
  FIBROLAMELLAR CARCINOMA                                    1
  HEPATOCELLULAR CARCINOMA                                  58
  HEPATOCHOLANGIOCARCINOMA (MIXED)                           3
                                  clus
vv                                 DEL PEAK  4(2Q37.3) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                      2
  HEPATOCELLULAR CARCINOMA                                   302
  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    54   2   0   6
  DEL PEAK  4(2Q37.3) WILD-TYPE 270  15   1  15
D31V10, multiclass
    clus
vv   DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE
  R0                          54                           270
  R1                           2                            15
  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                                  1    26
  DEL PEAK  4(2Q37.3) WILD-TYPE                                1   132
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  4(2Q37.3) MUTATED                           5    28
  DEL PEAK  4(2Q37.3) WILD-TYPE                        12   155
D31V11, multiclass
                                  clus
vv                                 DEL PEAK  4(2Q37.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                     26
  BLACK OR AFRICAN AMERICAN                                  5
  WHITE                                                     28
                                  clus
vv                                 DEL PEAK  4(2Q37.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                      132
  BLACK OR AFRICAN AMERICAN                                   12
  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"
D31V12, binary
                               cls
clus                              0   1
  DEL PEAK  4(2Q37.3) MUTATED     3  51
  DEL PEAK  4(2Q37.3) WILD-TYPE  13 284
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q37.3) MUTATED      3   51
  DEL PEAK  4(2Q37.3) WILD-TYPE   13  284
                        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                                13
  NOT HISPANIC OR LATINO                           284
[1] 2 2
[1] FALSE

Clustering(32) Variable = DEL PEAK  5(3P13) MUTATION ANALYSIS
D32V1, survival
                             sevent
clus2                           0   1
  DEL PEAK  5(3P13) MUTATED    45  25
  DEL PEAK  5(3P13) WILD-TYPE 190 104
  DEL PEAK  5(3P13) MUTATED DEL PEAK  5(3P13) WILD-TYPE 
                         70                         294 
  DEL PEAK  5(3P13) MUTATED DEL PEAK  5(3P13) WILD-TYPE 
                         25                         104 
$`DEL PEAK  5(3P13) MUTATED`
TCGA-BC-A112 TCGA-DD-A4NI TCGA-KR-A7K7 TCGA-UB-A7MF TCGA-ZP-A9D1 TCGA-ZS-A9CE 
        5.03        26.83        31.27         7.04         0.69        40.80 
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-A217 TCGA-CC-5260 TCGA-CC-5263 
        0.66        37.32        10.13        45.93         2.86         4.24 
TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IG TCGA-CC-A7II 
        9.96        10.36         8.94         7.13         9.83        13.12 
TCGA-CC-A7IJ TCGA-CC-A8HV TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A11A TCGA-DD-A1E9 
       12.56         9.17         8.15        79.73         2.60        90.71 
TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NH TCGA-DD-A4NO TCGA-DD-A73G TCGA-DD-AA3A 
       30.61        33.14        30.15        73.81       114.35        13.48 
TCGA-DD-AACO TCGA-DD-AAD2 TCGA-DD-AADC TCGA-DD-AADJ TCGA-DD-AADO TCGA-DD-AADY 
       61.68        21.63        13.97        35.05        14.89        18.25 
TCGA-DD-AAE3 TCGA-DD-AAVQ TCGA-DD-AAVU TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PZ 
       18.61        89.69        72.39         9.73         0.20         0.20 
TCGA-ED-A7XO TCGA-ED-A82E TCGA-ED-A97K TCGA-EP-A2KA TCGA-FV-A3I0 TCGA-FV-A3R3 
       14.04        13.41         0.20        20.61        27.88        12.03 
TCGA-G3-A25T TCGA-G3-A25X TCGA-G3-A7M5 TCGA-G3-AAV1 TCGA-G3-AAV6 TCGA-KR-A7K2 
       51.06        58.49        14.70        11.80         2.14        27.25 
TCGA-LG-A9QC TCGA-RC-A6M4 TCGA-RC-A6M5 TCGA-RC-A6M6 TCGA-RC-A7SH TCGA-UB-A7MC 
       13.97         0.72         0.49         0.30        15.39        16.44 
TCGA-UB-A7MD TCGA-WQ-AB4B TCGA-ZP-A9D0 TCGA-ZS-A9CF 
        1.71        12.99        35.87        79.30 

$`DEL PEAK  5(3P13) WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A5W4 
       83.24        11.74        38.40         8.61        69.57        17.98 
TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-AADV TCGA-DD-AAE7 TCGA-DD-AAE8 
       36.66         0.36        90.28        18.87        21.17        21.83 
TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-ES-A2HS TCGA-FV-A3I1 TCGA-FV-A3R2 
       18.90        23.64         9.96        22.62         8.12         6.38 
TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC TCGA-G3-A7M9 TCGA-K7-A5RF 
       81.73        30.74        22.13        22.06         1.84        20.75 
TCGA-KR-A7K0 TCGA-LG-A6GG TCGA-MI-A75H TCGA-T1-A6J8 TCGA-UB-AA0V TCGA-XR-A8TG 
        2.14        12.72        24.56         0.76        10.32        29.52 
TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GZ 
       23.80        53.39        63.75        41.79        80.28        27.88 
TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H4 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA 
      120.82        40.41        47.74        20.81        22.92         1.18 
TCGA-2Y-A9HB TCGA-5C-A9VH TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4072 
        8.55        10.59        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-A216 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A69H 
       23.38         1.12        44.42         0.26        22.36        14.60 
TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5258 
       12.72        18.48        44.81        13.45         0.66         4.24 
TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5264 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MC 
        3.19         3.39         3.35         3.32         9.86        11.93 
TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A7IF TCGA-CC-A7IH TCGA-CC-A7IK TCGA-CC-A7IL 
       11.41         9.99        21.34        12.00         8.61         9.14 
TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A9FS TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 
        4.60        11.31         6.94        37.78        83.57        53.33 
TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1EA 
      113.00         7.33         0.46        21.76        51.29        79.40 
TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG 
       66.31        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-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-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 
       70.06        17.59        20.12       102.74       107.11        13.78 
TCGA-DD-A4NB TCGA-DD-A4NF TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN 
       32.52        30.97        30.51        39.78        56.25        29.56 
TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A 
      108.76        12.26         0.30        80.75        78.84        23.93 
TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-AAC8 
        9.30        23.05        22.78         1.45        35.67         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        71.80 
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-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 
        5.62         4.50        18.54        42.58        44.22        22.09 
TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADF 
       40.08        40.54        40.83        40.47        39.52         3.78 
TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN 
       37.64        35.67        34.49        20.91         0.39        29.52 
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-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE9 
       18.25        18.15        20.98        19.99         4.64        23.74 
TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAEK 
       15.72        25.08        26.63        25.78        50.33        35.08 
TCGA-DD-AAVP TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVV TCGA-DD-AAVW TCGA-DD-AAVX 
       90.48        82.62        59.93        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        60.99        53.69 
TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A7PY 
       29.92        26.93        28.08        13.91        13.35        12.82 
TCGA-ED-A7XP TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KB 
       13.15        13.35         1.84        18.74        19.99        19.59 
TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR 
        0.62        11.93        14.40        60.89        23.97        19.10 
TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25V 
        0.03         0.33         0.39        13.68        53.79        28.27 
TCGA-G3-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-A7M6 TCGA-G3-A7M7 
       25.25        22.95        20.42        17.10        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-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ 
       11.64        11.87        28.90         1.02         2.20         2.99 
TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K8 TCGA-LG-A9QD 
       37.71        17.06        16.83        11.80        29.79        12.03 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO 
        9.57        16.67        22.95        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-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB 
       19.33        19.04        15.52        36.10        27.88        19.76 
TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WX-AA44 TCGA-WX-AA46 
       15.98        10.75        11.34         0.99        20.22        24.85 
TCGA-WX-AA47 TCGA-XR-A8TD TCGA-XR-A8TE TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CV 
       18.28        33.86        30.41        22.78        13.55        35.77 
TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CG 
       25.71        23.21        25.15        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 
                     14.005                      20.765 
[1] "0.2 - 114.3 (14.0)" "0.0 - 120.8 (20.8)"
[1] "hr=" "1.1"
D32V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  5(3P13) MUTATED        20       22         0         17          3
  DEL PEAK  5(3P13) WILD-TYPE     153       65         3         45          6
                             vv
clus                          STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK  5(3P13) MUTATED            3        1         1         1
  DEL PEAK  5(3P13) WILD-TYPE          4        1         0         1
D32V3, multiclass
            clus
vv           DEL PEAK  5(3P13) MUTATED DEL PEAK  5(3P13) WILD-TYPE
  STAGE I                           20                         153
  STAGE II                          22                          65
  STAGE III                          0                           3
  STAGE IIIA                        17                          45
  STAGE IIIB                         3                           6
  STAGE IIIC                         3                           4
  STAGE IV                           1                           1
  STAGE IVA                          1                           0
  STAGE IVB                          1                           1
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           T1  T2  T3  T4
  DEL PEAK  5(3P13) MUTATED    23  25  21   4
  DEL PEAK  5(3P13) WILD-TYPE 160  70  56   8
D32V4, multiclass
    clus
vv   DEL PEAK  5(3P13) MUTATED DEL PEAK  5(3P13) WILD-TYPE
  T1                        23                         160
  T2                        25                          70
  T3                        21                          56
  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"
D32V5, binary
                             cls
clus                            0   1
  DEL PEAK  5(3P13) MUTATED    48   2
  DEL PEAK  5(3P13) WILD-TYPE 206   1
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  5(3P13) MUTATED     48    2
  DEL PEAK  5(3P13) WILD-TYPE  206    1
   clus
vv  DEL PEAK  5(3P13) MUTATED DEL PEAK  5(3P13) WILD-TYPE
  0                        48                         206
  1                         2                           1
[1] 2 2
[1] FALSE
D32V6, binary
                             cls
clus                            0   1
  DEL PEAK  5(3P13) MUTATED    51   2
  DEL PEAK  5(3P13) WILD-TYPE 215   2
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  5(3P13) MUTATED     51    2
  DEL PEAK  5(3P13) WILD-TYPE  215    2
   clus
vv  DEL PEAK  5(3P13) MUTATED DEL PEAK  5(3P13) WILD-TYPE
  0                        51                         215
  1                         2                           2
[1] 2 2
[1] FALSE
D32V7, binary
                             cls
clus                            0   1
  DEL PEAK  5(3P13) MUTATED    32  41
  DEL PEAK  5(3P13) WILD-TYPE  86 211
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  5(3P13) MUTATED     32   41
  DEL PEAK  5(3P13) WILD-TYPE   86  211
        clus
vv       DEL PEAK  5(3P13) MUTATED DEL PEAK  5(3P13) WILD-TYPE
  FEMALE                        32                          86
  MALE                          41                         211
[1] 2 2
[1] FALSE
D32V8, binary
                             cls
clus                            0   1
  DEL PEAK  5(3P13) MUTATED    66   0
  DEL PEAK  5(3P13) WILD-TYPE 272   9
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  5(3P13) MUTATED     66    0
  DEL PEAK  5(3P13) WILD-TYPE  272    9
     clus
vv    DEL PEAK  5(3P13) MUTATED DEL PEAK  5(3P13) WILD-TYPE
  NO                         66                         272
  YES                         0                           9
[1] 2 2
[1] FALSE
                             vv
clus                          FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  DEL PEAK  5(3P13) MUTATED                         1                       67
  DEL PEAK  5(3P13) WILD-TYPE                       2                      293
                             vv
clus                          HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK  5(3P13) MUTATED                                  5
  DEL PEAK  5(3P13) WILD-TYPE                                2
D32V9, multiclass
                                  clus
vv                                 DEL PEAK  5(3P13) MUTATED
  FIBROLAMELLAR CARCINOMA                                  1
  HEPATOCELLULAR CARCINOMA                                67
  HEPATOCHOLANGIOCARCINOMA (MIXED)                         5
                                  clus
vv                                 DEL PEAK  5(3P13) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                    2
  HEPATOCELLULAR CARCINOMA                                 293
  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    66   3   0   4
  DEL PEAK  5(3P13) WILD-TYPE 258  14   1  17
D32V10, multiclass
    clus
vv   DEL PEAK  5(3P13) MUTATED DEL PEAK  5(3P13) WILD-TYPE
  R0                        66                         258
  R1                         3                          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                                  1    32
  DEL PEAK  5(3P13) WILD-TYPE                                1   126
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  5(3P13) MUTATED                           4    36
  DEL PEAK  5(3P13) WILD-TYPE                        13   147
D32V11, multiclass
                                  clus
vv                                 DEL PEAK  5(3P13) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         1
  ASIAN                                                   32
  BLACK OR AFRICAN AMERICAN                                4
  WHITE                                                   36
                                  clus
vv                                 DEL PEAK  5(3P13) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                    126
  BLACK OR AFRICAN AMERICAN                                 13
  WHITE                                                    147
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V12, binary
                             cls
clus                            0   1
  DEL PEAK  5(3P13) MUTATED     2  66
  DEL PEAK  5(3P13) WILD-TYPE  14 269
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  5(3P13) MUTATED      2   66
  DEL PEAK  5(3P13) WILD-TYPE   14  269
                        clus
vv                       DEL PEAK  5(3P13) MUTATED DEL PEAK  5(3P13) WILD-TYPE
  HISPANIC OR LATINO                             2                          14
  NOT HISPANIC OR LATINO                        66                         269
[1] 2 2
[1] FALSE

Clustering(33) Variable = DEL PEAK  6(4P16.3) MUTATION ANALYSIS
D33V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  6(4P16.3) MUTATED    48  33
  DEL PEAK  6(4P16.3) WILD-TYPE 187  96
  DEL PEAK  6(4P16.3) MUTATED DEL PEAK  6(4P16.3) WILD-TYPE 
                           81                           283 
  DEL PEAK  6(4P16.3) MUTATED DEL PEAK  6(4P16.3) WILD-TYPE 
                           33                            96 
$`DEL PEAK  6(4P16.3) MUTATED`
TCGA-BC-A112 TCGA-BC-A5W4 TCGA-DD-A4NI TCGA-DD-AADV TCGA-DD-AAE8 TCGA-FV-A4ZP 
        5.03        17.98        26.83        18.87        21.83        81.73 
TCGA-KR-A7K7 TCGA-UB-A7MF TCGA-ZS-A9CE TCGA-2Y-A9GS TCGA-3K-AAZ8 TCGA-5C-A9VG 
       31.27         7.04        40.80        23.80        13.02        10.78 
TCGA-5C-AAPD TCGA-BC-A10Y TCGA-BC-A69H TCGA-BW-A5NO TCGA-CC-5264 TCGA-CC-A3MC 
        0.66        23.38        14.60         0.66         3.35        11.93 
TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7II TCGA-CC-A7IK TCGA-CC-A7IL TCGA-CC-A8HV 
        7.13        21.34        13.12         8.61         9.14         9.17 
TCGA-CC-A9FW TCGA-DD-A114 TCGA-DD-A119 TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A39X 
        8.15        37.78         7.33         6.02        33.04        55.69 
TCGA-DD-A39Y TCGA-DD-A4NJ TCGA-DD-A4NN TCGA-DD-A73A TCGA-DD-AAC8 TCGA-DD-AACE 
        5.62        30.51        29.56        23.93         0.53        71.80 
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-AAED 
       47.67        44.22        40.08        13.97        40.47        25.08 
TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVQ TCGA-DD-AAVU TCGA-DD-AAVV TCGA-ED-A459 
       50.33        35.08        89.69        72.39        80.71        29.92 
TCGA-ED-A7XO TCGA-ED-A8O6 TCGA-EP-A2KB TCGA-EP-A2KC TCGA-FV-A2QQ TCGA-G3-A25S 
       14.04         1.84        19.59         0.62        23.97        13.68 
TCGA-G3-A25U TCGA-G3-A25X TCGA-G3-A3CH TCGA-G3-A7M5 TCGA-G3-AAUZ TCGA-G3-AAV1 
       53.79        58.49        25.64        14.70        15.78        11.80 
TCGA-G3-AAV4 TCGA-GJ-A3OU TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-KR-A7K2 TCGA-MI-A75G 
        0.89        28.90        37.71        17.06        27.25        22.95 
TCGA-PD-A5DF TCGA-RG-A7D4 TCGA-UB-A7MC TCGA-UB-A7ME TCGA-WQ-AB4B TCGA-WX-AA44 
       21.01        36.10        16.44        15.98        12.99        20.22 
TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9D2 
       22.78        13.55        25.15 

$`DEL PEAK  6(4P16.3) WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BD-A3ER 
       83.24        11.74        38.40         8.61        69.57        36.66 
TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-AAE7 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL 
        0.36        90.28        21.17        18.90        23.64         9.96 
TCGA-ES-A2HS TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC 
       22.62         8.12         6.38        30.74        22.13        22.06 
TCGA-G3-A7M9 TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-LG-A6GG TCGA-MI-A75H TCGA-T1-A6J8 
        1.84        20.75         2.14        12.72        24.56         0.76 
TCGA-UB-AA0V TCGA-XR-A8TG TCGA-ZP-A9D1 TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW 
       10.32        29.52         0.69        53.39        63.75        41.79 
TCGA-2Y-A9GX TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 
       80.28        24.89        27.88       120.82        40.41        56.91 
TCGA-2Y-A9H3 TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA 
       49.84        47.74        18.25        20.81        22.92         1.18 
TCGA-2Y-A9HB TCGA-5C-A9VH TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4072 
        8.55        10.59        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-A216 TCGA-BC-A217 TCGA-BC-A3KF 
        2.99        25.32         1.12        44.42        45.93         0.26 
TCGA-BC-A3KG TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-CC-5258 
       22.36        12.72        18.48        44.81        13.45         4.24 
TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 
        2.86         3.19         3.39         4.24         3.32         9.86 
TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IG 
        9.96        10.36        11.41         9.99         8.94         9.83 
TCGA-CC-A7IH TCGA-CC-A7IJ TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A9FS TCGA-DD-A113 
       12.00        12.56         4.60        11.31         6.94        79.73 
TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C 
       83.57        53.33       113.00         2.60         0.46        21.76 
TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED 
       51.29        90.71        79.40        66.31        19.79        75.65 
TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EK TCGA-DD-A1EL 
       11.47        12.95        45.11        49.15        18.35        13.64 
TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 
       21.14        27.19        19.76        25.81         7.66        70.06 
TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A9 
       17.59        20.12       102.74       107.11        13.78        30.61 
TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NK TCGA-DD-A4NL 
       33.14        32.52        30.97        30.15        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-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G 
        9.30        23.05        22.78         1.45        35.67       114.35 
TCGA-DD-AA3A TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD 
       13.48        11.41        75.65        76.41        55.40        12.53 
TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACO 
        6.41        53.19        69.11         0.30         3.52        61.68 
TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX 
       14.20        59.31        51.35        50.33        46.82         5.59 
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-AADA TCGA-DD-AADB TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI 
       40.54        40.83        39.52         3.78        37.64        35.67 
TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO 
       35.05        34.49        20.91         0.39        29.52        14.89 
TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW 
       15.06        14.33        66.67        15.58        18.21        19.30 
TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 
       18.25        18.25        18.15        20.98        18.61        19.99 
TCGA-DD-AAE6 TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAVP 
        4.64        23.74        15.72        26.63        25.78        90.48 
TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ 
       82.62        59.93        76.18        56.48        64.77        62.47 
TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A4XI TCGA-ED-A5KG 
       66.25        65.39        60.99        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-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S 
       13.15        13.41        13.35         0.20        18.74        19.99 
TCGA-EP-A2KA TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 
       20.61        11.93        14.40        60.89        19.10        27.88 
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-A25Y TCGA-G3-A25Z TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI 
       14.86        21.53         5.92        19.53        19.23        25.25 
TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 
       22.95        20.42        17.10        20.78        11.87        14.14 
TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 
       15.65        12.23        13.55        11.64         2.14        11.87 
TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K8 
        1.02         2.20         2.99        16.83        11.80        29.79 
TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75I TCGA-MR-A520 
       13.97        12.03         9.57        16.67        20.71         7.53 
TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-QA-A7B7 TCGA-RC-A6M4 
       10.85        58.88        26.27        17.69         3.09         0.72 
TCGA-RC-A6M5 TCGA-RC-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH 
        0.49         0.30        21.04        19.33        19.04        15.39 
TCGA-RC-A7SK TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MD TCGA-UB-AA0U TCGA-WJ-A86L 
       15.52        27.88        19.76         1.71        10.75        11.34 
TCGA-WQ-A9G7 TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TD TCGA-XR-A8TE TCGA-ZP-A9CV 
        0.99        24.85        18.28        33.86        30.41        35.77 
TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CF 
       25.71        23.21        35.87        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                         19.76 
[1] "0.5 - 89.7 (21.0)"  "0.0 - 120.8 (19.8)"
[1] "hr=" "1.3"
D33V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IIIA
  DEL PEAK  6(4P16.3) MUTATED        36       20         0         18
  DEL PEAK  6(4P16.3) WILD-TYPE     137       67         3         44
                               vv
clus                            STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK  6(4P16.3) MUTATED            2          2        2         0
  DEL PEAK  6(4P16.3) WILD-TYPE          7          5        0         1
                               vv
clus                            STAGE IVB
  DEL PEAK  6(4P16.3) MUTATED           0
  DEL PEAK  6(4P16.3) WILD-TYPE         2
D33V3, multiclass
            clus
vv           DEL PEAK  6(4P16.3) MUTATED DEL PEAK  6(4P16.3) WILD-TYPE
  STAGE I                             36                           137
  STAGE II                            20                            67
  STAGE III                            0                             3
  STAGE IIIA                          18                            44
  STAGE IIIB                           2                             7
  STAGE IIIC                           2                             5
  STAGE IV                             2                             0
  STAGE IVA                            0                             1
  STAGE IVB                            0                             2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  DEL PEAK  6(4P16.3) MUTATED    37  23  21   3
  DEL PEAK  6(4P16.3) WILD-TYPE 146  72  56   9
D33V4, multiclass
    clus
vv   DEL PEAK  6(4P16.3) MUTATED DEL PEAK  6(4P16.3) WILD-TYPE
  T1                          37                           146
  T2                          23                            72
  T3                          21                            56
  T4                           3                             9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V5, binary
                               cls
clus                              0   1
  DEL PEAK  6(4P16.3) MUTATED    58   1
  DEL PEAK  6(4P16.3) WILD-TYPE 196   2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(4P16.3) MUTATED     58    1
  DEL PEAK  6(4P16.3) WILD-TYPE  196    2
   clus
vv  DEL PEAK  6(4P16.3) MUTATED DEL PEAK  6(4P16.3) WILD-TYPE
  0                          58                           196
  1                           1                             2
[1] 2 2
[1] FALSE
D33V6, binary
                               cls
clus                              0   1
  DEL PEAK  6(4P16.3) MUTATED    63   2
  DEL PEAK  6(4P16.3) WILD-TYPE 203   2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(4P16.3) MUTATED     63    2
  DEL PEAK  6(4P16.3) WILD-TYPE  203    2
   clus
vv  DEL PEAK  6(4P16.3) MUTATED DEL PEAK  6(4P16.3) WILD-TYPE
  0                          63                           203
  1                           2                             2
[1] 2 2
[1] FALSE
D33V7, binary
                               cls
clus                              0   1
  DEL PEAK  6(4P16.3) MUTATED    17  68
  DEL PEAK  6(4P16.3) WILD-TYPE 101 184
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(4P16.3) MUTATED     17   68
  DEL PEAK  6(4P16.3) WILD-TYPE  101  184
        clus
vv       DEL PEAK  6(4P16.3) MUTATED DEL PEAK  6(4P16.3) WILD-TYPE
  FEMALE                          17                           101
  MALE                            68                           184
[1] 2 2
[1] FALSE
D33V8, binary
                               cls
clus                              0   1
  DEL PEAK  6(4P16.3) MUTATED    78   2
  DEL PEAK  6(4P16.3) WILD-TYPE 260   7
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(4P16.3) MUTATED     78    2
  DEL PEAK  6(4P16.3) WILD-TYPE  260    7
     clus
vv    DEL PEAK  6(4P16.3) MUTATED DEL PEAK  6(4P16.3) WILD-TYPE
  NO                           78                           260
  YES                           2                             7
[1] 2 2
[1] FALSE
                               vv
clus                            FIBROLAMELLAR CARCINOMA
  DEL PEAK  6(4P16.3) MUTATED                         0
  DEL PEAK  6(4P16.3) WILD-TYPE                       3
                               vv
clus                            HEPATOCELLULAR CARCINOMA
  DEL PEAK  6(4P16.3) MUTATED                         83
  DEL PEAK  6(4P16.3) WILD-TYPE                      277
                               vv
clus                            HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK  6(4P16.3) MUTATED                                  2
  DEL PEAK  6(4P16.3) WILD-TYPE                                5
D33V9, multiclass
                                  clus
vv                                 DEL PEAK  6(4P16.3) MUTATED
  FIBROLAMELLAR CARCINOMA                                    0
  HEPATOCELLULAR CARCINOMA                                  83
  HEPATOCHOLANGIOCARCINOMA (MIXED)                           2
                                  clus
vv                                 DEL PEAK  6(4P16.3) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                      3
  HEPATOCELLULAR CARCINOMA                                   277
  HEPATOCHOLANGIOCARCINOMA (MIXED)                             5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  6(4P16.3) MUTATED    73   3   1   7
  DEL PEAK  6(4P16.3) WILD-TYPE 251  14   0  14
D33V10, multiclass
    clus
vv   DEL PEAK  6(4P16.3) MUTATED DEL PEAK  6(4P16.3) WILD-TYPE
  R0                          73                           251
  R1                           3                            14
  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                                  1    44
  DEL PEAK  6(4P16.3) WILD-TYPE                                1   114
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  6(4P16.3) MUTATED                           6    32
  DEL PEAK  6(4P16.3) WILD-TYPE                        11   151
D33V11, multiclass
                                  clus
vv                                 DEL PEAK  6(4P16.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  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                                                      114
  BLACK OR AFRICAN AMERICAN                                   11
  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"
D33V12, binary
                               cls
clus                              0   1
  DEL PEAK  6(4P16.3) MUTATED     6  75
  DEL PEAK  6(4P16.3) WILD-TYPE  10 260
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(4P16.3) MUTATED      6   75
  DEL PEAK  6(4P16.3) WILD-TYPE   10  260
                        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                                10
  NOT HISPANIC OR LATINO                           260
[1] 2 2
[1] FALSE

Clustering(34) Variable = DEL PEAK  7(4Q21.3) MUTATION ANALYSIS
D34V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  7(4Q21.3) MUTATED   103  64
  DEL PEAK  7(4Q21.3) WILD-TYPE 132  65
  DEL PEAK  7(4Q21.3) MUTATED DEL PEAK  7(4Q21.3) WILD-TYPE 
                          167                           197 
  DEL PEAK  7(4Q21.3) MUTATED DEL PEAK  7(4Q21.3) WILD-TYPE 
                           64                            65 
$`DEL PEAK  7(4Q21.3) MUTATED`
TCGA-2Y-A9GV TCGA-BC-A112 TCGA-BC-A5W4 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV 
       83.24         5.03        17.98        90.28        26.83        18.87 
TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-FV-A3I1 TCGA-FV-A4ZP TCGA-G3-A7M9 TCGA-KR-A7K7 
       21.83        18.90         8.12        81.73         1.84        31.27 
TCGA-LG-A6GG TCGA-T1-A6J8 TCGA-UB-A7MF TCGA-XR-A8TG TCGA-ZS-A9CE TCGA-2Y-A9GS 
       12.72         0.76         7.04        29.52        40.80        23.80 
TCGA-2Y-A9GY TCGA-2Y-A9H0 TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H8 TCGA-3K-AAZ8 
       24.89       120.82        56.91        49.84        20.81        13.02 
TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10Y 
       10.78        10.59         0.66        27.52        27.52        23.38 
TCGA-BC-A10Z TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A69H TCGA-BD-A2L6 TCGA-BD-A3EP 
        1.12        45.93         0.26        14.60        44.81        13.45 
TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5261 TCGA-CC-5263 TCGA-CC-5264 TCGA-CC-A3M9 
        0.66         4.24         3.19         4.24         3.35         9.86 
TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IF 
       10.36        11.93         9.99         8.94         7.13        21.34 
TCGA-CC-A7IG TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A7IL TCGA-CC-A8HU 
        9.83        13.12        12.56         8.61         9.14        11.31 
TCGA-CC-A8HV TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A116 
        9.17         6.94         8.15        79.73        37.78        53.33 
TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A1EB TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH 
        7.33         2.60        66.31        12.95        45.11        49.15 
TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A3A5 
        6.02        33.04        13.64        55.69         5.62       102.74 
TCGA-DD-A3A9 TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NQ 
       30.61        30.15        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        71.80 
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-AADY TCGA-DD-AAE0 
       20.91        14.89        15.06        66.67        18.25        18.25 
TCGA-DD-AAE1 TCGA-DD-AAE6 TCGA-DD-AAED TCGA-DD-AAEK TCGA-DD-AAVQ TCGA-DD-AAVS 
       18.15         4.64        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-A496 
       13.35         0.20        19.59         0.62        23.97         0.33 
TCGA-G3-A25S TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A5SI TCGA-G3-A5SM 
       13.68        58.49        14.86        21.53        25.25        17.10 
TCGA-G3-A7M5 TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV4 TCGA-G3-AAV6 
       14.70        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        28.90         1.02        37.71        17.06        27.25 
TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-MI-A75G TCGA-O8-A75V TCGA-RC-A7SB TCGA-RC-A7SH 
       29.79        13.97        22.95        17.69        19.33        15.39 
TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7ME TCGA-WQ-A9G7 
       15.52        36.10        19.76        16.44        15.98         0.99 
TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9D2 
       12.99        20.22        22.78        13.55        25.15 

$`DEL PEAK  7(4Q21.3) WILD-TYPE`
TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BD-A3ER TCGA-DD-A3A8 
       11.74        38.40         8.61        69.57        36.66         0.36 
TCGA-DD-AAE7 TCGA-DD-AAEG TCGA-EP-A3JL TCGA-ES-A2HS TCGA-FV-A3R2 TCGA-G3-A25W 
       21.17        23.64         9.96        22.62         6.38        30.74 
TCGA-G3-A3CG TCGA-G3-A6UC TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-MI-A75H TCGA-UB-AA0V 
       22.13        22.06        20.75         2.14        24.56        10.32 
TCGA-ZP-A9D1 TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GZ 
        0.69        53.39        63.75        41.79        80.28        27.88 
TCGA-2Y-A9H1 TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB 
       40.41        47.74        18.25        22.92         1.18         8.55 
TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q 
       17.10        14.76         1.51        48.99        27.91        37.32 
TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A216 TCGA-BC-A3KG 
       10.13        46.78         2.99        25.32        44.42        22.36 
TCGA-BC-A69I TCGA-BC-A8YO TCGA-CC-5260 TCGA-CC-5262 TCGA-CC-A1HT TCGA-CC-A3MA 
       12.72        18.48         2.86         3.39         3.32         9.96 
TCGA-CC-A5UC TCGA-CC-A7IH TCGA-CC-A8HT TCGA-DD-A115 TCGA-DD-A118 TCGA-DD-A11B 
       11.41        12.00         4.60        83.57       113.00         0.46 
TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EC TCGA-DD-A1ED 
       21.76        51.29        90.71        79.40        19.79        75.65 
TCGA-DD-A1EE TCGA-DD-A1EK TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39Z TCGA-DD-A3A0 
       11.47        18.35        21.14        27.19        19.76        25.81 
TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A6 TCGA-DD-A3A7 
        7.66        70.06        17.59        20.12       107.11        13.78 
TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NF TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NP 
       33.14        32.52        30.97        39.78        56.25       108.76 
TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73C TCGA-DD-A73D 
        0.30        80.75        78.84        23.93        23.05        22.78 
TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-AA3A TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACD 
        1.45        35.67        13.48        11.41        75.65        12.53 
TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACO TCGA-DD-AACQ 
        6.41        53.19        69.11         0.30        61.68        14.20 
TCGA-DD-AACT TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 
       51.35         5.59        47.67         4.50        18.54        21.63 
TCGA-DD-AAD6 TCGA-DD-AADA TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADJ 
       22.09        40.54        39.52         3.78        37.64        35.05 
TCGA-DD-AADK TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADQ TCGA-DD-AADS TCGA-DD-AADU 
       34.49         0.39        29.52        14.33        15.58        18.21 
TCGA-DD-AADW TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE9 TCGA-DD-AAEB 
       19.30        20.98        18.61        19.99        23.74        15.72 
TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAVP TCGA-DD-AAVR TCGA-DD-AAVX 
       26.63        25.78        50.33        90.48        82.62        56.48 
TCGA-DD-AAVY TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A4XI TCGA-ED-A5KG 
       64.77        65.39        60.99        53.69        26.93        28.08 
TCGA-ED-A627 TCGA-ED-A66Y TCGA-ED-A82E TCGA-ED-A8O6 TCGA-EP-A12J TCGA-EP-A26S 
       13.91         9.73        13.41         1.84        18.74        19.99 
TCGA-EP-A2KA TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 
       20.61        11.93        14.40        60.89        19.10        27.88 
TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V 
       12.03         0.03         0.39        51.06        53.79        28.27 
TCGA-G3-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-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV3 TCGA-G3-AAV5 
       20.78        11.87        14.14        15.78        13.55        11.64 
TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-LG-A9QD TCGA-MI-A75C 
        2.20         2.99        16.83        11.80        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-A6M4 TCGA-RC-A6M5 TCGA-RC-A6M6 TCGA-RC-A7S9 
       21.01         3.09         0.72         0.49         0.30        21.04 
TCGA-RC-A7SF TCGA-UB-A7MA TCGA-UB-A7MD TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WX-AA46 
       19.04        27.88         1.71        10.75        11.34        24.85 
TCGA-WX-AA47 TCGA-XR-A8TD TCGA-XR-A8TE TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ 
       18.28        33.86        30.41        35.77        25.71        23.21 
TCGA-ZP-A9D0 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CF TCGA-ZS-A9CG 
       35.87        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 
                        17.98                         20.78 
[1] "0.2 - 120.8 (18.0)" "0.0 - 113.0 (20.8)"
[1] "hr=" "1.2"
D34V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IIIA
  DEL PEAK  7(4Q21.3) MUTATED        77       44         2         28
  DEL PEAK  7(4Q21.3) WILD-TYPE      96       43         1         34
                               vv
clus                            STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK  7(4Q21.3) MUTATED            4          2        2         0
  DEL PEAK  7(4Q21.3) WILD-TYPE          5          5        0         1
                               vv
clus                            STAGE IVB
  DEL PEAK  7(4Q21.3) MUTATED           1
  DEL PEAK  7(4Q21.3) WILD-TYPE         1
D34V3, multiclass
            clus
vv           DEL PEAK  7(4Q21.3) MUTATED DEL PEAK  7(4Q21.3) WILD-TYPE
  STAGE I                             77                            96
  STAGE II                            44                            43
  STAGE III                            2                             1
  STAGE IIIA                          28                            34
  STAGE IIIB                           4                             5
  STAGE IIIC                           2                             5
  STAGE IV                             2                             0
  STAGE IVA                            0                             1
  STAGE IVB                            1                             1
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  DEL PEAK  7(4Q21.3) MUTATED    80  49  36   5
  DEL PEAK  7(4Q21.3) WILD-TYPE 103  46  41   7
D34V4, multiclass
    clus
vv   DEL PEAK  7(4Q21.3) MUTATED DEL PEAK  7(4Q21.3) WILD-TYPE
  T1                          80                           103
  T2                          49                            46
  T3                          36                            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"
D34V5, binary
                               cls
clus                              0   1
  DEL PEAK  7(4Q21.3) MUTATED   121   1
  DEL PEAK  7(4Q21.3) WILD-TYPE 133   2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(4Q21.3) MUTATED    121    1
  DEL PEAK  7(4Q21.3) WILD-TYPE  133    2
   clus
vv  DEL PEAK  7(4Q21.3) MUTATED DEL PEAK  7(4Q21.3) WILD-TYPE
  0                         121                           133
  1                           1                             2
[1] 2 2
[1] FALSE
D34V6, binary
                               cls
clus                              0   1
  DEL PEAK  7(4Q21.3) MUTATED   134   3
  DEL PEAK  7(4Q21.3) WILD-TYPE 132   1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(4Q21.3) MUTATED    134    3
  DEL PEAK  7(4Q21.3) WILD-TYPE  132    1
   clus
vv  DEL PEAK  7(4Q21.3) MUTATED DEL PEAK  7(4Q21.3) WILD-TYPE
  0                         134                           132
  1                           3                             1
[1] 2 2
[1] FALSE
D34V7, binary
                               cls
clus                              0   1
  DEL PEAK  7(4Q21.3) MUTATED    50 121
  DEL PEAK  7(4Q21.3) WILD-TYPE  68 131
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(4Q21.3) MUTATED     50  121
  DEL PEAK  7(4Q21.3) WILD-TYPE   68  131
        clus
vv       DEL PEAK  7(4Q21.3) MUTATED DEL PEAK  7(4Q21.3) WILD-TYPE
  FEMALE                          50                            68
  MALE                           121                           131
[1] 2 2
[1] FALSE
D34V8, binary
                               cls
clus                              0   1
  DEL PEAK  7(4Q21.3) MUTATED   156   4
  DEL PEAK  7(4Q21.3) WILD-TYPE 182   5
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(4Q21.3) MUTATED    156    4
  DEL PEAK  7(4Q21.3) WILD-TYPE  182    5
     clus
vv    DEL PEAK  7(4Q21.3) MUTATED DEL PEAK  7(4Q21.3) WILD-TYPE
  NO                          156                           182
  YES                           4                             5
[1] 2 2
[1] FALSE
                               vv
clus                            FIBROLAMELLAR CARCINOMA
  DEL PEAK  7(4Q21.3) MUTATED                         0
  DEL PEAK  7(4Q21.3) WILD-TYPE                       3
                               vv
clus                            HEPATOCELLULAR CARCINOMA
  DEL PEAK  7(4Q21.3) MUTATED                        168
  DEL PEAK  7(4Q21.3) WILD-TYPE                      192
                               vv
clus                            HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK  7(4Q21.3) MUTATED                                  3
  DEL PEAK  7(4Q21.3) WILD-TYPE                                4
D34V9, multiclass
                                  clus
vv                                 DEL PEAK  7(4Q21.3) MUTATED
  FIBROLAMELLAR CARCINOMA                                    0
  HEPATOCELLULAR CARCINOMA                                 168
  HEPATOCHOLANGIOCARCINOMA (MIXED)                           3
                                  clus
vv                                 DEL PEAK  7(4Q21.3) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                      3
  HEPATOCELLULAR CARCINOMA                                   192
  HEPATOCHOLANGIOCARCINOMA (MIXED)                             4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  7(4Q21.3) MUTATED   152   6   1  12
  DEL PEAK  7(4Q21.3) WILD-TYPE 172  11   0   9
D34V10, multiclass
    clus
vv   DEL PEAK  7(4Q21.3) MUTATED DEL PEAK  7(4Q21.3) WILD-TYPE
  R0                         152                           172
  R1                           6                            11
  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                                  1    89
  DEL PEAK  7(4Q21.3) WILD-TYPE                                1    69
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  7(4Q21.3) MUTATED                           9    68
  DEL PEAK  7(4Q21.3) WILD-TYPE                         8   115
D34V11, multiclass
                                  clus
vv                                 DEL PEAK  7(4Q21.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                     89
  BLACK OR AFRICAN AMERICAN                                  9
  WHITE                                                     68
                                  clus
vv                                 DEL PEAK  7(4Q21.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                       69
  BLACK OR AFRICAN AMERICAN                                    8
  WHITE                                                      115
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V12, binary
                               cls
clus                              0   1
  DEL PEAK  7(4Q21.3) MUTATED    11 151
  DEL PEAK  7(4Q21.3) WILD-TYPE   5 184
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(4Q21.3) MUTATED     11  151
  DEL PEAK  7(4Q21.3) WILD-TYPE    5  184
                        clus
vv                       DEL PEAK  7(4Q21.3) MUTATED
  HISPANIC OR LATINO                              11
  NOT HISPANIC OR LATINO                         151
                        clus
vv                       DEL PEAK  7(4Q21.3) WILD-TYPE
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                           184
[1] 2 2
[1] FALSE

Clustering(35) Variable = DEL PEAK  8(4Q24) MUTATION ANALYSIS
D35V1, survival
                             sevent
clus2                           0   1
  DEL PEAK  8(4Q24) MUTATED   102  67
  DEL PEAK  8(4Q24) WILD-TYPE 133  62
  DEL PEAK  8(4Q24) MUTATED DEL PEAK  8(4Q24) WILD-TYPE 
                        169                         195 
  DEL PEAK  8(4Q24) MUTATED DEL PEAK  8(4Q24) WILD-TYPE 
                         67                          62 
$`DEL PEAK  8(4Q24) MUTATED`
TCGA-BC-A112 TCGA-BC-A5W4 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV TCGA-DD-AAE8 
        5.03        17.98        90.28        26.83        18.87        21.83 
TCGA-DD-AAEA TCGA-FV-A3I1 TCGA-FV-A4ZP TCGA-G3-A7M9 TCGA-KR-A7K7 TCGA-LG-A6GG 
       18.90         8.12        81.73         1.84        31.27        12.72 
TCGA-T1-A6J8 TCGA-UB-A7MF TCGA-XR-A8TG TCGA-ZS-A9CE TCGA-2Y-A9GS TCGA-2Y-A9GY 
        0.76         7.04        29.52        40.80        23.80        24.89 
TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H8 TCGA-2Y-A9HA 
       27.88       120.82        56.91        49.84        20.81         1.18 
TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-BC-4072 TCGA-BC-A10T 
       13.02        10.78        10.59         0.66        48.99        27.52 
TCGA-BC-A10U TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A69H 
       27.52        23.38         1.12        45.93         0.26        14.60 
TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5261 TCGA-CC-5263 TCGA-CC-5264 
       13.45         0.66         4.24         3.19         4.24         3.35 
TCGA-CC-A3M9 TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IE 
        9.86        10.36        11.93         9.99         8.94         7.13 
TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A7IL 
       21.34         9.83        13.12        12.56         8.61         9.14 
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-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A1EB 
       53.33         7.33         2.60         0.46        21.76        66.31 
TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EL 
       12.95        45.11        49.15         6.02        33.04        13.64 
TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A3A0 TCGA-DD-A3A5 TCGA-DD-A3A9 TCGA-DD-A4NH 
       55.69         5.62        25.81       102.74        30.61        30.15 
TCGA-DD-A4NJ TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NQ TCGA-DD-A73B TCGA-DD-A73G 
       30.51        29.56        73.81        12.26         9.30       114.35 
TCGA-DD-AAC8 TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG 
        0.53        76.41        55.40        71.80        12.00        15.42 
TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACP TCGA-DD-AACS TCGA-DD-AACU 
        3.52        58.16        42.81        13.64        59.31        51.52 
TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACZ TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD8 
       50.33        46.82         5.62        42.58        44.22        40.08 
TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADI TCGA-DD-AADL TCGA-DD-AADO 
       40.83        13.97        40.47        35.67        20.91        14.89 
TCGA-DD-AADP TCGA-DD-AADR TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE6 
       15.06        66.67        18.25        18.25        18.15         4.64 
TCGA-DD-AAED TCGA-DD-AAEK TCGA-DD-AAVQ TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVV 
       25.08        35.08        89.69        59.93        72.39        80.71 
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-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A8O5 TCGA-ED-A97K 
       12.82         0.20        14.04        13.15        13.35         0.20 
TCGA-EP-A2KB TCGA-EP-A2KC TCGA-FV-A2QQ TCGA-FV-A495 TCGA-FV-A496 TCGA-G3-A25S 
       19.59         0.62        23.97         0.03         0.33        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-AAV1 TCGA-G3-AAV4 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-HP-A5N0 
       11.80         0.89         2.14        11.87        28.90        37.71 
TCGA-K7-A5RG TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-MI-A75G TCGA-O8-A75V 
       17.06        27.25        29.79        13.97        22.95        17.69 
TCGA-RC-A7SB TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MB TCGA-UB-A7MC 
       19.33        15.39        15.52        36.10        19.76        16.44 
TCGA-UB-A7ME TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-XR-A8TF TCGA-YA-A8S7 
       15.98         0.99        12.99        20.22        22.78        13.55 
TCGA-ZP-A9D2 
       25.15 

$`DEL PEAK  8(4Q24) WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BD-A3ER 
       83.24        11.74        38.40         8.61        69.57        36.66 
TCGA-DD-A3A8 TCGA-DD-AAE7 TCGA-DD-AAEG TCGA-EP-A3JL TCGA-ES-A2HS TCGA-FV-A3R2 
        0.36        21.17        23.64         9.96        22.62         6.38 
TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-MI-A75H 
       30.74        22.13        22.06        20.75         2.14        24.56 
TCGA-UB-AA0V TCGA-ZP-A9D1 TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX 
       10.32         0.69        53.39        63.75        41.79        80.28 
TCGA-2Y-A9H1 TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H9 TCGA-2Y-A9HB TCGA-5R-AA1C 
       40.41        47.74        18.25        22.92         8.55        17.10 
TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S 
       14.76         1.51        27.91        37.32        10.13        46.78 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A216 TCGA-BC-A3KG TCGA-BC-A69I TCGA-BC-A8YO 
        2.99        25.32        44.42        22.36        12.72        18.48 
TCGA-BD-A2L6 TCGA-CC-5260 TCGA-CC-5262 TCGA-CC-A1HT TCGA-CC-A3MA TCGA-CC-A5UC 
       44.81         2.86         3.39         3.32         9.96        11.41 
TCGA-CC-A7IH TCGA-CC-A8HT TCGA-DD-A115 TCGA-DD-A118 TCGA-DD-A11D TCGA-DD-A1E9 
       12.00         4.60        83.57       113.00        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-A4NA TCGA-DD-A4NB TCGA-DD-A4NF TCGA-DD-A4NK 
      107.11        13.78        33.14        32.52        30.97        39.78 
TCGA-DD-A4NL TCGA-DD-A4NP TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A 
       56.25       108.76         0.30        80.75        78.84        23.93 
TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-AA3A TCGA-DD-AAC9 
       23.05        22.78         1.45        35.67        13.48        11.41 
TCGA-DD-AACA TCGA-DD-AACD TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK 
       75.65        12.53         6.41        53.19        69.11         0.30 
TCGA-DD-AACO TCGA-DD-AACQ TCGA-DD-AACT TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AAD0 
       61.68        14.20        51.35         5.59        47.67         4.50 
TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD6 TCGA-DD-AADA TCGA-DD-AADE TCGA-DD-AADF 
       18.54        21.63        22.09        40.54        39.52         3.78 
TCGA-DD-AADG TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADQ 
       37.64        35.05        34.49         0.39        29.52        14.33 
TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 
       15.58        18.21        19.30        20.98        18.61        19.99 
TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAVP 
       23.74        15.72        26.63        25.78        50.33        90.48 
TCGA-DD-AAVR TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 
       82.62        56.48        64.77        65.39        60.99        53.69 
TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66Y TCGA-ED-A82E TCGA-ED-A8O6 
       26.93        28.08        13.91         9.73        13.41         1.84 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B 
       18.74        19.99        20.61        11.93        14.40        60.89 
TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25U 
       19.10        27.88        12.03         0.39        51.06        53.79 
TCGA-G3-A25V TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SJ 
       28.27        25.64         5.92        19.53        19.23        22.95 
TCGA-G3-A5SL TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV0 
       20.42        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        11.64         1.02         2.20         2.99 
TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75I 
       16.83        11.80        12.03         9.57        16.67        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-A6M4 TCGA-RC-A6M5 TCGA-RC-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SF TCGA-UB-A7MA 
        0.72         0.49         0.30        21.04        19.04        27.88 
TCGA-UB-A7MD TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TD 
        1.71        10.75        11.34        24.85        18.28        33.86 
TCGA-XR-A8TE TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D4 
       30.41        35.77        25.71        23.21        35.87        12.99 
TCGA-ZS-A9CD TCGA-ZS-A9CF TCGA-ZS-A9CG 
       45.57        79.30        11.21 

  DEL PEAK  8(4Q24) MUTATED DEL PEAK  8(4Q24) WILD-TYPE 
                       0.03                        0.30 
  DEL PEAK  8(4Q24) MUTATED DEL PEAK  8(4Q24) WILD-TYPE 
                     120.82                      113.00 
  DEL PEAK  8(4Q24) MUTATED DEL PEAK  8(4Q24) WILD-TYPE 
                      18.15                       20.75 
[1] "0.0 - 120.8 (18.1)" "0.3 - 113.0 (20.8)"
[1] "hr=" "1.3"
D35V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  8(4Q24) MUTATED        77       46         2         29          4
  DEL PEAK  8(4Q24) WILD-TYPE      96       41         1         33          5
                             vv
clus                          STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK  8(4Q24) MUTATED            2        2         0         1
  DEL PEAK  8(4Q24) WILD-TYPE          5        0         1         1
D35V3, multiclass
            clus
vv           DEL PEAK  8(4Q24) MUTATED DEL PEAK  8(4Q24) WILD-TYPE
  STAGE I                           77                          96
  STAGE II                          46                          41
  STAGE III                          2                           1
  STAGE IIIA                        29                          33
  STAGE IIIB                         4                           5
  STAGE IIIC                         2                           5
  STAGE IV                           2                           0
  STAGE IVA                          0                           1
  STAGE IVB                          1                           1
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           T1  T2  T3  T4
  DEL PEAK  8(4Q24) MUTATED    80  50  37   5
  DEL PEAK  8(4Q24) WILD-TYPE 103  45  40   7
D35V4, multiclass
    clus
vv   DEL PEAK  8(4Q24) MUTATED DEL PEAK  8(4Q24) WILD-TYPE
  T1                        80                         103
  T2                        50                          45
  T3                        37                          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"
D35V5, binary
                             cls
clus                            0   1
  DEL PEAK  8(4Q24) MUTATED   122   1
  DEL PEAK  8(4Q24) WILD-TYPE 132   2
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  8(4Q24) MUTATED    122    1
  DEL PEAK  8(4Q24) WILD-TYPE  132    2
   clus
vv  DEL PEAK  8(4Q24) MUTATED DEL PEAK  8(4Q24) WILD-TYPE
  0                       122                         132
  1                         1                           2
[1] 2 2
[1] FALSE
D35V6, binary
                             cls
clus                            0   1
  DEL PEAK  8(4Q24) MUTATED   137   3
  DEL PEAK  8(4Q24) WILD-TYPE 129   1
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  8(4Q24) MUTATED    137    3
  DEL PEAK  8(4Q24) WILD-TYPE  129    1
   clus
vv  DEL PEAK  8(4Q24) MUTATED DEL PEAK  8(4Q24) WILD-TYPE
  0                       137                         129
  1                         3                           1
[1] 2 2
[1] FALSE
D35V7, binary
                             cls
clus                            0   1
  DEL PEAK  8(4Q24) MUTATED    51 122
  DEL PEAK  8(4Q24) WILD-TYPE  67 130
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  8(4Q24) MUTATED     51  122
  DEL PEAK  8(4Q24) WILD-TYPE   67  130
        clus
vv       DEL PEAK  8(4Q24) MUTATED DEL PEAK  8(4Q24) WILD-TYPE
  FEMALE                        51                          67
  MALE                         122                         130
[1] 2 2
[1] FALSE
D35V8, binary
                             cls
clus                            0   1
  DEL PEAK  8(4Q24) MUTATED   157   4
  DEL PEAK  8(4Q24) WILD-TYPE 181   5
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  8(4Q24) MUTATED    157    4
  DEL PEAK  8(4Q24) WILD-TYPE  181    5
     clus
vv    DEL PEAK  8(4Q24) MUTATED DEL PEAK  8(4Q24) WILD-TYPE
  NO                        157                         181
  YES                         4                           5
[1] 2 2
[1] FALSE
                             vv
clus                          FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  DEL PEAK  8(4Q24) MUTATED                         0                      170
  DEL PEAK  8(4Q24) WILD-TYPE                       3                      190
                             vv
clus                          HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK  8(4Q24) MUTATED                                  3
  DEL PEAK  8(4Q24) WILD-TYPE                                4
D35V9, multiclass
                                  clus
vv                                 DEL PEAK  8(4Q24) MUTATED
  FIBROLAMELLAR CARCINOMA                                  0
  HEPATOCELLULAR CARCINOMA                               170
  HEPATOCHOLANGIOCARCINOMA (MIXED)                         3
                                  clus
vv                                 DEL PEAK  8(4Q24) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                    3
  HEPATOCELLULAR CARCINOMA                                 190
  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(4Q24) MUTATED   152   7   1  13
  DEL PEAK  8(4Q24) WILD-TYPE 172  10   0   8
D35V10, multiclass
    clus
vv   DEL PEAK  8(4Q24) MUTATED DEL PEAK  8(4Q24) WILD-TYPE
  R0                       152                         172
  R1                         7                          10
  R2                         1                           0
  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  8(4Q24) MUTATED                                  1    88
  DEL PEAK  8(4Q24) WILD-TYPE                                1    70
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  8(4Q24) MUTATED                           9    71
  DEL PEAK  8(4Q24) WILD-TYPE                         8   112
D35V11, multiclass
                                  clus
vv                                 DEL PEAK  8(4Q24) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         1
  ASIAN                                                   88
  BLACK OR AFRICAN AMERICAN                                9
  WHITE                                                   71
                                  clus
vv                                 DEL PEAK  8(4Q24) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                     70
  BLACK OR AFRICAN AMERICAN                                  8
  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"
D35V12, binary
                             cls
clus                            0   1
  DEL PEAK  8(4Q24) MUTATED    11 154
  DEL PEAK  8(4Q24) WILD-TYPE   5 181
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  8(4Q24) MUTATED     11  154
  DEL PEAK  8(4Q24) WILD-TYPE    5  181
                        clus
vv                       DEL PEAK  8(4Q24) MUTATED DEL PEAK  8(4Q24) WILD-TYPE
  HISPANIC OR LATINO                            11                           5
  NOT HISPANIC OR LATINO                       154                         181
[1] 2 2
[1] FALSE

Clustering(36) Variable = DEL PEAK  9(4Q35.1) MUTATION ANALYSIS
D36V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  9(4Q35.1) MUTATED    99  69
  DEL PEAK  9(4Q35.1) WILD-TYPE 136  60
  DEL PEAK  9(4Q35.1) MUTATED DEL PEAK  9(4Q35.1) WILD-TYPE 
                          168                           196 
  DEL PEAK  9(4Q35.1) MUTATED DEL PEAK  9(4Q35.1) WILD-TYPE 
                           69                            60 
$`DEL PEAK  9(4Q35.1) MUTATED`
TCGA-BC-A112 TCGA-BC-A5W4 TCGA-DD-A4NI TCGA-DD-AADV TCGA-DD-AAE8 TCGA-FV-A3I1 
        5.03        17.98        26.83        18.87        21.83         8.12 
TCGA-FV-A4ZP TCGA-G3-A7M9 TCGA-KR-A7K7 TCGA-T1-A6J8 TCGA-UB-A7MF TCGA-ZS-A9CE 
       81.73         1.84        31.27         0.76         7.04        40.80 
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-A217 TCGA-BC-A3KF TCGA-BC-A3KG 
       27.52         2.99         1.12        45.93         0.26        22.36 
TCGA-BC-A69H TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5261 TCGA-CC-5264 
       14.60        13.45         0.66         4.24         3.19         3.35 
TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UD 
        3.32         9.86         9.96        10.36        11.93         9.99 
TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IK 
        7.13        21.34         9.83        13.12        12.56         8.61 
TCGA-CC-A7IL TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A113 
        9.14        11.31         9.17         6.94         8.15        79.73 
TCGA-DD-A114 TCGA-DD-A116 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A1EF 
       37.78        53.33         7.33         2.60         0.46        12.95 
TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39W 
       45.11        49.15         6.02        33.04        13.64        27.19 
TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A3A0 TCGA-DD-A3A2 TCGA-DD-A3A9 TCGA-DD-A4NH 
       55.69         5.62        25.81        70.06        30.61        30.15 
TCGA-DD-A4NJ TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A73B TCGA-DD-AAC8 TCGA-DD-AAC9 
       30.51        29.56        73.81         9.30         0.53        11.41 
TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH 
       76.41        55.40        71.80        12.00        15.42         6.41 
TCGA-DD-AACI TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACP TCGA-DD-AACQ 
       53.19         3.52        58.16        42.81        13.64        14.20 
TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACZ TCGA-DD-AAD2 
       59.31        51.52        50.33        46.82         5.62        21.63 
TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD8 TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD 
       42.58        44.22        40.08        40.83        13.97        40.47 
TCGA-DD-AADI TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADO TCGA-DD-AADP 
       35.67        34.49        20.91         0.39        14.89        15.06 
TCGA-DD-AADR TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE6 
       66.67        19.30        18.25        18.25        18.15         4.64 
TCGA-DD-AAEB TCGA-DD-AAEE TCGA-DD-AAEK TCGA-DD-AAVQ TCGA-DD-AAVS TCGA-DD-AAVU 
       15.72        26.63        35.08        89.69        59.93        72.39 
TCGA-DD-AAVW TCGA-DD-AAVY TCGA-DD-AAW0 TCGA-ED-A459 TCGA-ED-A66X TCGA-ED-A7PY 
       76.18        64.77        66.25        29.92        13.35        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-A2QR TCGA-FV-A496 TCGA-G3-A25S TCGA-G3-A25X 
        0.62        23.97        19.10         0.33        13.68        58.49 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A5SI TCGA-G3-A5SM TCGA-G3-A7M5 TCGA-G3-AAV1 
       14.86        21.53        25.25        17.10        14.70        11.80 
TCGA-G3-AAV4 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-K7-A5RG TCGA-KR-A7K2 
        0.89         2.14        11.87        28.90        17.06        27.25 
TCGA-LG-A9QC TCGA-MI-A75G TCGA-MI-A75I TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-RC-A7SB 
       13.97        22.95        20.71        58.88        26.27        19.33 
TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7ME 
       15.39        15.52        36.10        19.76        16.44        15.98 
TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9D2 
        0.99        12.99        20.22        22.78        13.55        25.15 

$`DEL PEAK  9(4Q35.1) WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BD-A3ER 
       83.24        11.74        38.40         8.61        69.57        36.66 
TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-AAE7 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL 
        0.36        90.28        21.17        18.90        23.64         9.96 
TCGA-ES-A2HS TCGA-FV-A3R2 TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC TCGA-K7-A5RF 
       22.62         6.38        30.74        22.13        22.06        20.75 
TCGA-KR-A7K0 TCGA-LG-A6GG TCGA-MI-A75H TCGA-UB-AA0V TCGA-XR-A8TG TCGA-ZP-A9D1 
        2.14        12.72        24.56        10.32        29.52         0.69 
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-A9H9 TCGA-2Y-A9HB TCGA-5R-AA1C TCGA-5R-AA1D 
       47.74        18.25        22.92         8.55        17.10        14.76 
TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10S TCGA-BC-A10U 
        1.51        48.99        27.91        37.32        46.78        27.52 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A216 TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A2L6 
       25.32        23.38        44.42        12.72        18.48        44.81 
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-A4NA TCGA-DD-A4NB TCGA-DD-A4NF TCGA-DD-A4NK 
      107.11        13.78        33.14        32.52        30.97        39.78 
TCGA-DD-A4NL TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV 
       56.25       108.76        12.26         0.30        80.75        78.84 
TCGA-DD-A73A TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G 
       23.93        23.05        22.78         1.45        35.67       114.35 
TCGA-DD-AA3A TCGA-DD-AACA TCGA-DD-AACD TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACO 
       13.48        75.65        12.53        69.11         0.30        61.68 
TCGA-DD-AACT TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD6 
       51.35         5.59        47.67         4.50        18.54        22.09 
TCGA-DD-AADA TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADJ TCGA-DD-AADN 
       40.54        39.52         3.78        37.64        35.05        29.52 
TCGA-DD-AADQ TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 
       14.33        15.58        18.21        20.98        18.61        19.99 
TCGA-DD-AAE9 TCGA-DD-AAED TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAVP TCGA-DD-AAVR 
       23.74        25.08        25.78        50.33        90.48        82.62 
TCGA-DD-AAVV TCGA-DD-AAVX TCGA-DD-AAVZ TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 
       80.71        56.48        62.47        65.39        60.99        53.69 
TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A82E 
       26.93        28.08        13.91         9.73         0.20        13.41 
TCGA-ED-A8O6 TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A3RK TCGA-ES-A2HT 
        1.84        18.74        19.99        20.61        11.93        14.40 
TCGA-FV-A23B TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A4ZQ TCGA-G3-A25T 
       60.89        27.88        12.03         0.03         0.39        51.06 
TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
       53.79        28.27        25.64         5.92        19.53        19.23 
TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ 
       22.95        20.42        20.78        11.87        14.14        15.78 
TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV5 TCGA-GJ-A6C0 TCGA-GJ-A9DB 
       15.65        12.23        13.55        11.64         1.02         2.20 
TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K8 TCGA-LG-A9QD 
        2.99        37.71        16.83        11.80        29.79        12.03 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MR-A520 TCGA-MR-A8JO TCGA-O8-A75V TCGA-PD-A5DF 
        9.57        16.67         7.53        10.85        17.69        21.01 
TCGA-QA-A7B7 TCGA-RC-A6M4 TCGA-RC-A6M5 TCGA-RC-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SF 
        3.09         0.72         0.49         0.30        21.04        19.04 
TCGA-UB-A7MA TCGA-UB-A7MD TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WX-AA46 TCGA-WX-AA47 
       27.88         1.71        10.75        11.34        24.85        18.28 
TCGA-XR-A8TD TCGA-XR-A8TE TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 
       33.86        30.41        35.77        25.71        23.21        35.87 
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 
                        17.08                         21.09 
[1] "0.2 - 120.8 (17.1)" "0.0 - 114.3 (21.1)"
[1] "hr=" "1.6"
D36V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IIIA
  DEL PEAK  9(4Q35.1) MUTATED        75       46         2         31
  DEL PEAK  9(4Q35.1) WILD-TYPE      98       41         1         31
                               vv
clus                            STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK  9(4Q35.1) MUTATED            3          2        2         0
  DEL PEAK  9(4Q35.1) WILD-TYPE          6          5        0         1
                               vv
clus                            STAGE IVB
  DEL PEAK  9(4Q35.1) MUTATED           1
  DEL PEAK  9(4Q35.1) WILD-TYPE         1
D36V3, multiclass
            clus
vv           DEL PEAK  9(4Q35.1) MUTATED DEL PEAK  9(4Q35.1) WILD-TYPE
  STAGE I                             75                            98
  STAGE II                            46                            41
  STAGE III                            2                             1
  STAGE IIIA                          31                            31
  STAGE IIIB                           3                             6
  STAGE IIIC                           2                             5
  STAGE IV                             2                             0
  STAGE IVA                            0                             1
  STAGE IVB                            1                             1
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  DEL PEAK  9(4Q35.1) MUTATED    78  50  40   4
  DEL PEAK  9(4Q35.1) WILD-TYPE 105  45  37   8
D36V4, multiclass
    clus
vv   DEL PEAK  9(4Q35.1) MUTATED DEL PEAK  9(4Q35.1) WILD-TYPE
  T1                          78                           105
  T2                          50                            45
  T3                          40                            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"
D36V5, binary
                               cls
clus                              0   1
  DEL PEAK  9(4Q35.1) MUTATED   125   1
  DEL PEAK  9(4Q35.1) WILD-TYPE 129   2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(4Q35.1) MUTATED    125    1
  DEL PEAK  9(4Q35.1) WILD-TYPE  129    2
   clus
vv  DEL PEAK  9(4Q35.1) MUTATED DEL PEAK  9(4Q35.1) WILD-TYPE
  0                         125                           129
  1                           1                             2
[1] 2 2
[1] FALSE
D36V6, binary
                               cls
clus                              0   1
  DEL PEAK  9(4Q35.1) MUTATED   135   3
  DEL PEAK  9(4Q35.1) WILD-TYPE 131   1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(4Q35.1) MUTATED    135    3
  DEL PEAK  9(4Q35.1) WILD-TYPE  131    1
   clus
vv  DEL PEAK  9(4Q35.1) MUTATED DEL PEAK  9(4Q35.1) WILD-TYPE
  0                         135                           131
  1                           3                             1
[1] 2 2
[1] FALSE
D36V7, binary
                               cls
clus                              0   1
  DEL PEAK  9(4Q35.1) MUTATED    46 126
  DEL PEAK  9(4Q35.1) WILD-TYPE  72 126
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(4Q35.1) MUTATED     46  126
  DEL PEAK  9(4Q35.1) WILD-TYPE   72  126
        clus
vv       DEL PEAK  9(4Q35.1) MUTATED DEL PEAK  9(4Q35.1) WILD-TYPE
  FEMALE                          46                            72
  MALE                           126                           126
[1] 2 2
[1] FALSE
D36V8, binary
                               cls
clus                              0   1
  DEL PEAK  9(4Q35.1) MUTATED   157   3
  DEL PEAK  9(4Q35.1) WILD-TYPE 181   6
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(4Q35.1) MUTATED    157    3
  DEL PEAK  9(4Q35.1) WILD-TYPE  181    6
     clus
vv    DEL PEAK  9(4Q35.1) MUTATED DEL PEAK  9(4Q35.1) WILD-TYPE
  NO                          157                           181
  YES                           3                             6
[1] 2 2
[1] FALSE
                               vv
clus                            FIBROLAMELLAR CARCINOMA
  DEL PEAK  9(4Q35.1) MUTATED                         0
  DEL PEAK  9(4Q35.1) WILD-TYPE                       3
                               vv
clus                            HEPATOCELLULAR CARCINOMA
  DEL PEAK  9(4Q35.1) MUTATED                        169
  DEL PEAK  9(4Q35.1) WILD-TYPE                      191
                               vv
clus                            HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK  9(4Q35.1) MUTATED                                  3
  DEL PEAK  9(4Q35.1) WILD-TYPE                                4
D36V9, multiclass
                                  clus
vv                                 DEL PEAK  9(4Q35.1) MUTATED
  FIBROLAMELLAR CARCINOMA                                    0
  HEPATOCELLULAR CARCINOMA                                 169
  HEPATOCHOLANGIOCARCINOMA (MIXED)                           3
                                  clus
vv                                 DEL PEAK  9(4Q35.1) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                      3
  HEPATOCELLULAR CARCINOMA                                   191
  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   153   5   1  12
  DEL PEAK  9(4Q35.1) WILD-TYPE 171  12   0   9
D36V10, multiclass
    clus
vv   DEL PEAK  9(4Q35.1) MUTATED DEL PEAK  9(4Q35.1) WILD-TYPE
  R0                         153                           171
  R1                           5                            12
  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                                  1    95
  DEL PEAK  9(4Q35.1) WILD-TYPE                                1    63
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  9(4Q35.1) MUTATED                          10    66
  DEL PEAK  9(4Q35.1) WILD-TYPE                         7   117
D36V11, multiclass
                                  clus
vv                                 DEL PEAK  9(4Q35.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  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                                                       63
  BLACK OR AFRICAN AMERICAN                                    7
  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"
D36V12, binary
                               cls
clus                              0   1
  DEL PEAK  9(4Q35.1) MUTATED     8 159
  DEL PEAK  9(4Q35.1) WILD-TYPE   8 176
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(4Q35.1) MUTATED      8  159
  DEL PEAK  9(4Q35.1) WILD-TYPE    8  176
                        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                                 8
  NOT HISPANIC OR LATINO                           176
[1] 2 2
[1] FALSE

Clustering(37) Variable = DEL PEAK 10(6Q27) MUTATION ANALYSIS
D37V1, survival
                             sevent
clus2                           0   1
  DEL PEAK 10(6Q27) MUTATED    87  48
  DEL PEAK 10(6Q27) WILD-TYPE 148  81
  DEL PEAK 10(6Q27) MUTATED DEL PEAK 10(6Q27) WILD-TYPE 
                        135                         229 
  DEL PEAK 10(6Q27) MUTATED DEL PEAK 10(6Q27) WILD-TYPE 
                         48                          81 
$`DEL PEAK 10(6Q27) MUTATED`
TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A5W4 TCGA-BD-A3ER TCGA-DD-A3A8 
       11.74        38.40         8.61        17.98        36.66         0.36 
TCGA-DD-AADV TCGA-DD-AAEG TCGA-ES-A2HS TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A3CG 
       18.87        23.64        22.62         6.38        81.73        22.13 
TCGA-G3-A6UC TCGA-G3-A7M9 TCGA-LG-A6GG TCGA-MI-A75H TCGA-T1-A6J8 TCGA-XR-A8TG 
       22.06         1.84        12.72        24.56         0.76        29.52 
TCGA-ZS-A9CE TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H2 TCGA-2Y-A9H5 TCGA-2Y-A9H8 
       40.80        27.88       120.82        56.91        18.25        20.81 
TCGA-2Y-A9HA TCGA-5R-AA1C TCGA-5R-AAAM TCGA-BC-A10Q TCGA-BC-A3KF TCGA-BC-A69I 
        1.18        17.10         1.51        37.32         0.26        12.72 
TCGA-CC-5260 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MC TCGA-CC-A7IF 
        2.86         3.32         9.86         9.96        11.93        21.34 
TCGA-CC-A7IL TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A118 
        9.14         6.94         8.15        37.78        83.57       113.00 
TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11C TCGA-DD-A1E9 TCGA-DD-A1EE TCGA-DD-A1EG 
        7.33         2.60        21.76        90.71        11.47        45.11 
TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A39X TCGA-DD-A39Z 
       49.15         6.02        33.04        18.35        55.69        19.76 
TCGA-DD-A3A0 TCGA-DD-A4NA TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NN 
       25.81        33.14        30.15        30.51        39.78        29.56 
TCGA-DD-A4NS TCGA-DD-A73E TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AACB TCGA-DD-AACD 
       80.75         1.45        13.48         0.53        76.41        12.53 
TCGA-DD-AACE TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACP TCGA-DD-AACU TCGA-DD-AACW 
       71.80         6.41        53.19        13.64        51.52        46.82 
TCGA-DD-AACY TCGA-DD-AAD0 TCGA-DD-AAD3 TCGA-DD-AAD8 TCGA-DD-AADF TCGA-DD-AADG 
       47.67         4.50        42.58        40.08         3.78        37.64 
TCGA-DD-AADJ TCGA-DD-AADL TCGA-DD-AADN TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR 
       35.05        20.91        29.52        15.06        14.33        66.67 
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-AAEH TCGA-DD-AAEK TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVY TCGA-DD-AAW0 
       25.78        35.08        59.93        72.39        64.77        66.25 
TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PZ 
       60.99        53.69        29.92         9.73         0.20         0.20 
TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A3RK 
       13.41        13.35         1.84         0.20        18.74        11.93 
TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A496 TCGA-G3-A25S TCGA-G3-A25T 
       60.89        19.10        27.88         0.33        13.68        51.06 
TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A5SL TCGA-G3-A7M5 TCGA-G3-AAV1 TCGA-G3-AAV3 
       58.49        14.86        20.42        14.70        11.80        13.55 
TCGA-G3-AAV4 TCGA-G3-AAV6 TCGA-HP-A5N0 TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I 
        0.89         2.14        37.71        16.67        22.95        20.71 
TCGA-NI-A8LF TCGA-RC-A6M4 TCGA-RC-A6M6 TCGA-RC-A7SK TCGA-UB-A7MB TCGA-UB-A7ME 
       26.27         0.72         0.30        15.52        19.76        15.98 
TCGA-UB-AA0U TCGA-WJ-A86L TCGA-ZS-A9CF 
       10.75        11.34        79.30 

$`DEL PEAK 10(6Q27) WILD-TYPE`
TCGA-2Y-A9GV TCGA-BC-A110 TCGA-BC-A112 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AAE7 
       83.24        69.57         5.03        90.28        26.83        21.17 
TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-EP-A3JL TCGA-FV-A3I1 TCGA-G3-A25W TCGA-K7-A5RF 
       21.83        18.90         9.96         8.12        30.74        20.75 
TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-UB-A7MF TCGA-UB-AA0V TCGA-ZP-A9D1 TCGA-2Y-A9GS 
        2.14        31.27         7.04        10.32         0.69        23.80 
TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GY TCGA-2Y-A9H1 
       53.39        63.75        41.79        80.28        24.89        40.41 
TCGA-2Y-A9H3 TCGA-2Y-A9H4 TCGA-2Y-A9H9 TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-5C-A9VG 
       49.84        47.74        22.92         8.55        13.02        10.78 
TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1D TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10R 
       10.59         0.66        14.76        48.99        27.91        10.13 
TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y 
       46.78        27.52        27.52         2.99        25.32        23.38 
TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A8YO 
        1.12        44.42        45.93        22.36        14.60        18.48 
TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5261 TCGA-CC-5262 
       44.81        13.45         0.66         4.24         3.19         3.39 
TCGA-CC-5263 TCGA-CC-5264 TCGA-CC-A3MB TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A5UE 
        4.24         3.35        10.36        11.41         9.99         8.94 
TCGA-CC-A7IE TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IK 
        7.13         9.83        12.00        13.12        12.56         8.61 
TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV TCGA-DD-A113 TCGA-DD-A116 TCGA-DD-A11B 
        4.60        11.31         9.17        79.73        53.33         0.46 
TCGA-DD-A11D TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EF 
       51.29        79.40        66.31        19.79        75.65        12.95 
TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39Y TCGA-DD-A3A1 TCGA-DD-A3A2 
       13.64        21.14        27.19         5.62         7.66        70.06 
TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A9 
       17.59        20.12       102.74       107.11        13.78        30.61 
TCGA-DD-A4NB TCGA-DD-A4NF TCGA-DD-A4NL TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ 
       32.52        30.97        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-AAEB TCGA-DD-AAED TCGA-DD-AAEI TCGA-DD-AAVP 
       19.99         4.64        15.72        25.08        50.33        90.48 
TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVV TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVZ 
       89.69        82.62        80.71        76.18        56.48        62.47 
TCGA-DD-AAW1 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A7PY 
       65.39        26.93        28.08        13.91        13.35        12.82 
TCGA-ED-A7XO TCGA-ED-A7XP TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC 
       14.04        13.15        19.99        20.61        19.59         0.62 
TCGA-ES-A2HT TCGA-FV-A2QQ TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A4ZQ TCGA-G3-A25U 
       14.40        23.97        12.03         0.03         0.39        53.79 
TCGA-G3-A25V TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
       28.27        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        11.64        11.87        28.90 
TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 
        1.02         2.20         2.99        17.06        16.83        11.80 
TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MR-A520 
       27.25        29.79        13.97        12.03         9.57         7.53 
TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A6M5 
       10.85        58.88        17.69        21.01         3.09         0.49 
TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RG-A7D4 TCGA-UB-A7MA 
       21.04        19.33        19.04        15.39        36.10        27.88 
TCGA-UB-A7MC TCGA-UB-A7MD TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-WX-AA46 
       16.44         1.71         0.99        12.99        20.22        24.85 
TCGA-WX-AA47 TCGA-XR-A8TD TCGA-XR-A8TE TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CV 
       18.28        33.86        30.41        22.78        13.55        35.77 
TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD 
       25.71        23.21        35.87        25.15        12.99        45.57 
TCGA-ZS-A9CG 
       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 
                      19.76                       19.79 
[1] "0.2 - 120.8 (19.8)" "0.0 - 114.3 (19.8)"
[1] "hr=" "1"  
D37V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 10(6Q27) MUTATED        62       32         1         24          3
  DEL PEAK 10(6Q27) WILD-TYPE     111       55         2         38          6
                             vv
clus                          STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 10(6Q27) MUTATED            5        2         0         1
  DEL PEAK 10(6Q27) WILD-TYPE          2        0         1         1
D37V3, multiclass
            clus
vv           DEL PEAK 10(6Q27) MUTATED DEL PEAK 10(6Q27) WILD-TYPE
  STAGE I                           62                         111
  STAGE II                          32                          55
  STAGE III                          1                           2
  STAGE IIIA                        24                          38
  STAGE IIIB                         3                           6
  STAGE IIIC                         5                           2
  STAGE IV                           2                           0
  STAGE IVA                          0                           1
  STAGE IVB                          1                           1
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           T1  T2  T3  T4
  DEL PEAK 10(6Q27) MUTATED    65  36  29   4
  DEL PEAK 10(6Q27) WILD-TYPE 118  59  48   8
D37V4, multiclass
    clus
vv   DEL PEAK 10(6Q27) MUTATED DEL PEAK 10(6Q27) WILD-TYPE
  T1                        65                         118
  T2                        36                          59
  T3                        29                          48
  T4                         4                           8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V5, binary
                             cls
clus                            0   1
  DEL PEAK 10(6Q27) MUTATED    93   2
  DEL PEAK 10(6Q27) WILD-TYPE 161   1
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 10(6Q27) MUTATED     93    2
  DEL PEAK 10(6Q27) WILD-TYPE  161    1
   clus
vv  DEL PEAK 10(6Q27) MUTATED DEL PEAK 10(6Q27) WILD-TYPE
  0                        93                         161
  1                         2                           1
[1] 2 2
[1] FALSE
D37V6, binary
                             cls
clus                            0   1
  DEL PEAK 10(6Q27) MUTATED   105   3
  DEL PEAK 10(6Q27) WILD-TYPE 161   1
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 10(6Q27) MUTATED    105    3
  DEL PEAK 10(6Q27) WILD-TYPE  161    1
   clus
vv  DEL PEAK 10(6Q27) MUTATED DEL PEAK 10(6Q27) WILD-TYPE
  0                       105                         161
  1                         3                           1
[1] 2 2
[1] FALSE
D37V7, binary
                             cls
clus                            0   1
  DEL PEAK 10(6Q27) MUTATED    48  88
  DEL PEAK 10(6Q27) WILD-TYPE  70 164
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 10(6Q27) MUTATED     48   88
  DEL PEAK 10(6Q27) WILD-TYPE   70  164
        clus
vv       DEL PEAK 10(6Q27) MUTATED DEL PEAK 10(6Q27) WILD-TYPE
  FEMALE                        48                          70
  MALE                          88                         164
[1] 2 2
[1] FALSE
D37V8, binary
                             cls
clus                            0   1
  DEL PEAK 10(6Q27) MUTATED   124   2
  DEL PEAK 10(6Q27) WILD-TYPE 214   7
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 10(6Q27) MUTATED    124    2
  DEL PEAK 10(6Q27) WILD-TYPE  214    7
     clus
vv    DEL PEAK 10(6Q27) MUTATED DEL PEAK 10(6Q27) WILD-TYPE
  NO                        124                         214
  YES                         2                           7
[1] 2 2
[1] FALSE
                             vv
clus                          FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  DEL PEAK 10(6Q27) MUTATED                         0                      133
  DEL PEAK 10(6Q27) WILD-TYPE                       3                      227
                             vv
clus                          HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK 10(6Q27) MUTATED                                  3
  DEL PEAK 10(6Q27) WILD-TYPE                                4
D37V9, multiclass
                                  clus
vv                                 DEL PEAK 10(6Q27) MUTATED
  FIBROLAMELLAR CARCINOMA                                  0
  HEPATOCELLULAR CARCINOMA                               133
  HEPATOCHOLANGIOCARCINOMA (MIXED)                         3
                                  clus
vv                                 DEL PEAK 10(6Q27) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                    3
  HEPATOCELLULAR CARCINOMA                                 227
  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   120   8   1   5
  DEL PEAK 10(6Q27) WILD-TYPE 204   9   0  16
D37V10, multiclass
    clus
vv   DEL PEAK 10(6Q27) MUTATED DEL PEAK 10(6Q27) WILD-TYPE
  R0                       120                         204
  R1                         8                           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                                2    96
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 10(6Q27) MUTATED                           4    68
  DEL PEAK 10(6Q27) WILD-TYPE                        13   115
D37V11, multiclass
                                  clus
vv                                 DEL PEAK 10(6Q27) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         0
  ASIAN                                                   62
  BLACK OR AFRICAN AMERICAN                                4
  WHITE                                                   68
                                  clus
vv                                 DEL PEAK 10(6Q27) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           2
  ASIAN                                                     96
  BLACK OR AFRICAN AMERICAN                                 13
  WHITE                                                    115
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V12, binary
                             cls
clus                            0   1
  DEL PEAK 10(6Q27) MUTATED     3 128
  DEL PEAK 10(6Q27) WILD-TYPE  13 207
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 10(6Q27) MUTATED      3  128
  DEL PEAK 10(6Q27) WILD-TYPE   13  207
                        clus
vv                       DEL PEAK 10(6Q27) MUTATED DEL PEAK 10(6Q27) WILD-TYPE
  HISPANIC OR LATINO                             3                          13
  NOT HISPANIC OR LATINO                       128                         207
[1] 2 2
[1] FALSE

Clustering(38) Variable = DEL PEAK 11(7Q36.3) MUTATION ANALYSIS
D38V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 11(7Q36.3) MUTATED    16  18
  DEL PEAK 11(7Q36.3) WILD-TYPE 219 111
  DEL PEAK 11(7Q36.3) MUTATED DEL PEAK 11(7Q36.3) WILD-TYPE 
                           34                           330 
  DEL PEAK 11(7Q36.3) MUTATED DEL PEAK 11(7Q36.3) WILD-TYPE 
                           18                           111 
$`DEL PEAK 11(7Q36.3) MUTATED`
TCGA-DD-A4ND TCGA-G3-A7M9 TCGA-UB-A7MF TCGA-BC-4072 TCGA-BC-A217 TCGA-BC-A3KG 
       90.28         1.84         7.04        48.99        45.93        22.36 
TCGA-CC-5261 TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A7IG TCGA-DD-A1EF TCGA-DD-A1EL 
        3.19        11.41         9.99         9.83        12.95        13.64 
TCGA-DD-A39X TCGA-DD-AAC9 TCGA-DD-AACB TCGA-DD-AACL TCGA-DD-AACZ TCGA-DD-AADB 
       55.69        11.41        76.41         3.52         5.62        40.83 
TCGA-DD-AADF TCGA-DD-AAE4 TCGA-DD-AAVZ TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A8O6 
        3.78        19.99        62.47         0.20        12.82         1.84 
TCGA-EP-A2KB TCGA-FV-A496 TCGA-G3-A25S TCGA-GJ-A6C0 TCGA-NI-A8LF TCGA-QA-A7B7 
       19.59         0.33        13.68         1.02        26.27         3.09 
TCGA-RC-A6M6 TCGA-UB-A7MA TCGA-WX-AA44 TCGA-ZS-A9CF 
        0.30        27.88        20.22        79.30 

$`DEL PEAK 11(7Q36.3) WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 
       83.24        11.74        38.40         8.61        69.57         5.03 
TCGA-BC-A5W4 TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4NI TCGA-DD-AADV TCGA-DD-AAE7 
       17.98        36.66         0.36        26.83        18.87        21.17 
TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-ES-A2HS TCGA-FV-A3I1 
       21.83        18.90        23.64         9.96        22.62         8.12 
TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC TCGA-K7-A5RF 
        6.38        81.73        30.74        22.13        22.06        20.75 
TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H TCGA-T1-A6J8 TCGA-UB-AA0V 
        2.14        31.27        12.72        24.56         0.76        10.32 
TCGA-XR-A8TG TCGA-ZP-A9D1 TCGA-ZS-A9CE TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU 
       29.52         0.69        40.80        23.80        53.39        63.75 
TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 
       41.79        80.28        24.89        27.88       120.82        40.41 
TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-2Y-A9H9 
       56.91        49.84        47.74        18.25        20.81        22.92 
TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD 
        1.18         8.55        13.02        10.78        10.59         0.66 
TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R 
       17.10        14.76         1.51        27.91        37.32        10.13 
TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y 
       46.78        27.52        27.52         2.99        25.32        23.38 
TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A3KF TCGA-BC-A69H TCGA-BC-A69I TCGA-BC-A8YO 
        1.12        44.42         0.26        14.60        12.72        18.48 
TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5262 
       44.81        13.45         0.66         4.24         2.86         3.39 
TCGA-CC-5263 TCGA-CC-5264 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB 
        4.24         3.35         3.32         9.86         9.96        10.36 
TCGA-CC-A3MC TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IH TCGA-CC-A7II 
       11.93         8.94         7.13        21.34        12.00        13.12 
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-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-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D 
      113.00         7.33         2.60         0.46        21.76        51.29 
TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE 
       90.71        79.40        66.31        19.79        75.65        11.47 
TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A39V 
       45.11        49.15         6.02        33.04        18.35        21.14 
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-A3A7 TCGA-DD-A3A9 
       17.59        20.12       102.74       107.11        13.78        30.61 
TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK 
       33.14        32.52        30.97        30.15        30.51        39.78 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR 
       56.25        29.56        73.81       108.76        12.26         0.30 
TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D 
       80.75        78.84        23.93         9.30        23.05        22.78 
TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AACA 
        1.45        35.67       114.35        13.48         0.53        75.65 
TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH 
       55.40        12.53        71.80        12.00        15.42         6.41 
TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO 
       53.19        69.11         0.30        58.16        42.81        61.68 
TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-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-AADC 
       42.58        44.22        22.09        40.08        40.54        13.97 
TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK 
       40.47        39.52        37.64        35.67        35.05        34.49 
TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ 
       20.91         0.39        29.52        14.89        15.06        14.33 
TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 
       66.67        15.58        18.21        19.30        18.25        18.25 
TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE6 TCGA-DD-AAE9 TCGA-DD-AAEB 
       18.15        20.98        18.61         4.64        23.74        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        90.48 
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-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 
       56.48        64.77        66.25        65.39        60.99        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-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A97K 
        0.20        14.04        13.15        13.41        13.35         0.20 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HT 
       18.74        19.99        20.61         0.62        11.93        14.40 
TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A495 
       60.89        23.97        19.10        27.88        12.03         0.03 
TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25X TCGA-G3-A25Y 
        0.39        51.06        53.79        28.27        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-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M7 
       22.95        20.42        17.10        14.70        20.78        11.87 
TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 
       14.14        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-A9DB 
        0.89        11.64         2.14        11.87        28.90         2.20 
TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K2 
        2.99        37.71        17.06        16.83        11.80        27.25 
TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G 
       29.79        13.97        12.03         9.57        16.67        22.95 
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-RC-A6M4 TCGA-RC-A6M5 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH 
        0.72         0.49        21.04        19.33        19.04        15.39 
TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME 
       15.52        36.10        19.76        16.44         1.71        15.98 
TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA46 TCGA-WX-AA47 
       10.75        11.34         0.99        12.99        24.85        18.28 
TCGA-XR-A8TD TCGA-XR-A8TE TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY 
       33.86        30.41        22.78        13.55        35.77        25.71 
TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CG 
       23.21        35.87        25.15        12.99        45.57        11.21 

  DEL PEAK 11(7Q36.3) MUTATED DEL PEAK 11(7Q36.3) WILD-TYPE 
                         0.20                          0.03 
  DEL PEAK 11(7Q36.3) MUTATED DEL PEAK 11(7Q36.3) WILD-TYPE 
                        90.28                        120.82 
  DEL PEAK 11(7Q36.3) MUTATED DEL PEAK 11(7Q36.3) WILD-TYPE 
                       12.885                        20.515 
[1] "0.2 - 90.3 (12.9)"  "0.0 - 120.8 (20.5)"
[1] "hr=" "2"  
D38V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IIIA
  DEL PEAK 11(7Q36.3) MUTATED        16       12         0          5
  DEL PEAK 11(7Q36.3) WILD-TYPE     157       75         3         57
                               vv
clus                            STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 11(7Q36.3) MUTATED            1          0        0         0
  DEL PEAK 11(7Q36.3) WILD-TYPE          8          7        2         1
                               vv
clus                            STAGE IVB
  DEL PEAK 11(7Q36.3) MUTATED           0
  DEL PEAK 11(7Q36.3) WILD-TYPE         2
D38V3, multiclass
            clus
vv           DEL PEAK 11(7Q36.3) MUTATED DEL PEAK 11(7Q36.3) WILD-TYPE
  STAGE I                             16                           157
  STAGE II                            12                            75
  STAGE III                            0                             3
  STAGE IIIA                           5                            57
  STAGE IIIB                           1                             8
  STAGE IIIC                           0                             7
  STAGE IV                             0                             2
  STAGE IVA                            0                             1
  STAGE IVB                            0                             2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  DEL PEAK 11(7Q36.3) MUTATED    16  12   6   0
  DEL PEAK 11(7Q36.3) WILD-TYPE 167  83  71  12
D38V4, multiclass
    clus
vv   DEL PEAK 11(7Q36.3) MUTATED DEL PEAK 11(7Q36.3) WILD-TYPE
  T1                          16                           167
  T2                          12                            83
  T3                           6                            71
  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"
D38V5, binary
                               cls
clus                              0   1
  DEL PEAK 11(7Q36.3) MUTATED    20   0
  DEL PEAK 11(7Q36.3) WILD-TYPE 234   3
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(7Q36.3) MUTATED     20    0
  DEL PEAK 11(7Q36.3) WILD-TYPE  234    3
   clus
vv  DEL PEAK 11(7Q36.3) MUTATED DEL PEAK 11(7Q36.3) WILD-TYPE
  0                          20                           234
  1                           0                             3
[1] 2 2
[1] FALSE
D38V6, binary
                               cls
clus                              0   1
  DEL PEAK 11(7Q36.3) MUTATED    26   0
  DEL PEAK 11(7Q36.3) WILD-TYPE 240   4
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(7Q36.3) MUTATED     26    0
  DEL PEAK 11(7Q36.3) WILD-TYPE  240    4
   clus
vv  DEL PEAK 11(7Q36.3) MUTATED DEL PEAK 11(7Q36.3) WILD-TYPE
  0                          26                           240
  1                           0                             4
[1] 2 2
[1] FALSE
D38V7, binary
                               cls
clus                              0   1
  DEL PEAK 11(7Q36.3) MUTATED    19  15
  DEL PEAK 11(7Q36.3) WILD-TYPE  99 237
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(7Q36.3) MUTATED     19   15
  DEL PEAK 11(7Q36.3) WILD-TYPE   99  237
        clus
vv       DEL PEAK 11(7Q36.3) MUTATED DEL PEAK 11(7Q36.3) WILD-TYPE
  FEMALE                          19                            99
  MALE                            15                           237
[1] 2 2
[1] FALSE
D38V8, binary
                               cls
clus                              0   1
  DEL PEAK 11(7Q36.3) MUTATED    30   1
  DEL PEAK 11(7Q36.3) WILD-TYPE 308   8
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(7Q36.3) MUTATED     30    1
  DEL PEAK 11(7Q36.3) WILD-TYPE  308    8
     clus
vv    DEL PEAK 11(7Q36.3) MUTATED DEL PEAK 11(7Q36.3) WILD-TYPE
  NO                           30                           308
  YES                           1                             8
[1] 2 2
[1] FALSE
                               vv
clus                            FIBROLAMELLAR CARCINOMA
  DEL PEAK 11(7Q36.3) MUTATED                         0
  DEL PEAK 11(7Q36.3) WILD-TYPE                       3
                               vv
clus                            HEPATOCELLULAR CARCINOMA
  DEL PEAK 11(7Q36.3) MUTATED                         33
  DEL PEAK 11(7Q36.3) WILD-TYPE                      327
                               vv
clus                            HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK 11(7Q36.3) MUTATED                                  1
  DEL PEAK 11(7Q36.3) WILD-TYPE                                6
D38V9, multiclass
                                  clus
vv                                 DEL PEAK 11(7Q36.3) MUTATED
  FIBROLAMELLAR CARCINOMA                                    0
  HEPATOCELLULAR CARCINOMA                                  33
  HEPATOCHOLANGIOCARCINOMA (MIXED)                           1
                                  clus
vv                                 DEL PEAK 11(7Q36.3) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                      3
  HEPATOCELLULAR CARCINOMA                                   327
  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 11(7Q36.3) MUTATED    26   4   0   4
  DEL PEAK 11(7Q36.3) WILD-TYPE 298  13   1  17
D38V10, multiclass
    clus
vv   DEL PEAK 11(7Q36.3) MUTATED DEL PEAK 11(7Q36.3) WILD-TYPE
  R0                          26                           298
  R1                           4                            13
  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 11(7Q36.3) MUTATED                                  0    15
  DEL PEAK 11(7Q36.3) WILD-TYPE                                2   143
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 11(7Q36.3) MUTATED                           2    17
  DEL PEAK 11(7Q36.3) WILD-TYPE                        15   166
D38V11, multiclass
                                  clus
vv                                 DEL PEAK 11(7Q36.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                     15
  BLACK OR AFRICAN AMERICAN                                  2
  WHITE                                                     17
                                  clus
vv                                 DEL PEAK 11(7Q36.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             2
  ASIAN                                                      143
  BLACK OR AFRICAN AMERICAN                                   15
  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"
D38V12, binary
                               cls
clus                              0   1
  DEL PEAK 11(7Q36.3) MUTATED     1  32
  DEL PEAK 11(7Q36.3) WILD-TYPE  15 303
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(7Q36.3) MUTATED      1   32
  DEL PEAK 11(7Q36.3) WILD-TYPE   15  303
                        clus
vv                       DEL PEAK 11(7Q36.3) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          32
                        clus
vv                       DEL PEAK 11(7Q36.3) WILD-TYPE
  HISPANIC OR LATINO                                15
  NOT HISPANIC OR LATINO                           303
[1] 2 2
[1] FALSE

Clustering(39) Variable = DEL PEAK 12(8P23.2) MUTATION ANALYSIS
D39V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 12(8P23.2) MUTATED   159  84
  DEL PEAK 12(8P23.2) WILD-TYPE  76  45
  DEL PEAK 12(8P23.2) MUTATED DEL PEAK 12(8P23.2) WILD-TYPE 
                          243                           121 
  DEL PEAK 12(8P23.2) MUTATED DEL PEAK 12(8P23.2) WILD-TYPE 
                           84                            45 
$`DEL PEAK 12(8P23.2) MUTATED`
TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-BC-A112 TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI 
       11.74        38.40         5.03         0.36        90.28        26.83 
TCGA-DD-AADV TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEG TCGA-EP-A3JL TCGA-ES-A2HS 
       18.87        21.17        21.83        23.64         9.96        22.62 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC 
        8.12         6.38        81.73        30.74        22.13        22.06 
TCGA-KR-A7K7 TCGA-MI-A75H TCGA-T1-A6J8 TCGA-UB-A7MF TCGA-XR-A8TG TCGA-ZS-A9CE 
       31.27        24.56         0.76         7.04        29.52        40.80 
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-A9H9 TCGA-2Y-A9HA 
       56.91        49.84        47.74        18.25        22.92         1.18 
TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-5C-A9VH TCGA-5R-AA1C TCGA-5R-AAAM TCGA-BC-4072 
        8.55        13.02        10.59        17.10         1.51        48.99 
TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A216 TCGA-BC-A217 
       10.13        46.78        27.52        27.52        44.42        45.93 
TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A69I TCGA-BD-A3EP TCGA-BW-A5NO 
        0.26        22.36        14.60        12.72        13.45         0.66 
TCGA-CC-5258 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 
        4.24         3.19         3.39         4.24         3.32         9.86 
TCGA-CC-A3MC TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7II 
       11.93         7.13        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-CC-A9FW TCGA-DD-A113 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 
        8.15        79.73        83.57        53.33       113.00         7.33 
TCGA-DD-A11C TCGA-DD-A1E9 TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EI 
       21.76        90.71        11.47        12.95        45.11         6.02 
TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y 
       33.04        18.35        13.64        21.14        55.69         5.62 
TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A3 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NA 
       19.76        25.81        17.59        13.78        30.61        33.14 
TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NN TCGA-DD-A4NO 
       30.97        30.15        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 
       71.80        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-AAE0 TCGA-DD-AAE4 
       14.89        15.06        14.33        66.67        18.25        19.99 
TCGA-DD-AAE6 TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEH 
        4.64        23.74        15.72        25.08        26.63        25.78 
TCGA-DD-AAEI TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU 
       50.33        90.48        89.69        82.62        59.93        72.39 
TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 
       64.77        62.47        66.25        60.99        53.69        29.92 
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-A3RK TCGA-ES-A2HT TCGA-FV-A2QQ 
       19.99        20.61         0.62        11.93        14.40        23.97 
TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A495 TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25V 
       19.10        27.88         0.03         0.39        13.68        28.27 
TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A3CJ TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A7M5 
       58.49        14.86        19.53        22.95        20.42        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 
       11.64         2.14        11.87         1.02         2.20         2.99 
TCGA-HP-A5N0 TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-LG-A9QC TCGA-LG-A9QD 
       37.71        16.83        11.80        27.25        13.97        12.03 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75I TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF 
        9.57        16.67        20.71        10.85        58.88        26.27 
TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A6M4 TCGA-RC-A6M6 TCGA-RC-A7S9 
       17.69        21.01         3.09         0.72         0.30        21.04 
TCGA-RC-A7SF TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MB TCGA-UB-A7MD TCGA-UB-A7ME 
       19.04        15.52        36.10        19.76         1.71        15.98 
TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-XR-A8TD 
       10.75        11.34         0.99        12.99        20.22        33.86 
TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 
       13.55        35.77        23.21        35.87        25.15        12.99 
TCGA-ZS-A9CD TCGA-ZS-A9CF TCGA-ZS-A9CG 
       45.57        79.30        11.21 

$`DEL PEAK 12(8P23.2) WILD-TYPE`
TCGA-2Y-A9GV TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A5W4 TCGA-BD-A3ER TCGA-DD-AAEA 
       83.24         8.61        69.57        17.98        36.66        18.90 
TCGA-G3-A7M9 TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-LG-A6GG TCGA-UB-AA0V TCGA-ZP-A9D1 
        1.84        20.75         2.14        12.72        10.32         0.69 
TCGA-2Y-A9GT TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H8 TCGA-5C-A9VG TCGA-5C-AAPD 
       53.39        27.88       120.82        20.81        10.78         0.66 
TCGA-5R-AA1D TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y 
       14.76        27.91        37.32         2.99        25.32        23.38 
TCGA-BC-A10Z TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-CC-5260 TCGA-CC-5264 TCGA-CC-A3MA 
        1.12        18.48        44.81         2.86         3.35         9.96 
TCGA-CC-A3MB TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IK TCGA-DD-A114 
       10.36        11.41         9.99         8.94         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-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A4 
       75.65        49.15        27.19         7.66        70.06        20.12 
TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A4NB TCGA-DD-A4NL TCGA-DD-A4NP TCGA-DD-A4NQ 
      102.74       107.11        32.52        56.25       108.76        12.26 
TCGA-DD-A73B TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACF 
        9.30        13.48         0.53        11.41        75.65        12.00 
TCGA-DD-AACI TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACT TCGA-DD-AACV TCGA-DD-AACW 
       53.19         0.30         3.52        51.35        50.33        46.82 
TCGA-DD-AACX TCGA-DD-AAD6 TCGA-DD-AADJ TCGA-DD-AADL TCGA-DD-AADS TCGA-DD-AADU 
        5.59        22.09        35.05        20.91        15.58        18.21 
TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAEK 
       19.30        18.25        18.15        20.98        18.61        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-AAV1 TCGA-G3-AAV3 TCGA-GJ-A3OU TCGA-K7-A5RG 
       17.10        14.14        11.80        13.55        28.90        17.06 
TCGA-KR-A7K8 TCGA-MI-A75G TCGA-MR-A520 TCGA-RC-A6M5 TCGA-RC-A7SB TCGA-RC-A7SH 
       29.79        22.95         7.53         0.49        19.33        15.39 
TCGA-UB-A7MA TCGA-UB-A7MC TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TE TCGA-XR-A8TF 
       27.88        16.44        24.85        18.28        30.41        22.78 
TCGA-ZP-A9CY 
       25.71 

  DEL PEAK 12(8P23.2) MUTATED DEL PEAK 12(8P23.2) WILD-TYPE 
                         0.03                          0.20 
  DEL PEAK 12(8P23.2) MUTATED DEL PEAK 12(8P23.2) WILD-TYPE 
                       114.35                        120.82 
  DEL PEAK 12(8P23.2) MUTATED DEL PEAK 12(8P23.2) WILD-TYPE 
                        20.22                         19.30 
[1] "0.0 - 114.3 (20.2)" "0.2 - 120.8 (19.3)"
[1] "hr=" "1"  
D39V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IIIA
  DEL PEAK 12(8P23.2) MUTATED       121       58         0         37
  DEL PEAK 12(8P23.2) WILD-TYPE      52       29         3         25
                               vv
clus                            STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 12(8P23.2) MUTATED            7          4        2         0
  DEL PEAK 12(8P23.2) WILD-TYPE          2          3        0         1
                               vv
clus                            STAGE IVB
  DEL PEAK 12(8P23.2) MUTATED           2
  DEL PEAK 12(8P23.2) WILD-TYPE         0
D39V3, multiclass
            clus
vv           DEL PEAK 12(8P23.2) MUTATED DEL PEAK 12(8P23.2) WILD-TYPE
  STAGE I                            121                            52
  STAGE II                            58                            29
  STAGE III                            0                             3
  STAGE IIIA                          37                            25
  STAGE IIIB                           7                             2
  STAGE IIIC                           4                             3
  STAGE IV                             2                             0
  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                             T1  T2  T3  T4
  DEL PEAK 12(8P23.2) MUTATED   127  64  48   6
  DEL PEAK 12(8P23.2) WILD-TYPE  56  31  29   6
D39V4, multiclass
    clus
vv   DEL PEAK 12(8P23.2) MUTATED DEL PEAK 12(8P23.2) WILD-TYPE
  T1                         127                            56
  T2                          64                            31
  T3                          48                            29
  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"
D39V5, binary
                               cls
clus                              0   1
  DEL PEAK 12(8P23.2) MUTATED   165   2
  DEL PEAK 12(8P23.2) WILD-TYPE  89   1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(8P23.2) MUTATED    165    2
  DEL PEAK 12(8P23.2) WILD-TYPE   89    1
   clus
vv  DEL PEAK 12(8P23.2) MUTATED DEL PEAK 12(8P23.2) WILD-TYPE
  0                         165                            89
  1                           2                             1
[1] 2 2
[1] FALSE
D39V6, binary
                               cls
clus                              0   1
  DEL PEAK 12(8P23.2) MUTATED   175   4
  DEL PEAK 12(8P23.2) WILD-TYPE  91   0
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(8P23.2) MUTATED    175    4
  DEL PEAK 12(8P23.2) WILD-TYPE   91    0
   clus
vv  DEL PEAK 12(8P23.2) MUTATED DEL PEAK 12(8P23.2) WILD-TYPE
  0                         175                            91
  1                           4                             0
[1] 2 2
[1] FALSE
D39V7, binary
                               cls
clus                              0   1
  DEL PEAK 12(8P23.2) MUTATED    75 172
  DEL PEAK 12(8P23.2) WILD-TYPE  43  80
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(8P23.2) MUTATED     75  172
  DEL PEAK 12(8P23.2) WILD-TYPE   43   80
        clus
vv       DEL PEAK 12(8P23.2) MUTATED DEL PEAK 12(8P23.2) WILD-TYPE
  FEMALE                          75                            43
  MALE                           172                            80
[1] 2 2
[1] FALSE
D39V8, binary
                               cls
clus                              0   1
  DEL PEAK 12(8P23.2) MUTATED   225   6
  DEL PEAK 12(8P23.2) WILD-TYPE 113   3
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(8P23.2) MUTATED    225    6
  DEL PEAK 12(8P23.2) WILD-TYPE  113    3
     clus
vv    DEL PEAK 12(8P23.2) MUTATED DEL PEAK 12(8P23.2) WILD-TYPE
  NO                          225                           113
  YES                           6                             3
[1] 2 2
[1] FALSE
                               vv
clus                            FIBROLAMELLAR CARCINOMA
  DEL PEAK 12(8P23.2) MUTATED                         1
  DEL PEAK 12(8P23.2) WILD-TYPE                       2
                               vv
clus                            HEPATOCELLULAR CARCINOMA
  DEL PEAK 12(8P23.2) MUTATED                        243
  DEL PEAK 12(8P23.2) WILD-TYPE                      117
                               vv
clus                            HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK 12(8P23.2) MUTATED                                  3
  DEL PEAK 12(8P23.2) WILD-TYPE                                4
D39V9, multiclass
                                  clus
vv                                 DEL PEAK 12(8P23.2) MUTATED
  FIBROLAMELLAR CARCINOMA                                    1
  HEPATOCELLULAR CARCINOMA                                 243
  HEPATOCHOLANGIOCARCINOMA (MIXED)                           3
                                  clus
vv                                 DEL PEAK 12(8P23.2) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                      2
  HEPATOCELLULAR CARCINOMA                                   117
  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 12(8P23.2) MUTATED   213  12   1  15
  DEL PEAK 12(8P23.2) WILD-TYPE 111   5   0   6
D39V10, multiclass
    clus
vv   DEL PEAK 12(8P23.2) MUTATED DEL PEAK 12(8P23.2) WILD-TYPE
  R0                         213                           111
  R1                          12                             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 12(8P23.2) MUTATED                                  2   102
  DEL PEAK 12(8P23.2) WILD-TYPE                                0    56
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 12(8P23.2) MUTATED                          13   123
  DEL PEAK 12(8P23.2) WILD-TYPE                         4    60
D39V11, multiclass
                                  clus
vv                                 DEL PEAK 12(8P23.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           2
  ASIAN                                                    102
  BLACK OR AFRICAN AMERICAN                                 13
  WHITE                                                    123
                                  clus
vv                                 DEL PEAK 12(8P23.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                       56
  BLACK OR AFRICAN AMERICAN                                    4
  WHITE                                                       60
[1] 4 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 12(8P23.2) MUTATED    11 223
  DEL PEAK 12(8P23.2) WILD-TYPE   5 112
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(8P23.2) MUTATED     11  223
  DEL PEAK 12(8P23.2) WILD-TYPE    5  112
                        clus
vv                       DEL PEAK 12(8P23.2) MUTATED
  HISPANIC OR LATINO                              11
  NOT HISPANIC OR LATINO                         223
                        clus
vv                       DEL PEAK 12(8P23.2) WILD-TYPE
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                           112
[1] 2 2
[1] FALSE

Clustering(40) Variable = DEL PEAK 13(8P12) MUTATION ANALYSIS
D40V1, survival
                             sevent
clus2                           0   1
  DEL PEAK 13(8P12) MUTATED   156  82
  DEL PEAK 13(8P12) WILD-TYPE  79  47
  DEL PEAK 13(8P12) MUTATED DEL PEAK 13(8P12) WILD-TYPE 
                        238                         126 
  DEL PEAK 13(8P12) MUTATED DEL PEAK 13(8P12) WILD-TYPE 
                         82                          47 
$`DEL PEAK 13(8P12) MUTATED`
TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-BC-A112 TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-AADV 
       11.74        38.40         5.03         0.36        90.28        18.87 
TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEG TCGA-EP-A3JL TCGA-ES-A2HS TCGA-FV-A3I1 
       21.17        21.83        23.64         9.96        22.62         8.12 
TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC TCGA-G3-A7M9 
        6.38        81.73        30.74        22.13        22.06         1.84 
TCGA-KR-A7K7 TCGA-MI-A75H TCGA-T1-A6J8 TCGA-UB-A7MF TCGA-XR-A8TG TCGA-ZS-A9CE 
       31.27        24.56         0.76         7.04        29.52        40.80 
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-A9H9 TCGA-2Y-A9HA 
       56.91        49.84        47.74        18.25        22.92         1.18 
TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-5C-A9VH TCGA-5R-AA1C TCGA-5R-AAAM TCGA-BC-4072 
        8.55        13.02        10.59        17.10         1.51        48.99 
TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A216 TCGA-BC-A217 
       37.32        10.13        46.78        27.52        44.42        45.93 
TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A69I TCGA-BD-A3EP TCGA-BW-A5NO 
        0.26        22.36        14.60        12.72        13.45         0.66 
TCGA-CC-5258 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 
        4.24         3.19         3.39         4.24         3.32         9.86 
TCGA-CC-A3MA TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7IJ 
        9.96         7.13        21.34         9.83        12.00        12.56 
TCGA-CC-A7IL TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FS TCGA-CC-A9FW 
        9.14         4.60        11.31         9.17         6.94         8.15 
TCGA-DD-A113 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11C 
       79.73        83.57        53.33       113.00         7.33        21.76 
TCGA-DD-A1E9 TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EI TCGA-DD-A1EJ 
       90.71        11.47        12.95        45.11         6.02        33.04 
TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A3 
       18.35        13.64        21.14         5.62        19.76        17.59 
TCGA-DD-A3A5 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NH TCGA-DD-A4NJ 
      102.74        13.78        30.61        33.14        30.15        30.51 
TCGA-DD-A4NK TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV 
       39.78        29.56        73.81         0.30        80.75        78.84 
TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F 
       23.93         9.30        23.05        22.78         1.45        35.67 
TCGA-DD-A73G TCGA-DD-AAC8 TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE 
      114.35         0.53        76.41        55.40        12.53        71.80 
TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACJ TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO 
       15.42         6.41        69.11        58.16        42.81        61.68 
TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 
       13.64        14.20        59.31         5.62         4.50        18.54 
TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB 
       21.63        42.58        44.22        40.08        40.54        40.83 
TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI 
       13.97        40.47        39.52         3.78        37.64        35.67 
TCGA-DD-AADK TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR 
       34.49        29.52        14.89        15.06        14.33        66.67 
TCGA-DD-AAE0 TCGA-DD-AAE4 TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE 
       18.25        19.99        23.74        15.72        25.08        26.63 
TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS 
       25.78        50.33        90.48        89.69        82.62        59.93 
TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW2 
       72.39        76.18        64.77        62.47        66.25        60.99 
TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A66X TCGA-ED-A7PY TCGA-ED-A7PZ 
       53.69        29.92        26.93        13.35        12.82         0.20 
TCGA-ED-A7XO TCGA-ED-A8O6 TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC 
       14.04         1.84        18.74        19.99        20.61         0.62 
TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A495 
       11.93        14.40        23.97        19.10        27.88         0.03 
TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25V TCGA-G3-A25X TCGA-G3-A3CJ TCGA-G3-A5SL 
        0.39        13.68        28.27        58.49        19.53        20.42 
TCGA-G3-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV2 
       14.70        20.78        11.87        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        11.64         2.14        11.87         2.99        16.83 
TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C 
       11.80        27.25        29.79        13.97        12.03         9.57 
TCGA-MI-A75E TCGA-MI-A75I TCGA-MR-A8JO TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF 
       16.67        20.71        10.85        26.27        17.69        21.01 
TCGA-QA-A7B7 TCGA-RC-A6M4 TCGA-RC-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SF TCGA-RC-A7SH 
        3.09         0.72         0.30        21.04        19.04        15.39 
TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MD TCGA-UB-A7ME 
       15.52        36.10        27.88        19.76         1.71        15.98 
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-A8TD TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 
       33.86        13.55        35.77        23.21        35.87        25.15 
TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CF TCGA-ZS-A9CG 
       12.99        45.57        79.30        11.21 

$`DEL PEAK 13(8P12) WILD-TYPE`
TCGA-2Y-A9GV TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A5W4 TCGA-BD-A3ER TCGA-DD-A4NI 
       83.24         8.61        69.57        17.98        36.66        26.83 
TCGA-DD-AAEA TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-LG-A6GG TCGA-UB-AA0V TCGA-ZP-A9D1 
       18.90        20.75         2.14        12.72        10.32         0.69 
TCGA-2Y-A9GT TCGA-2Y-A9GY TCGA-2Y-A9H0 TCGA-2Y-A9H8 TCGA-5C-A9VG TCGA-5C-AAPD 
       53.39        24.89       120.82        20.81        10.78         0.66 
TCGA-5R-AA1D TCGA-BC-4073 TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y 
       14.76        27.91        27.52         2.99        25.32        23.38 
TCGA-BC-A10Z TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-CC-5260 TCGA-CC-5264 TCGA-CC-A3MB 
        1.12        18.48        44.81         2.86         3.35        10.36 
TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7II TCGA-CC-A7IK 
       11.93        11.41         9.99         8.94        13.12         8.61 
TCGA-DD-A114 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11D TCGA-DD-A1EA TCGA-DD-A1EB 
       37.78         2.60         0.46        51.29        79.40        66.31 
TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EH TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A3A0 
       19.79        75.65        49.15        27.19        55.69        25.81 
TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A4 TCGA-DD-A3A6 TCGA-DD-A4NB TCGA-DD-A4NF 
        7.66        70.06        20.12       107.11        32.52        30.97 
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-AAEK TCGA-DD-AAVV 
       18.15        20.98        18.61         4.64        35.08        80.71 
TCGA-DD-AAVX TCGA-DD-AAW1 TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66Y TCGA-ED-A7PX 
       56.48        65.39        28.08        13.91         9.73         0.20 
TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A97K TCGA-EP-A2KB TCGA-FV-A23B 
       13.15        13.41        13.35         0.20        19.59        60.89 
TCGA-FV-A3R3 TCGA-FV-A496 TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25Y TCGA-G3-A25Z 
       12.03         0.33        51.06        53.79        14.86        21.53 
TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SM 
       25.64         5.92        19.23        25.25        22.95        17.10 
TCGA-G3-A7M8 TCGA-G3-AAV1 TCGA-G3-AAV3 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB 
       14.14        11.80        13.55        28.90         1.02         2.20 
TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-MI-A75G TCGA-MR-A520 TCGA-NI-A4U2 TCGA-RC-A6M5 
       37.71        17.06        22.95         7.53        58.88         0.49 
TCGA-RC-A7SB TCGA-UB-A7MC TCGA-WX-AA46 TCGA-XR-A8TE TCGA-XR-A8TF TCGA-ZP-A9CY 
       19.33        16.44        24.85        30.41        22.78        25.71 

  DEL PEAK 13(8P12) MUTATED DEL PEAK 13(8P12) WILD-TYPE 
                       0.03                        0.20 
  DEL PEAK 13(8P12) MUTATED DEL PEAK 13(8P12) WILD-TYPE 
                     114.35                      120.82 
  DEL PEAK 13(8P12) MUTATED DEL PEAK 13(8P12) WILD-TYPE 
                      19.99                       19.46 
[1] "0.0 - 114.3 (20.0)" "0.2 - 120.8 (19.5)"
[1] "hr=" "1.1"
D40V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 13(8P12) MUTATED       116       58         1         36          8
  DEL PEAK 13(8P12) WILD-TYPE      57       29         2         26          1
                             vv
clus                          STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 13(8P12) MUTATED            4        2         0         2
  DEL PEAK 13(8P12) WILD-TYPE          3        0         1         0
D40V3, multiclass
            clus
vv           DEL PEAK 13(8P12) MUTATED DEL PEAK 13(8P12) WILD-TYPE
  STAGE I                          116                          57
  STAGE II                          58                          29
  STAGE III                          1                           2
  STAGE IIIA                        36                          26
  STAGE IIIB                         8                           1
  STAGE IIIC                         4                           3
  STAGE IV                           2                           0
  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                           T1  T2  T3  T4
  DEL PEAK 13(8P12) MUTATED   122  64  49   6
  DEL PEAK 13(8P12) WILD-TYPE  61  31  28   6
D40V4, multiclass
    clus
vv   DEL PEAK 13(8P12) MUTATED DEL PEAK 13(8P12) WILD-TYPE
  T1                       122                          61
  T2                        64                          31
  T3                        49                          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 13(8P12) MUTATED   165   2
  DEL PEAK 13(8P12) WILD-TYPE  89   1
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 13(8P12) MUTATED    165    2
  DEL PEAK 13(8P12) WILD-TYPE   89    1
   clus
vv  DEL PEAK 13(8P12) MUTATED DEL PEAK 13(8P12) WILD-TYPE
  0                       165                          89
  1                         2                           1
[1] 2 2
[1] FALSE
D40V6, binary
                             cls
clus                            0   1
  DEL PEAK 13(8P12) MUTATED   171   4
  DEL PEAK 13(8P12) WILD-TYPE  95   0
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 13(8P12) MUTATED    171    4
  DEL PEAK 13(8P12) WILD-TYPE   95    0
   clus
vv  DEL PEAK 13(8P12) MUTATED DEL PEAK 13(8P12) WILD-TYPE
  0                       171                          95
  1                         4                           0
[1] 2 2
[1] FALSE
D40V7, binary
                             cls
clus                            0   1
  DEL PEAK 13(8P12) MUTATED    75 167
  DEL PEAK 13(8P12) WILD-TYPE  43  85
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 13(8P12) MUTATED     75  167
  DEL PEAK 13(8P12) WILD-TYPE   43   85
        clus
vv       DEL PEAK 13(8P12) MUTATED DEL PEAK 13(8P12) WILD-TYPE
  FEMALE                        75                          43
  MALE                         167                          85
[1] 2 2
[1] FALSE
D40V8, binary
                             cls
clus                            0   1
  DEL PEAK 13(8P12) MUTATED   219   7
  DEL PEAK 13(8P12) WILD-TYPE 119   2
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 13(8P12) MUTATED    219    7
  DEL PEAK 13(8P12) WILD-TYPE  119    2
     clus
vv    DEL PEAK 13(8P12) MUTATED DEL PEAK 13(8P12) WILD-TYPE
  NO                        219                         119
  YES                         7                           2
[1] 2 2
[1] FALSE
                             vv
clus                          FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  DEL PEAK 13(8P12) MUTATED                         1                      237
  DEL PEAK 13(8P12) WILD-TYPE                       2                      123
                             vv
clus                          HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK 13(8P12) MUTATED                                  4
  DEL PEAK 13(8P12) WILD-TYPE                                3
D40V9, multiclass
                                  clus
vv                                 DEL PEAK 13(8P12) MUTATED
  FIBROLAMELLAR CARCINOMA                                  1
  HEPATOCELLULAR CARCINOMA                               237
  HEPATOCHOLANGIOCARCINOMA (MIXED)                         4
                                  clus
vv                                 DEL PEAK 13(8P12) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                    2
  HEPATOCELLULAR CARCINOMA                                 123
  HEPATOCHOLANGIOCARCINOMA (MIXED)                           3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           R0  R1  R2  RX
  DEL PEAK 13(8P12) MUTATED   208  13   1  14
  DEL PEAK 13(8P12) WILD-TYPE 116   4   0   7
D40V10, multiclass
    clus
vv   DEL PEAK 13(8P12) MUTATED DEL PEAK 13(8P12) WILD-TYPE
  R0                       208                         116
  R1                        13                           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 13(8P12) MUTATED                                  2   100
  DEL PEAK 13(8P12) WILD-TYPE                                0    58
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 13(8P12) MUTATED                          13   120
  DEL PEAK 13(8P12) WILD-TYPE                         4    63
D40V11, multiclass
                                  clus
vv                                 DEL PEAK 13(8P12) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         2
  ASIAN                                                  100
  BLACK OR AFRICAN AMERICAN                               13
  WHITE                                                  120
                                  clus
vv                                 DEL PEAK 13(8P12) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                     58
  BLACK OR AFRICAN AMERICAN                                  4
  WHITE                                                     63
[1] 4 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 13(8P12) MUTATED    12 217
  DEL PEAK 13(8P12) WILD-TYPE   4 118
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 13(8P12) MUTATED     12  217
  DEL PEAK 13(8P12) WILD-TYPE    4  118
                        clus
vv                       DEL PEAK 13(8P12) MUTATED DEL PEAK 13(8P12) WILD-TYPE
  HISPANIC OR LATINO                            12                           4
  NOT HISPANIC OR LATINO                       217                         118
[1] 2 2
[1] FALSE

Clustering(41) Variable = DEL PEAK 14(9P21.3) MUTATION ANALYSIS
D41V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 14(9P21.3) MUTATED    90  58
  DEL PEAK 14(9P21.3) WILD-TYPE 145  71
  DEL PEAK 14(9P21.3) MUTATED DEL PEAK 14(9P21.3) WILD-TYPE 
                          148                           216 
  DEL PEAK 14(9P21.3) MUTATED DEL PEAK 14(9P21.3) WILD-TYPE 
                           58                            71 
$`DEL PEAK 14(9P21.3) MUTATED`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-BC-A112 TCGA-BC-A5W4 TCGA-DD-A4ND 
       83.24        11.74        38.40         5.03        17.98        90.28 
TCGA-DD-A4NI TCGA-DD-AADV TCGA-DD-AAE8 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A4ZP 
       26.83        18.87        21.83         8.12         6.38        81.73 
TCGA-KR-A7K7 TCGA-T1-A6J8 TCGA-UB-A7MF TCGA-ZP-A9D1 TCGA-2Y-A9GS TCGA-2Y-A9GU 
       31.27         0.76         7.04         0.69        23.80        63.75 
TCGA-2Y-A9GY TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-3K-AAZ8 
       24.89        56.91        49.84        18.25        20.81        13.02 
TCGA-5C-A9VG TCGA-5C-A9VH TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R 
       10.78        10.59        48.99        27.91        37.32        10.13 
TCGA-BC-A10S TCGA-BC-A10U TCGA-BC-A3KF TCGA-BC-A69H TCGA-CC-5258 TCGA-CC-5263 
       46.78        27.52         0.26        14.60         4.24         4.24 
TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UD TCGA-CC-A5UE 
        3.32         9.86        10.36        11.93         9.99         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-A8HU TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A115 TCGA-DD-A116 
       11.31         6.94         8.15        79.73        83.57        53.33 
TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A1EF TCGA-DD-A1EG 
        7.33         2.60         0.46        21.76        12.95        45.11 
TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A3A0 
        6.02        33.04        13.64        55.69         5.62        25.81 
TCGA-DD-A3A9 TCGA-DD-A4NO TCGA-DD-A73F TCGA-DD-AA3A TCGA-DD-AACA TCGA-DD-AACC 
       30.61        73.81        35.67        13.48        75.65        55.40 
TCGA-DD-AACE TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACS 
       71.80        15.42         6.41        61.68        13.64        59.31 
TCGA-DD-AACU TCGA-DD-AACW TCGA-DD-AACZ TCGA-DD-AAD3 TCGA-DD-AADC TCGA-DD-AADE 
       51.52        46.82         5.62        42.58        13.97        39.52 
TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADN TCGA-DD-AADP TCGA-DD-AADQ 
       35.05        34.49        20.91        29.52        15.06        14.33 
TCGA-DD-AADS TCGA-DD-AAE1 TCGA-DD-AAE3 TCGA-DD-AAE6 TCGA-DD-AAED TCGA-DD-AAEE 
       15.58        18.15        18.61         4.64        25.08        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-A4XI TCGA-ED-A66X TCGA-ED-A7PZ TCGA-ED-A7XP 
       66.25        29.92        26.93        13.35         0.20        13.15 
TCGA-ED-A82E TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC 
       13.41         1.84         0.20        20.61        19.59         0.62 
TCGA-EP-A3RK TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A3I0 TCGA-G3-A25S TCGA-G3-A25T 
       11.93        60.89        23.97        27.88        13.68        51.06 
TCGA-G3-A3CJ TCGA-G3-A7M5 TCGA-G3-A7M7 TCGA-G3-AAV1 TCGA-G3-AAV3 TCGA-G3-AAV6 
       19.53        14.70        11.87        11.80        13.55         2.14 
TCGA-G3-AAV7 TCGA-GJ-A9DB TCGA-KR-A7K8 TCGA-MI-A75G TCGA-MI-A75I TCGA-NI-A8LF 
       11.87         2.20        29.79        22.95        20.71        26.27 
TCGA-RC-A6M4 TCGA-RC-A6M5 TCGA-RC-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF 
        0.72         0.49         0.30        21.04        19.33        19.04 
TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WQ-A9G7 
       15.39        15.52        36.10        15.98        10.75         0.99 
TCGA-WQ-AB4B TCGA-XR-A8TF TCGA-ZP-A9D0 TCGA-ZP-A9D2 
       12.99        22.78        35.87        25.15 

$`DEL PEAK 14(9P21.3) WILD-TYPE`
TCGA-4R-AA8I TCGA-BC-A110 TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-AAE7 TCGA-DD-AAEA 
        8.61        69.57        36.66         0.36        21.17        18.90 
TCGA-DD-AAEG TCGA-EP-A3JL TCGA-ES-A2HS TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC 
       23.64         9.96        22.62        30.74        22.13        22.06 
TCGA-G3-A7M9 TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-LG-A6GG TCGA-MI-A75H TCGA-UB-AA0V 
        1.84        20.75         2.14        12.72        24.56        10.32 
TCGA-XR-A8TG TCGA-ZS-A9CE TCGA-2Y-A9GT TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GZ 
       29.52        40.80        53.39        41.79        80.28        27.88 
TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H4 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB 
      120.82        40.41        47.74        22.92         1.18         8.55 
TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-A10T TCGA-BC-A10W 
        0.66        17.10        14.76         1.51        27.52         2.99 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KG 
       25.32        23.38         1.12        44.42        45.93        22.36 
TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5260 
       12.72        18.48        44.81        13.45         0.66         2.86 
TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5264 TCGA-CC-A3MA TCGA-CC-A5UC TCGA-CC-A7IH 
        3.19         3.39         3.35         9.96        11.41        12.00 
TCGA-CC-A7II TCGA-CC-A8HT TCGA-CC-A8HV TCGA-DD-A114 TCGA-DD-A118 TCGA-DD-A11D 
       13.12         4.60         9.17        37.78       113.00        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-A1EH TCGA-DD-A1EK TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39Z TCGA-DD-A3A1 
       49.15        18.35        21.14        27.19        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-A4NA TCGA-DD-A4NB TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK 
       33.14        32.52        30.97        30.15        30.51        39.78 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS 
       56.25        29.56       108.76        12.26         0.30        80.75 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E 
       78.84        23.93         9.30        23.05        22.78         1.45 
TCGA-DD-A73G TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACB TCGA-DD-AACD TCGA-DD-AACF 
      114.35         0.53        11.41        76.41        12.53        12.00 
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-AACT TCGA-DD-AACV TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AAD0 
       14.20        51.35        50.33         5.59        47.67         4.50 
TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA 
       18.54        21.63        44.22        22.09        40.08        40.54 
TCGA-DD-AADB TCGA-DD-AADD TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADM 
       40.83        40.47         3.78        37.64        35.67         0.39 
TCGA-DD-AADO TCGA-DD-AADR TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 
       14.89        66.67        18.21        19.30        18.25        18.25 
TCGA-DD-AAE2 TCGA-DD-AAE4 TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAEH TCGA-DD-AAEI 
       20.98        19.99        23.74        15.72        25.78        50.33 
TCGA-DD-AAVP TCGA-DD-AAVR TCGA-DD-AAVV TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAW1 
       90.48        82.62        80.71        56.48        64.77        65.39 
TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66Y TCGA-ED-A7PX 
       60.99        53.69        28.08        13.91         9.73         0.20 
TCGA-ED-A7PY TCGA-ED-A7XO TCGA-ED-A8O5 TCGA-EP-A12J TCGA-EP-A26S TCGA-ES-A2HT 
       12.82        14.04        13.35        18.74        19.99        14.40 
TCGA-FV-A2QR TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25U 
       19.10        12.03         0.03         0.33         0.39        53.79 
TCGA-G3-A25V TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI 
       28.27        58.49        14.86        21.53        25.64         5.92 
TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A7M6 
       19.23        25.25        22.95        20.42        17.10        20.78 
TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV4 TCGA-G3-AAV5 
       14.14        15.78        15.65        12.23         0.89        11.64 
TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 
       28.90         1.02         2.99        37.71        17.06        16.83 
TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E 
       11.80        27.25        13.97        12.03         9.57        16.67 
TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 
        7.53        10.85        58.88        17.69        21.01         3.09 
TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-WJ-A86L TCGA-WX-AA44 
       27.88        19.76        16.44         1.71        11.34        20.22 
TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TD TCGA-XR-A8TE TCGA-YA-A8S7 TCGA-ZP-A9CV 
       24.85        18.28        33.86        30.41        13.55        35.77 
TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CF TCGA-ZS-A9CG 
       25.71        23.21        12.99        45.57        79.30        11.21 

  DEL PEAK 14(9P21.3) MUTATED DEL PEAK 14(9P21.3) WILD-TYPE 
                         0.20                          0.03 
  DEL PEAK 14(9P21.3) MUTATED DEL PEAK 14(9P21.3) WILD-TYPE 
                        90.28                        120.82 
  DEL PEAK 14(9P21.3) MUTATED DEL PEAK 14(9P21.3) WILD-TYPE 
                       18.430                        20.585 
[1] "0.2 - 90.3 (18.4)"  "0.0 - 120.8 (20.6)"
[1] "hr=" "1.3"
D41V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IIIA
  DEL PEAK 14(9P21.3) MUTATED        66       35         0         29
  DEL PEAK 14(9P21.3) WILD-TYPE     107       52         3         33
                               vv
clus                            STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 14(9P21.3) MUTATED            2          2        1         1
  DEL PEAK 14(9P21.3) WILD-TYPE          7          5        1         0
                               vv
clus                            STAGE IVB
  DEL PEAK 14(9P21.3) MUTATED           1
  DEL PEAK 14(9P21.3) WILD-TYPE         1
D41V3, multiclass
            clus
vv           DEL PEAK 14(9P21.3) MUTATED DEL PEAK 14(9P21.3) WILD-TYPE
  STAGE I                             66                           107
  STAGE II                            35                            52
  STAGE III                            0                             3
  STAGE IIIA                          29                            33
  STAGE IIIB                           2                             7
  STAGE IIIC                           2                             5
  STAGE IV                             1                             1
  STAGE IVA                            1                             0
  STAGE IVB                            1                             1
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  DEL PEAK 14(9P21.3) MUTATED    72  40  35   3
  DEL PEAK 14(9P21.3) WILD-TYPE 111  55  42   9
D41V4, multiclass
    clus
vv   DEL PEAK 14(9P21.3) MUTATED DEL PEAK 14(9P21.3) WILD-TYPE
  T1                          72                           111
  T2                          40                            55
  T3                          35                            42
  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"
D41V5, binary
                               cls
clus                              0   1
  DEL PEAK 14(9P21.3) MUTATED   102   2
  DEL PEAK 14(9P21.3) WILD-TYPE 152   1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(9P21.3) MUTATED    102    2
  DEL PEAK 14(9P21.3) WILD-TYPE  152    1
   clus
vv  DEL PEAK 14(9P21.3) MUTATED DEL PEAK 14(9P21.3) WILD-TYPE
  0                         102                           152
  1                           2                             1
[1] 2 2
[1] FALSE
D41V6, binary
                               cls
clus                              0   1
  DEL PEAK 14(9P21.3) MUTATED   108   2
  DEL PEAK 14(9P21.3) WILD-TYPE 158   2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(9P21.3) MUTATED    108    2
  DEL PEAK 14(9P21.3) WILD-TYPE  158    2
   clus
vv  DEL PEAK 14(9P21.3) MUTATED DEL PEAK 14(9P21.3) WILD-TYPE
  0                         108                           158
  1                           2                             2
[1] 2 2
[1] FALSE
D41V7, binary
                               cls
clus                              0   1
  DEL PEAK 14(9P21.3) MUTATED    44 106
  DEL PEAK 14(9P21.3) WILD-TYPE  74 146
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(9P21.3) MUTATED     44  106
  DEL PEAK 14(9P21.3) WILD-TYPE   74  146
        clus
vv       DEL PEAK 14(9P21.3) MUTATED DEL PEAK 14(9P21.3) WILD-TYPE
  FEMALE                          44                            74
  MALE                           106                           146
[1] 2 2
[1] FALSE
D41V8, binary
                               cls
clus                              0   1
  DEL PEAK 14(9P21.3) MUTATED   136   2
  DEL PEAK 14(9P21.3) WILD-TYPE 202   7
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(9P21.3) MUTATED    136    2
  DEL PEAK 14(9P21.3) WILD-TYPE  202    7
     clus
vv    DEL PEAK 14(9P21.3) MUTATED DEL PEAK 14(9P21.3) WILD-TYPE
  NO                          136                           202
  YES                           2                             7
[1] 2 2
[1] FALSE
                               vv
clus                            FIBROLAMELLAR CARCINOMA
  DEL PEAK 14(9P21.3) MUTATED                         1
  DEL PEAK 14(9P21.3) WILD-TYPE                       2
                               vv
clus                            HEPATOCELLULAR CARCINOMA
  DEL PEAK 14(9P21.3) MUTATED                        146
  DEL PEAK 14(9P21.3) WILD-TYPE                      214
                               vv
clus                            HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK 14(9P21.3) MUTATED                                  3
  DEL PEAK 14(9P21.3) WILD-TYPE                                4
D41V9, multiclass
                                  clus
vv                                 DEL PEAK 14(9P21.3) MUTATED
  FIBROLAMELLAR CARCINOMA                                    1
  HEPATOCELLULAR CARCINOMA                                 146
  HEPATOCHOLANGIOCARCINOMA (MIXED)                           3
                                  clus
vv                                 DEL PEAK 14(9P21.3) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                      2
  HEPATOCELLULAR CARCINOMA                                   214
  HEPATOCHOLANGIOCARCINOMA (MIXED)                             4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 14(9P21.3) MUTATED   130  10   1   7
  DEL PEAK 14(9P21.3) WILD-TYPE 194   7   0  14
D41V10, multiclass
    clus
vv   DEL PEAK 14(9P21.3) MUTATED DEL PEAK 14(9P21.3) WILD-TYPE
  R0                         130                           194
  R1                          10                             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 14(9P21.3) MUTATED                                  1    74
  DEL PEAK 14(9P21.3) WILD-TYPE                                1    84
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 14(9P21.3) MUTATED                           7    67
  DEL PEAK 14(9P21.3) WILD-TYPE                        10   116
D41V11, multiclass
                                  clus
vv                                 DEL PEAK 14(9P21.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                     74
  BLACK OR AFRICAN AMERICAN                                  7
  WHITE                                                     67
                                  clus
vv                                 DEL PEAK 14(9P21.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                       84
  BLACK OR AFRICAN AMERICAN                                   10
  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"
D41V12, binary
                               cls
clus                              0   1
  DEL PEAK 14(9P21.3) MUTATED     3 142
  DEL PEAK 14(9P21.3) WILD-TYPE  13 193
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(9P21.3) MUTATED      3  142
  DEL PEAK 14(9P21.3) WILD-TYPE   13  193
                        clus
vv                       DEL PEAK 14(9P21.3) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                         142
                        clus
vv                       DEL PEAK 14(9P21.3) WILD-TYPE
  HISPANIC OR LATINO                                13
  NOT HISPANIC OR LATINO                           193
[1] 2 2
[1] FALSE

Clustering(42) Variable = DEL PEAK 15(9Q31.3) MUTATION ANALYSIS
D42V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 15(9Q31.3) MUTATED    72  45
  DEL PEAK 15(9Q31.3) WILD-TYPE 163  84
  DEL PEAK 15(9Q31.3) MUTATED DEL PEAK 15(9Q31.3) WILD-TYPE 
                          117                           247 
  DEL PEAK 15(9Q31.3) MUTATED DEL PEAK 15(9Q31.3) WILD-TYPE 
                           45                            84 
$`DEL PEAK 15(9Q31.3) MUTATED`
TCGA-2Y-A9H6 TCGA-BC-A112 TCGA-BC-A5W4 TCGA-DD-A4NI TCGA-DD-AADV TCGA-DD-AAE8 
       11.74         5.03        17.98        26.83        18.87        21.83 
TCGA-DD-AAEA TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-T1-A6J8 TCGA-UB-A7MF 
       18.90         8.12         6.38        81.73         0.76         7.04 
TCGA-ZS-A9CE TCGA-2Y-A9GS TCGA-2Y-A9GU TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H5 
       40.80        23.80        63.75        56.91        49.84        18.25 
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-A217 
       27.91        37.32        10.13        46.78        27.52        45.93 
TCGA-BC-A69H TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MB 
       14.60         4.24         2.86         3.32         9.86        10.36 
TCGA-CC-A3MC TCGA-CC-A5UE TCGA-CC-A7IF TCGA-CC-A7IJ TCGA-CC-A7IL TCGA-CC-A9FW 
       11.93         8.94        21.34        12.56         9.14         8.15 
TCGA-DD-A113 TCGA-DD-A116 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C 
       79.73        53.33         7.33         2.60         0.46        21.76 
TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A39X 
       12.95        45.11         6.02        33.04        18.35        55.69 
TCGA-DD-A39Y TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NJ TCGA-DD-A4NN TCGA-DD-A4NO 
        5.62        30.61        33.14        30.51        29.56        73.81 
TCGA-DD-AA3A TCGA-DD-AACB TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACO TCGA-DD-AACP 
       13.48        76.41        12.53        71.80        61.68        13.64 
TCGA-DD-AACU TCGA-DD-AACZ TCGA-DD-AAD3 TCGA-DD-AAD8 TCGA-DD-AADJ TCGA-DD-AADK 
       51.52         5.62        42.58        40.08        35.05        34.49 
TCGA-DD-AADL TCGA-DD-AADO TCGA-DD-AAED TCGA-DD-AAEK TCGA-DD-AAVQ TCGA-DD-AAVU 
       20.91        14.89        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-A3R3 TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A3CH TCGA-G3-A7M5 TCGA-G3-AAV1 
       12.03        13.68        51.06        25.64        14.70        11.80 
TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-MI-A75G TCGA-MI-A75I TCGA-PD-A5DF 
       11.87         1.02         2.20        22.95        20.71        21.01 
TCGA-RC-A6M5 TCGA-RC-A6M6 TCGA-RC-A7SB TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 
        0.49         0.30        19.33        15.39        15.52        36.10 
TCGA-UB-A7MB TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WQ-AB4B TCGA-XR-A8TD TCGA-ZP-A9CZ 
       19.76        15.98        10.75        12.99        33.86        23.21 
TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZS-A9CF 
       35.87        25.15        79.30 

$`DEL PEAK 15(9Q31.3) WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BD-A3ER TCGA-DD-A3A8 
       83.24        38.40         8.61        69.57        36.66         0.36 
TCGA-DD-A4ND TCGA-DD-AAE7 TCGA-DD-AAEG TCGA-EP-A3JL TCGA-ES-A2HS TCGA-G3-A25W 
       90.28        21.17        23.64         9.96        22.62        30.74 
TCGA-G3-A3CG TCGA-G3-A6UC TCGA-G3-A7M9 TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-KR-A7K7 
       22.13        22.06         1.84        20.75         2.14        31.27 
TCGA-LG-A6GG TCGA-MI-A75H TCGA-UB-AA0V TCGA-XR-A8TG TCGA-ZP-A9D1 TCGA-2Y-A9GT 
       12.72        24.56        10.32        29.52         0.69        53.39 
TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 
       41.79        80.28        24.89        27.88       120.82        40.41 
TCGA-2Y-A9H4 TCGA-2Y-A9HB TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM 
       47.74         8.55         0.66        17.10        14.76         1.51 
TCGA-BC-4072 TCGA-BC-A10T TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z 
       48.99        27.52         2.99        25.32        23.38         1.12 
TCGA-BC-A216 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A2L6 
       44.42         0.26        22.36        12.72        18.48        44.81 
TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-5264 
       13.45         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-A4NB 
       17.59        20.12       102.74       107.11        13.78        32.52 
TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NP TCGA-DD-A4NQ 
       30.97        30.15        39.78        56.25       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-AAC8 TCGA-DD-AAC9 
       22.78         1.45        35.67       114.35         0.53        11.41 
TCGA-DD-AACA TCGA-DD-AACC TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI 
       75.65        55.40        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-AACQ 
       69.11         0.30         3.52        58.16        42.81        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-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-AADF TCGA-DD-AADG 
       40.83        13.97        40.47        39.52         3.78        37.64 
TCGA-DD-AADI TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR 
       35.67         0.39        29.52        15.06        14.33        66.67 
TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 
       15.58        18.21        19.30        18.25        18.25        18.15 
TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE9 TCGA-DD-AAEB 
       20.98        18.61        19.99         4.64        23.74        15.72 
TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAVP TCGA-DD-AAVR TCGA-DD-AAVS 
       26.63        25.78        50.33        90.48        82.62        59.93 
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        60.99        53.69 
TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66Y TCGA-ED-A7PY TCGA-ED-A7XO 
       26.93        28.08        13.91         9.73        12.82        14.04 
TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S 
       13.41        13.35         1.84         0.20        18.74        19.99 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A495 
       20.61        19.59        14.40        60.89        19.10         0.03 
TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25X TCGA-G3-A25Y 
        0.33         0.39        53.79        28.27        58.49        14.86 
TCGA-G3-A25Z TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ 
       21.53         5.92        19.53        19.23        25.25        22.95 
TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ 
       20.42        17.10        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        11.64         2.14 
TCGA-GJ-A3OU TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 
       28.90         2.99        37.71        17.06        16.83        11.80 
TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E 
       27.25        29.79        13.97        12.03         9.57        16.67 
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-A6M4 TCGA-RC-A7S9 TCGA-RC-A7SF TCGA-UB-A7MA TCGA-UB-A7MC TCGA-UB-A7MD 
        0.72        21.04        19.04        27.88        16.44         1.71 
TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TE 
       11.34         0.99        20.22        24.85        18.28        30.41 
TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9D4 TCGA-ZS-A9CD 
       22.78        13.55        35.77        25.71        12.99        45.57 
TCGA-ZS-A9CG 
       11.21 

  DEL PEAK 15(9Q31.3) MUTATED DEL PEAK 15(9Q31.3) WILD-TYPE 
                         0.20                          0.03 
  DEL PEAK 15(9Q31.3) MUTATED DEL PEAK 15(9Q31.3) WILD-TYPE 
                        89.69                        120.82 
  DEL PEAK 15(9Q31.3) MUTATED DEL PEAK 15(9Q31.3) WILD-TYPE 
                        19.33                         19.99 
[1] "0.2 - 89.7 (19.3)"  "0.0 - 120.8 (20.0)"
[1] "hr=" "1.3"
D42V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IIIA
  DEL PEAK 15(9Q31.3) MUTATED        47       31         0         17
  DEL PEAK 15(9Q31.3) WILD-TYPE     126       56         3         45
                               vv
clus                            STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 15(9Q31.3) MUTATED            4          4        1         1
  DEL PEAK 15(9Q31.3) WILD-TYPE          5          3        1         0
                               vv
clus                            STAGE IVB
  DEL PEAK 15(9Q31.3) MUTATED           2
  DEL PEAK 15(9Q31.3) WILD-TYPE         0
D42V3, multiclass
            clus
vv           DEL PEAK 15(9Q31.3) MUTATED DEL PEAK 15(9Q31.3) WILD-TYPE
  STAGE I                             47                           126
  STAGE II                            31                            56
  STAGE III                            0                             3
  STAGE IIIA                          17                            45
  STAGE IIIB                           4                             5
  STAGE IIIC                           4                             3
  STAGE IV                             1                             1
  STAGE IVA                            1                             0
  STAGE IVB                            2                             0
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  DEL PEAK 15(9Q31.3) MUTATED    53  37  23   6
  DEL PEAK 15(9Q31.3) WILD-TYPE 130  58  54   6
D42V4, multiclass
    clus
vv   DEL PEAK 15(9Q31.3) MUTATED DEL PEAK 15(9Q31.3) WILD-TYPE
  T1                          53                           130
  T2                          37                            58
  T3                          23                            54
  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"
D42V5, binary
                               cls
clus                              0   1
  DEL PEAK 15(9Q31.3) MUTATED    74   3
  DEL PEAK 15(9Q31.3) WILD-TYPE 180   0
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(9Q31.3) MUTATED     74    3
  DEL PEAK 15(9Q31.3) WILD-TYPE  180    0
   clus
vv  DEL PEAK 15(9Q31.3) MUTATED DEL PEAK 15(9Q31.3) WILD-TYPE
  0                          74                           180
  1                           3                             0
[1] 2 2
[1] FALSE
D42V6, binary
                               cls
clus                              0   1
  DEL PEAK 15(9Q31.3) MUTATED    79   3
  DEL PEAK 15(9Q31.3) WILD-TYPE 187   1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(9Q31.3) MUTATED     79    3
  DEL PEAK 15(9Q31.3) WILD-TYPE  187    1
   clus
vv  DEL PEAK 15(9Q31.3) MUTATED DEL PEAK 15(9Q31.3) WILD-TYPE
  0                          79                           187
  1                           3                             1
[1] 2 2
[1] FALSE
D42V7, binary
                               cls
clus                              0   1
  DEL PEAK 15(9Q31.3) MUTATED    37  82
  DEL PEAK 15(9Q31.3) WILD-TYPE  81 170
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(9Q31.3) MUTATED     37   82
  DEL PEAK 15(9Q31.3) WILD-TYPE   81  170
        clus
vv       DEL PEAK 15(9Q31.3) MUTATED DEL PEAK 15(9Q31.3) WILD-TYPE
  FEMALE                          37                            81
  MALE                            82                           170
[1] 2 2
[1] FALSE
D42V8, binary
                               cls
clus                              0   1
  DEL PEAK 15(9Q31.3) MUTATED   107   2
  DEL PEAK 15(9Q31.3) WILD-TYPE 231   7
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(9Q31.3) MUTATED    107    2
  DEL PEAK 15(9Q31.3) WILD-TYPE  231    7
     clus
vv    DEL PEAK 15(9Q31.3) MUTATED DEL PEAK 15(9Q31.3) WILD-TYPE
  NO                          107                           231
  YES                           2                             7
[1] 2 2
[1] FALSE
                               vv
clus                            FIBROLAMELLAR CARCINOMA
  DEL PEAK 15(9Q31.3) MUTATED                         1
  DEL PEAK 15(9Q31.3) WILD-TYPE                       2
                               vv
clus                            HEPATOCELLULAR CARCINOMA
  DEL PEAK 15(9Q31.3) MUTATED                        116
  DEL PEAK 15(9Q31.3) WILD-TYPE                      244
                               vv
clus                            HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK 15(9Q31.3) MUTATED                                  2
  DEL PEAK 15(9Q31.3) WILD-TYPE                                5
D42V9, multiclass
                                  clus
vv                                 DEL PEAK 15(9Q31.3) MUTATED
  FIBROLAMELLAR CARCINOMA                                    1
  HEPATOCELLULAR CARCINOMA                                 116
  HEPATOCHOLANGIOCARCINOMA (MIXED)                           2
                                  clus
vv                                 DEL PEAK 15(9Q31.3) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                      2
  HEPATOCELLULAR CARCINOMA                                   244
  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 15(9Q31.3) MUTATED    99   8   1   8
  DEL PEAK 15(9Q31.3) WILD-TYPE 225   9   0  13
D42V10, multiclass
    clus
vv   DEL PEAK 15(9Q31.3) MUTATED DEL PEAK 15(9Q31.3) WILD-TYPE
  R0                          99                           225
  R1                           8                             9
  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 15(9Q31.3) MUTATED                                  0    53
  DEL PEAK 15(9Q31.3) WILD-TYPE                                2   105
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 15(9Q31.3) MUTATED                           6    60
  DEL PEAK 15(9Q31.3) WILD-TYPE                        11   123
D42V11, multiclass
                                  clus
vv                                 DEL PEAK 15(9Q31.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                     53
  BLACK OR AFRICAN AMERICAN                                  6
  WHITE                                                     60
                                  clus
vv                                 DEL PEAK 15(9Q31.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             2
  ASIAN                                                      105
  BLACK OR AFRICAN AMERICAN                                   11
  WHITE                                                      123
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V12, binary
                               cls
clus                              0   1
  DEL PEAK 15(9Q31.3) MUTATED     3 114
  DEL PEAK 15(9Q31.3) WILD-TYPE  13 221
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(9Q31.3) MUTATED      3  114
  DEL PEAK 15(9Q31.3) WILD-TYPE   13  221
                        clus
vv                       DEL PEAK 15(9Q31.3) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                         114
                        clus
vv                       DEL PEAK 15(9Q31.3) WILD-TYPE
  HISPANIC OR LATINO                                13
  NOT HISPANIC OR LATINO                           221
[1] 2 2
[1] FALSE

Clustering(43) Variable = DEL PEAK 16(10Q23.31) MUTATION ANALYSIS
D43V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 16(10Q23.31) MUTATED    59  37
  DEL PEAK 16(10Q23.31) WILD-TYPE 176  92
  DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(10Q23.31) WILD-TYPE 
                             96                             268 
  DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(10Q23.31) WILD-TYPE 
                             37                              92 
$`DEL PEAK 16(10Q23.31) MUTATED`
TCGA-BC-A5W4 TCGA-DD-A4NI TCGA-DD-AAE8 TCGA-KR-A7K7 TCGA-ZP-A9D1 TCGA-ZS-A9CE 
       17.98        26.83        21.83        31.27         0.69        40.80 
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-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5260 
       22.36        18.48        44.81        13.45         0.66         2.86 
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-A5UD TCGA-CC-A5UE TCGA-CC-A7II TCGA-CC-A8HT TCGA-DD-A114 TCGA-DD-A115 
        9.99         8.94        13.12         4.60        37.78        83.57 
TCGA-DD-A118 TCGA-DD-A11A TCGA-DD-A11C TCGA-DD-A1EG TCGA-DD-A1EL TCGA-DD-A39Y 
      113.00         2.60        21.76        45.11        13.64         5.62 
TCGA-DD-A3A0 TCGA-DD-A4NA TCGA-DD-A4NQ TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI 
       25.81        33.14        12.26        15.42         6.41        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-AAD0 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADL 
        4.50        42.58        44.22        40.08        40.54        20.91 
TCGA-DD-AADN TCGA-DD-AADR TCGA-DD-AADY TCGA-DD-AAE2 TCGA-ED-A459 TCGA-ED-A66Y 
       29.52        66.67        18.25        20.98        29.92         9.73 
TCGA-ED-A7PX TCGA-ED-A7XO TCGA-ED-A8O6 TCGA-ED-A97K TCGA-FV-A2QQ TCGA-FV-A2QR 
        0.20        14.04         1.84         0.20        23.97        19.10 
TCGA-FV-A3I0 TCGA-FV-A496 TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25X TCGA-G3-A5SJ 
       27.88         0.33        51.06        53.79        58.49        22.95 
TCGA-G3-A7M5 TCGA-G3-AAV1 TCGA-G3-AAV4 TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-KR-A7K2 
       14.70        11.80         0.89        37.71        17.06        27.25 
TCGA-NI-A4U2 TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A6M6 TCGA-RC-A7SB TCGA-RC-A7SK 
       58.88        21.01         3.09         0.30        19.33        15.52 
TCGA-RG-A7D4 TCGA-UB-A7MB TCGA-UB-A7MD TCGA-WJ-A86L TCGA-XR-A8TD TCGA-YA-A8S7 
       36.10        19.76         1.71        11.34        33.86        13.55 

$`DEL PEAK 16(10Q23.31) WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 
       83.24        11.74        38.40         8.61        69.57         5.03 
TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-AADV TCGA-DD-AAE7 TCGA-DD-AAEA 
       36.66         0.36        90.28        18.87        21.17        18.90 
TCGA-DD-AAEG TCGA-EP-A3JL TCGA-ES-A2HS TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A4ZP 
       23.64         9.96        22.62         8.12         6.38        81.73 
TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC TCGA-G3-A7M9 TCGA-K7-A5RF TCGA-KR-A7K0 
       30.74        22.13        22.06         1.84        20.75         2.14 
TCGA-LG-A6GG TCGA-MI-A75H TCGA-T1-A6J8 TCGA-UB-A7MF TCGA-UB-AA0V TCGA-XR-A8TG 
       12.72        24.56         0.76         7.04        10.32        29.52 
TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GY TCGA-2Y-A9GZ 
       53.39        63.75        41.79        80.28        24.89        27.88 
TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H3 TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-2Y-A9HA 
      120.82        40.41        49.84        18.25        20.81         1.18 
TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5R-AA1C TCGA-5R-AA1D 
        8.55        13.02        10.78        10.59        17.10        14.76 
TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10X 
        1.51        48.99        46.78        27.52        27.52        25.32 
TCGA-BC-A10Z TCGA-BC-A3KF TCGA-BC-A69H TCGA-BC-A69I TCGA-CC-5258 TCGA-CC-5261 
        1.12         0.26        14.60        12.72         4.24         3.19 
TCGA-CC-5262 TCGA-CC-A3M9 TCGA-CC-A5UC TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IG 
        3.39         9.86        11.41         7.13        21.34         9.83 
TCGA-CC-A7IH TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A7IL TCGA-CC-A8HU TCGA-CC-A8HV 
       12.00        12.56         8.61         9.14        11.31         9.17 
TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A116 TCGA-DD-A119 TCGA-DD-A11B 
        6.94         8.15        79.73        53.33         7.33         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-A1EE TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK 
       11.47        12.95        49.15         6.02        33.04        18.35 
TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Z TCGA-DD-A3A1 TCGA-DD-A3A2 
       21.14        27.19        55.69        19.76         7.66        70.06 
TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A9 
       17.59        20.12       102.74       107.11        13.78        30.61 
TCGA-DD-A4NB TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL 
       32.52        30.97        30.15        30.51        39.78        56.25 
TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV 
       29.56        73.81       108.76         0.30        80.75        78.84 
TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F 
       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-AACA TCGA-DD-AACB 
      114.35        13.48         0.53        11.41        75.65        76.41 
TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACJ TCGA-DD-AACK 
       55.40        12.53        71.80        12.00        69.11         0.30 
TCGA-DD-AACL TCGA-DD-AACN TCGA-DD-AACP TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACW 
        3.52        42.81        13.64        59.31        51.35        46.82 
TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD6 TCGA-DD-AADB 
        5.59        47.67        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-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-AADW TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE3 
       15.58        18.21        19.30        18.25        18.15        18.61 
TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE 
       19.99         4.64        23.74        15.72        25.08        26.63 
TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR 
       25.78        50.33        35.08        90.48        89.69        82.62 
TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVV TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY 
       59.93        72.39        80.71        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        60.99        53.69        26.93 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XP 
       28.08        13.91        13.35        12.82         0.20        13.15 
TCGA-ED-A82E TCGA-ED-A8O5 TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB 
       13.41        13.35        18.74        19.99        20.61        19.59 
TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A3R3 TCGA-FV-A495 
        0.62        11.93        14.40        60.89        12.03         0.03 
TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25V TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH 
        0.39        13.68        28.27        14.86        21.53        25.64 
TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SL TCGA-G3-A5SM 
        5.92        19.53        19.23        25.25        20.42        17.10 
TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV2 
       20.78        11.87        14.14        15.78        15.65        12.23 
TCGA-G3-AAV3 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 
       13.55        11.64         2.14        11.87        28.90         1.02 
TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K8 TCGA-LG-A9QC 
        2.20         2.99        16.83        11.80        29.79        13.97 
TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A520 
       12.03         9.57        16.67        22.95        20.71         7.53 
TCGA-MR-A8JO TCGA-NI-A8LF TCGA-O8-A75V TCGA-RC-A6M4 TCGA-RC-A6M5 TCGA-RC-A7S9 
       10.85        26.27        17.69         0.72         0.49        21.04 
TCGA-RC-A7SF TCGA-RC-A7SH TCGA-UB-A7MA TCGA-UB-A7MC TCGA-UB-A7ME TCGA-UB-AA0U 
       19.04        15.39        27.88        16.44        15.98        10.75 
TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TE 
        0.99        12.99        20.22        24.85        18.28        30.41 
TCGA-XR-A8TF TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 
       22.78        35.77        25.71        23.21        35.87        25.15 
TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CF TCGA-ZS-A9CG 
       12.99        45.57        79.30        11.21 

  DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(10Q23.31) WILD-TYPE 
                           0.20                            0.03 
  DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(10Q23.31) WILD-TYPE 
                         113.00                          120.82 
  DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(10Q23.31) WILD-TYPE 
                         20.335                          19.775 
[1] "0.2 - 113.0 (20.3)" "0.0 - 120.8 (19.8)"
[1] "hr=" "1.3"
D43V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE III STAGE IIIA
  DEL PEAK 16(10Q23.31) MUTATED        37       24         0         21
  DEL PEAK 16(10Q23.31) WILD-TYPE     136       63         3         41
                                 vv
clus                              STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 16(10Q23.31) MUTATED            3          4        0         0
  DEL PEAK 16(10Q23.31) WILD-TYPE          6          3        2         1
                                 vv
clus                              STAGE IVB
  DEL PEAK 16(10Q23.31) MUTATED           0
  DEL PEAK 16(10Q23.31) WILD-TYPE         2
D43V3, multiclass
            clus
vv           DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(10Q23.31) WILD-TYPE
  STAGE I                               37                             136
  STAGE II                              24                              63
  STAGE III                              0                               3
  STAGE IIIA                            21                              41
  STAGE IIIB                             3                               6
  STAGE IIIC                             4                               3
  STAGE IV                               0                               2
  STAGE IVA                              0                               1
  STAGE IVB                              0                               2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               T1  T2  T3  T4
  DEL PEAK 16(10Q23.31) MUTATED    38  28  23   7
  DEL PEAK 16(10Q23.31) WILD-TYPE 145  67  54   5
D43V4, multiclass
    clus
vv   DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(10Q23.31) WILD-TYPE
  T1                            38                             145
  T2                            28                              67
  T3                            23                              54
  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"
D43V5, binary
                                 cls
clus                                0   1
  DEL PEAK 16(10Q23.31) MUTATED    66   1
  DEL PEAK 16(10Q23.31) WILD-TYPE 188   2
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 16(10Q23.31) MUTATED     66    1
  DEL PEAK 16(10Q23.31) WILD-TYPE  188    2
   clus
vv  DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(10Q23.31) WILD-TYPE
  0                            66                             188
  1                             1                               2
[1] 2 2
[1] FALSE
D43V6, binary
                                 cls
clus                                0   1
  DEL PEAK 16(10Q23.31) MUTATED    73   0
  DEL PEAK 16(10Q23.31) WILD-TYPE 193   4
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 16(10Q23.31) MUTATED     73    0
  DEL PEAK 16(10Q23.31) WILD-TYPE  193    4
   clus
vv  DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(10Q23.31) WILD-TYPE
  0                            73                             193
  1                             0                               4
[1] 2 2
[1] FALSE
D43V7, binary
                                 cls
clus                                0   1
  DEL PEAK 16(10Q23.31) MUTATED    31  66
  DEL PEAK 16(10Q23.31) WILD-TYPE  87 186
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 16(10Q23.31) MUTATED     31   66
  DEL PEAK 16(10Q23.31) WILD-TYPE   87  186
        clus
vv       DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(10Q23.31) WILD-TYPE
  FEMALE                            31                              87
  MALE                              66                             186
[1] 2 2
[1] FALSE
D43V8, binary
                                 cls
clus                                0   1
  DEL PEAK 16(10Q23.31) MUTATED    92   1
  DEL PEAK 16(10Q23.31) WILD-TYPE 246   8
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 16(10Q23.31) MUTATED     92    1
  DEL PEAK 16(10Q23.31) WILD-TYPE  246    8
     clus
vv    DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(10Q23.31) WILD-TYPE
  NO                             92                             246
  YES                             1                               8
[1] 2 2
[1] FALSE
                                 vv
clus                              FIBROLAMELLAR CARCINOMA
  DEL PEAK 16(10Q23.31) MUTATED                         0
  DEL PEAK 16(10Q23.31) WILD-TYPE                       3
                                 vv
clus                              HEPATOCELLULAR CARCINOMA
  DEL PEAK 16(10Q23.31) MUTATED                         93
  DEL PEAK 16(10Q23.31) WILD-TYPE                      267
                                 vv
clus                              HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK 16(10Q23.31) MUTATED                                  4
  DEL PEAK 16(10Q23.31) WILD-TYPE                                3
D43V9, multiclass
                                  clus
vv                                 DEL PEAK 16(10Q23.31) MUTATED
  FIBROLAMELLAR CARCINOMA                                      0
  HEPATOCELLULAR CARCINOMA                                    93
  HEPATOCHOLANGIOCARCINOMA (MIXED)                             4
                                  clus
vv                                 DEL PEAK 16(10Q23.31) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                        3
  HEPATOCELLULAR CARCINOMA                                     267
  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(10Q23.31) MUTATED    82   5   0   8
  DEL PEAK 16(10Q23.31) WILD-TYPE 242  12   1  13
D43V10, multiclass
    clus
vv   DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(10Q23.31) WILD-TYPE
  R0                            82                             242
  R1                             5                              12
  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(10Q23.31) MUTATED                                  0    46
  DEL PEAK 16(10Q23.31) WILD-TYPE                                2   112
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 16(10Q23.31) MUTATED                          10    40
  DEL PEAK 16(10Q23.31) WILD-TYPE                         7   143
D43V11, multiclass
                                  clus
vv                                 DEL PEAK 16(10Q23.31) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                       46
  BLACK OR AFRICAN AMERICAN                                   10
  WHITE                                                       40
                                  clus
vv                                 DEL PEAK 16(10Q23.31) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               2
  ASIAN                                                        112
  BLACK OR AFRICAN AMERICAN                                      7
  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"
D43V12, binary
                                 cls
clus                                0   1
  DEL PEAK 16(10Q23.31) MUTATED     4  86
  DEL PEAK 16(10Q23.31) WILD-TYPE  12 249
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 16(10Q23.31) MUTATED      4   86
  DEL PEAK 16(10Q23.31) WILD-TYPE   12  249
                        clus
vv                       DEL PEAK 16(10Q23.31) MUTATED
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                            86
                        clus
vv                       DEL PEAK 16(10Q23.31) WILD-TYPE
  HISPANIC OR LATINO                                  12
  NOT HISPANIC OR LATINO                             249
[1] 2 2
[1] FALSE

Clustering(44) Variable = DEL PEAK 17(10Q26.13) MUTATION ANALYSIS
D44V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 17(10Q26.13) MUTATED    64  40
  DEL PEAK 17(10Q26.13) WILD-TYPE 171  89
  DEL PEAK 17(10Q26.13) MUTATED DEL PEAK 17(10Q26.13) WILD-TYPE 
                            104                             260 
  DEL PEAK 17(10Q26.13) MUTATED DEL PEAK 17(10Q26.13) WILD-TYPE 
                             40                              89 
$`DEL PEAK 17(10Q26.13) MUTATED`
TCGA-2Y-A9GV TCGA-BC-A112 TCGA-BC-A5W4 TCGA-DD-A4NI TCGA-DD-AAE8 TCGA-KR-A7K7 
       83.24         5.03        17.98        26.83        21.83        31.27 
TCGA-ZP-A9D1 TCGA-ZS-A9CE TCGA-2Y-A9GS TCGA-2Y-A9GU TCGA-2Y-A9H2 TCGA-2Y-A9H4 
        0.69        40.80        23.80        63.75        56.91        47.74 
TCGA-2Y-A9H9 TCGA-5C-AAPD TCGA-5R-AAAM TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R 
       22.92         0.66         1.51        27.91        37.32        10.13 
TCGA-BC-A10W TCGA-BC-A10Y TCGA-BC-A217 TCGA-BC-A3KG TCGA-BC-A8YO TCGA-BD-A3EP 
        2.99        23.38        45.93        22.36        18.48        13.45 
TCGA-BW-A5NO TCGA-CC-5260 TCGA-CC-5264 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA 
        0.66         2.86         3.35         3.32         9.86         9.96 
TCGA-CC-A3MC TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A8HT 
       11.93         9.99         8.94        13.12        12.56         4.60 
TCGA-CC-A8HV TCGA-CC-A9FW TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A11A TCGA-DD-A11C 
        9.17         8.15        37.78        83.57         2.60        21.76 
TCGA-DD-A1EB TCGA-DD-A1EG TCGA-DD-A1EL TCGA-DD-A39Y TCGA-DD-A3A0 TCGA-DD-A4NA 
       66.31        45.11        13.64         5.62        25.81        33.14 
TCGA-DD-A4NQ TCGA-DD-A73F TCGA-DD-AACG TCGA-DD-AACI TCGA-DD-AACM TCGA-DD-AACO 
       12.26        35.67        15.42        53.19        58.16        61.68 
TCGA-DD-AACQ TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACZ TCGA-DD-AAD3 TCGA-DD-AAD5 
       14.20        51.52        50.33         5.62        42.58        44.22 
TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADR 
       40.08        40.54        20.91         0.39        29.52        66.67 
TCGA-DD-AADY TCGA-DD-AAE2 TCGA-ED-A459 TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7XO 
       18.25        20.98        29.92         9.73         0.20        14.04 
TCGA-ED-A8O6 TCGA-ED-A97K TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A496 
        1.84         0.20        23.97        19.10        27.88         0.33 
TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A5SJ TCGA-G3-A7M5 
       51.06        53.79        58.49        14.86        22.95        14.70 
TCGA-G3-AAV1 TCGA-G3-AAV4 TCGA-K7-A5RG TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-MR-A8JO 
       11.80         0.89        17.06        27.25        29.79        10.85 
TCGA-NI-A4U2 TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A6M4 TCGA-RC-A6M6 TCGA-RC-A7SB 
       58.88        21.01         3.09         0.72         0.30        19.33 
TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MB TCGA-UB-A7MD TCGA-UB-AA0U TCGA-WQ-A9G7 
       15.52        36.10        19.76         1.71        10.75         0.99 
TCGA-XR-A8TD TCGA-YA-A8S7 
       33.86        13.55 

$`DEL PEAK 17(10Q26.13) WILD-TYPE`
TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BD-A3ER TCGA-DD-A3A8 
       11.74        38.40         8.61        69.57        36.66         0.36 
TCGA-DD-A4ND TCGA-DD-AADV TCGA-DD-AAE7 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL 
       90.28        18.87        21.17        18.90        23.64         9.96 
TCGA-ES-A2HS TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A3CG 
       22.62         8.12         6.38        81.73        30.74        22.13 
TCGA-G3-A6UC TCGA-G3-A7M9 TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-LG-A6GG TCGA-MI-A75H 
       22.06         1.84        20.75         2.14        12.72        24.56 
TCGA-T1-A6J8 TCGA-UB-A7MF TCGA-UB-AA0V TCGA-XR-A8TG TCGA-2Y-A9GT TCGA-2Y-A9GW 
        0.76         7.04        10.32        29.52        53.39        41.79 
TCGA-2Y-A9GX TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H3 
       80.28        24.89        27.88       120.82        40.41        49.84 
TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-5C-A9VG 
       18.25        20.81         1.18         8.55        13.02        10.78 
TCGA-5C-A9VH TCGA-5R-AA1C TCGA-5R-AA1D TCGA-BC-4072 TCGA-BC-A10S TCGA-BC-A10T 
       10.59        17.10        14.76        48.99        46.78        27.52 
TCGA-BC-A10U TCGA-BC-A10X TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A3KF TCGA-BC-A69H 
       27.52        25.32         1.12        44.42         0.26        14.60 
TCGA-BC-A69I TCGA-BD-A2L6 TCGA-CC-5258 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 
       12.72        44.81         4.24         3.19         3.39         4.24 
TCGA-CC-A3MB TCGA-CC-A5UC TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7IH 
       10.36        11.41         7.13        21.34         9.83        12.00 
TCGA-CC-A7IK TCGA-CC-A7IL TCGA-CC-A8HU TCGA-CC-A9FS TCGA-DD-A113 TCGA-DD-A116 
        8.61         9.14        11.31         6.94        79.73        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-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-A39V TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Z 
       33.04        18.35        21.14        27.19        55.69        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-A3A9 TCGA-DD-A4NB TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NJ 
       13.78        30.61        32.52        30.97        30.15        30.51 
TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NR 
       39.78        56.25        29.56        73.81       108.76         0.30 
TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D 
       80.75        78.84        23.93         9.30        23.05        22.78 
TCGA-DD-A73E TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA 
        1.45       114.35        13.48         0.53        11.41        75.65 
TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACH 
       76.41        55.40        12.53        71.80        12.00         6.41 
TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACN TCGA-DD-AACP TCGA-DD-AACS 
       69.11         0.30         3.52        42.81        13.64        59.31 
TCGA-DD-AACT TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AAD0 TCGA-DD-AAD1 
       51.35        46.82         5.59        47.67         4.50        18.54 
TCGA-DD-AAD2 TCGA-DD-AAD6 TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE 
       21.63        22.09        40.83        13.97        40.47        39.52 
TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADO 
        3.78        37.64        35.67        35.05        34.49        14.89 
TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AAE0 
       15.06        14.33        15.58        18.21        19.30        18.25 
TCGA-DD-AAE1 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE9 TCGA-DD-AAEB 
       18.15        18.61        19.99         4.64        23.74        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        90.48 
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        60.99 
TCGA-DD-AAW3 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A7PY 
       53.69        26.93        28.08        13.91        13.35        12.82 
TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-EP-A12J TCGA-EP-A26S 
        0.20        13.15        13.41        13.35        18.74        19.99 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B 
       20.61        19.59         0.62        11.93        14.40        60.89 
TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25V TCGA-G3-A25Z 
       12.03         0.03         0.39        13.68        28.27        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-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV0 
       17.10        20.78        11.87        14.14        15.78        15.65 
TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A3OU 
       12.23        13.55        11.64         2.14        11.87        28.90 
TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A6G5 TCGA-K7-AAU7 
        1.02         2.20         2.99        37.71        16.83        11.80 
TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I 
       13.97        12.03         9.57        16.67        22.95        20.71 
TCGA-MR-A520 TCGA-NI-A8LF TCGA-O8-A75V TCGA-RC-A6M5 TCGA-RC-A7S9 TCGA-RC-A7SF 
        7.53        26.27        17.69         0.49        21.04        19.04 
TCGA-RC-A7SH TCGA-UB-A7MA TCGA-UB-A7MC TCGA-UB-A7ME TCGA-WJ-A86L TCGA-WQ-AB4B 
       15.39        27.88        16.44        15.98        11.34        12.99 
TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TE TCGA-XR-A8TF TCGA-ZP-A9CV 
       20.22        24.85        18.28        30.41        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-A9CF TCGA-ZS-A9CG 
       79.30        11.21 

  DEL PEAK 17(10Q26.13) MUTATED DEL PEAK 17(10Q26.13) WILD-TYPE 
                           0.20                            0.03 
  DEL PEAK 17(10Q26.13) MUTATED DEL PEAK 17(10Q26.13) WILD-TYPE 
                          83.57                          120.82 
  DEL PEAK 17(10Q26.13) MUTATED DEL PEAK 17(10Q26.13) WILD-TYPE 
                         18.790                          20.055 
[1] "0.2 - 83.6 (18.8)"  "0.0 - 120.8 (20.1)"
[1] "hr=" "1.4"
D44V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE III STAGE IIIA
  DEL PEAK 17(10Q26.13) MUTATED        42       27         0         21
  DEL PEAK 17(10Q26.13) WILD-TYPE     131       60         3         41
                                 vv
clus                              STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 17(10Q26.13) MUTATED            3          4        0         0
  DEL PEAK 17(10Q26.13) WILD-TYPE          6          3        2         1
                                 vv
clus                              STAGE IVB
  DEL PEAK 17(10Q26.13) MUTATED           0
  DEL PEAK 17(10Q26.13) WILD-TYPE         2
D44V3, multiclass
            clus
vv           DEL PEAK 17(10Q26.13) MUTATED DEL PEAK 17(10Q26.13) WILD-TYPE
  STAGE I                               42                             131
  STAGE II                              27                              60
  STAGE III                              0                               3
  STAGE IIIA                            21                              41
  STAGE IIIB                             3                               6
  STAGE IIIC                             4                               3
  STAGE IV                               0                               2
  STAGE IVA                              0                               1
  STAGE IVB                              0                               2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               T1  T2  T3  T4
  DEL PEAK 17(10Q26.13) MUTATED    43  30  25   7
  DEL PEAK 17(10Q26.13) WILD-TYPE 140  65  52   5
D44V4, multiclass
    clus
vv   DEL PEAK 17(10Q26.13) MUTATED DEL PEAK 17(10Q26.13) WILD-TYPE
  T1                            43                             140
  T2                            30                              65
  T3                            25                              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 17(10Q26.13) MUTATED    72   1
  DEL PEAK 17(10Q26.13) WILD-TYPE 182   2
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 17(10Q26.13) MUTATED     72    1
  DEL PEAK 17(10Q26.13) WILD-TYPE  182    2
   clus
vv  DEL PEAK 17(10Q26.13) MUTATED DEL PEAK 17(10Q26.13) WILD-TYPE
  0                            72                             182
  1                             1                               2
[1] 2 2
[1] FALSE
D44V6, binary
                                 cls
clus                                0   1
  DEL PEAK 17(10Q26.13) MUTATED    77   0
  DEL PEAK 17(10Q26.13) WILD-TYPE 189   4
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 17(10Q26.13) MUTATED     77    0
  DEL PEAK 17(10Q26.13) WILD-TYPE  189    4
   clus
vv  DEL PEAK 17(10Q26.13) MUTATED DEL PEAK 17(10Q26.13) WILD-TYPE
  0                            77                             189
  1                             0                               4
[1] 2 2
[1] FALSE
D44V7, binary
                                 cls
clus                                0   1
  DEL PEAK 17(10Q26.13) MUTATED    35  70
  DEL PEAK 17(10Q26.13) WILD-TYPE  83 182
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 17(10Q26.13) MUTATED     35   70
  DEL PEAK 17(10Q26.13) WILD-TYPE   83  182
        clus
vv       DEL PEAK 17(10Q26.13) MUTATED DEL PEAK 17(10Q26.13) WILD-TYPE
  FEMALE                            35                              83
  MALE                              70                             182
[1] 2 2
[1] FALSE
D44V8, binary
                                 cls
clus                                0   1
  DEL PEAK 17(10Q26.13) MUTATED    99   1
  DEL PEAK 17(10Q26.13) WILD-TYPE 239   8
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 17(10Q26.13) MUTATED     99    1
  DEL PEAK 17(10Q26.13) WILD-TYPE  239    8
     clus
vv    DEL PEAK 17(10Q26.13) MUTATED DEL PEAK 17(10Q26.13) WILD-TYPE
  NO                             99                             239
  YES                             1                               8
[1] 2 2
[1] FALSE
                                 vv
clus                              FIBROLAMELLAR CARCINOMA
  DEL PEAK 17(10Q26.13) MUTATED                         1
  DEL PEAK 17(10Q26.13) WILD-TYPE                       2
                                 vv
clus                              HEPATOCELLULAR CARCINOMA
  DEL PEAK 17(10Q26.13) MUTATED                        100
  DEL PEAK 17(10Q26.13) WILD-TYPE                      260
                                 vv
clus                              HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK 17(10Q26.13) MUTATED                                  4
  DEL PEAK 17(10Q26.13) WILD-TYPE                                3
D44V9, multiclass
                                  clus
vv                                 DEL PEAK 17(10Q26.13) MUTATED
  FIBROLAMELLAR CARCINOMA                                      1
  HEPATOCELLULAR CARCINOMA                                   100
  HEPATOCHOLANGIOCARCINOMA (MIXED)                             4
                                  clus
vv                                 DEL PEAK 17(10Q26.13) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                        2
  HEPATOCELLULAR CARCINOMA                                     260
  HEPATOCHOLANGIOCARCINOMA (MIXED)                               3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 17(10Q26.13) MUTATED    88   7   0   8
  DEL PEAK 17(10Q26.13) WILD-TYPE 236  10   1  13
D44V10, multiclass
    clus
vv   DEL PEAK 17(10Q26.13) MUTATED DEL PEAK 17(10Q26.13) WILD-TYPE
  R0                            88                             236
  R1                             7                              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 17(10Q26.13) MUTATED                                  0    48
  DEL PEAK 17(10Q26.13) WILD-TYPE                                2   110
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 17(10Q26.13) MUTATED                          10    45
  DEL PEAK 17(10Q26.13) WILD-TYPE                         7   138
D44V11, multiclass
                                  clus
vv                                 DEL PEAK 17(10Q26.13) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                       48
  BLACK OR AFRICAN AMERICAN                                   10
  WHITE                                                       45
                                  clus
vv                                 DEL PEAK 17(10Q26.13) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               2
  ASIAN                                                        110
  BLACK OR AFRICAN AMERICAN                                      7
  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"
D44V12, binary
                                 cls
clus                                0   1
  DEL PEAK 17(10Q26.13) MUTATED     4  94
  DEL PEAK 17(10Q26.13) WILD-TYPE  12 241
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 17(10Q26.13) MUTATED      4   94
  DEL PEAK 17(10Q26.13) WILD-TYPE   12  241
                        clus
vv                       DEL PEAK 17(10Q26.13) MUTATED
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                            94
                        clus
vv                       DEL PEAK 17(10Q26.13) WILD-TYPE
  HISPANIC OR LATINO                                  12
  NOT HISPANIC OR LATINO                             241
[1] 2 2
[1] FALSE

Clustering(45) Variable = DEL PEAK 18(11Q14.1) MUTATION ANALYSIS
D45V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 18(11Q14.1) MUTATED    47  27
  DEL PEAK 18(11Q14.1) WILD-TYPE 188 102
  DEL PEAK 18(11Q14.1) MUTATED DEL PEAK 18(11Q14.1) WILD-TYPE 
                            74                            290 
  DEL PEAK 18(11Q14.1) MUTATED DEL PEAK 18(11Q14.1) WILD-TYPE 
                            27                            102 
$`DEL PEAK 18(11Q14.1) MUTATED`
TCGA-BC-A112 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-FV-A4ZP TCGA-KR-A7K7 TCGA-UB-A7MF 
        5.03        90.28        26.83        81.73        31.27         7.04 
TCGA-XR-A8TG TCGA-2Y-A9GS TCGA-2Y-A9GY TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-3K-AAZ8 
       29.52        23.80        24.89        56.91        49.84        13.02 
TCGA-5C-A9VG TCGA-5C-AAPD TCGA-5R-AA1D TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10S 
       10.78         0.66        14.76        27.91        37.32        46.78 
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-A73B TCGA-DD-AACB TCGA-DD-AACP TCGA-DD-AACV TCGA-DD-AACY 
       32.52         9.30        76.41        13.64        50.33        47.67 
TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADD TCGA-DD-AADO TCGA-DD-AADP 
       44.22        22.09        40.08        40.47        14.89        15.06 
TCGA-DD-AADY TCGA-DD-AAE3 TCGA-DD-AAE6 TCGA-DD-AAED TCGA-DD-AAEK TCGA-ED-A7PZ 
       18.25        18.61         4.64        25.08        35.08         0.20 
TCGA-ED-A7XO TCGA-ED-A8O6 TCGA-EP-A2KC TCGA-FV-A2QQ TCGA-G3-A25S TCGA-G3-A5SJ 
       14.04         1.84         0.62        23.97        13.68        22.95 
TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV6 TCGA-K7-A5RG TCGA-KR-A7K2 TCGA-RC-A6M4 
       11.80        12.23         2.14        17.06        27.25         0.72 
TCGA-RC-A6M5 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MC 
        0.49        19.33        19.04        36.10        27.88        16.44 
TCGA-XR-A8TD TCGA-YA-A8S7 
       33.86        13.55 

$`DEL PEAK 18(11Q14.1) WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A5W4 
       83.24        11.74        38.40         8.61        69.57        17.98 
TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-AADV TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEA 
       36.66         0.36        18.87        21.17        21.83        18.90 
TCGA-DD-AAEG TCGA-EP-A3JL TCGA-ES-A2HS TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-G3-A25W 
       23.64         9.96        22.62         8.12         6.38        30.74 
TCGA-G3-A3CG TCGA-G3-A6UC TCGA-G3-A7M9 TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-LG-A6GG 
       22.13        22.06         1.84        20.75         2.14        12.72 
TCGA-MI-A75H TCGA-T1-A6J8 TCGA-UB-AA0V TCGA-ZP-A9D1 TCGA-ZS-A9CE TCGA-2Y-A9GT 
       24.56         0.76        10.32         0.69        40.80        53.39 
TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 
       63.75        41.79        80.28        27.88       120.82        40.41 
TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB 
       47.74        18.25        20.81        22.92         1.18         8.55 
TCGA-5C-A9VH TCGA-5R-AA1C TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-A10R TCGA-BC-A10T 
       10.59        17.10         1.51        48.99        10.13        27.52 
TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A216 
       27.52         2.99        25.32        23.38         1.12        44.42 
TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP 
       22.36        14.60        12.72        18.48        44.81        13.45 
TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-A1HT 
        0.66         4.24         2.86         3.19         3.39         3.32 
TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A5UC TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IF 
        9.96        10.36        11.41         8.94         7.13        21.34 
TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A8HT TCGA-CC-A8HV TCGA-CC-A9FS TCGA-CC-A9FW 
       12.00        13.12         4.60         9.17         6.94         8.15 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11B 
       37.78        83.57        53.33       113.00         7.33         0.46 
TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED 
       21.76        51.29        79.40        66.31        19.79        75.65 
TCGA-DD-A1EE TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EK TCGA-DD-A1EL 
       11.47        45.11        49.15         6.02        18.35        13.64 
TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 
       21.14        27.19         5.62        19.76        25.81         7.66 
TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 
       70.06        17.59        20.12       102.74       107.11        13.78 
TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK 
       30.61        33.14        30.97        30.15        30.51        39.78 
TCGA-DD-A4NL TCGA-DD-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-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH 
       55.40        12.53        71.80        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-AACQ TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACW 
       61.68        14.20        59.31        51.35        51.52        46.82 
TCGA-DD-AACX TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 
        5.59         5.62         4.50        18.54        21.63        42.58 
TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG 
       40.54        40.83        13.97        39.52         3.78        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-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AAE0 
       14.33        66.67        15.58        18.21        19.30        18.25 
TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE4 TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAEE 
       18.15        20.98        19.99        23.74        15.72        26.63 
TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS 
       25.78        50.33        90.48        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        60.99        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-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S 
       13.15        13.41        13.35         0.20        18.74        19.99 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR 
       20.61        19.59        11.93        14.40        60.89        19.10 
TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25T 
       27.88        12.03         0.03         0.33         0.39        51.06 
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-A5SL TCGA-G3-A5SM 
        5.92        19.53        19.23        25.25        20.42        17.10 
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-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 
       13.55         0.89        11.64        11.87        28.90         1.02 
TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K8 
        2.20         2.99        37.71        16.83        11.80        29.79 
TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I 
       13.97        12.03         9.57        16.67        22.95        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-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SH TCGA-RC-A7SK TCGA-UB-A7MB 
        3.09         0.30        21.04        15.39        15.52        19.76 
TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B 
        1.71        15.98        10.75        11.34         0.99        12.99 
TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TE TCGA-XR-A8TF TCGA-ZP-A9CV 
       20.22        24.85        18.28        30.41        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-A9CF TCGA-ZS-A9CG 
       79.30        11.21 

  DEL PEAK 18(11Q14.1) MUTATED DEL PEAK 18(11Q14.1) WILD-TYPE 
                          0.20                           0.03 
  DEL PEAK 18(11Q14.1) MUTATED DEL PEAK 18(11Q14.1) WILD-TYPE 
                         90.71                         120.82 
  DEL PEAK 18(11Q14.1) MUTATED DEL PEAK 18(11Q14.1) WILD-TYPE 
                        17.655                         20.170 
[1] "0.2 - 90.7 (17.7)"  "0.0 - 120.8 (20.2)"
[1] "hr=" "1.2"
D45V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IIIA
  DEL PEAK 18(11Q14.1) MUTATED        31       16         0         20
  DEL PEAK 18(11Q14.1) WILD-TYPE     142       71         3         42
                                vv
clus                             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 18(11Q14.1) MUTATED            2          2        1         1
  DEL PEAK 18(11Q14.1) WILD-TYPE          7          5        1         0
                                vv
clus                             STAGE IVB
  DEL PEAK 18(11Q14.1) MUTATED           0
  DEL PEAK 18(11Q14.1) WILD-TYPE         2
D45V3, multiclass
            clus
vv           DEL PEAK 18(11Q14.1) MUTATED DEL PEAK 18(11Q14.1) WILD-TYPE
  STAGE I                              31                            142
  STAGE II                             16                             71
  STAGE III                             0                              3
  STAGE IIIA                           20                             42
  STAGE IIIB                            2                              7
  STAGE IIIC                            2                              5
  STAGE IV                              1                              1
  STAGE IVA                             1                              0
  STAGE IVB                             0                              2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 18(11Q14.1) MUTATED    33  19  24   1
  DEL PEAK 18(11Q14.1) WILD-TYPE 150  76  53  11
D45V4, multiclass
    clus
vv   DEL PEAK 18(11Q14.1) MUTATED DEL PEAK 18(11Q14.1) WILD-TYPE
  T1                           33                            150
  T2                           19                             76
  T3                           24                             53
  T4                            1                             11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V5, binary
                                cls
clus                               0   1
  DEL PEAK 18(11Q14.1) MUTATED    56   2
  DEL PEAK 18(11Q14.1) WILD-TYPE 198   1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(11Q14.1) MUTATED     56    2
  DEL PEAK 18(11Q14.1) WILD-TYPE  198    1
   clus
vv  DEL PEAK 18(11Q14.1) MUTATED DEL PEAK 18(11Q14.1) WILD-TYPE
  0                           56                            198
  1                            2                              1
[1] 2 2
[1] FALSE
D45V6, binary
                                cls
clus                               0   1
  DEL PEAK 18(11Q14.1) MUTATED    60   1
  DEL PEAK 18(11Q14.1) WILD-TYPE 206   3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(11Q14.1) MUTATED     60    1
  DEL PEAK 18(11Q14.1) WILD-TYPE  206    3
   clus
vv  DEL PEAK 18(11Q14.1) MUTATED DEL PEAK 18(11Q14.1) WILD-TYPE
  0                           60                            206
  1                            1                              3
[1] 2 2
[1] FALSE
D45V7, binary
                                cls
clus                               0   1
  DEL PEAK 18(11Q14.1) MUTATED    26  51
  DEL PEAK 18(11Q14.1) WILD-TYPE  92 201
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(11Q14.1) MUTATED     26   51
  DEL PEAK 18(11Q14.1) WILD-TYPE   92  201
        clus
vv       DEL PEAK 18(11Q14.1) MUTATED DEL PEAK 18(11Q14.1) WILD-TYPE
  FEMALE                           26                             92
  MALE                             51                            201
[1] 2 2
[1] FALSE
D45V8, binary
                                cls
clus                               0   1
  DEL PEAK 18(11Q14.1) MUTATED    68   2
  DEL PEAK 18(11Q14.1) WILD-TYPE 270   7
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(11Q14.1) MUTATED     68    2
  DEL PEAK 18(11Q14.1) WILD-TYPE  270    7
     clus
vv    DEL PEAK 18(11Q14.1) MUTATED DEL PEAK 18(11Q14.1) WILD-TYPE
  NO                            68                            270
  YES                            2                              7
[1] 2 2
[1] FALSE
                                vv
clus                             FIBROLAMELLAR CARCINOMA
  DEL PEAK 18(11Q14.1) MUTATED                         2
  DEL PEAK 18(11Q14.1) WILD-TYPE                       1
                                vv
clus                             HEPATOCELLULAR CARCINOMA
  DEL PEAK 18(11Q14.1) MUTATED                         72
  DEL PEAK 18(11Q14.1) WILD-TYPE                      288
                                vv
clus                             HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK 18(11Q14.1) MUTATED                                  3
  DEL PEAK 18(11Q14.1) WILD-TYPE                                4
D45V9, multiclass
                                  clus
vv                                 DEL PEAK 18(11Q14.1) MUTATED
  FIBROLAMELLAR CARCINOMA                                     2
  HEPATOCELLULAR CARCINOMA                                   72
  HEPATOCHOLANGIOCARCINOMA (MIXED)                            3
                                  clus
vv                                 DEL PEAK 18(11Q14.1) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                       1
  HEPATOCELLULAR CARCINOMA                                    288
  HEPATOCHOLANGIOCARCINOMA (MIXED)                              4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 18(11Q14.1) MUTATED    67   6   0   4
  DEL PEAK 18(11Q14.1) WILD-TYPE 257  11   1  17
D45V10, multiclass
    clus
vv   DEL PEAK 18(11Q14.1) MUTATED DEL PEAK 18(11Q14.1) WILD-TYPE
  R0                           67                            257
  R1                            6                             11
  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 18(11Q14.1) MUTATED                                  1    33
  DEL PEAK 18(11Q14.1) WILD-TYPE                                1   125
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 18(11Q14.1) MUTATED                           5    38
  DEL PEAK 18(11Q14.1) WILD-TYPE                        12   145
D45V11, multiclass
                                  clus
vv                                 DEL PEAK 18(11Q14.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                      33
  BLACK OR AFRICAN AMERICAN                                   5
  WHITE                                                      38
                                  clus
vv                                 DEL PEAK 18(11Q14.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                       125
  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"
D45V12, binary
                                cls
clus                               0   1
  DEL PEAK 18(11Q14.1) MUTATED     7  64
  DEL PEAK 18(11Q14.1) WILD-TYPE   9 271
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(11Q14.1) MUTATED      7   64
  DEL PEAK 18(11Q14.1) WILD-TYPE    9  271
                        clus
vv                       DEL PEAK 18(11Q14.1) MUTATED
  HISPANIC OR LATINO                                7
  NOT HISPANIC OR LATINO                           64
                        clus
vv                       DEL PEAK 18(11Q14.1) WILD-TYPE
  HISPANIC OR LATINO                                  9
  NOT HISPANIC OR LATINO                            271
[1] 2 2
[1] FALSE

Clustering(46) Variable = DEL PEAK 19(11Q23.3) MUTATION ANALYSIS
D46V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 19(11Q23.3) MUTATED    58  32
  DEL PEAK 19(11Q23.3) WILD-TYPE 177  97
  DEL PEAK 19(11Q23.3) MUTATED DEL PEAK 19(11Q23.3) WILD-TYPE 
                            90                            274 
  DEL PEAK 19(11Q23.3) MUTATED DEL PEAK 19(11Q23.3) WILD-TYPE 
                            32                             97 
$`DEL PEAK 19(11Q23.3) MUTATED`
TCGA-BC-A112 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-FV-A4ZP TCGA-KR-A7K7 TCGA-UB-A7MF 
        5.03        90.28        26.83        81.73        31.27         7.04 
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-A3KF 
        0.66        14.76        27.91        37.32        46.78         0.26 
TCGA-BC-A69H TCGA-BW-A5NO TCGA-CC-5263 TCGA-CC-5264 TCGA-CC-A3MA TCGA-CC-A3MC 
       14.60         0.66         4.24         3.35         9.96        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-CC-A8HV TCGA-DD-A113 TCGA-DD-A11A TCGA-DD-A1E9 TCGA-DD-A1EF TCGA-DD-A1EJ 
        9.17        79.73         2.60        90.71        12.95        33.04 
TCGA-DD-A39X TCGA-DD-A4NB TCGA-DD-A4NN TCGA-DD-A73B TCGA-DD-AACB TCGA-DD-AACI 
       55.69        32.52        29.56         9.30        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        90.48        80.71 
TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A8O6 TCGA-EP-A2KC TCGA-FV-A2QQ TCGA-G3-A25S 
        0.20        14.04         1.84         0.62        23.97        13.68 
TCGA-G3-A25U TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 
       53.79        25.25        22.95        15.65        11.80        12.23 
TCGA-G3-AAV6 TCGA-GJ-A6C0 TCGA-K7-A5RG TCGA-KR-A7K2 TCGA-PD-A5DF TCGA-RC-A6M4 
        2.14         1.02        17.06        27.25        21.01         0.72 
TCGA-RC-A6M5 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MC 
        0.49        19.33        19.04        36.10        27.88        16.44 
TCGA-UB-A7ME TCGA-WQ-AB4B TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CZ TCGA-ZP-A9D0 
       15.98        12.99        22.78        13.55        23.21        35.87 

$`DEL PEAK 19(11Q23.3) WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A5W4 
       83.24        11.74        38.40         8.61        69.57        17.98 
TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-AADV TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEA 
       36.66         0.36        18.87        21.17        21.83        18.90 
TCGA-DD-AAEG TCGA-EP-A3JL TCGA-ES-A2HS TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-G3-A25W 
       23.64         9.96        22.62         8.12         6.38        30.74 
TCGA-G3-A3CG TCGA-G3-A6UC TCGA-G3-A7M9 TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-LG-A6GG 
       22.13        22.06         1.84        20.75         2.14        12.72 
TCGA-MI-A75H TCGA-T1-A6J8 TCGA-UB-AA0V TCGA-XR-A8TG TCGA-ZP-A9D1 TCGA-ZS-A9CE 
       24.56         0.76        10.32        29.52         0.69        40.80 
TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GZ TCGA-2Y-A9H0 
       53.39        63.75        41.79        80.28        27.88       120.82 
TCGA-2Y-A9H1 TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA 
       40.41        47.74        18.25        20.81        22.92         1.18 
TCGA-2Y-A9HB TCGA-5C-A9VH TCGA-5R-AA1C TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-A10R 
        8.55        10.59        17.10         1.51        48.99        10.13 
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-A216 TCGA-BC-A217 TCGA-BC-A3KG TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A2L6 
       44.42        45.93        22.36        12.72        18.48        44.81 
TCGA-BD-A3EP TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-A1HT 
       13.45         4.24         2.86         3.19         3.39         3.32 
TCGA-CC-A3M9 TCGA-CC-A3MB TCGA-CC-A5UC TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IF 
        9.86        10.36        11.41         8.94         7.13        21.34 
TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A8HT TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A114 
       12.00        13.12         4.60         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-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-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V 
       45.11        49.15         6.02        18.35        13.64        21.14 
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-A3A7 TCGA-DD-A3A9 
       17.59        20.12       102.74       107.11        13.78        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-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-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-AACJ TCGA-DD-AACK 
       71.80        12.00        15.42         6.41        69.11         0.30 
TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT 
        3.52        58.16        42.81        14.20        59.31        51.35 
TCGA-DD-AACU TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 
       51.52        46.82         5.59         5.62         4.50        18.54 
TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADE 
       21.63        42.58        40.54        40.83        13.97        39.52 
TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL 
        3.78        37.64        35.67        35.05        34.49        20.91 
TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADQ TCGA-DD-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-AAE4 TCGA-DD-AAE9 TCGA-DD-AAEB 
       19.30        18.25        18.15        19.99        23.74        15.72 
TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS 
       26.63        25.78        50.33        89.69        82.62        59.93 
TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 
       72.39        76.18        56.48        64.77        62.47        66.25 
TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG 
       65.39        60.99        53.69        29.92        26.93        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-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
       13.41        13.35         0.20        18.74        19.99        20.61 
TCGA-EP-A2KB TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 
       19.59        11.93        14.40        60.89        19.10        27.88 
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-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ 
       58.49        14.86        21.53        25.64         5.92        19.53 
TCGA-G3-A3CK TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M7 
       19.23        20.42        17.10        14.70        20.78        11.87 
TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV7 
       14.14        15.78        13.55         0.89        11.64        11.87 
TCGA-GJ-A3OU TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A6G5 TCGA-K7-AAU7 
       28.90         2.20         2.99        37.71        16.83        11.80 
TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G 
       29.79        13.97        12.03         9.57        16.67        22.95 
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-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SH TCGA-RC-A7SK TCGA-UB-A7MB 
        3.09         0.30        21.04        15.39        15.52        19.76 
TCGA-UB-A7MD TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WX-AA44 TCGA-WX-AA46 
        1.71        10.75        11.34         0.99        20.22        24.85 
TCGA-WX-AA47 TCGA-XR-A8TD TCGA-XR-A8TE TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9D2 
       18.28        33.86        30.41        35.77        25.71        25.15 
TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CF TCGA-ZS-A9CG 
       12.99        45.57        79.30        11.21 

  DEL PEAK 19(11Q23.3) MUTATED DEL PEAK 19(11Q23.3) WILD-TYPE 
                          0.20                           0.03 
  DEL PEAK 19(11Q23.3) MUTATED DEL PEAK 19(11Q23.3) WILD-TYPE 
                         90.71                         120.82 
  DEL PEAK 19(11Q23.3) MUTATED DEL PEAK 19(11Q23.3) WILD-TYPE 
                        18.430                         20.055 
[1] "0.2 - 90.7 (18.4)"  "0.0 - 120.8 (20.1)"
[1] "hr=" "1.1"
D46V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IIIA
  DEL PEAK 19(11Q23.3) MUTATED        38       22         0         21
  DEL PEAK 19(11Q23.3) WILD-TYPE     135       65         3         41
                                vv
clus                             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 19(11Q23.3) MUTATED            2          2        1         1
  DEL PEAK 19(11Q23.3) WILD-TYPE          7          5        1         0
                                vv
clus                             STAGE IVB
  DEL PEAK 19(11Q23.3) MUTATED           0
  DEL PEAK 19(11Q23.3) WILD-TYPE         2
D46V3, multiclass
            clus
vv           DEL PEAK 19(11Q23.3) MUTATED DEL PEAK 19(11Q23.3) WILD-TYPE
  STAGE I                              38                            135
  STAGE II                             22                             65
  STAGE III                             0                              3
  STAGE IIIA                           21                             41
  STAGE IIIB                            2                              7
  STAGE IIIC                            2                              5
  STAGE IV                              1                              1
  STAGE IVA                             1                              0
  STAGE IVB                             0                              2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 19(11Q23.3) MUTATED    42  25  24   2
  DEL PEAK 19(11Q23.3) WILD-TYPE 141  70  53  10
D46V4, multiclass
    clus
vv   DEL PEAK 19(11Q23.3) MUTATED DEL PEAK 19(11Q23.3) WILD-TYPE
  T1                           42                            141
  T2                           25                             70
  T3                           24                             53
  T4                            2                             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V5, binary
                                cls
clus                               0   1
  DEL PEAK 19(11Q23.3) MUTATED    66   2
  DEL PEAK 19(11Q23.3) WILD-TYPE 188   1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(11Q23.3) MUTATED     66    2
  DEL PEAK 19(11Q23.3) WILD-TYPE  188    1
   clus
vv  DEL PEAK 19(11Q23.3) MUTATED DEL PEAK 19(11Q23.3) WILD-TYPE
  0                           66                            188
  1                            2                              1
[1] 2 2
[1] FALSE
D46V6, binary
                                cls
clus                               0   1
  DEL PEAK 19(11Q23.3) MUTATED    70   1
  DEL PEAK 19(11Q23.3) WILD-TYPE 196   3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(11Q23.3) MUTATED     70    1
  DEL PEAK 19(11Q23.3) WILD-TYPE  196    3
   clus
vv  DEL PEAK 19(11Q23.3) MUTATED DEL PEAK 19(11Q23.3) WILD-TYPE
  0                           70                            196
  1                            1                              3
[1] 2 2
[1] FALSE
D46V7, binary
                                cls
clus                               0   1
  DEL PEAK 19(11Q23.3) MUTATED    30  63
  DEL PEAK 19(11Q23.3) WILD-TYPE  88 189
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(11Q23.3) MUTATED     30   63
  DEL PEAK 19(11Q23.3) WILD-TYPE   88  189
        clus
vv       DEL PEAK 19(11Q23.3) MUTATED DEL PEAK 19(11Q23.3) WILD-TYPE
  FEMALE                           30                             88
  MALE                             63                            189
[1] 2 2
[1] FALSE
D46V8, binary
                                cls
clus                               0   1
  DEL PEAK 19(11Q23.3) MUTATED    85   1
  DEL PEAK 19(11Q23.3) WILD-TYPE 253   8
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(11Q23.3) MUTATED     85    1
  DEL PEAK 19(11Q23.3) WILD-TYPE  253    8
     clus
vv    DEL PEAK 19(11Q23.3) MUTATED DEL PEAK 19(11Q23.3) WILD-TYPE
  NO                            85                            253
  YES                            1                              8
[1] 2 2
[1] FALSE
                                vv
clus                             FIBROLAMELLAR CARCINOMA
  DEL PEAK 19(11Q23.3) MUTATED                         2
  DEL PEAK 19(11Q23.3) WILD-TYPE                       1
                                vv
clus                             HEPATOCELLULAR CARCINOMA
  DEL PEAK 19(11Q23.3) MUTATED                         88
  DEL PEAK 19(11Q23.3) WILD-TYPE                      272
                                vv
clus                             HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK 19(11Q23.3) MUTATED                                  3
  DEL PEAK 19(11Q23.3) WILD-TYPE                                4
D46V9, multiclass
                                  clus
vv                                 DEL PEAK 19(11Q23.3) MUTATED
  FIBROLAMELLAR CARCINOMA                                     2
  HEPATOCELLULAR CARCINOMA                                   88
  HEPATOCHOLANGIOCARCINOMA (MIXED)                            3
                                  clus
vv                                 DEL PEAK 19(11Q23.3) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                       1
  HEPATOCELLULAR CARCINOMA                                    272
  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 19(11Q23.3) MUTATED    80   6   0   6
  DEL PEAK 19(11Q23.3) WILD-TYPE 244  11   1  15
D46V10, multiclass
    clus
vv   DEL PEAK 19(11Q23.3) MUTATED DEL PEAK 19(11Q23.3) WILD-TYPE
  R0                           80                            244
  R1                            6                             11
  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 19(11Q23.3) MUTATED                                  1    44
  DEL PEAK 19(11Q23.3) WILD-TYPE                                1   114
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 19(11Q23.3) MUTATED                           7    41
  DEL PEAK 19(11Q23.3) WILD-TYPE                        10   142
D46V11, multiclass
                                  clus
vv                                 DEL PEAK 19(11Q23.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                      44
  BLACK OR AFRICAN AMERICAN                                   7
  WHITE                                                      41
                                  clus
vv                                 DEL PEAK 19(11Q23.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                       114
  BLACK OR AFRICAN AMERICAN                                    10
  WHITE                                                       142
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V12, binary
                                cls
clus                               0   1
  DEL PEAK 19(11Q23.3) MUTATED     6  82
  DEL PEAK 19(11Q23.3) WILD-TYPE  10 253
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(11Q23.3) MUTATED      6   82
  DEL PEAK 19(11Q23.3) WILD-TYPE   10  253
                        clus
vv                       DEL PEAK 19(11Q23.3) MUTATED
  HISPANIC OR LATINO                                6
  NOT HISPANIC OR LATINO                           82
                        clus
vv                       DEL PEAK 19(11Q23.3) WILD-TYPE
  HISPANIC OR LATINO                                 10
  NOT HISPANIC OR LATINO                            253
[1] 2 2
[1] FALSE

Clustering(47) Variable = DEL PEAK 20(12P12.1) MUTATION ANALYSIS
D47V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 20(12P12.1) MUTATED    48  27
  DEL PEAK 20(12P12.1) WILD-TYPE 187 102
  DEL PEAK 20(12P12.1) MUTATED DEL PEAK 20(12P12.1) WILD-TYPE 
                            75                            289 
  DEL PEAK 20(12P12.1) MUTATED DEL PEAK 20(12P12.1) WILD-TYPE 
                            27                            102 
$`DEL PEAK 20(12P12.1) MUTATED`
TCGA-BC-A5W4 TCGA-DD-A4NI TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-T1-A6J8 TCGA-ZP-A9D1 
       17.98        26.83         8.12         6.38         0.76         0.69 
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-BD-A2L6 TCGA-BD-A3EP TCGA-CC-A1HT TCGA-CC-A3MA TCGA-CC-A3MC 
        0.26        44.81        13.45         3.32         9.96        11.93 
TCGA-CC-A5UE TCGA-CC-A7IK TCGA-CC-A7IL TCGA-CC-A8HT TCGA-CC-A8HV TCGA-DD-A119 
        8.94         8.61         9.14         4.60         9.17         7.33 
TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39X TCGA-DD-A39Y 
       45.11        49.15        33.04        13.64        55.69         5.62 
TCGA-DD-A3A1 TCGA-DD-A3A7 TCGA-DD-A4NA TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NO 
        7.66        13.78        33.14        30.15        30.51        73.81 
TCGA-DD-A73F TCGA-DD-AACE TCGA-DD-AACG TCGA-DD-AACN TCGA-DD-AACU TCGA-DD-AACY 
       35.67        71.80        15.42        42.81        51.52        47.67 
TCGA-DD-AAD5 TCGA-DD-AAD8 TCGA-DD-AADD TCGA-DD-AADJ TCGA-DD-AADM TCGA-DD-AADO 
       44.22        40.08        40.47        35.05         0.39        14.89 
TCGA-DD-AAE3 TCGA-DD-AAEE TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVU 
       18.61        26.63        50.33        35.08        90.48        72.39 
TCGA-DD-AAVV TCGA-ED-A7XP TCGA-EP-A2KC TCGA-FV-A496 TCGA-G3-A25S TCGA-G3-A25Z 
       80.71        13.15         0.62         0.33        13.68        21.53 
TCGA-G3-A7M6 TCGA-G3-AAV0 TCGA-G3-AAV3 TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-K7-AAU7 
       20.78        15.65        13.55        11.87         1.02        11.80 
TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A8JO TCGA-PD-A5DF TCGA-RC-A6M4 TCGA-RC-A6M5 
       22.95        20.71        10.85        21.01         0.72         0.49 
TCGA-RC-A6M6 TCGA-RC-A7SK TCGA-UB-AA0U 
        0.30        15.52        10.75 

$`DEL PEAK 20(12P12.1) WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 
       83.24        11.74        38.40         8.61        69.57         5.03 
TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-AADV TCGA-DD-AAE7 TCGA-DD-AAE8 
       36.66         0.36        90.28        18.87        21.17        21.83 
TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-ES-A2HS TCGA-FV-A4ZP TCGA-G3-A25W 
       18.90        23.64         9.96        22.62        81.73        30.74 
TCGA-G3-A3CG TCGA-G3-A6UC TCGA-G3-A7M9 TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-KR-A7K7 
       22.13        22.06         1.84        20.75         2.14        31.27 
TCGA-LG-A6GG TCGA-MI-A75H TCGA-UB-A7MF TCGA-UB-AA0V TCGA-XR-A8TG TCGA-ZS-A9CE 
       12.72        24.56         7.04        10.32        29.52        40.80 
TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GY TCGA-2Y-A9GZ 
       53.39        63.75        41.79        80.28        24.89        27.88 
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-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD 
       20.81        22.92         1.18        10.78        10.59         0.66 
TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-A10Q TCGA-BC-A10R 
       17.10        14.76         1.51        48.99        37.32        10.13 
TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Z 
       46.78        27.52        27.52         2.99        25.32         1.12 
TCGA-BC-A216 TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A69I TCGA-BC-A8YO TCGA-BW-A5NO 
       44.42        22.36        14.60        12.72        18.48         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-A3MB TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A7IE TCGA-CC-A7IF 
        9.86        10.36        11.41         9.99         7.13        21.34 
TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A8HU TCGA-CC-A9FS 
        9.83        12.00        13.12        12.56        11.31         6.94 
TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 
        8.15        79.73        37.78        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-A1EI 
       66.31        19.79        75.65        11.47        12.95         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-A3A9 TCGA-DD-A4NB 
       17.59        20.12       102.74       107.11        30.61        32.52 
TCGA-DD-A4NF TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NP TCGA-DD-A4NQ 
       30.97        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-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 
       22.78         1.45       114.35        13.48         0.53        11.41 
TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACF TCGA-DD-AACH 
       75.65        76.41        55.40        12.53        12.00         6.41 
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-AACS TCGA-DD-AACT TCGA-DD-AACV TCGA-DD-AACW 
       13.64        14.20        59.31        51.35        50.33        46.82 
TCGA-DD-AACX TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 
        5.59         5.62         4.50        18.54        21.63        42.58 
TCGA-DD-AAD6 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADE TCGA-DD-AADF 
       22.09        40.54        40.83        13.97        39.52         3.78 
TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADN TCGA-DD-AADP 
       37.64        35.67        34.49        20.91        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-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE9 
       18.25        18.15        20.98        19.99         4.64        23.74 
TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEH TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS 
       15.72        25.08        25.78        89.69        82.62        59.93 
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 
       60.99        53.69        29.92        26.93        28.08        13.91 
TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO 
       13.35         9.73         0.20        12.82         0.20        14.04 
TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S 
       13.41        13.35         1.84         0.20        18.74        19.99 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ 
       20.61        19.59        11.93        14.40        60.89        23.97 
TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A4ZQ TCGA-G3-A25T 
       19.10        27.88        12.03         0.03         0.39        51.06 
TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A3CH TCGA-G3-A3CI 
       53.79        28.27        58.49        14.86        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-A7M5 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV1 TCGA-G3-AAV2 
       14.70        11.87        14.14        15.78        11.80        12.23 
TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-GJ-A3OU TCGA-GJ-A9DB TCGA-HP-A5MZ 
        0.89        11.64         2.14        28.90         2.20         2.99 
TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A9QC 
       37.71        17.06        16.83        27.25        29.79        13.97 
TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MR-A520 TCGA-NI-A4U2 TCGA-NI-A8LF 
       12.03         9.57        16.67         7.53        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-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME 
       36.10        27.88        19.76        16.44         1.71        15.98 
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-A8TD TCGA-XR-A8TE TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY 
       33.86        30.41        22.78        13.55        35.77        25.71 
TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CF 
       23.21        35.87        25.15        12.99        45.57        79.30 
TCGA-ZS-A9CG 
       11.21 

  DEL PEAK 20(12P12.1) MUTATED DEL PEAK 20(12P12.1) WILD-TYPE 
                          0.26                           0.03 
  DEL PEAK 20(12P12.1) MUTATED DEL PEAK 20(12P12.1) WILD-TYPE 
                         90.48                         120.82 
  DEL PEAK 20(12P12.1) MUTATED DEL PEAK 20(12P12.1) WILD-TYPE 
                         15.52                          20.12 
[1] "0.3 - 90.5 (15.5)"  "0.0 - 120.8 (20.1)"
[1] "hr=" "1.2"
D47V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IIIA
  DEL PEAK 20(12P12.1) MUTATED        30       20         1         11
  DEL PEAK 20(12P12.1) WILD-TYPE     143       67         2         51
                                vv
clus                             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 20(12P12.1) MUTATED            5          2        2         1
  DEL PEAK 20(12P12.1) WILD-TYPE          4          5        0         0
                                vv
clus                             STAGE IVB
  DEL PEAK 20(12P12.1) MUTATED           0
  DEL PEAK 20(12P12.1) WILD-TYPE         2
D47V3, multiclass
            clus
vv           DEL PEAK 20(12P12.1) MUTATED DEL PEAK 20(12P12.1) WILD-TYPE
  STAGE I                              30                            143
  STAGE II                             20                             67
  STAGE III                             1                              2
  STAGE IIIA                           11                             51
  STAGE IIIB                            5                              4
  STAGE IIIC                            2                              5
  STAGE IV                              2                              0
  STAGE IVA                             1                              0
  STAGE IVB                             0                              2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 20(12P12.1) MUTATED    34  25  16   3
  DEL PEAK 20(12P12.1) WILD-TYPE 149  70  61   9
D47V4, multiclass
    clus
vv   DEL PEAK 20(12P12.1) MUTATED DEL PEAK 20(12P12.1) WILD-TYPE
  T1                           34                            149
  T2                           25                             70
  T3                           16                             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"
D47V5, binary
                                cls
clus                               0   1
  DEL PEAK 20(12P12.1) MUTATED    51   3
  DEL PEAK 20(12P12.1) WILD-TYPE 203   0
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(12P12.1) MUTATED     51    3
  DEL PEAK 20(12P12.1) WILD-TYPE  203    0
   clus
vv  DEL PEAK 20(12P12.1) MUTATED DEL PEAK 20(12P12.1) WILD-TYPE
  0                           51                            203
  1                            3                              0
[1] 2 2
[1] FALSE
D47V6, binary
                                cls
clus                               0   1
  DEL PEAK 20(12P12.1) MUTATED    58   2
  DEL PEAK 20(12P12.1) WILD-TYPE 208   2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(12P12.1) MUTATED     58    2
  DEL PEAK 20(12P12.1) WILD-TYPE  208    2
   clus
vv  DEL PEAK 20(12P12.1) MUTATED DEL PEAK 20(12P12.1) WILD-TYPE
  0                           58                            208
  1                            2                              2
[1] 2 2
[1] FALSE
D47V7, binary
                                cls
clus                               0   1
  DEL PEAK 20(12P12.1) MUTATED    24  54
  DEL PEAK 20(12P12.1) WILD-TYPE  94 198
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(12P12.1) MUTATED     24   54
  DEL PEAK 20(12P12.1) WILD-TYPE   94  198
        clus
vv       DEL PEAK 20(12P12.1) MUTATED DEL PEAK 20(12P12.1) WILD-TYPE
  FEMALE                           24                             94
  MALE                             54                            198
[1] 2 2
[1] FALSE
D47V8, binary
                                cls
clus                               0   1
  DEL PEAK 20(12P12.1) MUTATED    70   0
  DEL PEAK 20(12P12.1) WILD-TYPE 268   9
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(12P12.1) MUTATED     70    0
  DEL PEAK 20(12P12.1) WILD-TYPE  268    9
     clus
vv    DEL PEAK 20(12P12.1) MUTATED DEL PEAK 20(12P12.1) WILD-TYPE
  NO                            70                            268
  YES                            0                              9
[1] 2 2
[1] FALSE
                                vv
clus                             FIBROLAMELLAR CARCINOMA
  DEL PEAK 20(12P12.1) MUTATED                         2
  DEL PEAK 20(12P12.1) WILD-TYPE                       1
                                vv
clus                             HEPATOCELLULAR CARCINOMA
  DEL PEAK 20(12P12.1) MUTATED                         75
  DEL PEAK 20(12P12.1) WILD-TYPE                      285
                                vv
clus                             HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK 20(12P12.1) MUTATED                                  1
  DEL PEAK 20(12P12.1) WILD-TYPE                                6
D47V9, multiclass
                                  clus
vv                                 DEL PEAK 20(12P12.1) MUTATED
  FIBROLAMELLAR CARCINOMA                                     2
  HEPATOCELLULAR CARCINOMA                                   75
  HEPATOCHOLANGIOCARCINOMA (MIXED)                            1
                                  clus
vv                                 DEL PEAK 20(12P12.1) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                       1
  HEPATOCELLULAR CARCINOMA                                    285
  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(12P12.1) MUTATED    63   6   1   6
  DEL PEAK 20(12P12.1) WILD-TYPE 261  11   0  15
D47V10, multiclass
    clus
vv   DEL PEAK 20(12P12.1) MUTATED DEL PEAK 20(12P12.1) WILD-TYPE
  R0                           63                            261
  R1                            6                             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 20(12P12.1) MUTATED                                  0    35
  DEL PEAK 20(12P12.1) WILD-TYPE                                2   123
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 20(12P12.1) MUTATED                           5    35
  DEL PEAK 20(12P12.1) WILD-TYPE                        12   148
D47V11, multiclass
                                  clus
vv                                 DEL PEAK 20(12P12.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                      35
  BLACK OR AFRICAN AMERICAN                                   5
  WHITE                                                      35
                                  clus
vv                                 DEL PEAK 20(12P12.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              2
  ASIAN                                                       123
  BLACK OR AFRICAN AMERICAN                                    12
  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"
D47V12, binary
                                cls
clus                               0   1
  DEL PEAK 20(12P12.1) MUTATED     3  68
  DEL PEAK 20(12P12.1) WILD-TYPE  13 267
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(12P12.1) MUTATED      3   68
  DEL PEAK 20(12P12.1) WILD-TYPE   13  267
                        clus
vv                       DEL PEAK 20(12P12.1) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           68
                        clus
vv                       DEL PEAK 20(12P12.1) WILD-TYPE
  HISPANIC OR LATINO                                 13
  NOT HISPANIC OR LATINO                            267
[1] 2 2
[1] FALSE

Clustering(48) Variable = DEL PEAK 21(12Q24.33) MUTATION ANALYSIS
D48V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 21(12Q24.33) MUTATED    31  25
  DEL PEAK 21(12Q24.33) WILD-TYPE 204 104
  DEL PEAK 21(12Q24.33) MUTATED DEL PEAK 21(12Q24.33) WILD-TYPE 
                             56                             308 
  DEL PEAK 21(12Q24.33) MUTATED DEL PEAK 21(12Q24.33) WILD-TYPE 
                             25                             104 
$`DEL PEAK 21(12Q24.33) MUTATED`
TCGA-BC-A5W4 TCGA-DD-A4NI TCGA-FV-A3I1 TCGA-G3-A25W TCGA-ZP-A9D1 TCGA-2Y-A9GS 
       17.98        26.83         8.12        30.74         0.69        23.80 
TCGA-2Y-A9GY TCGA-2Y-A9H2 TCGA-2Y-A9H8 TCGA-3K-AAZ8 TCGA-BC-A217 TCGA-CC-5260 
       24.89        56.91        20.81        13.02        45.93         2.86 
TCGA-CC-A1HT TCGA-CC-A3MA TCGA-CC-A3MC TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IL 
        3.32         9.96        11.93         9.99         8.94         9.14 
TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EL TCGA-DD-A39X TCGA-DD-A39Z TCGA-DD-A3A0 
       45.11        49.15        13.64        55.69        19.76        25.81 
TCGA-DD-A3A5 TCGA-DD-A3A9 TCGA-DD-A4NJ TCGA-DD-A4NO TCGA-DD-AAC8 TCGA-DD-AACA 
      102.74        30.61        30.51        73.81         0.53        75.65 
TCGA-DD-AACE TCGA-DD-AACG TCGA-DD-AACN TCGA-DD-AACU TCGA-DD-AAD3 TCGA-DD-AAD8 
       71.80        15.42        42.81        51.52        42.58        40.08 
TCGA-DD-AADF TCGA-DD-AADM TCGA-DD-AADY TCGA-DD-AAE3 TCGA-DD-AAEK TCGA-DD-AAVU 
        3.78         0.39        18.25        18.61        35.08        72.39 
TCGA-ED-A459 TCGA-ED-A82E TCGA-ED-A97K TCGA-EP-A2KC TCGA-FV-A496 TCGA-G3-A25Y 
       29.92        13.41         0.20         0.62         0.33        14.86 
TCGA-MI-A75G TCGA-NI-A8LF TCGA-RC-A6M4 TCGA-RC-A6M5 TCGA-RC-A6M6 TCGA-RC-A7SB 
       22.95        26.27         0.72         0.49         0.30        19.33 
TCGA-RC-A7SK TCGA-XR-A8TD 
       15.52        33.86 

$`DEL PEAK 21(12Q24.33) WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 
       83.24        11.74        38.40         8.61        69.57         5.03 
TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-AADV TCGA-DD-AAE7 TCGA-DD-AAE8 
       36.66         0.36        90.28        18.87        21.17        21.83 
TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-ES-A2HS TCGA-FV-A3R2 TCGA-FV-A4ZP 
       18.90        23.64         9.96        22.62         6.38        81.73 
TCGA-G3-A3CG TCGA-G3-A6UC TCGA-G3-A7M9 TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-KR-A7K7 
       22.13        22.06         1.84        20.75         2.14        31.27 
TCGA-LG-A6GG TCGA-MI-A75H TCGA-T1-A6J8 TCGA-UB-A7MF TCGA-UB-AA0V TCGA-XR-A8TG 
       12.72        24.56         0.76         7.04        10.32        29.52 
TCGA-ZS-A9CE TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GZ 
       40.80        53.39        63.75        41.79        80.28        27.88 
TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H3 TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H9 
      120.82        40.41        49.84        47.74        18.25        22.92 
TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C 
        1.18         8.55        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-A10W TCGA-BC-A10X TCGA-BC-A10Y 
       46.78        27.52        27.52         2.99        25.32        23.38 
TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A69I 
        1.12        44.42         0.26        22.36        14.60        12.72 
TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5261 
       18.48        44.81        13.45         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-A4NA 
       70.06        17.59        20.12       107.11        13.78        33.14 
TCGA-DD-A4NB TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN 
       32.52        30.97        30.15        39.78        56.25        29.56 
TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A 
      108.76        12.26         0.30        80.75        78.84        23.93 
TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G 
        9.30        23.05        22.78         1.45        35.67       114.35 
TCGA-DD-AA3A TCGA-DD-AAC9 TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACF 
       13.48        11.41        76.41        55.40        12.53        12.00 
TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM 
        6.41        53.19        69.11         0.30         3.52        58.16 
TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACV 
       61.68        13.64        14.20        59.31        51.35        50.33 
TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 
       46.82         5.59        47.67         5.62         4.50        18.54 
TCGA-DD-AAD2 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC 
       21.63        44.22        22.09        40.54        40.83        13.97 
TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK 
       40.47        39.52        37.64        35.67        35.05        34.49 
TCGA-DD-AADL TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR 
       20.91        29.52        14.89        15.06        14.33        66.67 
TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 
       15.58        18.21        19.30        18.25        18.15        20.98 
TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE 
       19.99         4.64        23.74        15.72        25.08        26.63 
TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS 
       25.78        50.33        90.48        89.69        82.62        59.93 
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        60.99        53.69        26.93        28.08        13.91 
TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO 
       13.35         9.73         0.20        12.82         0.20        14.04 
TCGA-ED-A7XP TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
       13.15        13.35         1.84        18.74        19.99        20.61 
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-A4ZQ TCGA-G3-A25S TCGA-G3-A25T 
       27.88        12.03         0.03         0.39        13.68        51.06 
TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25X TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI 
       53.79        28.27        58.49        21.53        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-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        11.64         2.14 
TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 
       11.87        28.90         1.02         2.20         2.99        37.71 
TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A9QC 
       17.06        16.83        11.80        27.25        29.79        13.97 
TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO 
       12.03         9.57        16.67        20.71         7.53        10.85 
TCGA-NI-A4U2 TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SF 
       58.88        17.69        21.01         3.09        21.04        19.04 
TCGA-RC-A7SH TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD 
       15.39        36.10        27.88        19.76        16.44         1.71 
TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA44 
       15.98        10.75        11.34         0.99        12.99        20.22 
TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TE TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CV 
       24.85        18.28        30.41        22.78        13.55        35.77 
TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD 
       25.71        23.21        35.87        25.15        12.99        45.57 
TCGA-ZS-A9CF TCGA-ZS-A9CG 
       79.30        11.21 

  DEL PEAK 21(12Q24.33) MUTATED DEL PEAK 21(12Q24.33) WILD-TYPE 
                           0.20                            0.03 
  DEL PEAK 21(12Q24.33) MUTATED DEL PEAK 21(12Q24.33) WILD-TYPE 
                         102.74                          120.82 
  DEL PEAK 21(12Q24.33) MUTATED DEL PEAK 21(12Q24.33) WILD-TYPE 
                         19.545                          19.890 
[1] "0.2 - 102.7 (19.5)" "0.0 - 120.8 (19.9)"
[1] "hr=" "1.4"
D48V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE III STAGE IIIA
  DEL PEAK 21(12Q24.33) MUTATED        20       16         2         10
  DEL PEAK 21(12Q24.33) WILD-TYPE     153       71         1         52
                                 vv
clus                              STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 21(12Q24.33) MUTATED            4          1        1         1
  DEL PEAK 21(12Q24.33) WILD-TYPE          5          6        1         0
                                 vv
clus                              STAGE IVB
  DEL PEAK 21(12Q24.33) MUTATED           1
  DEL PEAK 21(12Q24.33) WILD-TYPE         1
D48V3, multiclass
            clus
vv           DEL PEAK 21(12Q24.33) MUTATED DEL PEAK 21(12Q24.33) WILD-TYPE
  STAGE I                               20                             153
  STAGE II                              16                              71
  STAGE III                              2                               1
  STAGE IIIA                            10                              52
  STAGE IIIB                             4                               5
  STAGE IIIC                             1                               6
  STAGE IV                               1                               1
  STAGE IVA                              1                               0
  STAGE IVB                              1                               1
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               T1  T2  T3  T4
  DEL PEAK 21(12Q24.33) MUTATED    23  18  15   3
  DEL PEAK 21(12Q24.33) WILD-TYPE 160  77  62   9
D48V4, multiclass
    clus
vv   DEL PEAK 21(12Q24.33) MUTATED DEL PEAK 21(12Q24.33) WILD-TYPE
  T1                            23                             160
  T2                            18                              77
  T3                            15                              62
  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 21(12Q24.33) MUTATED    42   1
  DEL PEAK 21(12Q24.33) WILD-TYPE 212   2
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 21(12Q24.33) MUTATED     42    1
  DEL PEAK 21(12Q24.33) WILD-TYPE  212    2
   clus
vv  DEL PEAK 21(12Q24.33) MUTATED DEL PEAK 21(12Q24.33) WILD-TYPE
  0                            42                             212
  1                             1                               2
[1] 2 2
[1] FALSE
D48V6, binary
                                 cls
clus                                0   1
  DEL PEAK 21(12Q24.33) MUTATED    47   2
  DEL PEAK 21(12Q24.33) WILD-TYPE 219   2
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 21(12Q24.33) MUTATED     47    2
  DEL PEAK 21(12Q24.33) WILD-TYPE  219    2
   clus
vv  DEL PEAK 21(12Q24.33) MUTATED DEL PEAK 21(12Q24.33) WILD-TYPE
  0                            47                             219
  1                             2                               2
[1] 2 2
[1] FALSE
D48V7, binary
                                 cls
clus                                0   1
  DEL PEAK 21(12Q24.33) MUTATED    24  35
  DEL PEAK 21(12Q24.33) WILD-TYPE  94 217
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 21(12Q24.33) MUTATED     24   35
  DEL PEAK 21(12Q24.33) WILD-TYPE   94  217
        clus
vv       DEL PEAK 21(12Q24.33) MUTATED DEL PEAK 21(12Q24.33) WILD-TYPE
  FEMALE                            24                              94
  MALE                              35                             217
[1] 2 2
[1] FALSE
D48V8, binary
                                 cls
clus                                0   1
  DEL PEAK 21(12Q24.33) MUTATED    50   1
  DEL PEAK 21(12Q24.33) WILD-TYPE 288   8
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 21(12Q24.33) MUTATED     50    1
  DEL PEAK 21(12Q24.33) WILD-TYPE  288    8
     clus
vv    DEL PEAK 21(12Q24.33) MUTATED DEL PEAK 21(12Q24.33) WILD-TYPE
  NO                             50                             288
  YES                             1                               8
[1] 2 2
[1] FALSE
                                 vv
clus                              FIBROLAMELLAR CARCINOMA
  DEL PEAK 21(12Q24.33) MUTATED                         1
  DEL PEAK 21(12Q24.33) WILD-TYPE                       2
                                 vv
clus                              HEPATOCELLULAR CARCINOMA
  DEL PEAK 21(12Q24.33) MUTATED                         57
  DEL PEAK 21(12Q24.33) WILD-TYPE                      303
                                 vv
clus                              HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK 21(12Q24.33) MUTATED                                  1
  DEL PEAK 21(12Q24.33) WILD-TYPE                                6
D48V9, multiclass
                                  clus
vv                                 DEL PEAK 21(12Q24.33) MUTATED
  FIBROLAMELLAR CARCINOMA                                      1
  HEPATOCELLULAR CARCINOMA                                    57
  HEPATOCHOLANGIOCARCINOMA (MIXED)                             1
                                  clus
vv                                 DEL PEAK 21(12Q24.33) 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 21(12Q24.33) MUTATED    52   3   0   3
  DEL PEAK 21(12Q24.33) WILD-TYPE 272  14   1  18
D48V10, multiclass
    clus
vv   DEL PEAK 21(12Q24.33) MUTATED DEL PEAK 21(12Q24.33) WILD-TYPE
  R0                            52                             272
  R1                             3                              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 21(12Q24.33) MUTATED                                  1    28
  DEL PEAK 21(12Q24.33) WILD-TYPE                                1   130
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 21(12Q24.33) MUTATED                           3    26
  DEL PEAK 21(12Q24.33) WILD-TYPE                        14   157
D48V11, multiclass
                                  clus
vv                                 DEL PEAK 21(12Q24.33) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                       28
  BLACK OR AFRICAN AMERICAN                                    3
  WHITE                                                       26
                                  clus
vv                                 DEL PEAK 21(12Q24.33) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               1
  ASIAN                                                        130
  BLACK OR AFRICAN AMERICAN                                     14
  WHITE                                                        157
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V12, binary
                                 cls
clus                                0   1
  DEL PEAK 21(12Q24.33) MUTATED     3  52
  DEL PEAK 21(12Q24.33) WILD-TYPE  13 283
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 21(12Q24.33) MUTATED      3   52
  DEL PEAK 21(12Q24.33) WILD-TYPE   13  283
                        clus
vv                       DEL PEAK 21(12Q24.33) MUTATED
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                            52
                        clus
vv                       DEL PEAK 21(12Q24.33) WILD-TYPE
  HISPANIC OR LATINO                                  13
  NOT HISPANIC OR LATINO                             283
[1] 2 2
[1] FALSE

Clustering(49) Variable = DEL PEAK 22(13Q14.2) MUTATION ANALYSIS
D49V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 22(13Q14.2) MUTATED   105  71
  DEL PEAK 22(13Q14.2) WILD-TYPE 130  58
  DEL PEAK 22(13Q14.2) MUTATED DEL PEAK 22(13Q14.2) WILD-TYPE 
                           176                            188 
  DEL PEAK 22(13Q14.2) MUTATED DEL PEAK 22(13Q14.2) WILD-TYPE 
                            71                             58 
$`DEL PEAK 22(13Q14.2) MUTATED`
TCGA-2Y-A9GV TCGA-4R-AA8I TCGA-BC-A112 TCGA-BC-A5W4 TCGA-DD-AADV TCGA-DD-AAE8 
       83.24         8.61         5.03        17.98        18.87        21.83 
TCGA-DD-AAEA TCGA-DD-AAEG TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-UB-A7MF TCGA-XR-A8TG 
       18.90        23.64         8.12         6.38         7.04        29.52 
TCGA-ZS-A9CE TCGA-2Y-A9GS TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H2 
       40.80        23.80        24.89        27.88       120.82        56.91 
TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-2Y-A9HA TCGA-3K-AAZ8 TCGA-5C-A9VG 
       47.74        18.25        20.81         1.18        13.02        10.78 
TCGA-5C-A9VH TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10W TCGA-BC-A10Y 
       10.59        37.32        10.13        27.52         2.99        23.38 
TCGA-BC-A10Z TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A8YO 
        1.12        45.93         0.26        22.36        14.60        18.48 
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-A3MC TCGA-CC-A5UC 
        3.35         3.32         9.86         9.96        11.93        11.41 
TCGA-CC-A5UE TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IK 
        8.94        21.34         9.83        13.12        12.56         8.61 
TCGA-CC-A7IL TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A113 
        9.14        11.31         9.17         6.94         8.15        79.73 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A11A TCGA-DD-A11C 
       37.78        83.57        53.33       113.00         2.60        21.76 
TCGA-DD-A1EF TCGA-DD-A1EI TCGA-DD-A1EK TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A3A0 
       12.95         6.02        18.35        55.69         5.62        25.81 
TCGA-DD-A3A5 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NN 
      102.74        30.61        33.14        30.15        30.51        29.56 
TCGA-DD-A4NO TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G 
       73.81        12.26         0.30         1.45        35.67       114.35 
TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI 
       13.48         0.53        12.00        15.42         6.41        53.19 
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-AACU TCGA-DD-AACV TCGA-DD-AAD1 TCGA-DD-AAD8 TCGA-DD-AADC 
       59.31        51.52        50.33        18.54        40.08        13.97 
TCGA-DD-AADD TCGA-DD-AADF TCGA-DD-AADI TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM 
       40.47         3.78        35.67        34.49        20.91         0.39 
TCGA-DD-AADO TCGA-DD-AADR TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE2 
       14.89        66.67        19.30        18.25        18.25        20.98 
TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEI TCGA-DD-AAEK 
       18.61        19.99        25.08        26.63        50.33        35.08 
TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVV TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A66Y 
       90.48        89.69        80.71        29.92        26.93         9.73 
TCGA-ED-A7PX TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-EP-A3RK TCGA-FV-A3I0 
        0.20         0.20        14.04        13.15        11.93        27.88 
TCGA-FV-A495 TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A3CH 
        0.03        13.68        51.06        58.49        14.86        25.64 
TCGA-G3-A5SI TCGA-G3-A5SM TCGA-G3-A7M5 TCGA-G3-A7M6 TCGA-G3-AAUZ TCGA-G3-AAV4 
       25.25        17.10        14.70        20.78        15.78         0.89 
TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-K7-A5RG TCGA-KR-A7K2 
       11.87        28.90         1.02         2.20        17.06        27.25 
TCGA-KR-A7K8 TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A8JO TCGA-NI-A8LF TCGA-PD-A5DF 
       29.79        22.95        20.71        10.85        26.27        21.01 
TCGA-RC-A6M4 TCGA-RC-A6M5 TCGA-RC-A7S9 TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK 
        0.72         0.49        21.04        19.04        15.39        15.52 
TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MC TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WX-AA44 
       36.10        27.88        16.44        10.75        11.34        20.22 
TCGA-WX-AA47 TCGA-XR-A8TD TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CY TCGA-ZP-A9CZ 
       18.28        33.86        22.78        13.55        25.71        23.21 
TCGA-ZP-A9D0 TCGA-ZS-A9CG 
       35.87        11.21 

$`DEL PEAK 22(13Q14.2) WILD-TYPE`
TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-BC-A110 TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND 
       11.74        38.40        69.57        36.66         0.36        90.28 
TCGA-DD-A4NI TCGA-DD-AAE7 TCGA-EP-A3JL TCGA-ES-A2HS TCGA-FV-A4ZP TCGA-G3-A25W 
       26.83        21.17         9.96        22.62        81.73        30.74 
TCGA-G3-A3CG TCGA-G3-A6UC TCGA-G3-A7M9 TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-KR-A7K7 
       22.13        22.06         1.84        20.75         2.14        31.27 
TCGA-LG-A6GG TCGA-MI-A75H TCGA-T1-A6J8 TCGA-UB-AA0V TCGA-ZP-A9D1 TCGA-2Y-A9GT 
       12.72        24.56         0.76        10.32         0.69        53.39 
TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9H1 TCGA-2Y-A9H3 TCGA-2Y-A9H9 
       63.75        41.79        80.28        40.41        49.84        22.92 
TCGA-2Y-A9HB TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4072 
        8.55         0.66        17.10        14.76         1.51        48.99 
TCGA-BC-4073 TCGA-BC-A10S TCGA-BC-A10U TCGA-BC-A10X TCGA-BC-A216 TCGA-BC-A69I 
       27.91        46.78        27.52        25.32        44.42        12.72 
TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-CC-A3MB TCGA-CC-A5UD TCGA-CC-A7IE TCGA-CC-A7IH 
       44.81        13.45        10.36         9.99         7.13        12.00 
TCGA-CC-A8HT TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA 
        4.60         7.33         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-A1EJ TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39Z TCGA-DD-A3A1 
       33.04        13.64        21.14        27.19        19.76         7.66 
TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A4NB 
       70.06        17.59        20.12       107.11        13.78        32.52 
TCGA-DD-A4NF TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NP TCGA-DD-A4NS TCGA-DD-A4NV 
       30.97        39.78        56.25       108.76        80.75        78.84 
TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-AAC9 TCGA-DD-AACA 
       23.93         9.30        23.05        22.78        11.41        75.65 
TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACJ TCGA-DD-AACK 
       76.41        55.40        12.53        71.80        69.11         0.30 
TCGA-DD-AACT TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD0 
       51.35        46.82         5.59        47.67         5.62         4.50 
TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AADA TCGA-DD-AADB 
       21.63        42.58        44.22        22.09        40.54        40.83 
TCGA-DD-AADE TCGA-DD-AADG TCGA-DD-AADJ TCGA-DD-AADN TCGA-DD-AADP TCGA-DD-AADQ 
       39.52        37.64        35.05        29.52        15.06        14.33 
TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AAE1 TCGA-DD-AAE6 TCGA-DD-AAE9 TCGA-DD-AAEB 
       15.58        18.21        18.15         4.64        23.74        15.72 
TCGA-DD-AAEH TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVX 
       25.78        82.62        59.93        72.39        76.18        56.48 
TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 
       64.77        62.47        66.25        65.39        60.99        53.69 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A7PY TCGA-ED-A82E TCGA-ED-A8O5 
       28.08        13.91        13.35        12.82        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-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3R3 
        0.62        14.40        60.89        23.97        19.10        12.03 
TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25Z TCGA-G3-A3CI 
        0.33         0.39        53.79        28.27        21.53         5.92 
TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A7M7 TCGA-G3-A7M8 
       19.53        19.23        22.95        20.42        11.87        14.14 
TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV5 TCGA-G3-AAV6 
       15.65        11.80        12.23        13.55        11.64         2.14 
TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-LG-A9QC TCGA-LG-A9QD 
        2.99        37.71        16.83        11.80        13.97        12.03 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MR-A520 TCGA-NI-A4U2 TCGA-O8-A75V TCGA-QA-A7B7 
        9.57        16.67         7.53        58.88        17.69         3.09 
TCGA-RC-A6M6 TCGA-RC-A7SB TCGA-UB-A7MB TCGA-UB-A7MD TCGA-UB-A7ME TCGA-WQ-A9G7 
        0.30        19.33        19.76         1.71        15.98         0.99 
TCGA-WQ-AB4B TCGA-WX-AA46 TCGA-XR-A8TE TCGA-ZP-A9CV TCGA-ZP-A9D2 TCGA-ZP-A9D4 
       12.99        24.85        30.41        35.77        25.15        12.99 
TCGA-ZS-A9CD TCGA-ZS-A9CF 
       45.57        79.30 

  DEL PEAK 22(13Q14.2) MUTATED DEL PEAK 22(13Q14.2) WILD-TYPE 
                          0.03                           0.20 
  DEL PEAK 22(13Q14.2) MUTATED DEL PEAK 22(13Q14.2) WILD-TYPE 
                        120.82                         108.76 
  DEL PEAK 22(13Q14.2) MUTATED DEL PEAK 22(13Q14.2) WILD-TYPE 
                        18.415                         21.155 
[1] "0.0 - 120.8 (18.4)" "0.2 - 108.8 (21.2)"
[1] "hr=" "1.5"
D49V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IIIA
  DEL PEAK 22(13Q14.2) MUTATED        75       49         1         30
  DEL PEAK 22(13Q14.2) WILD-TYPE      98       38         2         32
                                vv
clus                             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 22(13Q14.2) MUTATED            5          4        0         1
  DEL PEAK 22(13Q14.2) WILD-TYPE          4          3        2         0
                                vv
clus                             STAGE IVB
  DEL PEAK 22(13Q14.2) MUTATED           2
  DEL PEAK 22(13Q14.2) WILD-TYPE         0
D49V3, multiclass
            clus
vv           DEL PEAK 22(13Q14.2) MUTATED DEL PEAK 22(13Q14.2) WILD-TYPE
  STAGE I                              75                             98
  STAGE II                             49                             38
  STAGE III                             1                              2
  STAGE IIIA                           30                             32
  STAGE IIIB                            5                              4
  STAGE IIIC                            4                              3
  STAGE IV                              0                              2
  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                              T1  T2  T3  T4
  DEL PEAK 22(13Q14.2) MUTATED    80  53  36  10
  DEL PEAK 22(13Q14.2) WILD-TYPE 103  42  41   2
D49V4, multiclass
    clus
vv   DEL PEAK 22(13Q14.2) MUTATED DEL PEAK 22(13Q14.2) WILD-TYPE
  T1                           80                            103
  T2                           53                             42
  T3                           36                             41
  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"
D49V5, binary
                                cls
clus                               0   1
  DEL PEAK 22(13Q14.2) MUTATED   126   2
  DEL PEAK 22(13Q14.2) WILD-TYPE 128   1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 22(13Q14.2) MUTATED    126    2
  DEL PEAK 22(13Q14.2) WILD-TYPE  128    1
   clus
vv  DEL PEAK 22(13Q14.2) MUTATED DEL PEAK 22(13Q14.2) WILD-TYPE
  0                          126                            128
  1                            2                              1
[1] 2 2
[1] FALSE
D49V6, binary
                                cls
clus                               0   1
  DEL PEAK 22(13Q14.2) MUTATED   130   2
  DEL PEAK 22(13Q14.2) WILD-TYPE 136   2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 22(13Q14.2) MUTATED    130    2
  DEL PEAK 22(13Q14.2) WILD-TYPE  136    2
   clus
vv  DEL PEAK 22(13Q14.2) MUTATED DEL PEAK 22(13Q14.2) WILD-TYPE
  0                          130                            136
  1                            2                              2
[1] 2 2
[1] FALSE
D49V7, binary
                                cls
clus                               0   1
  DEL PEAK 22(13Q14.2) MUTATED    65 114
  DEL PEAK 22(13Q14.2) WILD-TYPE  53 138
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 22(13Q14.2) MUTATED     65  114
  DEL PEAK 22(13Q14.2) WILD-TYPE   53  138
        clus
vv       DEL PEAK 22(13Q14.2) MUTATED DEL PEAK 22(13Q14.2) WILD-TYPE
  FEMALE                           65                             53
  MALE                            114                            138
[1] 2 2
[1] FALSE
D49V8, binary
                                cls
clus                               0   1
  DEL PEAK 22(13Q14.2) MUTATED   163   5
  DEL PEAK 22(13Q14.2) WILD-TYPE 175   4
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 22(13Q14.2) MUTATED    163    5
  DEL PEAK 22(13Q14.2) WILD-TYPE  175    4
     clus
vv    DEL PEAK 22(13Q14.2) MUTATED DEL PEAK 22(13Q14.2) WILD-TYPE
  NO                           163                            175
  YES                            5                              4
[1] 2 2
[1] FALSE
                                vv
clus                             FIBROLAMELLAR CARCINOMA
  DEL PEAK 22(13Q14.2) MUTATED                         2
  DEL PEAK 22(13Q14.2) WILD-TYPE                       1
                                vv
clus                             HEPATOCELLULAR CARCINOMA
  DEL PEAK 22(13Q14.2) MUTATED                        173
  DEL PEAK 22(13Q14.2) WILD-TYPE                      187
                                vv
clus                             HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK 22(13Q14.2) MUTATED                                  4
  DEL PEAK 22(13Q14.2) WILD-TYPE                                3
D49V9, multiclass
                                  clus
vv                                 DEL PEAK 22(13Q14.2) MUTATED
  FIBROLAMELLAR CARCINOMA                                     2
  HEPATOCELLULAR CARCINOMA                                  173
  HEPATOCHOLANGIOCARCINOMA (MIXED)                            4
                                  clus
vv                                 DEL PEAK 22(13Q14.2) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                       1
  HEPATOCELLULAR CARCINOMA                                    187
  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(13Q14.2) MUTATED   153   9   0  13
  DEL PEAK 22(13Q14.2) WILD-TYPE 171   8   1   8
D49V10, multiclass
    clus
vv   DEL PEAK 22(13Q14.2) MUTATED DEL PEAK 22(13Q14.2) WILD-TYPE
  R0                          153                            171
  R1                            9                              8
  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 22(13Q14.2) MUTATED                                  1    87
  DEL PEAK 22(13Q14.2) WILD-TYPE                                1    71
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 22(13Q14.2) MUTATED                           9    80
  DEL PEAK 22(13Q14.2) WILD-TYPE                         8   103
D49V11, multiclass
                                  clus
vv                                 DEL PEAK 22(13Q14.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                      87
  BLACK OR AFRICAN AMERICAN                                   9
  WHITE                                                      80
                                  clus
vv                                 DEL PEAK 22(13Q14.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        71
  BLACK OR AFRICAN AMERICAN                                     8
  WHITE                                                       103
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V12, binary
                                cls
clus                               0   1
  DEL PEAK 22(13Q14.2) MUTATED     9 162
  DEL PEAK 22(13Q14.2) WILD-TYPE   7 173
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 22(13Q14.2) MUTATED      9  162
  DEL PEAK 22(13Q14.2) WILD-TYPE    7  173
                        clus
vv                       DEL PEAK 22(13Q14.2) MUTATED
  HISPANIC OR LATINO                                9
  NOT HISPANIC OR LATINO                          162
                        clus
vv                       DEL PEAK 22(13Q14.2) WILD-TYPE
  HISPANIC OR LATINO                                  7
  NOT HISPANIC OR LATINO                            173
[1] 2 2
[1] FALSE

Clustering(50) Variable = DEL PEAK 23(14Q23.3) MUTATION ANALYSIS
D50V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 23(14Q23.3) MUTATED    79  49
  DEL PEAK 23(14Q23.3) WILD-TYPE 156  80
  DEL PEAK 23(14Q23.3) MUTATED DEL PEAK 23(14Q23.3) WILD-TYPE 
                           128                            236 
  DEL PEAK 23(14Q23.3) MUTATED DEL PEAK 23(14Q23.3) WILD-TYPE 
                            49                             80 
$`DEL PEAK 23(14Q23.3) MUTATED`
TCGA-BC-A112 TCGA-DD-A4NI TCGA-DD-AADV TCGA-DD-AAE8 TCGA-DD-AAEG TCGA-FV-A4ZP 
        5.03        26.83        18.87        21.83        23.64        81.73 
TCGA-G3-A7M9 TCGA-KR-A7K7 TCGA-UB-A7MF TCGA-XR-A8TG TCGA-2Y-A9GS TCGA-2Y-A9GX 
        1.84        31.27         7.04        29.52        23.80        80.28 
TCGA-2Y-A9GY TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H4 TCGA-2Y-A9H9 
       24.89        40.41        56.91        49.84        47.74        22.92 
TCGA-5C-A9VG TCGA-5C-AAPD TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10Z TCGA-BC-A216 
       10.78         0.66        27.91        37.32         1.12        44.42 
TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BD-A3EP TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 
        0.26        22.36        13.45         4.24         2.86         3.19 
TCGA-CC-5264 TCGA-CC-A1HT TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UE 
        3.35         3.32         9.96        10.36        11.93         8.94 
TCGA-CC-A7IE TCGA-CC-A7IG TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A8HT 
        7.13         9.83        13.12        12.56         8.61         4.60 
TCGA-CC-A8HU TCGA-CC-A8HV TCGA-DD-A113 TCGA-DD-A115 TCGA-DD-A118 TCGA-DD-A11A 
       11.31         9.17        79.73        83.57       113.00         2.60 
TCGA-DD-A11C TCGA-DD-A1E9 TCGA-DD-A1EG TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EL 
       21.76        90.71        45.11         6.02        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-A4NO TCGA-DD-A4NQ TCGA-DD-A73F TCGA-DD-AA3A TCGA-DD-AAC8 
       30.15        73.81        12.26        35.67        13.48         0.53 
TCGA-DD-AACA TCGA-DD-AACE TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACN TCGA-DD-AACS 
       75.65        71.80        15.42         6.41        42.81        59.31 
TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACX TCGA-DD-AACZ TCGA-DD-AAD5 TCGA-DD-AAD6 
       51.52        50.33         5.59         5.62        44.22        22.09 
TCGA-DD-AADB TCGA-DD-AADD TCGA-DD-AADF TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN 
       40.83        40.47         3.78        20.91         0.39        29.52 
TCGA-DD-AADO TCGA-DD-AADR TCGA-DD-AADW TCGA-DD-AAE0 TCGA-DD-AAE3 TCGA-DD-AAE6 
       14.89        66.67        19.30        18.25        18.61         4.64 
TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAVP TCGA-DD-AAVU TCGA-DD-AAVV TCGA-DD-AAW3 
       25.08        26.63        90.48        72.39        80.71        53.69 
TCGA-ED-A459 TCGA-ED-A7PX TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O6 
       29.92         0.20         0.20        13.15        13.41         1.84 
TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A2KB TCGA-EP-A3RK TCGA-FV-A3I0 TCGA-G3-A25S 
        0.20        18.74        19.59        11.93        27.88        13.68 
TCGA-G3-A25X TCGA-G3-A3CH TCGA-G3-A5SM TCGA-G3-AAV1 TCGA-G3-AAV7 TCGA-GJ-A6C0 
       58.49        25.64        17.10        11.80        11.87         1.02 
TCGA-K7-A5RG TCGA-NI-A8LF TCGA-PD-A5DF TCGA-RC-A6M5 TCGA-RC-A7SF TCGA-RC-A7SH 
       17.06        26.27        21.01         0.49        19.04        15.39 
TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MC TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA44 
       15.52        36.10        16.44         0.99        12.99        20.22 
TCGA-XR-A8TF TCGA-ZP-A9D2 
       22.78        25.15 

$`DEL PEAK 23(14Q23.3) WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A5W4 
       83.24        11.74        38.40         8.61        69.57        17.98 
TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-AAE7 TCGA-DD-AAEA TCGA-EP-A3JL 
       36.66         0.36        90.28        21.17        18.90         9.96 
TCGA-ES-A2HS TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC 
       22.62         8.12         6.38        30.74        22.13        22.06 
TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-LG-A6GG TCGA-MI-A75H TCGA-T1-A6J8 TCGA-UB-AA0V 
       20.75         2.14        12.72        24.56         0.76        10.32 
TCGA-ZP-A9D1 TCGA-ZS-A9CE TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GZ 
        0.69        40.80        53.39        63.75        41.79        27.88 
TCGA-2Y-A9H0 TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 
      120.82        18.25        20.81         1.18         8.55        13.02 
TCGA-5C-A9VH TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-A10R 
       10.59        17.10        14.76         1.51        48.99        10.13 
TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y 
       46.78        27.52        27.52         2.99        25.32        23.38 
TCGA-BC-A217 TCGA-BC-A69H TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BW-A5NO 
       45.93        14.60        12.72        18.48        44.81         0.66 
TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A3M9 TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A7IF 
        3.39         4.24         9.86        11.41         9.99        21.34 
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-A119 TCGA-DD-A11B TCGA-DD-A11D TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC 
        7.33         0.46        51.29        79.40        66.31        19.79 
TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EK TCGA-DD-A39V 
       75.65        11.47        12.95        49.15        18.35        21.14 
TCGA-DD-A39W TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 
       27.19        19.76        25.81        70.06        17.59        20.12 
TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A4NA TCGA-DD-A4NF TCGA-DD-A4NJ TCGA-DD-A4NK 
      102.74       107.11        33.14        30.97        30.51        39.78 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NP TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV 
       56.25        29.56       108.76         0.30        80.75        78.84 
TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73G 
       23.93         9.30        23.05        22.78         1.45       114.35 
TCGA-DD-AAC9 TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACF TCGA-DD-AACI 
       11.41        76.41        55.40        12.53        12.00        53.19 
TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACO TCGA-DD-AACP 
       69.11         0.30         3.52        58.16        61.68        13.64 
TCGA-DD-AACQ TCGA-DD-AACT TCGA-DD-AACW TCGA-DD-AACY TCGA-DD-AAD0 TCGA-DD-AAD1 
       14.20        51.35        46.82        47.67         4.50        18.54 
TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADC TCGA-DD-AADE 
       21.63        42.58        40.08        40.54        13.97        39.52 
TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADP TCGA-DD-AADQ 
       37.64        35.67        35.05        34.49        15.06        14.33 
TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADY TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE4 
       15.58        18.21        18.25        18.15        20.98        19.99 
TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVQ 
       23.74        15.72        25.78        50.33        35.08        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-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 
       66.25        65.39        60.99        26.93        28.08        13.91 
TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PY TCGA-ED-A7XO TCGA-ED-A8O5 TCGA-EP-A26S 
       13.35         9.73        12.82        14.04        13.35        19.99 
TCGA-EP-A2KA TCGA-EP-A2KC TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR 
       20.61         0.62        14.40        60.89        23.97        19.10 
TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25U 
       12.03         0.03         0.33         0.39        51.06        53.79 
TCGA-G3-A25V TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
       28.27        14.86        21.53         5.92        19.53        19.23 
TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M7 
       25.25        22.95        20.42        14.70        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-AAV6 TCGA-GJ-A3OU TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 
       11.64         2.14        28.90         2.20         2.99        37.71 
TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD 
       16.83        11.80        27.25        29.79        13.97        12.03 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO 
        9.57        16.67        22.95        20.71         7.53        10.85 
TCGA-NI-A4U2 TCGA-O8-A75V TCGA-QA-A7B7 TCGA-RC-A6M4 TCGA-RC-A6M6 TCGA-RC-A7S9 
       58.88        17.69         3.09         0.72         0.30        21.04 
TCGA-RC-A7SB TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0U 
       19.33        27.88        19.76         1.71        15.98        10.75 
TCGA-WJ-A86L TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TD TCGA-XR-A8TE TCGA-YA-A8S7 
       11.34        24.85        18.28        33.86        30.41        13.55 
TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D4 TCGA-ZS-A9CD 
       35.77        25.71        23.21        35.87        12.99        45.57 
TCGA-ZS-A9CF TCGA-ZS-A9CG 
       79.30        11.21 

  DEL PEAK 23(14Q23.3) MUTATED DEL PEAK 23(14Q23.3) WILD-TYPE 
                          0.20                           0.03 
  DEL PEAK 23(14Q23.3) MUTATED DEL PEAK 23(14Q23.3) WILD-TYPE 
                        113.00                         120.82 
  DEL PEAK 23(14Q23.3) MUTATED DEL PEAK 23(14Q23.3) WILD-TYPE 
                        18.805                         20.270 
[1] "0.2 - 113.0 (18.8)" "0.0 - 120.8 (20.3)"
[1] "hr=" "1.2"
D50V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IIIA
  DEL PEAK 23(14Q23.3) MUTATED        56       34         0         25
  DEL PEAK 23(14Q23.3) WILD-TYPE     117       53         3         37
                                vv
clus                             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 23(14Q23.3) MUTATED            5          3        1         1
  DEL PEAK 23(14Q23.3) WILD-TYPE          4          4        1         0
                                vv
clus                             STAGE IVB
  DEL PEAK 23(14Q23.3) MUTATED           1
  DEL PEAK 23(14Q23.3) WILD-TYPE         1
D50V3, multiclass
            clus
vv           DEL PEAK 23(14Q23.3) MUTATED DEL PEAK 23(14Q23.3) WILD-TYPE
  STAGE I                              56                            117
  STAGE II                             34                             53
  STAGE III                             0                              3
  STAGE IIIA                           25                             37
  STAGE IIIB                            5                              4
  STAGE IIIC                            3                              4
  STAGE IV                              1                              1
  STAGE IVA                             1                              0
  STAGE IVB                             1                              1
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 23(14Q23.3) MUTATED    58  38  30   5
  DEL PEAK 23(14Q23.3) WILD-TYPE 125  57  47   7
D50V4, multiclass
    clus
vv   DEL PEAK 23(14Q23.3) MUTATED DEL PEAK 23(14Q23.3) WILD-TYPE
  T1                           58                            125
  T2                           38                             57
  T3                           30                             47
  T4                            5                              7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V5, binary
                                cls
clus                               0   1
  DEL PEAK 23(14Q23.3) MUTATED    96   2
  DEL PEAK 23(14Q23.3) WILD-TYPE 158   1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(14Q23.3) MUTATED     96    2
  DEL PEAK 23(14Q23.3) WILD-TYPE  158    1
   clus
vv  DEL PEAK 23(14Q23.3) MUTATED DEL PEAK 23(14Q23.3) WILD-TYPE
  0                           96                            158
  1                            2                              1
[1] 2 2
[1] FALSE
D50V6, binary
                                cls
clus                               0   1
  DEL PEAK 23(14Q23.3) MUTATED   102   2
  DEL PEAK 23(14Q23.3) WILD-TYPE 164   2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(14Q23.3) MUTATED    102    2
  DEL PEAK 23(14Q23.3) WILD-TYPE  164    2
   clus
vv  DEL PEAK 23(14Q23.3) MUTATED DEL PEAK 23(14Q23.3) WILD-TYPE
  0                          102                            164
  1                            2                              2
[1] 2 2
[1] FALSE
D50V7, binary
                                cls
clus                               0   1
  DEL PEAK 23(14Q23.3) MUTATED    38  93
  DEL PEAK 23(14Q23.3) WILD-TYPE  80 159
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(14Q23.3) MUTATED     38   93
  DEL PEAK 23(14Q23.3) WILD-TYPE   80  159
        clus
vv       DEL PEAK 23(14Q23.3) MUTATED DEL PEAK 23(14Q23.3) WILD-TYPE
  FEMALE                           38                             80
  MALE                             93                            159
[1] 2 2
[1] FALSE
D50V8, binary
                                cls
clus                               0   1
  DEL PEAK 23(14Q23.3) MUTATED   121   3
  DEL PEAK 23(14Q23.3) WILD-TYPE 217   6
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(14Q23.3) MUTATED    121    3
  DEL PEAK 23(14Q23.3) WILD-TYPE  217    6
     clus
vv    DEL PEAK 23(14Q23.3) MUTATED DEL PEAK 23(14Q23.3) WILD-TYPE
  NO                           121                            217
  YES                            3                              6
[1] 2 2
[1] FALSE
                                vv
clus                             FIBROLAMELLAR CARCINOMA
  DEL PEAK 23(14Q23.3) MUTATED                         2
  DEL PEAK 23(14Q23.3) WILD-TYPE                       1
                                vv
clus                             HEPATOCELLULAR CARCINOMA
  DEL PEAK 23(14Q23.3) MUTATED                        125
  DEL PEAK 23(14Q23.3) WILD-TYPE                      235
                                vv
clus                             HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK 23(14Q23.3) MUTATED                                  4
  DEL PEAK 23(14Q23.3) WILD-TYPE                                3
D50V9, multiclass
                                  clus
vv                                 DEL PEAK 23(14Q23.3) MUTATED
  FIBROLAMELLAR CARCINOMA                                     2
  HEPATOCELLULAR CARCINOMA                                  125
  HEPATOCHOLANGIOCARCINOMA (MIXED)                            4
                                  clus
vv                                 DEL PEAK 23(14Q23.3) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                       1
  HEPATOCELLULAR CARCINOMA                                    235
  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 23(14Q23.3) MUTATED   114   5   0   9
  DEL PEAK 23(14Q23.3) WILD-TYPE 210  12   1  12
D50V10, multiclass
    clus
vv   DEL PEAK 23(14Q23.3) MUTATED DEL PEAK 23(14Q23.3) WILD-TYPE
  R0                          114                            210
  R1                            5                             12
  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(14Q23.3) MUTATED                                  0    69
  DEL PEAK 23(14Q23.3) WILD-TYPE                                2    89
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 23(14Q23.3) MUTATED                           7    53
  DEL PEAK 23(14Q23.3) WILD-TYPE                        10   130
D50V11, multiclass
                                  clus
vv                                 DEL PEAK 23(14Q23.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                      69
  BLACK OR AFRICAN AMERICAN                                   7
  WHITE                                                      53
                                  clus
vv                                 DEL PEAK 23(14Q23.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              2
  ASIAN                                                        89
  BLACK OR AFRICAN AMERICAN                                    10
  WHITE                                                       130
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V12, binary
                                cls
clus                               0   1
  DEL PEAK 23(14Q23.3) MUTATED     7 117
  DEL PEAK 23(14Q23.3) WILD-TYPE   9 218
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(14Q23.3) MUTATED      7  117
  DEL PEAK 23(14Q23.3) WILD-TYPE    9  218
                        clus
vv                       DEL PEAK 23(14Q23.3) MUTATED
  HISPANIC OR LATINO                                7
  NOT HISPANIC OR LATINO                          117
                        clus
vv                       DEL PEAK 23(14Q23.3) WILD-TYPE
  HISPANIC OR LATINO                                  9
  NOT HISPANIC OR LATINO                            218
[1] 2 2
[1] FALSE

Clustering(51) Variable = DEL PEAK 24(14Q32.33) MUTATION ANALYSIS
D51V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 24(14Q32.33) MUTATED    84  46
  DEL PEAK 24(14Q32.33) WILD-TYPE 151  83
  DEL PEAK 24(14Q32.33) MUTATED DEL PEAK 24(14Q32.33) WILD-TYPE 
                            130                             234 
  DEL PEAK 24(14Q32.33) MUTATED DEL PEAK 24(14Q32.33) WILD-TYPE 
                             46                              83 
$`DEL PEAK 24(14Q32.33) MUTATED`
TCGA-2Y-A9H6 TCGA-BC-A112 TCGA-DD-A4NI TCGA-DD-AADV TCGA-DD-AAE8 TCGA-DD-AAEG 
       11.74         5.03        26.83        18.87        21.83        23.64 
TCGA-FV-A4ZP TCGA-G3-A7M9 TCGA-KR-A7K7 TCGA-UB-A7MF TCGA-2Y-A9GS TCGA-2Y-A9GX 
       81.73         1.84        31.27         7.04        23.80        80.28 
TCGA-2Y-A9GY TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H4 TCGA-2Y-A9H9 
       24.89        40.41        56.91        49.84        47.74        22.92 
TCGA-5C-A9VG TCGA-5C-AAPD TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10Z 
       10.78         0.66        37.32        10.13        27.52         1.12 
TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 
       45.93         0.26        22.36         4.24         2.86         3.19 
TCGA-CC-5264 TCGA-CC-A1HT TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UE 
        3.35         3.32         9.96        10.36        11.93         8.94 
TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV 
       13.12        12.56         8.61         4.60        11.31         9.17 
TCGA-DD-A113 TCGA-DD-A115 TCGA-DD-A11A TCGA-DD-A11C TCGA-DD-A1E9 TCGA-DD-A1EG 
       79.73        83.57         2.60        21.76        90.71        45.11 
TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A3A1 TCGA-DD-A3A7 
       33.04        13.64        55.69         5.62         7.66        13.78 
TCGA-DD-A3A9 TCGA-DD-A4NB TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NO TCGA-DD-A4NQ 
       30.61        32.52        30.15        30.51        73.81        12.26 
TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AACA TCGA-DD-AACE TCGA-DD-AACG 
       35.67       114.35        13.48        75.65        71.80        15.42 
TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACS TCGA-DD-AACU 
        6.41        53.19        42.81        61.68        59.31        51.52 
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-AADW TCGA-DD-AAE0 TCGA-DD-AAE6 TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEK 
       19.30        18.25         4.64        25.08        26.63        35.08 
TCGA-DD-AAVP TCGA-DD-AAVU TCGA-DD-AAVV TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A7PX 
       90.48        72.39        80.71        53.69        29.92         0.20 
TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J 
        0.20        13.15        13.41         1.84         0.20        18.74 
TCGA-EP-A2KB TCGA-EP-A3RK TCGA-FV-A3I0 TCGA-FV-A495 TCGA-G3-A25S TCGA-G3-A25X 
       19.59        11.93        27.88         0.03        13.68        58.49 
TCGA-G3-A3CH TCGA-G3-A5SM TCGA-G3-AAV1 TCGA-G3-AAV3 TCGA-G3-AAV7 TCGA-K7-A5RG 
       25.64        17.10        11.80        13.55        11.87        17.06 
TCGA-KR-A7K8 TCGA-NI-A8LF TCGA-QA-A7B7 TCGA-RC-A6M5 TCGA-RC-A7SH TCGA-RC-A7SK 
       29.79        26.27         3.09         0.49        15.39        15.52 
TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-WJ-A86L TCGA-WQ-A9G7 
       36.10        27.88        19.76        16.44        11.34         0.99 
TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-ZP-A9D0 TCGA-ZP-A9D2 
       12.99        20.22        35.87        25.15 

$`DEL PEAK 24(14Q32.33) WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A5W4 TCGA-BD-A3ER 
       83.24        38.40         8.61        69.57        17.98        36.66 
TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-AAE7 TCGA-DD-AAEA TCGA-EP-A3JL TCGA-ES-A2HS 
        0.36        90.28        21.17        18.90         9.96        22.62 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC TCGA-K7-A5RF 
        8.12         6.38        30.74        22.13        22.06        20.75 
TCGA-KR-A7K0 TCGA-LG-A6GG TCGA-MI-A75H TCGA-T1-A6J8 TCGA-UB-AA0V TCGA-XR-A8TG 
        2.14        12.72        24.56         0.76        10.32        29.52 
TCGA-ZP-A9D1 TCGA-ZS-A9CE TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GZ 
        0.69        40.80        53.39        63.75        41.79        27.88 
TCGA-2Y-A9H0 TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 
      120.82        18.25        20.81         1.18         8.55        13.02 
TCGA-5C-A9VH TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-4073 
       10.59        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-A216 
       46.78        27.52         2.99        25.32        23.38        44.42 
TCGA-BC-A69H TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BW-A5NO 
       14.60        12.72        18.48        44.81        13.45         0.66 
TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A3M9 TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A7IE 
        3.39         4.24         9.86        11.41         9.99         7.13 
TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7IL TCGA-CC-A9FS TCGA-CC-A9FW 
       21.34         9.83        12.00         9.14         6.94         8.15 
TCGA-DD-A114 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11D 
       37.78        53.33       113.00         7.33         0.46        51.29 
TCGA-DD-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-A39Z 
       49.15         6.02        18.35        21.14        27.19        19.76 
TCGA-DD-A3A0 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 
       25.81        70.06        17.59        20.12       102.74       107.11 
TCGA-DD-A4NA TCGA-DD-A4NF TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NP 
       33.14        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-AAC8 TCGA-DD-AAC9 TCGA-DD-AACB TCGA-DD-AACC 
       22.78         1.45         0.53        11.41        76.41        55.40 
TCGA-DD-AACD TCGA-DD-AACF TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM 
       12.53        12.00        69.11         0.30         3.52        58.16 
TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACT TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACY 
       13.64        14.20        51.35        50.33        46.82        47.67 
TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD8 TCGA-DD-AADA 
        4.50        18.54        21.63        42.58        40.08        40.54 
TCGA-DD-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-AADP TCGA-DD-AADQ TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADY TCGA-DD-AAE1 
       15.06        14.33        15.58        18.21        18.25        18.15 
TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAEH 
       20.98        18.61        19.99        23.74        15.72        25.78 
TCGA-DD-AAEI TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVW TCGA-DD-AAVX 
       50.33        89.69        82.62        59.93        76.18        56.48 
TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-ED-A4XI 
       64.77        62.47        66.25        65.39        60.99        26.93 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PY TCGA-ED-A7XO 
       28.08        13.91        13.35         9.73        12.82        14.04 
TCGA-ED-A8O5 TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC TCGA-ES-A2HT TCGA-FV-A23B 
       13.35        19.99        20.61         0.62        14.40        60.89 
TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3R3 TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25T 
       23.97        19.10        12.03         0.33         0.39        51.06 
TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CI TCGA-G3-A3CJ 
       53.79        28.27        14.86        21.53         5.92        19.53 
TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A7M5 TCGA-G3-A7M6 
       19.23        25.25        22.95        20.42        14.70        20.78 
TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV4 
       11.87        14.14        15.78        15.65        12.23         0.89 
TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ 
       11.64         2.14        28.90         1.02         2.20         2.99 
TCGA-HP-A5N0 TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-LG-A9QC TCGA-LG-A9QD 
       37.71        16.83        11.80        27.25        13.97        12.03 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO 
        9.57        16.67        22.95        20.71         7.53        10.85 
TCGA-NI-A4U2 TCGA-O8-A75V TCGA-PD-A5DF TCGA-RC-A6M4 TCGA-RC-A6M6 TCGA-RC-A7S9 
       58.88        17.69        21.01         0.72         0.30        21.04 
TCGA-RC-A7SB TCGA-RC-A7SF TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WX-AA46 
       19.33        19.04         1.71        15.98        10.75        24.85 
TCGA-WX-AA47 TCGA-XR-A8TD TCGA-XR-A8TE TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CV 
       18.28        33.86        30.41        22.78        13.55        35.77 
TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CF TCGA-ZS-A9CG 
       25.71        23.21        12.99        45.57        79.30        11.21 

  DEL PEAK 24(14Q32.33) MUTATED DEL PEAK 24(14Q32.33) WILD-TYPE 
                           0.03                            0.30 
  DEL PEAK 24(14Q32.33) MUTATED DEL PEAK 24(14Q32.33) WILD-TYPE 
                         114.35                          120.82 
  DEL PEAK 24(14Q32.33) MUTATED DEL PEAK 24(14Q32.33) WILD-TYPE 
                         19.445                          19.990 
[1] "0.0 - 114.3 (19.4)" "0.3 - 120.8 (20.0)"
[1] "hr=" "1"  
D51V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE III STAGE IIIA
  DEL PEAK 24(14Q32.33) MUTATED        53       40         0         22
  DEL PEAK 24(14Q32.33) WILD-TYPE     120       47         3         40
                                 vv
clus                              STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 24(14Q32.33) MUTATED            4          3        1         1
  DEL PEAK 24(14Q32.33) WILD-TYPE          5          4        1         0
                                 vv
clus                              STAGE IVB
  DEL PEAK 24(14Q32.33) MUTATED           1
  DEL PEAK 24(14Q32.33) WILD-TYPE         1
D51V3, multiclass
            clus
vv           DEL PEAK 24(14Q32.33) MUTATED DEL PEAK 24(14Q32.33) WILD-TYPE
  STAGE I                               53                             120
  STAGE II                              40                              47
  STAGE III                              0                               3
  STAGE IIIA                            22                              40
  STAGE IIIB                             4                               5
  STAGE IIIC                             3                               4
  STAGE IV                               1                               1
  STAGE IVA                              1                               0
  STAGE IVB                              1                               1
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               T1  T2  T3  T4
  DEL PEAK 24(14Q32.33) MUTATED    56  44  28   5
  DEL PEAK 24(14Q32.33) WILD-TYPE 127  51  49   7
D51V4, multiclass
    clus
vv   DEL PEAK 24(14Q32.33) MUTATED DEL PEAK 24(14Q32.33) WILD-TYPE
  T1                            56                             127
  T2                            44                              51
  T3                            28                              49
  T4                             5                               7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V5, binary
                                 cls
clus                                0   1
  DEL PEAK 24(14Q32.33) MUTATED    93   2
  DEL PEAK 24(14Q32.33) WILD-TYPE 161   1
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 24(14Q32.33) MUTATED     93    2
  DEL PEAK 24(14Q32.33) WILD-TYPE  161    1
   clus
vv  DEL PEAK 24(14Q32.33) MUTATED DEL PEAK 24(14Q32.33) WILD-TYPE
  0                            93                             161
  1                             2                               1
[1] 2 2
[1] FALSE
D51V6, binary
                                 cls
clus                                0   1
  DEL PEAK 24(14Q32.33) MUTATED   100   2
  DEL PEAK 24(14Q32.33) WILD-TYPE 166   2
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 24(14Q32.33) MUTATED    100    2
  DEL PEAK 24(14Q32.33) WILD-TYPE  166    2
   clus
vv  DEL PEAK 24(14Q32.33) MUTATED DEL PEAK 24(14Q32.33) WILD-TYPE
  0                           100                             166
  1                             2                               2
[1] 2 2
[1] FALSE
D51V7, binary
                                 cls
clus                                0   1
  DEL PEAK 24(14Q32.33) MUTATED    43  90
  DEL PEAK 24(14Q32.33) WILD-TYPE  75 162
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 24(14Q32.33) MUTATED     43   90
  DEL PEAK 24(14Q32.33) WILD-TYPE   75  162
        clus
vv       DEL PEAK 24(14Q32.33) MUTATED DEL PEAK 24(14Q32.33) WILD-TYPE
  FEMALE                            43                              75
  MALE                              90                             162
[1] 2 2
[1] FALSE
D51V8, binary
                                 cls
clus                                0   1
  DEL PEAK 24(14Q32.33) MUTATED   124   2
  DEL PEAK 24(14Q32.33) WILD-TYPE 214   7
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 24(14Q32.33) MUTATED    124    2
  DEL PEAK 24(14Q32.33) WILD-TYPE  214    7
     clus
vv    DEL PEAK 24(14Q32.33) MUTATED DEL PEAK 24(14Q32.33) WILD-TYPE
  NO                            124                             214
  YES                             2                               7
[1] 2 2
[1] FALSE
                                 vv
clus                              FIBROLAMELLAR CARCINOMA
  DEL PEAK 24(14Q32.33) MUTATED                         2
  DEL PEAK 24(14Q32.33) WILD-TYPE                       1
                                 vv
clus                              HEPATOCELLULAR CARCINOMA
  DEL PEAK 24(14Q32.33) MUTATED                        126
  DEL PEAK 24(14Q32.33) WILD-TYPE                      234
                                 vv
clus                              HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK 24(14Q32.33) MUTATED                                  5
  DEL PEAK 24(14Q32.33) WILD-TYPE                                2
D51V9, multiclass
                                  clus
vv                                 DEL PEAK 24(14Q32.33) MUTATED
  FIBROLAMELLAR CARCINOMA                                      2
  HEPATOCELLULAR CARCINOMA                                   126
  HEPATOCHOLANGIOCARCINOMA (MIXED)                             5
                                  clus
vv                                 DEL PEAK 24(14Q32.33) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                        1
  HEPATOCELLULAR CARCINOMA                                     234
  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 24(14Q32.33) MUTATED   116   6   0   9
  DEL PEAK 24(14Q32.33) WILD-TYPE 208  11   1  12
D51V10, multiclass
    clus
vv   DEL PEAK 24(14Q32.33) MUTATED DEL PEAK 24(14Q32.33) WILD-TYPE
  R0                           116                             208
  R1                             6                              11
  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 24(14Q32.33) MUTATED                                  0    65
  DEL PEAK 24(14Q32.33) WILD-TYPE                                2    93
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 24(14Q32.33) MUTATED                           8    57
  DEL PEAK 24(14Q32.33) WILD-TYPE                         9   126
D51V11, multiclass
                                  clus
vv                                 DEL PEAK 24(14Q32.33) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                       65
  BLACK OR AFRICAN AMERICAN                                    8
  WHITE                                                       57
                                  clus
vv                                 DEL PEAK 24(14Q32.33) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               2
  ASIAN                                                         93
  BLACK OR AFRICAN AMERICAN                                      9
  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 24(14Q32.33) MUTATED     5 120
  DEL PEAK 24(14Q32.33) WILD-TYPE  11 215
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 24(14Q32.33) MUTATED      5  120
  DEL PEAK 24(14Q32.33) WILD-TYPE   11  215
                        clus
vv                       DEL PEAK 24(14Q32.33) MUTATED
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                           120
                        clus
vv                       DEL PEAK 24(14Q32.33) WILD-TYPE
  HISPANIC OR LATINO                                  11
  NOT HISPANIC OR LATINO                             215
[1] 2 2
[1] FALSE

Clustering(52) Variable = DEL PEAK 25(15Q26.3) MUTATION ANALYSIS
D52V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 25(15Q26.3) MUTATED    41  35
  DEL PEAK 25(15Q26.3) WILD-TYPE 194  94
  DEL PEAK 25(15Q26.3) MUTATED DEL PEAK 25(15Q26.3) WILD-TYPE 
                            76                            288 
  DEL PEAK 25(15Q26.3) MUTATED DEL PEAK 25(15Q26.3) WILD-TYPE 
                            35                             94 
$`DEL PEAK 25(15Q26.3) MUTATED`
TCGA-BC-A112 TCGA-BC-A5W4 TCGA-DD-AADV TCGA-DD-AAE7 TCGA-FV-A4ZP TCGA-G3-A7M9 
        5.03        17.98        18.87        21.17        81.73         1.84 
TCGA-KR-A7K7 TCGA-2Y-A9GZ TCGA-2Y-A9H8 TCGA-3K-AAZ8 TCGA-5C-A9VH TCGA-5C-AAPD 
       31.27        27.88        20.81        13.02        10.59         0.66 
TCGA-BC-A216 TCGA-BC-A69H TCGA-CC-5258 TCGA-CC-5264 TCGA-CC-A3MA TCGA-CC-A5UC 
       44.42        14.60         4.24         3.35         9.96        11.41 
TCGA-CC-A5UD TCGA-CC-A7IG TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A8HV 
        9.99         9.83        13.12        12.56         8.61         9.17 
TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A11C TCGA-DD-A1E9 TCGA-DD-A1EI 
       79.73        37.78        83.57        21.76        90.71         6.02 
TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39Y TCGA-DD-A3A5 TCGA-DD-A4NA TCGA-DD-A4NQ 
       33.04        13.64         5.62       102.74        33.14        12.26 
TCGA-DD-A73B TCGA-DD-A73F TCGA-DD-AAC8 TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACL 
        9.30        35.67         0.53        15.42         6.41         3.52 
TCGA-DD-AACS TCGA-DD-AADB TCGA-DD-AADF TCGA-DD-AADK TCGA-DD-AAE1 TCGA-DD-AAE4 
       59.31        40.83         3.78        34.49        18.15        19.99 
TCGA-DD-AAEK TCGA-DD-AAVQ TCGA-DD-AAVV TCGA-DD-AAVX TCGA-ED-A459 TCGA-ED-A66Y 
       35.08        89.69        80.71        56.48        29.92         9.73 
TCGA-ED-A7PX TCGA-ED-A82E TCGA-EP-A2KB TCGA-FV-A3I0 TCGA-FV-A496 TCGA-G3-A25Z 
        0.20        13.41        19.59        27.88         0.33        21.53 
TCGA-G3-A5SI TCGA-G3-A5SM TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV4 TCGA-G3-AAV6 
       25.25        17.10        15.65        11.80         0.89         2.14 
TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-K7-A5RG TCGA-KR-A7K2 TCGA-NI-A8LF TCGA-RC-A6M4 
       11.87        28.90        17.06        27.25        26.27         0.72 
TCGA-RG-A7D4 TCGA-WQ-A9G7 TCGA-YA-A8S7 TCGA-ZS-A9CF 
       36.10         0.99        13.55        79.30 

$`DEL PEAK 25(15Q26.3) WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BD-A3ER 
       83.24        11.74        38.40         8.61        69.57        36.66 
TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG 
        0.36        90.28        26.83        21.83        18.90        23.64 
TCGA-EP-A3JL TCGA-ES-A2HS TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-G3-A25W TCGA-G3-A3CG 
        9.96        22.62         8.12         6.38        30.74        22.13 
TCGA-G3-A6UC TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-LG-A6GG TCGA-MI-A75H TCGA-T1-A6J8 
       22.06        20.75         2.14        12.72        24.56         0.76 
TCGA-UB-A7MF TCGA-UB-AA0V TCGA-XR-A8TG TCGA-ZP-A9D1 TCGA-ZS-A9CE TCGA-2Y-A9GS 
        7.04        10.32        29.52         0.69        40.80        23.80 
TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GY TCGA-2Y-A9H0 
       53.39        63.75        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-A9H9 
       40.41        56.91        49.84        47.74        18.25        22.92 
TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-5C-A9VG TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM 
        1.18         8.55        10.78        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-A10Y TCGA-BC-A10Z TCGA-BC-A217 
       27.52         2.99        25.32        23.38         1.12        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-BW-A5NO TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT 
        0.66         2.86         3.19         3.39         4.24         3.32 
TCGA-CC-A3M9 TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IF 
        9.86        10.36        11.93         8.94         7.13        21.34 
TCGA-CC-A7IH TCGA-CC-A7IL TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A9FS TCGA-CC-A9FW 
       12.00         9.14         4.60        11.31         6.94         8.15 
TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11D 
       53.33       113.00         7.33         2.60         0.46        51.29 
TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF 
       79.40        66.31        19.79        75.65        11.47        12.95 
TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EK TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39X 
       45.11        49.15        18.35        21.14        27.19        55.69 
TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 
       19.76        25.81         7.66        70.06        17.59        20.12 
TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NB TCGA-DD-A4NF TCGA-DD-A4NH 
      107.11        13.78        30.61        32.52        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-A73C TCGA-DD-A73D 
        0.30        80.75        78.84        23.93        23.05        22.78 
TCGA-DD-A73E TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB 
        1.45       114.35        13.48        11.41        75.65        76.41 
TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACI TCGA-DD-AACJ 
       55.40        12.53        71.80        12.00        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-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-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE 
       22.09        40.08        40.54        13.97        40.47        39.52 
TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN 
       37.64        35.67        35.05        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-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE6 
       19.30        18.25        18.25        20.98        18.61         4.64 
TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAEI 
       23.74        15.72        25.08        26.63        25.78        50.33 
TCGA-DD-AAVP TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVY 
       90.48        82.62        59.93        72.39        76.18        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        60.99        53.69        26.93 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO 
       28.08        13.91        13.35        12.82         0.20        14.04 
TCGA-ED-A7XP TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S 
       13.15        13.35         1.84         0.20        18.74        19.99 
TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ 
       20.61         0.62        11.93        14.40        60.89        23.97 
TCGA-FV-A2QR TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T 
       19.10        12.03         0.03         0.39        13.68        51.06 
TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A3CH TCGA-G3-A3CI 
       53.79        28.27        58.49        14.86        25.64         5.92 
TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A7M5 TCGA-G3-A7M6 
       19.53        19.23        22.95        20.42        14.70        20.78 
TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV5 
       11.87        14.14        15.78        12.23        13.55        11.64 
TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A6G5 TCGA-K7-AAU7 
        1.02         2.20         2.99        37.71        16.83        11.80 
TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G 
       29.79        13.97        12.03         9.57        16.67        22.95 
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-A6M5 TCGA-RC-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF 
        3.09         0.49         0.30        21.04        19.33        19.04 
TCGA-RC-A7SH TCGA-RC-A7SK TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD 
       15.39        15.52        27.88        19.76        16.44         1.71 
TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-WX-AA46 
       15.98        10.75        11.34        12.99        20.22        24.85 
TCGA-WX-AA47 TCGA-XR-A8TD TCGA-XR-A8TE TCGA-XR-A8TF TCGA-ZP-A9CV TCGA-ZP-A9CY 
       18.28        33.86        30.41        22.78        35.77        25.71 
TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CG 
       23.21        35.87        25.15        12.99        45.57        11.21 

  DEL PEAK 25(15Q26.3) MUTATED DEL PEAK 25(15Q26.3) WILD-TYPE 
                          0.20                           0.03 
  DEL PEAK 25(15Q26.3) MUTATED DEL PEAK 25(15Q26.3) WILD-TYPE 
                        102.74                         120.82 
  DEL PEAK 25(15Q26.3) MUTATED DEL PEAK 25(15Q26.3) WILD-TYPE 
                        16.355                         20.660 
[1] "0.2 - 102.7 (16.4)" "0.0 - 120.8 (20.7)"
[1] "hr=" "1.6"
D52V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IIIA
  DEL PEAK 25(15Q26.3) MUTATED        27       27         1         16
  DEL PEAK 25(15Q26.3) WILD-TYPE     146       60         2         46
                                vv
clus                             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 25(15Q26.3) MUTATED            2          3        0         0
  DEL PEAK 25(15Q26.3) WILD-TYPE          7          4        2         1
                                vv
clus                             STAGE IVB
  DEL PEAK 25(15Q26.3) MUTATED           0
  DEL PEAK 25(15Q26.3) WILD-TYPE         2
D52V3, multiclass
            clus
vv           DEL PEAK 25(15Q26.3) MUTATED DEL PEAK 25(15Q26.3) WILD-TYPE
  STAGE I                              27                            146
  STAGE II                             27                             60
  STAGE III                             1                              2
  STAGE IIIA                           16                             46
  STAGE IIIB                            2                              7
  STAGE IIIC                            3                              4
  STAGE IV                              0                              2
  STAGE IVA                             0                              1
  STAGE IVB                             0                              2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 25(15Q26.3) MUTATED    29  28  21   1
  DEL PEAK 25(15Q26.3) WILD-TYPE 154  67  56  11
D52V4, multiclass
    clus
vv   DEL PEAK 25(15Q26.3) MUTATED DEL PEAK 25(15Q26.3) WILD-TYPE
  T1                           29                            154
  T2                           28                             67
  T3                           21                             56
  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"
D52V5, binary
                                cls
clus                               0   1
  DEL PEAK 25(15Q26.3) MUTATED    54   2
  DEL PEAK 25(15Q26.3) WILD-TYPE 200   1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(15Q26.3) MUTATED     54    2
  DEL PEAK 25(15Q26.3) WILD-TYPE  200    1
   clus
vv  DEL PEAK 25(15Q26.3) MUTATED DEL PEAK 25(15Q26.3) WILD-TYPE
  0                           54                            200
  1                            2                              1
[1] 2 2
[1] FALSE
D52V6, binary
                                cls
clus                               0   1
  DEL PEAK 25(15Q26.3) MUTATED    66   0
  DEL PEAK 25(15Q26.3) WILD-TYPE 200   4
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(15Q26.3) MUTATED     66    0
  DEL PEAK 25(15Q26.3) WILD-TYPE  200    4
   clus
vv  DEL PEAK 25(15Q26.3) MUTATED DEL PEAK 25(15Q26.3) WILD-TYPE
  0                           66                            200
  1                            0                              4
[1] 2 2
[1] FALSE
D52V7, binary
                                cls
clus                               0   1
  DEL PEAK 25(15Q26.3) MUTATED    26  53
  DEL PEAK 25(15Q26.3) WILD-TYPE  92 199
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(15Q26.3) MUTATED     26   53
  DEL PEAK 25(15Q26.3) WILD-TYPE   92  199
        clus
vv       DEL PEAK 25(15Q26.3) MUTATED DEL PEAK 25(15Q26.3) WILD-TYPE
  FEMALE                           26                             92
  MALE                             53                            199
[1] 2 2
[1] FALSE
D52V8, binary
                                cls
clus                               0   1
  DEL PEAK 25(15Q26.3) MUTATED    71   2
  DEL PEAK 25(15Q26.3) WILD-TYPE 267   7
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(15Q26.3) MUTATED     71    2
  DEL PEAK 25(15Q26.3) WILD-TYPE  267    7
     clus
vv    DEL PEAK 25(15Q26.3) MUTATED DEL PEAK 25(15Q26.3) WILD-TYPE
  NO                            71                            267
  YES                            2                              7
[1] 2 2
[1] FALSE
                                vv
clus                             FIBROLAMELLAR CARCINOMA
  DEL PEAK 25(15Q26.3) MUTATED                         0
  DEL PEAK 25(15Q26.3) WILD-TYPE                       3
                                vv
clus                             HEPATOCELLULAR CARCINOMA
  DEL PEAK 25(15Q26.3) MUTATED                         76
  DEL PEAK 25(15Q26.3) WILD-TYPE                      284
                                vv
clus                             HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK 25(15Q26.3) MUTATED                                  3
  DEL PEAK 25(15Q26.3) WILD-TYPE                                4
D52V9, multiclass
                                  clus
vv                                 DEL PEAK 25(15Q26.3) MUTATED
  FIBROLAMELLAR CARCINOMA                                     0
  HEPATOCELLULAR CARCINOMA                                   76
  HEPATOCHOLANGIOCARCINOMA (MIXED)                            3
                                  clus
vv                                 DEL PEAK 25(15Q26.3) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                       3
  HEPATOCELLULAR CARCINOMA                                    284
  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(15Q26.3) MUTATED    70   3   0   6
  DEL PEAK 25(15Q26.3) WILD-TYPE 254  14   1  15
D52V10, multiclass
    clus
vv   DEL PEAK 25(15Q26.3) MUTATED DEL PEAK 25(15Q26.3) WILD-TYPE
  R0                           70                            254
  R1                            3                             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 25(15Q26.3) MUTATED                                  1    39
  DEL PEAK 25(15Q26.3) WILD-TYPE                                1   119
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 25(15Q26.3) MUTATED                           5    34
  DEL PEAK 25(15Q26.3) WILD-TYPE                        12   149
D52V11, multiclass
                                  clus
vv                                 DEL PEAK 25(15Q26.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                      39
  BLACK OR AFRICAN AMERICAN                                   5
  WHITE                                                      34
                                  clus
vv                                 DEL PEAK 25(15Q26.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                       119
  BLACK OR AFRICAN AMERICAN                                    12
  WHITE                                                       149
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V12, binary
                                cls
clus                               0   1
  DEL PEAK 25(15Q26.3) MUTATED     3  71
  DEL PEAK 25(15Q26.3) WILD-TYPE  13 264
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(15Q26.3) MUTATED      3   71
  DEL PEAK 25(15Q26.3) WILD-TYPE   13  264
                        clus
vv                       DEL PEAK 25(15Q26.3) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           71
                        clus
vv                       DEL PEAK 25(15Q26.3) WILD-TYPE
  HISPANIC OR LATINO                                 13
  NOT HISPANIC OR LATINO                            264
[1] 2 2
[1] FALSE

Clustering(53) Variable = DEL PEAK 26(16Q23.1) MUTATION ANALYSIS
D53V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 26(16Q23.1) MUTATED   100  59
  DEL PEAK 26(16Q23.1) WILD-TYPE 135  70
  DEL PEAK 26(16Q23.1) MUTATED DEL PEAK 26(16Q23.1) WILD-TYPE 
                           159                            205 
  DEL PEAK 26(16Q23.1) MUTATED DEL PEAK 26(16Q23.1) WILD-TYPE 
                            59                             70 
$`DEL PEAK 26(16Q23.1) MUTATED`
TCGA-2Y-A9H7 TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV TCGA-DD-AAE8 
       38.40         0.36        90.28        26.83        18.87        21.83 
TCGA-DD-AAEG TCGA-ES-A2HS TCGA-FV-A3R2 TCGA-G3-A7M9 TCGA-KR-A7K7 TCGA-LG-A6GG 
       23.64        22.62         6.38         1.84        31.27        12.72 
TCGA-T1-A6J8 TCGA-UB-A7MF TCGA-ZP-A9D1 TCGA-2Y-A9GY TCGA-2Y-A9H2 TCGA-2Y-A9H3 
        0.76         7.04         0.69        24.89        56.91        49.84 
TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-2Y-A9HA TCGA-5C-A9VG TCGA-5C-AAPD TCGA-BC-4073 
       18.25        20.81         1.18        10.78         0.66        27.91 
TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10W TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A216 
       10.13        46.78         2.99        23.38         1.12        44.42 
TCGA-BC-A217 TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A8YO TCGA-BD-A3EP TCGA-BW-A5NO 
       45.93        22.36        14.60        18.48        13.45         0.66 
TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5263 TCGA-CC-5264 TCGA-CC-A3M9 
        4.24         2.86         3.19         4.24         3.35         9.86 
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-A8HT TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FS 
       21.34         9.83         4.60        11.31         9.17         6.94 
TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A116 TCGA-DD-A11A TCGA-DD-A11B 
        8.15        79.73        37.78        53.33         2.60         0.46 
TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A39Y TCGA-DD-A39Z 
       12.95        49.15         6.02        33.04         5.62        19.76 
TCGA-DD-A3A9 TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NQ 
       30.61        30.15        30.51        29.56        73.81        12.26 
TCGA-DD-A73B TCGA-DD-A73F TCGA-DD-AACC TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH 
        9.30        35.67        55.40        12.00        15.42         6.41 
TCGA-DD-AACI TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP 
       53.19         3.52        58.16        42.81        61.68        13.64 
TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACZ 
       14.20        59.31        51.52        50.33        46.82         5.62 
TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD3 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADI 
        4.50        18.54        42.58        40.54        40.83        35.67 
TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADO TCGA-DD-AADP 
       35.05        34.49        20.91         0.39        14.89        15.06 
TCGA-DD-AADR TCGA-DD-AADW TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE6 TCGA-DD-AAED 
       66.67        19.30        18.25        18.15         4.64        25.08 
TCGA-DD-AAEH TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVS TCGA-DD-AAVU 
       25.78        35.08        90.48        89.69        59.93        72.39 
TCGA-DD-AAVV TCGA-DD-AAVW TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-ED-A459 TCGA-ED-A5KG 
       80.71        76.18        62.47        66.25        29.92        28.08 
TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PY TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-EP-A2KB 
       13.35         9.73        12.82        13.35         1.84        19.59 
TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A3I0 TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25X 
       60.89        23.97        27.88        13.68        53.79        58.49 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A5SI TCGA-G3-A7M5 TCGA-G3-AAUZ 
       14.86        21.53        25.64        25.25        14.70        15.78 
TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-KR-A7K8 TCGA-MI-A75G TCGA-MI-A75I TCGA-NI-A8LF 
        2.14        11.87        29.79        22.95        20.71        26.27 
TCGA-O8-A75V TCGA-QA-A7B7 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RG-A7D4 
       17.69         3.09        19.33        19.04        15.39        36.10 
TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-XR-A8TD 
       27.88        19.76        10.75        11.34         0.99        33.86 
TCGA-XR-A8TF TCGA-ZP-A9CZ TCGA-ZS-A9CG 
       22.78        23.21        11.21 

$`DEL PEAK 26(16Q23.1) WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A5W4 
       83.24        11.74         8.61        69.57         5.03        17.98 
TCGA-BD-A3ER TCGA-DD-AAE7 TCGA-DD-AAEA TCGA-EP-A3JL TCGA-FV-A3I1 TCGA-FV-A4ZP 
       36.66        21.17        18.90         9.96         8.12        81.73 
TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-MI-A75H 
       30.74        22.13        22.06        20.75         2.14        24.56 
TCGA-UB-AA0V TCGA-XR-A8TG TCGA-ZS-A9CE TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU 
       10.32        29.52        40.80        23.80        53.39        63.75 
TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H4 
       41.79        80.28        27.88       120.82        40.41        47.74 
TCGA-2Y-A9H9 TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-5C-A9VH TCGA-5R-AA1C TCGA-5R-AA1D 
       22.92         8.55        13.02        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-A3KF TCGA-BC-A69I TCGA-BD-A2L6 TCGA-CC-5262 TCGA-CC-A1HT TCGA-CC-A3MA 
        0.26        12.72        44.81         3.39         3.32         9.96 
TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A7IL TCGA-DD-A115 
       12.00        13.12        12.56         8.61         9.14        83.57 
TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA 
      113.00         7.33        21.76        51.29        90.71        79.40 
TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EG TCGA-DD-A1EK 
       66.31        19.79        75.65        11.47        45.11        18.35 
TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A3A0 TCGA-DD-A3A1 
       13.64        21.14        27.19        55.69        25.81         7.66 
TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 
       70.06        17.59        20.12       102.74       107.11        13.78 
TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NF TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NP 
       33.14        32.52        30.97        39.78        56.25       108.76 
TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73C TCGA-DD-A73D 
        0.30        80.75        78.84        23.93        23.05        22.78 
TCGA-DD-A73E TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA 
        1.45       114.35        13.48         0.53        11.41        75.65 
TCGA-DD-AACB TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACT 
       76.41        12.53        71.80        69.11         0.30        51.35 
TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AAD2 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 
        5.59        47.67        21.63        44.22        22.09        40.08 
TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADN 
       13.97        40.47        39.52         3.78        37.64        29.52 
TCGA-DD-AADQ TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADY TCGA-DD-AAE2 TCGA-DD-AAE3 
       14.33        15.58        18.21        18.25        20.98        18.61 
TCGA-DD-AAE4 TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAEE TCGA-DD-AAEI TCGA-DD-AAVR 
       19.99        23.74        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        60.99        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-A3RK 
        0.20        18.74        19.99        20.61         0.62        11.93 
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-A25T TCGA-G3-A25V TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SJ 
       51.06        28.27         5.92        19.53        19.23        22.95 
TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAV0 
       20.42        17.10        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        11.64        28.90 
TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 
        1.02         2.20         2.99        37.71        17.06        16.83 
TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E 
       11.80        27.25        13.97        12.03         9.57        16.67 
TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-PD-A5DF TCGA-RC-A6M4 TCGA-RC-A6M5 
        7.53        10.85        58.88        21.01         0.72         0.49 
TCGA-RC-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SK TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME 
        0.30        21.04        15.52        16.44         1.71        15.98 
TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TE TCGA-YA-A8S7 
       12.99        20.22        24.85        18.28        30.41        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-A9CF 
       79.30 

  DEL PEAK 26(16Q23.1) MUTATED DEL PEAK 26(16Q23.1) WILD-TYPE 
                          0.36                           0.03 
  DEL PEAK 26(16Q23.1) MUTATED DEL PEAK 26(16Q23.1) WILD-TYPE 
                         90.48                         120.82 
  DEL PEAK 26(16Q23.1) MUTATED DEL PEAK 26(16Q23.1) WILD-TYPE 
                         19.33                          20.12 
[1] "0.4 - 90.5 (19.3)"  "0.0 - 120.8 (20.1)"
[1] "hr=" "1.2"
D53V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IIIA
  DEL PEAK 26(16Q23.1) MUTATED        68       49         1         25
  DEL PEAK 26(16Q23.1) WILD-TYPE     105       38         2         37
                                vv
clus                             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 26(16Q23.1) MUTATED            4          3        1         0
  DEL PEAK 26(16Q23.1) WILD-TYPE          5          4        1         1
                                vv
clus                             STAGE IVB
  DEL PEAK 26(16Q23.1) MUTATED           1
  DEL PEAK 26(16Q23.1) WILD-TYPE         1
D53V3, multiclass
            clus
vv           DEL PEAK 26(16Q23.1) MUTATED DEL PEAK 26(16Q23.1) WILD-TYPE
  STAGE I                              68                            105
  STAGE II                             49                             38
  STAGE III                             1                              2
  STAGE IIIA                           25                             37
  STAGE IIIB                            4                              5
  STAGE IIIC                            3                              4
  STAGE IV                              1                              1
  STAGE IVA                             0                              1
  STAGE IVB                             1                              1
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 26(16Q23.1) MUTATED    73  51  32   6
  DEL PEAK 26(16Q23.1) WILD-TYPE 110  44  45   6
D53V4, multiclass
    clus
vv   DEL PEAK 26(16Q23.1) MUTATED DEL PEAK 26(16Q23.1) WILD-TYPE
  T1                           73                            110
  T2                           51                             44
  T3                           32                             45
  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"
D53V5, binary
                                cls
clus                               0   1
  DEL PEAK 26(16Q23.1) MUTATED   122   1
  DEL PEAK 26(16Q23.1) WILD-TYPE 132   2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(16Q23.1) MUTATED    122    1
  DEL PEAK 26(16Q23.1) WILD-TYPE  132    2
   clus
vv  DEL PEAK 26(16Q23.1) MUTATED DEL PEAK 26(16Q23.1) WILD-TYPE
  0                          122                            132
  1                            1                              2
[1] 2 2
[1] FALSE
D53V6, binary
                                cls
clus                               0   1
  DEL PEAK 26(16Q23.1) MUTATED   127   2
  DEL PEAK 26(16Q23.1) WILD-TYPE 139   2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(16Q23.1) MUTATED    127    2
  DEL PEAK 26(16Q23.1) WILD-TYPE  139    2
   clus
vv  DEL PEAK 26(16Q23.1) MUTATED DEL PEAK 26(16Q23.1) WILD-TYPE
  0                          127                            139
  1                            2                              2
[1] 2 2
[1] FALSE
D53V7, binary
                                cls
clus                               0   1
  DEL PEAK 26(16Q23.1) MUTATED    57 105
  DEL PEAK 26(16Q23.1) WILD-TYPE  61 147
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(16Q23.1) MUTATED     57  105
  DEL PEAK 26(16Q23.1) WILD-TYPE   61  147
        clus
vv       DEL PEAK 26(16Q23.1) MUTATED DEL PEAK 26(16Q23.1) WILD-TYPE
  FEMALE                           57                             61
  MALE                            105                            147
[1] 2 2
[1] FALSE
D53V8, binary
                                cls
clus                               0   1
  DEL PEAK 26(16Q23.1) MUTATED   151   2
  DEL PEAK 26(16Q23.1) WILD-TYPE 187   7
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(16Q23.1) MUTATED    151    2
  DEL PEAK 26(16Q23.1) WILD-TYPE  187    7
     clus
vv    DEL PEAK 26(16Q23.1) MUTATED DEL PEAK 26(16Q23.1) WILD-TYPE
  NO                           151                            187
  YES                            2                              7
[1] 2 2
[1] FALSE
                                vv
clus                             FIBROLAMELLAR CARCINOMA
  DEL PEAK 26(16Q23.1) MUTATED                         0
  DEL PEAK 26(16Q23.1) WILD-TYPE                       3
                                vv
clus                             HEPATOCELLULAR CARCINOMA
  DEL PEAK 26(16Q23.1) MUTATED                        159
  DEL PEAK 26(16Q23.1) WILD-TYPE                      201
                                vv
clus                             HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK 26(16Q23.1) MUTATED                                  3
  DEL PEAK 26(16Q23.1) WILD-TYPE                                4
D53V9, multiclass
                                  clus
vv                                 DEL PEAK 26(16Q23.1) MUTATED
  FIBROLAMELLAR CARCINOMA                                     0
  HEPATOCELLULAR CARCINOMA                                  159
  HEPATOCHOLANGIOCARCINOMA (MIXED)                            3
                                  clus
vv                                 DEL PEAK 26(16Q23.1) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                       3
  HEPATOCELLULAR CARCINOMA                                    201
  HEPATOCHOLANGIOCARCINOMA (MIXED)                              4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 26(16Q23.1) MUTATED   144   7   0  11
  DEL PEAK 26(16Q23.1) WILD-TYPE 180  10   1  10
D53V10, multiclass
    clus
vv   DEL PEAK 26(16Q23.1) MUTATED DEL PEAK 26(16Q23.1) WILD-TYPE
  R0                          144                            180
  R1                            7                             10
  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 26(16Q23.1) MUTATED                                  0    91
  DEL PEAK 26(16Q23.1) WILD-TYPE                                2    67
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 26(16Q23.1) MUTATED                           7    60
  DEL PEAK 26(16Q23.1) WILD-TYPE                        10   123
D53V11, multiclass
                                  clus
vv                                 DEL PEAK 26(16Q23.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                      91
  BLACK OR AFRICAN AMERICAN                                   7
  WHITE                                                      60
                                  clus
vv                                 DEL PEAK 26(16Q23.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              2
  ASIAN                                                        67
  BLACK OR AFRICAN AMERICAN                                    10
  WHITE                                                       123
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V12, binary
                                cls
clus                               0   1
  DEL PEAK 26(16Q23.1) MUTATED     8 149
  DEL PEAK 26(16Q23.1) WILD-TYPE   8 186
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(16Q23.1) MUTATED      8  149
  DEL PEAK 26(16Q23.1) WILD-TYPE    8  186
                        clus
vv                       DEL PEAK 26(16Q23.1) MUTATED
  HISPANIC OR LATINO                                8
  NOT HISPANIC OR LATINO                          149
                        clus
vv                       DEL PEAK 26(16Q23.1) WILD-TYPE
  HISPANIC OR LATINO                                  8
  NOT HISPANIC OR LATINO                            186
[1] 2 2
[1] FALSE

Clustering(54) Variable = DEL PEAK 27(17P13.1) MUTATION ANALYSIS
D54V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 27(17P13.1) MUTATED   132  90
  DEL PEAK 27(17P13.1) WILD-TYPE 103  39
  DEL PEAK 27(17P13.1) MUTATED DEL PEAK 27(17P13.1) WILD-TYPE 
                           222                            142 
  DEL PEAK 27(17P13.1) MUTATED DEL PEAK 27(17P13.1) WILD-TYPE 
                            90                             39 
$`DEL PEAK 27(17P13.1) MUTATED`
TCGA-2Y-A9GV TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A5W4 TCGA-DD-A4NI 
       83.24         8.61        69.57         5.03        17.98        26.83 
TCGA-DD-AADV TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-ES-A2HS TCGA-FV-A3I1 TCGA-FV-A3R2 
       18.87        21.83        18.90        22.62         8.12         6.38 
TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A7M9 TCGA-KR-A7K0 TCGA-LG-A6GG TCGA-T1-A6J8 
       81.73        30.74         1.84         2.14        12.72         0.76 
TCGA-UB-A7MF TCGA-XR-A8TG TCGA-ZP-A9D1 TCGA-ZS-A9CE TCGA-2Y-A9GS TCGA-2Y-A9GT 
        7.04        29.52         0.69        40.80        23.80        53.39 
TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H2 TCGA-2Y-A9H4 TCGA-2Y-A9H5 
       24.89        27.88       120.82        56.91        47.74        18.25 
TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-5C-AAPD TCGA-5R-AAAM TCGA-BC-4072 
       20.81        22.92         1.18         0.66         1.51        48.99 
TCGA-BC-4073 TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10Y TCGA-BC-A10Z 
       27.91        10.13        27.52        27.52        23.38         1.12 
TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A8YO 
       44.42        45.93         0.26        22.36        14.60        18.48 
TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 
       44.81        13.45         0.66         4.24         2.86         3.19 
TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-5264 TCGA-CC-A1HT TCGA-CC-A3MA TCGA-CC-A3MB 
        3.39         4.24         3.35         3.32         9.96        10.36 
TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IF TCGA-CC-A7IG 
       11.93        11.41         9.99         8.94        21.34         9.83 
TCGA-CC-A7II TCGA-CC-A7IK TCGA-CC-A7IL TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV 
       13.12         8.61         9.14         4.60        11.31         9.17 
TCGA-CC-A9FS TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 
        6.94        37.78        83.57        53.33       113.00         7.33 
TCGA-DD-A11A TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EG 
        2.60        21.76        51.29        79.40        66.31        45.11 
TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39Y 
       49.15         6.02        33.04        18.35        13.64         5.62 
TCGA-DD-A3A0 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A7 TCGA-DD-A3A9 
       25.81        17.59        20.12       102.74        13.78        30.61 
TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NO TCGA-DD-A4NQ 
       33.14        32.52        30.15        30.51        73.81        12.26 
TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73E TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB 
       23.93         9.30         1.45        11.41        75.65        76.41 
TCGA-DD-AACC TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACJ 
       55.40        71.80        12.00        15.42         6.41        69.11 
TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACV 
        3.52        58.16        14.20        59.31        51.52        50.33 
TCGA-DD-AACX TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD3 TCGA-DD-AAD5 
        5.59         5.62         4.50        18.54        42.58        44.22 
TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE 
       22.09        40.08        40.83        13.97        40.47        39.52 
TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADL TCGA-DD-AADN TCGA-DD-AADR TCGA-DD-AADW 
        3.78        37.64        20.91        29.52        66.67        19.30 
TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE4 TCGA-DD-AAE6 
       18.25        18.25        18.15        20.98        19.99         4.64 
TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP 
       15.72        25.08        26.63        50.33        35.08        90.48 
TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVU TCGA-DD-AAVV TCGA-DD-AAVW TCGA-DD-AAW1 
       89.69        82.62        72.39        80.71        76.18        65.39 
TCGA-ED-A459 TCGA-ED-A7PX TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E 
       29.92         0.20         0.20        14.04        13.15        13.41 
TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A2KC TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR 
        1.84         0.20         0.62        60.89        23.97        19.10 
TCGA-FV-A3I0 TCGA-FV-A495 TCGA-FV-A496 TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25V 
       27.88         0.03         0.33        13.68        53.79        28.27 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL 
       14.86        21.53        25.64        25.25        22.95        20.42 
TCGA-G3-A5SM TCGA-G3-A7M5 TCGA-G3-A7M6 TCGA-G3-AAUZ TCGA-G3-AAV1 TCGA-G3-AAV4 
       17.10        14.70        20.78        15.78        11.80         0.89 
TCGA-G3-AAV5 TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5N0 
       11.64        11.87        28.90         1.02         2.20        37.71 
TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I TCGA-NI-A4U2 
       11.80        27.25        16.67        22.95        20.71        58.88 
TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A6M4 TCGA-RC-A6M5 
       26.27        17.69        21.01         3.09         0.72         0.49 
TCGA-RC-A6M6 TCGA-RC-A7SB TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MB 
        0.30        19.33        15.39        15.52        36.10        19.76 
TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-AB4B 
       16.44         1.71        15.98        10.75        11.34        12.99 
TCGA-WX-AA44 TCGA-XR-A8TD TCGA-YA-A8S7 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CF 
       20.22        33.86        13.55        25.15        12.99        79.30 

$`DEL PEAK 27(17P13.1) WILD-TYPE`
TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-AAE7 
       11.74        38.40        36.66         0.36        90.28        21.17 
TCGA-DD-AAEG TCGA-EP-A3JL TCGA-G3-A3CG TCGA-G3-A6UC TCGA-K7-A5RF TCGA-KR-A7K7 
       23.64         9.96        22.13        22.06        20.75        31.27 
TCGA-MI-A75H TCGA-UB-AA0V TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9H1 
       24.56        10.32        63.75        41.79        80.28        40.41 
TCGA-2Y-A9H3 TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5R-AA1C 
       49.84         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-CC-A3M9 TCGA-CC-A7IE TCGA-CC-A7IH TCGA-CC-A7IJ TCGA-CC-A9FW TCGA-DD-A113 
        9.86         7.13        12.00        12.56         8.15        79.73 
TCGA-DD-A11B TCGA-DD-A1E9 TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF 
        0.46        90.71        19.79        75.65        11.47        12.95 
TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Z TCGA-DD-A3A1 TCGA-DD-A3A2 
       21.14        27.19        55.69        19.76         7.66        70.06 
TCGA-DD-A3A6 TCGA-DD-A4NF TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NP 
      107.11        30.97        39.78        56.25        29.56       108.76 
TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73F 
        0.30        80.75        78.84        23.05        22.78        35.67 
TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AACD TCGA-DD-AACI TCGA-DD-AACK 
      114.35        13.48         0.53        12.53        53.19         0.30 
TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACT TCGA-DD-AACW TCGA-DD-AACY 
       42.81        61.68        13.64        51.35        46.82        47.67 
TCGA-DD-AAD2 TCGA-DD-AADA TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADM 
       21.63        40.54        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-AAE3 
       14.89        15.06        14.33        15.58        18.21        18.61 
TCGA-DD-AAE9 TCGA-DD-AAEH TCGA-DD-AAVS TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ 
       23.74        25.78        59.93        56.48        64.77        62.47 
TCGA-DD-AAW0 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 
       66.25        60.99        53.69        26.93        28.08        13.91 
TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PY TCGA-ED-A8O5 TCGA-EP-A12J TCGA-EP-A26S 
       13.35         9.73        12.82        13.35        18.74        19.99 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A3R3 TCGA-FV-A4ZQ 
       20.61        19.59        11.93        14.40        12.03         0.39 
TCGA-G3-A25T TCGA-G3-A25X TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A7M7 
       51.06        58.49         5.92        19.53        19.23        11.87 
TCGA-G3-A7M8 TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV6 TCGA-HP-A5MZ 
       14.14        15.65        12.23        13.55         2.14         2.99 
TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C 
       17.06        16.83        29.79        13.97        12.03         9.57 
TCGA-MR-A520 TCGA-MR-A8JO TCGA-RC-A7S9 TCGA-RC-A7SF TCGA-UB-A7MA TCGA-WQ-A9G7 
        7.53        10.85        21.04        19.04        27.88         0.99 
TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TE TCGA-XR-A8TF TCGA-ZP-A9CV TCGA-ZP-A9CY 
       24.85        18.28        30.41        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(17P13.1) MUTATED DEL PEAK 27(17P13.1) WILD-TYPE 
                          0.03                           0.30 
  DEL PEAK 27(17P13.1) MUTATED DEL PEAK 27(17P13.1) WILD-TYPE 
                        120.82                         114.35 
  DEL PEAK 27(17P13.1) MUTATED DEL PEAK 27(17P13.1) WILD-TYPE 
                        19.000                         20.895 
[1] "0.0 - 120.8 (19.0)" "0.3 - 114.3 (20.9)"
[1] "hr=" "1.7"
D54V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IIIA
  DEL PEAK 27(17P13.1) MUTATED        93       58         2         39
  DEL PEAK 27(17P13.1) WILD-TYPE      80       29         1         23
                                vv
clus                             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 27(17P13.1) MUTATED            7          7        2         1
  DEL PEAK 27(17P13.1) WILD-TYPE          2          0        0         0
                                vv
clus                             STAGE IVB
  DEL PEAK 27(17P13.1) MUTATED           2
  DEL PEAK 27(17P13.1) WILD-TYPE         0
D54V3, multiclass
            clus
vv           DEL PEAK 27(17P13.1) MUTATED DEL PEAK 27(17P13.1) WILD-TYPE
  STAGE I                              93                             80
  STAGE II                             58                             29
  STAGE III                             2                              1
  STAGE IIIA                           39                             23
  STAGE IIIB                            7                              2
  STAGE IIIC                            7                              0
  STAGE IV                              2                              0
  STAGE IVA                             1                              0
  STAGE IVB                             2                              0
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 27(17P13.1) MUTATED   100  65  49  11
  DEL PEAK 27(17P13.1) WILD-TYPE  83  30  28   1
D54V4, multiclass
    clus
vv   DEL PEAK 27(17P13.1) MUTATED DEL PEAK 27(17P13.1) WILD-TYPE
  T1                          100                             83
  T2                           65                             30
  T3                           49                             28
  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"
D54V5, binary
                                cls
clus                               0   1
  DEL PEAK 27(17P13.1) MUTATED   155   3
  DEL PEAK 27(17P13.1) WILD-TYPE  99   0
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(17P13.1) MUTATED    155    3
  DEL PEAK 27(17P13.1) WILD-TYPE   99    0
   clus
vv  DEL PEAK 27(17P13.1) MUTATED DEL PEAK 27(17P13.1) WILD-TYPE
  0                          155                             99
  1                            3                              0
[1] 2 2
[1] FALSE
D54V6, binary
                                cls
clus                               0   1
  DEL PEAK 27(17P13.1) MUTATED   166   4
  DEL PEAK 27(17P13.1) WILD-TYPE 100   0
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(17P13.1) MUTATED    166    4
  DEL PEAK 27(17P13.1) WILD-TYPE  100    0
   clus
vv  DEL PEAK 27(17P13.1) MUTATED DEL PEAK 27(17P13.1) WILD-TYPE
  0                          166                            100
  1                            4                              0
[1] 2 2
[1] FALSE
D54V7, binary
                                cls
clus                               0   1
  DEL PEAK 27(17P13.1) MUTATED    70 156
  DEL PEAK 27(17P13.1) WILD-TYPE  48  96
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(17P13.1) MUTATED     70  156
  DEL PEAK 27(17P13.1) WILD-TYPE   48   96
        clus
vv       DEL PEAK 27(17P13.1) MUTATED DEL PEAK 27(17P13.1) WILD-TYPE
  FEMALE                           70                             48
  MALE                            156                             96
[1] 2 2
[1] FALSE
D54V8, binary
                                cls
clus                               0   1
  DEL PEAK 27(17P13.1) MUTATED   205   5
  DEL PEAK 27(17P13.1) WILD-TYPE 133   4
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(17P13.1) MUTATED    205    5
  DEL PEAK 27(17P13.1) WILD-TYPE  133    4
     clus
vv    DEL PEAK 27(17P13.1) MUTATED DEL PEAK 27(17P13.1) WILD-TYPE
  NO                           205                            133
  YES                            5                              4
[1] 2 2
[1] FALSE
                                vv
clus                             FIBROLAMELLAR CARCINOMA
  DEL PEAK 27(17P13.1) MUTATED                         2
  DEL PEAK 27(17P13.1) WILD-TYPE                       1
                                vv
clus                             HEPATOCELLULAR CARCINOMA
  DEL PEAK 27(17P13.1) MUTATED                        219
  DEL PEAK 27(17P13.1) WILD-TYPE                      141
                                vv
clus                             HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK 27(17P13.1) MUTATED                                  5
  DEL PEAK 27(17P13.1) WILD-TYPE                                2
D54V9, multiclass
                                  clus
vv                                 DEL PEAK 27(17P13.1) MUTATED
  FIBROLAMELLAR CARCINOMA                                     2
  HEPATOCELLULAR CARCINOMA                                  219
  HEPATOCHOLANGIOCARCINOMA (MIXED)                            5
                                  clus
vv                                 DEL PEAK 27(17P13.1) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                       1
  HEPATOCELLULAR CARCINOMA                                    141
  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(17P13.1) MUTATED   194  12   1  16
  DEL PEAK 27(17P13.1) WILD-TYPE 130   5   0   5
D54V10, multiclass
    clus
vv   DEL PEAK 27(17P13.1) MUTATED DEL PEAK 27(17P13.1) WILD-TYPE
  R0                          194                            130
  R1                           12                              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 27(17P13.1) MUTATED                                  1   104
  DEL PEAK 27(17P13.1) WILD-TYPE                                1    54
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 27(17P13.1) MUTATED                          12   104
  DEL PEAK 27(17P13.1) WILD-TYPE                         5    79
D54V11, multiclass
                                  clus
vv                                 DEL PEAK 27(17P13.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                     104
  BLACK OR AFRICAN AMERICAN                                  12
  WHITE                                                     104
                                  clus
vv                                 DEL PEAK 27(17P13.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        54
  BLACK OR AFRICAN AMERICAN                                     5
  WHITE                                                        79
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V12, binary
                                cls
clus                               0   1
  DEL PEAK 27(17P13.1) MUTATED    11 203
  DEL PEAK 27(17P13.1) WILD-TYPE   5 132
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(17P13.1) MUTATED     11  203
  DEL PEAK 27(17P13.1) WILD-TYPE    5  132
                        clus
vv                       DEL PEAK 27(17P13.1) MUTATED
  HISPANIC OR LATINO                               11
  NOT HISPANIC OR LATINO                          203
                        clus
vv                       DEL PEAK 27(17P13.1) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                            132
[1] 2 2
[1] FALSE

Clustering(55) Variable = DEL PEAK 28(17P11.2) MUTATION ANALYSIS
D55V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 28(17P11.2) MUTATED   110  81
  DEL PEAK 28(17P11.2) WILD-TYPE 125  48
  DEL PEAK 28(17P11.2) MUTATED DEL PEAK 28(17P11.2) WILD-TYPE 
                           191                            173 
  DEL PEAK 28(17P11.2) MUTATED DEL PEAK 28(17P11.2) WILD-TYPE 
                            81                             48 
$`DEL PEAK 28(17P11.2) MUTATED`
TCGA-2Y-A9GV TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A5W4 TCGA-DD-A4NI TCGA-DD-AADV 
       83.24        69.57         5.03        17.98        26.83        18.87 
TCGA-DD-AAEA TCGA-ES-A2HS TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25W 
       18.90        22.62         8.12         6.38        81.73        30.74 
TCGA-G3-A3CG TCGA-G3-A7M9 TCGA-KR-A7K0 TCGA-LG-A6GG TCGA-T1-A6J8 TCGA-UB-A7MF 
       22.13         1.84         2.14        12.72         0.76         7.04 
TCGA-XR-A8TG TCGA-ZP-A9D1 TCGA-ZS-A9CE TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GY 
       29.52         0.69        40.80        23.80        53.39        24.89 
TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H2 TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-2Y-A9H9 
       27.88       120.82        56.91        18.25        20.81        22.92 
TCGA-2Y-A9HA TCGA-5C-AAPD TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10R 
        1.18         0.66         1.51        48.99        27.91        10.13 
TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A217 TCGA-BC-A3KF 
       27.52        27.52        23.38         1.12        45.93         0.26 
TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BW-A5NO 
       22.36        14.60        18.48        44.81        13.45         0.66 
TCGA-CC-5258 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3MA 
        4.24         3.19         3.39         4.24         3.32         9.96 
TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IF 
       10.36        11.93        11.41         8.94         7.13        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-A11C TCGA-DD-A11D TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EG 
        7.33        21.76        51.29        79.40        66.31        45.11 
TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39Y TCGA-DD-A3A3 
        6.02        33.04        18.35        13.64         5.62        17.59 
TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A7 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NH 
       20.12       102.74        13.78        33.14        32.52        30.15 
TCGA-DD-A4NJ TCGA-DD-A4NO TCGA-DD-A4NQ TCGA-DD-A73B TCGA-DD-A73E TCGA-DD-AAC9 
       30.51        73.81        12.26         9.30         1.45        11.41 
TCGA-DD-AACA TCGA-DD-AACC TCGA-DD-AACE TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACJ 
       75.65        55.40        71.80        15.42         6.41        69.11 
TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACX TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 
        3.52        58.16         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-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADJ TCGA-DD-AADL TCGA-DD-AADN 
       39.52         3.78        37.64        35.05        20.91        29.52 
TCGA-DD-AADO TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE2 TCGA-DD-AAE4 
       14.89        19.30        18.25        18.25        20.98        19.99 
TCGA-DD-AAEB TCGA-DD-AAEE TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ 
       15.72        26.63        50.33        35.08        90.48        89.69 
TCGA-DD-AAVR TCGA-DD-AAVU TCGA-DD-AAVV TCGA-DD-AAW1 TCGA-ED-A459 TCGA-ED-A7PX 
       82.62        72.39        80.71        65.39        29.92         0.20 
TCGA-ED-A82E TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A2KC TCGA-FV-A23B TCGA-FV-A2QQ 
       13.41         1.84         0.20         0.62        60.89        23.97 
TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A495 TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25V 
       19.10        27.88         0.03        13.68        53.79        28.27 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A7M6 
       14.86        21.53        25.64        20.42        17.10        20.78 
TCGA-G3-AAUZ TCGA-G3-AAV1 TCGA-G3-AAV5 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB 
       15.78        11.80        11.64        28.90         1.02         2.20 
TCGA-HP-A5N0 TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I 
       37.71        11.80        27.25        16.67        22.95        20.71 
TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A6M4 TCGA-RC-A6M5 
       58.88        26.27        21.01         3.09         0.72         0.49 
TCGA-RC-A6M6 TCGA-RC-A7SB TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MB TCGA-UB-A7MC 
        0.30        19.33        15.52        36.10        19.76        16.44 
TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-AB4B TCGA-WX-AA44 
        1.71        15.98        10.75        11.34        12.99        20.22 
TCGA-XR-A8TD TCGA-YA-A8S7 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CF 
       33.86        13.55        25.15        12.99        79.30 

$`DEL PEAK 28(17P11.2) WILD-TYPE`
TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND 
       11.74        38.40         8.61        36.66         0.36        90.28 
TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEG TCGA-EP-A3JL TCGA-G3-A6UC TCGA-K7-A5RF 
       21.17        21.83        23.64         9.96        22.06        20.75 
TCGA-KR-A7K7 TCGA-MI-A75H TCGA-UB-AA0V TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX 
       31.27        24.56        10.32        63.75        41.79        80.28 
TCGA-2Y-A9H1 TCGA-2Y-A9H3 TCGA-2Y-A9H4 TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-5C-A9VG 
       40.41        49.84        47.74         8.55        13.02        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-CC-5260 TCGA-CC-5264 TCGA-CC-A3M9 
       25.32        44.42        12.72         2.86         3.35         9.86 
TCGA-CC-A5UD TCGA-CC-A7IH TCGA-CC-A7IJ TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A11A 
        9.99        12.00        12.56         8.15        79.73         2.60 
TCGA-DD-A11B TCGA-DD-A1E9 TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF 
        0.46        90.71        19.79        75.65        11.47        12.95 
TCGA-DD-A1EH TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Z TCGA-DD-A3A0 
       49.15        21.14        27.19        55.69        19.76        25.81 
TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A6 TCGA-DD-A3A9 TCGA-DD-A4NF TCGA-DD-A4NK 
        7.66        70.06       107.11        30.61        30.97        39.78 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NP TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV 
       56.25        29.56       108.76         0.30        80.75        78.84 
TCGA-DD-A73A TCGA-DD-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-AACB TCGA-DD-AACD TCGA-DD-AACF TCGA-DD-AACI TCGA-DD-AACK 
        0.53        76.41        12.53        12.00        53.19         0.30 
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-AACY TCGA-DD-AAD2 TCGA-DD-AADA 
       51.52        50.33        46.82        47.67        21.63        40.54 
TCGA-DD-AADD TCGA-DD-AADI TCGA-DD-AADK TCGA-DD-AADM TCGA-DD-AADP TCGA-DD-AADQ 
       40.47        35.67        34.49         0.39        15.06        14.33 
TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AAE1 TCGA-DD-AAE3 TCGA-DD-AAE6 
       66.67        15.58        18.21        18.15        18.61         4.64 
TCGA-DD-AAE9 TCGA-DD-AAED TCGA-DD-AAEH TCGA-DD-AAVS TCGA-DD-AAVW TCGA-DD-AAVX 
       23.74        25.08        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        60.99        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-A3RK TCGA-ES-A2HT TCGA-FV-A3R3 TCGA-FV-A496 TCGA-FV-A4ZQ 
       19.59        11.93        14.40        12.03         0.33         0.39 
TCGA-G3-A25T TCGA-G3-A25X TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI 
       51.06        58.49         5.92        19.53        19.23        25.25 
TCGA-G3-A5SJ TCGA-G3-A7M5 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAV0 TCGA-G3-AAV2 
       22.95        14.70        11.87        14.14        15.65        12.23 
TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-HP-A5MZ TCGA-K7-A5RG 
       13.55         0.89         2.14        11.87         2.99        17.06 
TCGA-K7-A6G5 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MR-A520 
       16.83        29.79        13.97        12.03         9.57         7.53 
TCGA-MR-A8JO TCGA-O8-A75V TCGA-RC-A7S9 TCGA-RC-A7SF TCGA-RC-A7SH TCGA-UB-A7MA 
       10.85        17.69        21.04        19.04        15.39        27.88 
TCGA-WQ-A9G7 TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TE TCGA-XR-A8TF TCGA-ZP-A9CV 
        0.99        24.85        18.28        30.41        22.78        35.77 
TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZS-A9CD TCGA-ZS-A9CG 
       25.71        23.21        35.87        45.57        11.21 

  DEL PEAK 28(17P11.2) MUTATED DEL PEAK 28(17P11.2) WILD-TYPE 
                          0.03                           0.20 
  DEL PEAK 28(17P11.2) MUTATED DEL PEAK 28(17P11.2) WILD-TYPE 
                        120.82                         114.35 
  DEL PEAK 28(17P11.2) MUTATED DEL PEAK 28(17P11.2) WILD-TYPE 
                         19.10                          20.75 
[1] "0.0 - 120.8 (19.1)" "0.2 - 114.3 (20.8)"
[1] "hr=" "1.7"
D55V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IIIA
  DEL PEAK 28(17P11.2) MUTATED        75       51         1         36
  DEL PEAK 28(17P11.2) WILD-TYPE      98       36         2         26
                                vv
clus                             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 28(17P11.2) MUTATED            7          6        2         1
  DEL PEAK 28(17P11.2) WILD-TYPE          2          1        0         0
                                vv
clus                             STAGE IVB
  DEL PEAK 28(17P11.2) MUTATED           1
  DEL PEAK 28(17P11.2) WILD-TYPE         1
D55V3, multiclass
            clus
vv           DEL PEAK 28(17P11.2) MUTATED DEL PEAK 28(17P11.2) WILD-TYPE
  STAGE I                              75                             98
  STAGE II                             51                             36
  STAGE III                             1                              2
  STAGE IIIA                           36                             26
  STAGE IIIB                            7                              2
  STAGE IIIC                            6                              1
  STAGE IV                              2                              0
  STAGE IVA                             1                              0
  STAGE IVB                             1                              1
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 28(17P11.2) MUTATED    82  58  45   9
  DEL PEAK 28(17P11.2) WILD-TYPE 101  37  32   3
D55V4, multiclass
    clus
vv   DEL PEAK 28(17P11.2) MUTATED DEL PEAK 28(17P11.2) WILD-TYPE
  T1                           82                            101
  T2                           58                             37
  T3                           45                             32
  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"
D55V5, binary
                                cls
clus                               0   1
  DEL PEAK 28(17P11.2) MUTATED   132   3
  DEL PEAK 28(17P11.2) WILD-TYPE 122   0
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 28(17P11.2) MUTATED    132    3
  DEL PEAK 28(17P11.2) WILD-TYPE  122    0
   clus
vv  DEL PEAK 28(17P11.2) MUTATED DEL PEAK 28(17P11.2) WILD-TYPE
  0                          132                            122
  1                            3                              0
[1] 2 2
[1] FALSE
D55V6, binary
                                cls
clus                               0   1
  DEL PEAK 28(17P11.2) MUTATED   140   3
  DEL PEAK 28(17P11.2) WILD-TYPE 126   1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 28(17P11.2) MUTATED    140    3
  DEL PEAK 28(17P11.2) WILD-TYPE  126    1
   clus
vv  DEL PEAK 28(17P11.2) MUTATED DEL PEAK 28(17P11.2) WILD-TYPE
  0                          140                            126
  1                            3                              1
[1] 2 2
[1] FALSE
D55V7, binary
                                cls
clus                               0   1
  DEL PEAK 28(17P11.2) MUTATED    63 132
  DEL PEAK 28(17P11.2) WILD-TYPE  55 120
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 28(17P11.2) MUTATED     63  132
  DEL PEAK 28(17P11.2) WILD-TYPE   55  120
        clus
vv       DEL PEAK 28(17P11.2) MUTATED DEL PEAK 28(17P11.2) WILD-TYPE
  FEMALE                           63                             55
  MALE                            132                            120
[1] 2 2
[1] FALSE
D55V8, binary
                                cls
clus                               0   1
  DEL PEAK 28(17P11.2) MUTATED   177   5
  DEL PEAK 28(17P11.2) WILD-TYPE 161   4
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 28(17P11.2) MUTATED    177    5
  DEL PEAK 28(17P11.2) WILD-TYPE  161    4
     clus
vv    DEL PEAK 28(17P11.2) MUTATED DEL PEAK 28(17P11.2) WILD-TYPE
  NO                           177                            161
  YES                            5                              4
[1] 2 2
[1] FALSE
                                vv
clus                             FIBROLAMELLAR CARCINOMA
  DEL PEAK 28(17P11.2) MUTATED                         2
  DEL PEAK 28(17P11.2) WILD-TYPE                       1
                                vv
clus                             HEPATOCELLULAR CARCINOMA
  DEL PEAK 28(17P11.2) MUTATED                        188
  DEL PEAK 28(17P11.2) WILD-TYPE                      172
                                vv
clus                             HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK 28(17P11.2) MUTATED                                  5
  DEL PEAK 28(17P11.2) WILD-TYPE                                2
D55V9, multiclass
                                  clus
vv                                 DEL PEAK 28(17P11.2) MUTATED
  FIBROLAMELLAR CARCINOMA                                     2
  HEPATOCELLULAR CARCINOMA                                  188
  HEPATOCHOLANGIOCARCINOMA (MIXED)                            5
                                  clus
vv                                 DEL PEAK 28(17P11.2) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                       1
  HEPATOCELLULAR CARCINOMA                                    172
  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 28(17P11.2) MUTATED   165  12   1  14
  DEL PEAK 28(17P11.2) WILD-TYPE 159   5   0   7
D55V10, multiclass
    clus
vv   DEL PEAK 28(17P11.2) MUTATED DEL PEAK 28(17P11.2) WILD-TYPE
  R0                          165                            159
  R1                           12                              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 28(17P11.2) MUTATED                                  1    84
  DEL PEAK 28(17P11.2) WILD-TYPE                                1    74
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 28(17P11.2) MUTATED                          10    96
  DEL PEAK 28(17P11.2) WILD-TYPE                         7    87
D55V11, multiclass
                                  clus
vv                                 DEL PEAK 28(17P11.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                      84
  BLACK OR AFRICAN AMERICAN                                  10
  WHITE                                                      96
                                  clus
vv                                 DEL PEAK 28(17P11.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        74
  BLACK OR AFRICAN AMERICAN                                     7
  WHITE                                                        87
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V12, binary
                                cls
clus                               0   1
  DEL PEAK 28(17P11.2) MUTATED    10 174
  DEL PEAK 28(17P11.2) WILD-TYPE   6 161
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 28(17P11.2) MUTATED     10  174
  DEL PEAK 28(17P11.2) WILD-TYPE    6  161
                        clus
vv                       DEL PEAK 28(17P11.2) MUTATED
  HISPANIC OR LATINO                               10
  NOT HISPANIC OR LATINO                          174
                        clus
vv                       DEL PEAK 28(17P11.2) WILD-TYPE
  HISPANIC OR LATINO                                  6
  NOT HISPANIC OR LATINO                            161
[1] 2 2
[1] FALSE

Clustering(56) Variable = DEL PEAK 29(18Q21.2) MUTATION ANALYSIS
D56V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 29(18Q21.2) MUTATED    62  30
  DEL PEAK 29(18Q21.2) WILD-TYPE 173  99
  DEL PEAK 29(18Q21.2) MUTATED DEL PEAK 29(18Q21.2) WILD-TYPE 
                            92                            272 
  DEL PEAK 29(18Q21.2) MUTATED DEL PEAK 29(18Q21.2) WILD-TYPE 
                            30                             99 
$`DEL PEAK 29(18Q21.2) MUTATED`
TCGA-BC-A112 TCGA-DD-A4NI TCGA-DD-AADV TCGA-DD-AAEG TCGA-ES-A2HS TCGA-FV-A3R2 
        5.03        26.83        18.87        23.64        22.62         6.38 
TCGA-KR-A7K7 TCGA-T1-A6J8 TCGA-UB-A7MF TCGA-ZS-A9CE TCGA-2Y-A9H3 TCGA-2Y-A9H5 
       31.27         0.76         7.04        40.80        49.84        18.25 
TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1D TCGA-BC-A10R TCGA-BC-A10U TCGA-BC-A216 
       10.59         0.66        14.76        10.13        27.52        44.42 
TCGA-BC-A217 TCGA-BC-A3KF TCGA-CC-A3MB TCGA-CC-A5UD TCGA-CC-A7IK TCGA-CC-A8HV 
       45.93         0.26        10.36         9.99         8.61         9.17 
TCGA-DD-A118 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A1EF TCGA-DD-A1EJ TCGA-DD-A1EL 
      113.00         2.60         0.46        12.95        33.04        13.64 
TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A3A4 TCGA-DD-A3A9 TCGA-DD-A4NB TCGA-DD-A4NN 
       55.69         5.62        20.12        30.61        32.52        29.56 
TCGA-DD-A4NO TCGA-DD-A73B TCGA-DD-A73E TCGA-DD-A73G TCGA-DD-AAC8 TCGA-DD-AACB 
       73.81         9.30         1.45       114.35         0.53        76.41 
TCGA-DD-AACE TCGA-DD-AACI TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACV 
       71.80        53.19        42.81        61.68        13.64        50.33 
TCGA-DD-AACX TCGA-DD-AACZ TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AADA TCGA-DD-AADI 
        5.59         5.62        44.22        22.09        40.54        35.67 
TCGA-DD-AADJ TCGA-DD-AADO TCGA-DD-AADW TCGA-DD-AAE0 TCGA-DD-AAE2 TCGA-DD-AAEK 
       35.05        14.89        19.30        18.25        20.98        35.08 
TCGA-DD-AAVP TCGA-DD-AAVV TCGA-ED-A459 TCGA-ED-A66X TCGA-ED-A7XP TCGA-ED-A82E 
       90.48        80.71        29.92        13.35        13.15        13.41 
TCGA-ED-A8O6 TCGA-FV-A3I0 TCGA-FV-A496 TCGA-G3-A25S TCGA-G3-A7M5 TCGA-G3-AAV1 
        1.84        27.88         0.33        13.68        14.70        11.80 
TCGA-G3-AAV6 TCGA-GJ-A3OU TCGA-MI-A75G TCGA-MR-A8JO TCGA-NI-A8LF TCGA-QA-A7B7 
        2.14        28.90        22.95        10.85        26.27         3.09 
TCGA-RC-A6M4 TCGA-RC-A6M5 TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 
        0.72         0.49        19.04        15.39        15.52        36.10 
TCGA-UB-A7MC TCGA-WX-AA44 TCGA-WX-AA47 TCGA-YA-A8S7 TCGA-ZP-A9CZ TCGA-ZP-A9D0 
       16.44        20.22        18.28        13.55        23.21        35.87 
TCGA-ZS-A9CF TCGA-ZS-A9CG 
       79.30        11.21 

$`DEL PEAK 29(18Q21.2) WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A5W4 
       83.24        11.74        38.40         8.61        69.57        17.98 
TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEA 
       36.66         0.36        90.28        21.17        21.83        18.90 
TCGA-EP-A3JL TCGA-FV-A3I1 TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC 
        9.96         8.12        81.73        30.74        22.13        22.06 
TCGA-G3-A7M9 TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-LG-A6GG TCGA-MI-A75H TCGA-UB-AA0V 
        1.84        20.75         2.14        12.72        24.56        10.32 
TCGA-XR-A8TG TCGA-ZP-A9D1 TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW 
       29.52         0.69        23.80        53.39        63.75        41.79 
TCGA-2Y-A9GX TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 
       80.28        24.89        27.88       120.82        40.41        56.91 
TCGA-2Y-A9H4 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 
       47.74        20.81        22.92         1.18         8.55        13.02 
TCGA-5C-A9VG TCGA-5R-AA1C TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q 
       10.78        17.10         1.51        48.99        27.91        37.32 
TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z 
       46.78        27.52         2.99        25.32        23.38         1.12 
TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP 
       22.36        14.60        12.72        18.48        44.81        13.45 
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-A3MC TCGA-CC-A5UC 
        3.35         3.32         9.86         9.96        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-A7IJ TCGA-CC-A7IL TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A9FS TCGA-CC-A9FW 
       12.56         9.14         4.60        11.31         6.94         8.15 
TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A119 TCGA-DD-A11C 
       79.73        37.78        83.57        53.33         7.33        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-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EK TCGA-DD-A39V 
       11.47        45.11        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-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A4NA TCGA-DD-A4NF TCGA-DD-A4NH 
      102.74       107.11        13.78        33.14        30.97        30.15 
TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR 
       30.51        39.78        56.25       108.76        12.26         0.30 
TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73F 
       80.75        78.84        23.93        23.05        22.78        35.67 
TCGA-DD-AA3A TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACF 
       13.48        11.41        75.65        55.40        12.53        12.00 
TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM 
       15.42         6.41        69.11         0.30         3.52        58.16 
TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACW TCGA-DD-AACY 
       14.20        59.31        51.35        51.52        46.82        47.67 
TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD8 TCGA-DD-AADB 
        4.50        18.54        21.63        42.58        40.08        40.83 
TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADK 
       13.97        40.47        39.52         3.78        37.64        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-AADY TCGA-DD-AAE1 TCGA-DD-AAE3 TCGA-DD-AAE4 
       15.58        18.21        18.25        18.15        18.61        19.99 
TCGA-DD-AAE6 TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEH 
        4.64        23.74        15.72        25.08        26.63        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        60.99 
TCGA-DD-AAW3 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66Y TCGA-ED-A7PX 
       53.69        26.93        28.08        13.91         9.73         0.20 
TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A8O5 TCGA-ED-A97K TCGA-EP-A12J 
       12.82         0.20        14.04        13.35         0.20        18.74 
TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HT 
       19.99        20.61        19.59         0.62        11.93        14.40 
TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A4ZQ 
       60.89        23.97        19.10        12.03         0.03         0.39 
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-A5SJ 
       25.64         5.92        19.53        19.23        25.25        22.95 
TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ 
       20.42        17.10        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-AAV7 
       15.65        12.23        13.55         0.89        11.64        11.87 
TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 
        1.02         2.20         2.99        37.71        17.06        16.83 
TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C 
       11.80        27.25        29.79        13.97        12.03         9.57 
TCGA-MI-A75E TCGA-MI-A75I TCGA-MR-A520 TCGA-NI-A4U2 TCGA-O8-A75V TCGA-PD-A5DF 
       16.67        20.71         7.53        58.88        17.69        21.01 
TCGA-RC-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MD 
        0.30        21.04        19.33        27.88        19.76         1.71 
TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA46 
       15.98        10.75        11.34         0.99        12.99        24.85 
TCGA-XR-A8TD TCGA-XR-A8TE TCGA-XR-A8TF TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9D2 
       33.86        30.41        22.78        35.77        25.71        25.15 
TCGA-ZP-A9D4 TCGA-ZS-A9CD 
       12.99        45.57 

  DEL PEAK 29(18Q21.2) MUTATED DEL PEAK 29(18Q21.2) WILD-TYPE 
                          0.26                           0.03 
  DEL PEAK 29(18Q21.2) MUTATED DEL PEAK 29(18Q21.2) WILD-TYPE 
                        114.35                         120.82 
  DEL PEAK 29(18Q21.2) MUTATED DEL PEAK 29(18Q21.2) WILD-TYPE 
                        18.575                         20.205 
[1] "0.3 - 114.3 (18.6)" "0.0 - 120.8 (20.2)"
[1] "hr=" "1"  
D56V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IIIA
  DEL PEAK 29(18Q21.2) MUTATED        44       22         0         17
  DEL PEAK 29(18Q21.2) WILD-TYPE     129       65         3         45
                                vv
clus                             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 29(18Q21.2) MUTATED            0          2        1         1
  DEL PEAK 29(18Q21.2) WILD-TYPE          9          5        1         0
                                vv
clus                             STAGE IVB
  DEL PEAK 29(18Q21.2) MUTATED           1
  DEL PEAK 29(18Q21.2) WILD-TYPE         1
D56V3, multiclass
            clus
vv           DEL PEAK 29(18Q21.2) MUTATED DEL PEAK 29(18Q21.2) WILD-TYPE
  STAGE I                              44                            129
  STAGE II                             22                             65
  STAGE III                             0                              3
  STAGE IIIA                           17                             45
  STAGE IIIB                            0                              9
  STAGE IIIC                            2                              5
  STAGE IV                              1                              1
  STAGE IVA                             1                              0
  STAGE IVB                             1                              1
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 29(18Q21.2) MUTATED    49  24  19   2
  DEL PEAK 29(18Q21.2) WILD-TYPE 134  71  58  10
D56V4, multiclass
    clus
vv   DEL PEAK 29(18Q21.2) MUTATED DEL PEAK 29(18Q21.2) WILD-TYPE
  T1                           49                            134
  T2                           24                             71
  T3                           19                             58
  T4                            2                             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V5, binary
                                cls
clus                               0   1
  DEL PEAK 29(18Q21.2) MUTATED    63   2
  DEL PEAK 29(18Q21.2) WILD-TYPE 191   1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(18Q21.2) MUTATED     63    2
  DEL PEAK 29(18Q21.2) WILD-TYPE  191    1
   clus
vv  DEL PEAK 29(18Q21.2) MUTATED DEL PEAK 29(18Q21.2) WILD-TYPE
  0                           63                            191
  1                            2                              1
[1] 2 2
[1] FALSE
D56V6, binary
                                cls
clus                               0   1
  DEL PEAK 29(18Q21.2) MUTATED    68   2
  DEL PEAK 29(18Q21.2) WILD-TYPE 198   2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(18Q21.2) MUTATED     68    2
  DEL PEAK 29(18Q21.2) WILD-TYPE  198    2
   clus
vv  DEL PEAK 29(18Q21.2) MUTATED DEL PEAK 29(18Q21.2) WILD-TYPE
  0                           68                            198
  1                            2                              2
[1] 2 2
[1] FALSE
D56V7, binary
                                cls
clus                               0   1
  DEL PEAK 29(18Q21.2) MUTATED    36  58
  DEL PEAK 29(18Q21.2) WILD-TYPE  82 194
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(18Q21.2) MUTATED     36   58
  DEL PEAK 29(18Q21.2) WILD-TYPE   82  194
        clus
vv       DEL PEAK 29(18Q21.2) MUTATED DEL PEAK 29(18Q21.2) WILD-TYPE
  FEMALE                           36                             82
  MALE                             58                            194
[1] 2 2
[1] FALSE
D56V8, binary
                                cls
clus                               0   1
  DEL PEAK 29(18Q21.2) MUTATED    80   4
  DEL PEAK 29(18Q21.2) WILD-TYPE 258   5
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(18Q21.2) MUTATED     80    4
  DEL PEAK 29(18Q21.2) WILD-TYPE  258    5
     clus
vv    DEL PEAK 29(18Q21.2) MUTATED DEL PEAK 29(18Q21.2) WILD-TYPE
  NO                            80                            258
  YES                            4                              5
[1] 2 2
[1] FALSE
                                vv
clus                             FIBROLAMELLAR CARCINOMA
  DEL PEAK 29(18Q21.2) MUTATED                         3
  DEL PEAK 29(18Q21.2) WILD-TYPE                       0
                                vv
clus                             HEPATOCELLULAR CARCINOMA
  DEL PEAK 29(18Q21.2) MUTATED                         89
  DEL PEAK 29(18Q21.2) WILD-TYPE                      271
                                vv
clus                             HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK 29(18Q21.2) MUTATED                                  2
  DEL PEAK 29(18Q21.2) WILD-TYPE                                5
D56V9, multiclass
                                  clus
vv                                 DEL PEAK 29(18Q21.2) MUTATED
  FIBROLAMELLAR CARCINOMA                                     3
  HEPATOCELLULAR CARCINOMA                                   89
  HEPATOCHOLANGIOCARCINOMA (MIXED)                            2
                                  clus
vv                                 DEL PEAK 29(18Q21.2) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                       0
  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 29(18Q21.2) MUTATED    83   3   0   8
  DEL PEAK 29(18Q21.2) WILD-TYPE 241  14   1  13
D56V10, multiclass
    clus
vv   DEL PEAK 29(18Q21.2) MUTATED DEL PEAK 29(18Q21.2) WILD-TYPE
  R0                           83                            241
  R1                            3                             14
  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 29(18Q21.2) MUTATED                                  0    41
  DEL PEAK 29(18Q21.2) WILD-TYPE                                2   117
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 29(18Q21.2) MUTATED                           5    48
  DEL PEAK 29(18Q21.2) WILD-TYPE                        12   135
D56V11, multiclass
                                  clus
vv                                 DEL PEAK 29(18Q21.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                      41
  BLACK OR AFRICAN AMERICAN                                   5
  WHITE                                                      48
                                  clus
vv                                 DEL PEAK 29(18Q21.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              2
  ASIAN                                                       117
  BLACK OR AFRICAN AMERICAN                                    12
  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"
D56V12, binary
                                cls
clus                               0   1
  DEL PEAK 29(18Q21.2) MUTATED     5  83
  DEL PEAK 29(18Q21.2) WILD-TYPE  11 252
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(18Q21.2) MUTATED      5   83
  DEL PEAK 29(18Q21.2) WILD-TYPE   11  252
                        clus
vv                       DEL PEAK 29(18Q21.2) MUTATED
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                           83
                        clus
vv                       DEL PEAK 29(18Q21.2) WILD-TYPE
  HISPANIC OR LATINO                                 11
  NOT HISPANIC OR LATINO                            252
[1] 2 2
[1] FALSE

Clustering(57) Variable = DEL PEAK 30(19P13.3) MUTATION ANALYSIS
D57V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 30(19P13.3) MUTATED    51  34
  DEL PEAK 30(19P13.3) WILD-TYPE 184  95
  DEL PEAK 30(19P13.3) MUTATED DEL PEAK 30(19P13.3) WILD-TYPE 
                            85                            279 
  DEL PEAK 30(19P13.3) MUTATED DEL PEAK 30(19P13.3) WILD-TYPE 
                            34                             95 
$`DEL PEAK 30(19P13.3) MUTATED`
TCGA-4R-AA8I TCGA-BC-A112 TCGA-DD-AADV TCGA-DD-AAE8 TCGA-DD-AAEG TCGA-FV-A3I1 
        8.61         5.03        18.87        21.83        23.64         8.12 
TCGA-FV-A4ZP TCGA-T1-A6J8 TCGA-2Y-A9GS TCGA-2Y-A9GU TCGA-2Y-A9GY TCGA-2Y-A9GZ 
       81.73         0.76        23.80        63.75        24.89        27.88 
TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9HA TCGA-BC-A10W TCGA-BC-A3KF TCGA-BC-A69H 
       56.91        49.84         1.18         2.99         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        71.80        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-AAE6 TCGA-DD-AAVR TCGA-DD-AAVV TCGA-ED-A459 
       40.47        20.91         4.64        82.62        80.71        29.92 
TCGA-ED-A4XI TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A8O6 TCGA-ED-A97K TCGA-FV-A496 
       26.93         0.20        14.04         1.84         0.20         0.33 
TCGA-G3-A25S TCGA-G3-A25X TCGA-G3-A3CH TCGA-G3-A5SM TCGA-G3-A7M6 TCGA-G3-AAV1 
       13.68        58.49        25.64        17.10        20.78        11.80 
TCGA-G3-AAV7 TCGA-MI-A75C TCGA-NI-A8LF TCGA-RC-A6M4 TCGA-RC-A6M6 TCGA-RC-A7SK 
       11.87         9.57        26.27         0.72         0.30        15.52 
TCGA-RG-A7D4 
       36.10 

$`DEL PEAK 30(19P13.3) WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-BC-A110 TCGA-BC-A5W4 TCGA-BD-A3ER 
       83.24        11.74        38.40        69.57        17.98        36.66 
TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AAE7 TCGA-DD-AAEA TCGA-EP-A3JL 
        0.36        90.28        26.83        21.17        18.90         9.96 
TCGA-ES-A2HS TCGA-FV-A3R2 TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC TCGA-G3-A7M9 
       22.62         6.38        30.74        22.13        22.06         1.84 
TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H TCGA-UB-A7MF 
       20.75         2.14        31.27        12.72        24.56         7.04 
TCGA-UB-AA0V TCGA-XR-A8TG TCGA-ZP-A9D1 TCGA-ZS-A9CE TCGA-2Y-A9GT TCGA-2Y-A9GW 
       10.32        29.52         0.69        40.80        53.39        41.79 
TCGA-2Y-A9GX TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H8 
       80.28       120.82        40.41        47.74        18.25        20.81 
TCGA-2Y-A9H9 TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD 
       22.92         8.55        13.02        10.78        10.59         0.66 
TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q 
       17.10        14.76         1.51        48.99        27.91        37.32 
TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10X TCGA-BC-A10Y 
       10.13        46.78        27.52        27.52        25.32        23.38 
TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KG TCGA-BC-A69I TCGA-BD-A2L6 
        1.12        44.42        45.93        22.36        12.72        44.81 
TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5264 
       13.45         0.66         2.86         3.19         3.39         3.35 
TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A5UC TCGA-CC-A7IE TCGA-CC-A7IH 
        9.86         9.96        10.36        11.41         7.13        12.00 
TCGA-CC-A7IJ TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FS TCGA-CC-A9FW 
       12.56         4.60        11.31         9.17         6.94         8.15 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11C 
       37.78        83.57        53.33         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-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-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-A4NA TCGA-DD-A4NB TCGA-DD-A4NF 
      102.74       107.11        13.78        33.14        32.52        30.97 
TCGA-DD-A4NH TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP 
       30.15        39.78        56.25        29.56        73.81       108.76 
TCGA-DD-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-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 
        1.45        35.67       114.35        13.48         0.53        11.41 
TCGA-DD-AACA TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACF TCGA-DD-AACI TCGA-DD-AACJ 
       75.65        55.40        12.53        12.00        53.19        69.11 
TCGA-DD-AACK TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACT TCGA-DD-AACW TCGA-DD-AACX 
        0.30        58.16        42.81        51.35        46.82         5.59 
TCGA-DD-AACY TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AADA 
       47.67         4.50        18.54        21.63        42.58        40.54 
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-AADP TCGA-DD-AADQ TCGA-DD-AADR 
        0.39        29.52        14.89        15.06        14.33        66.67 
TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 
       15.58        18.21        19.30        18.25        18.25        18.15 
TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAED 
       20.98        18.61        19.99        23.74        15.72        25.08 
TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ 
       26.63        25.78        50.33        35.08        90.48        89.69 
TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ 
       59.93        72.39        76.18        56.48        64.77        62.47 
TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A5KG TCGA-ED-A627 
       66.25        65.39        60.99        53.69        28.08        13.91 
TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7XP TCGA-ED-A82E 
       13.35         9.73         0.20        12.82        13.15        13.41 
TCGA-ED-A8O5 TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC 
       13.35        18.74        19.99        20.61        19.59         0.62 
TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 
       11.93        14.40        60.89        23.97        19.10        27.88 
TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V 
       12.03         0.03         0.39        51.06        53.79        28.27 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI 
       14.86        21.53         5.92        19.53        19.23        25.25 
TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A7M5 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ 
       22.95        20.42        14.70        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        11.64         2.14 
TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RG 
       28.90         1.02         2.20         2.99        37.71        17.06 
TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD 
       16.83        11.80        27.25        29.79        13.97        12.03 
TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 
       16.67        22.95        20.71         7.53        10.85        58.88 
TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A6M5 TCGA-RC-A7S9 TCGA-RC-A7SB 
       17.69        21.01         3.09         0.49        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        27.88        19.76        16.44         1.71 
TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA44 
       15.98        10.75        11.34         0.99        12.99        20.22 
TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TD TCGA-XR-A8TE TCGA-XR-A8TF TCGA-YA-A8S7 
       24.85        18.28        33.86        30.41        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-A9CF TCGA-ZS-A9CG 
       45.57        79.30        11.21 

  DEL PEAK 30(19P13.3) MUTATED DEL PEAK 30(19P13.3) WILD-TYPE 
                          0.20                           0.03 
  DEL PEAK 30(19P13.3) MUTATED DEL PEAK 30(19P13.3) WILD-TYPE 
                        113.00                         120.82 
  DEL PEAK 30(19P13.3) MUTATED DEL PEAK 30(19P13.3) WILD-TYPE 
                         15.52                          20.12 
[1] "0.2 - 113.0 (15.5)" "0.0 - 120.8 (20.1)"
[1] "hr=" "1.3"
D57V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IIIA
  DEL PEAK 30(19P13.3) MUTATED        35       27         0         16
  DEL PEAK 30(19P13.3) WILD-TYPE     138       60         3         46
                                vv
clus                             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 30(19P13.3) MUTATED            1          3        0         0
  DEL PEAK 30(19P13.3) WILD-TYPE          8          4        2         1
                                vv
clus                             STAGE IVB
  DEL PEAK 30(19P13.3) MUTATED           1
  DEL PEAK 30(19P13.3) WILD-TYPE         1
D57V3, multiclass
            clus
vv           DEL PEAK 30(19P13.3) MUTATED DEL PEAK 30(19P13.3) WILD-TYPE
  STAGE I                              35                            138
  STAGE II                             27                             60
  STAGE III                             0                              3
  STAGE IIIA                           16                             46
  STAGE IIIB                            1                              8
  STAGE IIIC                            3                              4
  STAGE IV                              0                              2
  STAGE IVA                             0                              1
  STAGE IVB                             1                              1
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 30(19P13.3) MUTATED    37  28  17   5
  DEL PEAK 30(19P13.3) WILD-TYPE 146  67  60   7
D57V4, multiclass
    clus
vv   DEL PEAK 30(19P13.3) MUTATED DEL PEAK 30(19P13.3) WILD-TYPE
  T1                           37                            146
  T2                           28                             67
  T3                           17                             60
  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"
D57V5, binary
                                cls
clus                               0   1
  DEL PEAK 30(19P13.3) MUTATED    62   1
  DEL PEAK 30(19P13.3) WILD-TYPE 192   2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(19P13.3) MUTATED     62    1
  DEL PEAK 30(19P13.3) WILD-TYPE  192    2
   clus
vv  DEL PEAK 30(19P13.3) MUTATED DEL PEAK 30(19P13.3) WILD-TYPE
  0                           62                            192
  1                            1                              2
[1] 2 2
[1] FALSE
D57V6, binary
                                cls
clus                               0   1
  DEL PEAK 30(19P13.3) MUTATED    70   1
  DEL PEAK 30(19P13.3) WILD-TYPE 196   3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(19P13.3) MUTATED     70    1
  DEL PEAK 30(19P13.3) WILD-TYPE  196    3
   clus
vv  DEL PEAK 30(19P13.3) MUTATED DEL PEAK 30(19P13.3) WILD-TYPE
  0                           70                            196
  1                            1                              3
[1] 2 2
[1] FALSE
D57V7, binary
                                cls
clus                               0   1
  DEL PEAK 30(19P13.3) MUTATED    25  62
  DEL PEAK 30(19P13.3) WILD-TYPE  93 190
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(19P13.3) MUTATED     25   62
  DEL PEAK 30(19P13.3) WILD-TYPE   93  190
        clus
vv       DEL PEAK 30(19P13.3) MUTATED DEL PEAK 30(19P13.3) WILD-TYPE
  FEMALE                           25                             93
  MALE                             62                            190
[1] 2 2
[1] FALSE
D57V8, binary
                                cls
clus                               0   1
  DEL PEAK 30(19P13.3) MUTATED    76   1
  DEL PEAK 30(19P13.3) WILD-TYPE 262   8
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(19P13.3) MUTATED     76    1
  DEL PEAK 30(19P13.3) WILD-TYPE  262    8
     clus
vv    DEL PEAK 30(19P13.3) MUTATED DEL PEAK 30(19P13.3) WILD-TYPE
  NO                            76                            262
  YES                            1                              8
[1] 2 2
[1] FALSE
                                vv
clus                             FIBROLAMELLAR CARCINOMA
  DEL PEAK 30(19P13.3) MUTATED                         0
  DEL PEAK 30(19P13.3) WILD-TYPE                       3
                                vv
clus                             HEPATOCELLULAR CARCINOMA
  DEL PEAK 30(19P13.3) MUTATED                         86
  DEL PEAK 30(19P13.3) WILD-TYPE                      274
                                vv
clus                             HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK 30(19P13.3) MUTATED                                  1
  DEL PEAK 30(19P13.3) WILD-TYPE                                6
D57V9, multiclass
                                  clus
vv                                 DEL PEAK 30(19P13.3) MUTATED
  FIBROLAMELLAR CARCINOMA                                     0
  HEPATOCELLULAR CARCINOMA                                   86
  HEPATOCHOLANGIOCARCINOMA (MIXED)                            1
                                  clus
vv                                 DEL PEAK 30(19P13.3) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                       3
  HEPATOCELLULAR CARCINOMA                                    274
  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(19P13.3) MUTATED    77   5   0   4
  DEL PEAK 30(19P13.3) WILD-TYPE 247  12   1  17
D57V10, multiclass
    clus
vv   DEL PEAK 30(19P13.3) MUTATED DEL PEAK 30(19P13.3) WILD-TYPE
  R0                           77                            247
  R1                            5                             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 30(19P13.3) MUTATED                                  0    51
  DEL PEAK 30(19P13.3) WILD-TYPE                                2   107
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 30(19P13.3) MUTATED                           3    33
  DEL PEAK 30(19P13.3) WILD-TYPE                        14   150
D57V11, multiclass
                                  clus
vv                                 DEL PEAK 30(19P13.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                      51
  BLACK OR AFRICAN AMERICAN                                   3
  WHITE                                                      33
                                  clus
vv                                 DEL PEAK 30(19P13.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              2
  ASIAN                                                       107
  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"
D57V12, binary
                                cls
clus                               0   1
  DEL PEAK 30(19P13.3) MUTATED     3  83
  DEL PEAK 30(19P13.3) WILD-TYPE  13 252
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(19P13.3) MUTATED      3   83
  DEL PEAK 30(19P13.3) WILD-TYPE   13  252
                        clus
vv                       DEL PEAK 30(19P13.3) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           83
                        clus
vv                       DEL PEAK 30(19P13.3) WILD-TYPE
  HISPANIC OR LATINO                                 13
  NOT HISPANIC OR LATINO                            252
[1] 2 2
[1] FALSE

Clustering(58) Variable = DEL PEAK 31(20P12.1) MUTATION ANALYSIS
D58V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 31(20P12.1) MUTATED    18  10
  DEL PEAK 31(20P12.1) WILD-TYPE 217 119
  DEL PEAK 31(20P12.1) MUTATED DEL PEAK 31(20P12.1) WILD-TYPE 
                            28                            336 
  DEL PEAK 31(20P12.1) MUTATED DEL PEAK 31(20P12.1) WILD-TYPE 
                            10                            119 
$`DEL PEAK 31(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 TCGA-XR-A8TD 
        0.20         0.20        10.85        33.86 

$`DEL PEAK 31(20P12.1) WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A5W4 
       83.24        38.40         8.61        69.57         5.03        17.98 
TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV TCGA-DD-AAE7 
       36.66         0.36        90.28        26.83        18.87        21.17 
TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-ES-A2HS TCGA-FV-A3I1 
       21.83        18.90        23.64         9.96        22.62         8.12 
TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC TCGA-G3-A7M9 
        6.38        81.73        30.74        22.13        22.06         1.84 
TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H TCGA-T1-A6J8 
       20.75         2.14        31.27        12.72        24.56         0.76 
TCGA-UB-A7MF TCGA-UB-AA0V TCGA-XR-A8TG TCGA-ZP-A9D1 TCGA-ZS-A9CE TCGA-2Y-A9GS 
        7.04        10.32        29.52         0.69        40.80        23.80 
TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GY TCGA-2Y-A9GZ 
       53.39        63.75        41.79        80.28        24.89        27.88 
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-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-5C-A9VH TCGA-5C-AAPD 
       20.81        22.92         1.18         8.55        10.59         0.66 
TCGA-5R-AA1C TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R 
       17.10         1.51        48.99        27.91        37.32        10.13 
TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y 
       46.78        27.52        27.52         2.99        25.32        23.38 
TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A69I 
       44.42        45.93         0.26        22.36        14.60        12.72 
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-A3M9 
        3.19         3.39         4.24         3.35         3.32         9.86 
TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IE 
        9.96        10.36        11.41         9.99         8.94         7.13 
TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A8HT 
       21.34         9.83        13.12        12.56         8.61         4.60 
TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 
       11.31         9.17         8.15        79.73        37.78        83.57 
TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C 
       53.33       113.00         7.33         2.60         0.46        21.76 
TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED 
       51.29        90.71        79.40        66.31        19.79        75.65 
TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ 
       11.47        12.95        45.11        49.15         6.02        33.04 
TCGA-DD-A1EL TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 
       13.64        27.19        55.69        19.76        25.81         7.66 
TCGA-DD-A3A2 TCGA-DD-A3A4 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NA 
       70.06        20.12       107.11        13.78        30.61        33.14 
TCGA-DD-A4NB TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL 
       32.52        30.97        30.15        30.51        39.78        56.25 
TCGA-DD-A4NN TCGA-DD-A4NP TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A 
       29.56       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-AACG TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ 
       71.80        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-AACT TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACY 
       14.20        51.35        51.52        50.33        46.82        47.67 
TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD6 TCGA-DD-AAD8 
        4.50        18.54        21.63        42.58        22.09        40.08 
TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG 
       40.83        13.97        40.47        39.52         3.78        37.64 
TCGA-DD-AADI TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP 
       35.67        34.49        20.91        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-AAE9 TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAEI 
       23.74        15.72        25.08        26.63        25.78        50.33 
TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU 
       35.08        90.48        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-A5KG 
       65.39        60.99        53.69        29.92        26.93        28.08 
TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO 
       13.91        13.35         9.73        12.82         0.20        14.04 
TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-EP-A12J TCGA-EP-A26S 
       13.15        13.41        13.35         1.84        18.74        19.99 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B 
       20.61        19.59         0.62        11.93        14.40        60.89 
TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 
       23.97        19.10        27.88        12.03         0.03         0.33 
TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25X 
        0.39        13.68        51.06        53.79        28.27        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-A7M5 TCGA-G3-A7M6 
       25.25        22.95        20.42        17.10        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        11.64         2.14        11.87        28.90 
TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 
        1.02         2.20         2.99        37.71        17.06        16.83 
TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C 
       11.80        27.25        29.79        13.97        12.03         9.57 
TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A520 TCGA-NI-A4U2 TCGA-NI-A8LF 
       16.67        22.95        20.71         7.53        58.88        26.27 
TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A6M4 TCGA-RC-A6M5 TCGA-RC-A6M6 
       17.69        21.01         3.09         0.72         0.49         0.30 
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-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0U 
       27.88        19.76        16.44         1.71        15.98        10.75 
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-A8TE TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ 
       30.41        22.78        13.55        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 31(20P12.1) MUTATED DEL PEAK 31(20P12.1) WILD-TYPE 
                          0.20                           0.03 
  DEL PEAK 31(20P12.1) MUTATED DEL PEAK 31(20P12.1) WILD-TYPE 
                        102.74                         120.82 
  DEL PEAK 31(20P12.1) MUTATED DEL PEAK 31(20P12.1) WILD-TYPE 
                         12.13                          20.32 
[1] "0.2 - 102.7 (12.1)" "0.0 - 120.8 (20.3)"
[1] "hr=" "1.2"
D58V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IIIA
  DEL PEAK 31(20P12.1) MUTATED        12        8         1          5
  DEL PEAK 31(20P12.1) WILD-TYPE     161       79         2         57
                                vv
clus                             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 31(20P12.1) MUTATED            2          0        0         0
  DEL PEAK 31(20P12.1) WILD-TYPE          7          7        2         1
                                vv
clus                             STAGE IVB
  DEL PEAK 31(20P12.1) MUTATED           1
  DEL PEAK 31(20P12.1) WILD-TYPE         1
D58V3, multiclass
            clus
vv           DEL PEAK 31(20P12.1) MUTATED DEL PEAK 31(20P12.1) WILD-TYPE
  STAGE I                              12                            161
  STAGE II                              8                             79
  STAGE III                             1                              2
  STAGE IIIA                            5                             57
  STAGE IIIB                            2                              7
  STAGE IIIC                            0                              7
  STAGE IV                              0                              2
  STAGE IVA                             0                              1
  STAGE IVB                             1                              1
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 31(20P12.1) MUTATED    12   8   8   1
  DEL PEAK 31(20P12.1) WILD-TYPE 171  87  69  11
D58V4, multiclass
    clus
vv   DEL PEAK 31(20P12.1) MUTATED DEL PEAK 31(20P12.1) WILD-TYPE
  T1                           12                            171
  T2                            8                             87
  T3                            8                             69
  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"
D58V5, binary
                                cls
clus                               0   1
  DEL PEAK 31(20P12.1) MUTATED    24   0
  DEL PEAK 31(20P12.1) WILD-TYPE 230   3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(20P12.1) MUTATED     24    0
  DEL PEAK 31(20P12.1) WILD-TYPE  230    3
   clus
vv  DEL PEAK 31(20P12.1) MUTATED DEL PEAK 31(20P12.1) WILD-TYPE
  0                           24                            230
  1                            0                              3
[1] 2 2
[1] FALSE
D58V6, binary
                                cls
clus                               0   1
  DEL PEAK 31(20P12.1) MUTATED    24   1
  DEL PEAK 31(20P12.1) WILD-TYPE 242   3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(20P12.1) MUTATED     24    1
  DEL PEAK 31(20P12.1) WILD-TYPE  242    3
   clus
vv  DEL PEAK 31(20P12.1) MUTATED DEL PEAK 31(20P12.1) WILD-TYPE
  0                           24                            242
  1                            1                              3
[1] 2 2
[1] FALSE
D58V7, binary
                                cls
clus                               0   1
  DEL PEAK 31(20P12.1) MUTATED    11  18
  DEL PEAK 31(20P12.1) WILD-TYPE 107 234
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(20P12.1) MUTATED     11   18
  DEL PEAK 31(20P12.1) WILD-TYPE  107  234
        clus
vv       DEL PEAK 31(20P12.1) MUTATED DEL PEAK 31(20P12.1) WILD-TYPE
  FEMALE                           11                            107
  MALE                             18                            234
[1] 2 2
[1] FALSE
D58V8, binary
                                cls
clus                               0   1
  DEL PEAK 31(20P12.1) MUTATED    25   2
  DEL PEAK 31(20P12.1) WILD-TYPE 313   7
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(20P12.1) MUTATED     25    2
  DEL PEAK 31(20P12.1) WILD-TYPE  313    7
     clus
vv    DEL PEAK 31(20P12.1) MUTATED DEL PEAK 31(20P12.1) WILD-TYPE
  NO                            25                            313
  YES                            2                              7
[1] 2 2
[1] FALSE
                                vv
clus                             FIBROLAMELLAR CARCINOMA
  DEL PEAK 31(20P12.1) MUTATED                         1
  DEL PEAK 31(20P12.1) WILD-TYPE                       2
                                vv
clus                             HEPATOCELLULAR CARCINOMA
  DEL PEAK 31(20P12.1) MUTATED                         27
  DEL PEAK 31(20P12.1) WILD-TYPE                      333
                                vv
clus                             HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK 31(20P12.1) MUTATED                                  1
  DEL PEAK 31(20P12.1) WILD-TYPE                                6
D58V9, multiclass
                                  clus
vv                                 DEL PEAK 31(20P12.1) MUTATED
  FIBROLAMELLAR CARCINOMA                                     1
  HEPATOCELLULAR CARCINOMA                                   27
  HEPATOCHOLANGIOCARCINOMA (MIXED)                            1
                                  clus
vv                                 DEL PEAK 31(20P12.1) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                       2
  HEPATOCELLULAR CARCINOMA                                    333
  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 31(20P12.1) MUTATED    27   0   0   2
  DEL PEAK 31(20P12.1) WILD-TYPE 297  17   1  19
D58V10, multiclass
    clus
vv   DEL PEAK 31(20P12.1) MUTATED DEL PEAK 31(20P12.1) WILD-TYPE
  R0                           27                            297
  R1                            0                             17
  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 31(20P12.1) MUTATED                                  1    15
  DEL PEAK 31(20P12.1) WILD-TYPE                                1   143
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 31(20P12.1) MUTATED                           1    12
  DEL PEAK 31(20P12.1) WILD-TYPE                        16   171
D58V11, multiclass
                                  clus
vv                                 DEL PEAK 31(20P12.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                      15
  BLACK OR AFRICAN AMERICAN                                   1
  WHITE                                                      12
                                  clus
vv                                 DEL PEAK 31(20P12.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                       143
  BLACK OR AFRICAN AMERICAN                                    16
  WHITE                                                       171
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V12, binary
                                cls
clus                               0   1
  DEL PEAK 31(20P12.1) MUTATED     2  25
  DEL PEAK 31(20P12.1) WILD-TYPE  14 310
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(20P12.1) MUTATED      2   25
  DEL PEAK 31(20P12.1) WILD-TYPE   14  310
                        clus
vv                       DEL PEAK 31(20P12.1) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           25
                        clus
vv                       DEL PEAK 31(20P12.1) WILD-TYPE
  HISPANIC OR LATINO                                 14
  NOT HISPANIC OR LATINO                            310
[1] 2 2
[1] FALSE

Clustering(59) Variable = DEL PEAK 32(22Q12.1) MUTATION ANALYSIS
D59V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 32(22Q12.1) MUTATED    48  28
  DEL PEAK 32(22Q12.1) WILD-TYPE 187 101
  DEL PEAK 32(22Q12.1) MUTATED DEL PEAK 32(22Q12.1) WILD-TYPE 
                            76                            288 
  DEL PEAK 32(22Q12.1) MUTATED DEL PEAK 32(22Q12.1) WILD-TYPE 
                            28                            101 
$`DEL PEAK 32(22Q12.1) MUTATED`
TCGA-BC-A5W4 TCGA-DD-A4NI TCGA-FV-A4ZP TCGA-G3-A7M9 TCGA-KR-A7K7 TCGA-T1-A6J8 
       17.98        26.83        81.73         1.84        31.27         0.76 
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-A69H 
       14.76        37.32        27.52        45.93         0.26        14.60 
TCGA-BC-A8YO TCGA-BD-A3EP TCGA-CC-5260 TCGA-CC-5264 TCGA-CC-A1HT TCGA-CC-A5UD 
       18.48        13.45         2.86         3.35         3.32         9.99 
TCGA-CC-A7IK TCGA-CC-A8HU TCGA-CC-A8HV TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A11A 
        8.61        11.31         9.17        79.73        37.78         2.60 
TCGA-DD-A1EB TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A3A4 TCGA-DD-A3A6 TCGA-DD-A4NB 
       66.31        55.69         5.62        20.12       107.11        32.52 
TCGA-DD-A4NJ TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A73B TCGA-DD-AAC8 TCGA-DD-AACZ 
       30.51        73.81       108.76         9.30         0.53         5.62 
TCGA-DD-AAD5 TCGA-DD-AADF TCGA-DD-AADJ TCGA-DD-AADQ TCGA-DD-AADS TCGA-DD-AAE3 
       44.22         3.78        35.05        14.33        15.58        18.61 
TCGA-DD-AAEE TCGA-DD-AAVR TCGA-ED-A459 TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7XO 
       26.63        82.62        29.92         9.73         0.20        14.04 
TCGA-ED-A7XP TCGA-EP-A2KB TCGA-FV-A495 TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A5SI 
       13.15        19.59         0.03        13.68        51.06        25.25 
TCGA-G3-A7M5 TCGA-G3-AAV3 TCGA-K7-A5RG TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-MI-A75G 
       14.70        13.55        17.06        11.80        27.25        22.95 
TCGA-MI-A75I TCGA-MR-A8JO TCGA-QA-A7B7 TCGA-RC-A6M5 TCGA-RC-A6M6 TCGA-RG-A7D4 
       20.71        10.85         3.09         0.49         0.30        36.10 
TCGA-UB-A7MC TCGA-WQ-AB4B TCGA-XR-A8TD TCGA-ZS-A9CF 
       16.44        12.99        33.86        79.30 

$`DEL PEAK 32(22Q12.1) WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 
       83.24        11.74        38.40         8.61        69.57         5.03 
TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-AADV TCGA-DD-AAE7 TCGA-DD-AAE8 
       36.66         0.36        90.28        18.87        21.17        21.83 
TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-ES-A2HS TCGA-FV-A3I1 TCGA-FV-A3R2 
       18.90        23.64         9.96        22.62         8.12         6.38 
TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-LG-A6GG 
       30.74        22.13        22.06        20.75         2.14        12.72 
TCGA-MI-A75H TCGA-UB-A7MF TCGA-UB-AA0V TCGA-XR-A8TG TCGA-ZP-A9D1 TCGA-ZS-A9CE 
       24.56         7.04        10.32        29.52         0.69        40.80 
TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GY TCGA-2Y-A9GZ 
       53.39        63.75        41.79        80.28        24.89        27.88 
TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HB 
       40.41        56.91        18.25        20.81        22.92         8.55 
TCGA-3K-AAZ8 TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AAAM TCGA-BC-4072 
       13.02        10.59         0.66        17.10         1.51        48.99 
TCGA-BC-4073 TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X 
       27.91        10.13        46.78        27.52         2.99        25.32 
TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A3KG TCGA-BC-A69I TCGA-BD-A2L6 
       23.38         1.12        44.42        22.36        12.72        44.81 
TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A3M9 
        0.66         4.24         3.19         3.39         4.24         9.86 
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-A9FS TCGA-CC-A9FW TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 
        4.60         6.94         8.15        83.57        53.33       113.00 
TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA 
        7.33         0.46        21.76        51.29        90.71        79.40 
TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH 
       19.79        75.65        11.47        12.95        45.11        49.15 
TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W 
        6.02        33.04        18.35        13.64        21.14        27.19 
TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A5 
       19.76        25.81         7.66        70.06        17.59       102.74 
TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NK 
       13.78        30.61        33.14        30.97        30.15        39.78 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV 
       56.25        29.56        12.26         0.30        80.75        78.84 
TCGA-DD-A73A TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G 
       23.93        23.05        22.78         1.45        35.67       114.35 
TCGA-DD-AA3A TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD 
       13.48        11.41        75.65        76.41        55.40        12.53 
TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ 
       71.80        12.00        15.42         6.41        53.19        69.11 
TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP 
        0.30         3.52        58.16        42.81        61.68        13.64 
TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW 
       14.20        59.31        51.35        51.52        50.33        46.82 
TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 
        5.59        47.67         4.50        18.54        21.63        42.58 
TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD 
       22.09        40.08        40.54        40.83        13.97        40.47 
TCGA-DD-AADE TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM 
       39.52        37.64        35.67        34.49        20.91         0.39 
TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADR TCGA-DD-AADU TCGA-DD-AADW 
       29.52        14.89        15.06        66.67        18.21        19.30 
TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE4 TCGA-DD-AAE6 
       18.25        18.25        18.15        20.98        19.99         4.64 
TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAEK 
       23.74        15.72        25.08        25.78        50.33        35.08 
TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVV TCGA-DD-AAVW 
       90.48        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        60.99 
TCGA-DD-AAW3 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A7PY 
       53.69        26.93        28.08        13.91        13.35        12.82 
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-A26S TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B 
       19.99        20.61         0.62        11.93        14.40        60.89 
TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A496 TCGA-FV-A4ZQ 
       23.97        19.10        27.88        12.03         0.33         0.39 
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-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM 
        5.92        19.53        19.23        22.95        20.42        17.10 
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-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A3OU 
       12.23         0.89        11.64         2.14        11.87        28.90 
TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A6G5 TCGA-KR-A7K8 
        1.02         2.20         2.99        37.71        16.83        29.79 
TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MR-A520 TCGA-NI-A4U2 
       13.97        12.03         9.57        16.67         7.53        58.88 
TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-RC-A6M4 TCGA-RC-A7S9 TCGA-RC-A7SB 
       26.27        17.69        21.01         0.72        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        27.88        19.76         1.71 
TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WX-AA44 TCGA-WX-AA46 
       15.98        10.75        11.34         0.99        20.22        24.85 
TCGA-WX-AA47 TCGA-XR-A8TE TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY 
       18.28        30.41        22.78        13.55        35.77        25.71 
TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CG 
       23.21        35.87        25.15        12.99        45.57        11.21 

  DEL PEAK 32(22Q12.1) MUTATED DEL PEAK 32(22Q12.1) WILD-TYPE 
                          0.03                           0.20 
  DEL PEAK 32(22Q12.1) MUTATED DEL PEAK 32(22Q12.1) WILD-TYPE 
                        120.82                         114.35 
  DEL PEAK 32(22Q12.1) MUTATED DEL PEAK 32(22Q12.1) WILD-TYPE 
                        16.750                         20.515 
[1] "0.0 - 120.8 (16.8)" "0.2 - 114.3 (20.5)"
[1] "hr=" "1.1"
D59V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IIIA
  DEL PEAK 32(22Q12.1) MUTATED        27       27         0         14
  DEL PEAK 32(22Q12.1) WILD-TYPE     146       60         3         48
                                vv
clus                             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 32(22Q12.1) MUTATED            2          2        1         1
  DEL PEAK 32(22Q12.1) WILD-TYPE          7          5        1         0
                                vv
clus                             STAGE IVB
  DEL PEAK 32(22Q12.1) MUTATED           0
  DEL PEAK 32(22Q12.1) WILD-TYPE         2
D59V3, multiclass
            clus
vv           DEL PEAK 32(22Q12.1) MUTATED DEL PEAK 32(22Q12.1) WILD-TYPE
  STAGE I                              27                            146
  STAGE II                             27                             60
  STAGE III                             0                              3
  STAGE IIIA                           14                             48
  STAGE IIIB                            2                              7
  STAGE IIIC                            2                              5
  STAGE IV                              1                              1
  STAGE IVA                             1                              0
  STAGE IVB                             0                              2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 32(22Q12.1) MUTATED    29  31  16   3
  DEL PEAK 32(22Q12.1) WILD-TYPE 154  64  61   9
D59V4, multiclass
    clus
vv   DEL PEAK 32(22Q12.1) MUTATED DEL PEAK 32(22Q12.1) WILD-TYPE
  T1                           29                            154
  T2                           31                             64
  T3                           16                             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"
D59V5, binary
                                cls
clus                               0   1
  DEL PEAK 32(22Q12.1) MUTATED    50   1
  DEL PEAK 32(22Q12.1) WILD-TYPE 204   2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 32(22Q12.1) MUTATED     50    1
  DEL PEAK 32(22Q12.1) WILD-TYPE  204    2
   clus
vv  DEL PEAK 32(22Q12.1) MUTATED DEL PEAK 32(22Q12.1) WILD-TYPE
  0                           50                            204
  1                            1                              2
[1] 2 2
[1] FALSE
D59V6, binary
                                cls
clus                               0   1
  DEL PEAK 32(22Q12.1) MUTATED    61   1
  DEL PEAK 32(22Q12.1) WILD-TYPE 205   3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 32(22Q12.1) MUTATED     61    1
  DEL PEAK 32(22Q12.1) WILD-TYPE  205    3
   clus
vv  DEL PEAK 32(22Q12.1) MUTATED DEL PEAK 32(22Q12.1) WILD-TYPE
  0                           61                            205
  1                            1                              3
[1] 2 2
[1] FALSE
D59V7, binary
                                cls
clus                               0   1
  DEL PEAK 32(22Q12.1) MUTATED    29  50
  DEL PEAK 32(22Q12.1) WILD-TYPE  89 202
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 32(22Q12.1) MUTATED     29   50
  DEL PEAK 32(22Q12.1) WILD-TYPE   89  202
        clus
vv       DEL PEAK 32(22Q12.1) MUTATED DEL PEAK 32(22Q12.1) WILD-TYPE
  FEMALE                           29                             89
  MALE                             50                            202
[1] 2 2
[1] FALSE
D59V8, binary
                                cls
clus                               0   1
  DEL PEAK 32(22Q12.1) MUTATED    69   2
  DEL PEAK 32(22Q12.1) WILD-TYPE 269   7
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 32(22Q12.1) MUTATED     69    2
  DEL PEAK 32(22Q12.1) WILD-TYPE  269    7
     clus
vv    DEL PEAK 32(22Q12.1) MUTATED DEL PEAK 32(22Q12.1) WILD-TYPE
  NO                            69                            269
  YES                            2                              7
[1] 2 2
[1] FALSE
                                vv
clus                             FIBROLAMELLAR CARCINOMA
  DEL PEAK 32(22Q12.1) MUTATED                         3
  DEL PEAK 32(22Q12.1) WILD-TYPE                       0
                                vv
clus                             HEPATOCELLULAR CARCINOMA
  DEL PEAK 32(22Q12.1) MUTATED                         74
  DEL PEAK 32(22Q12.1) WILD-TYPE                      286
                                vv
clus                             HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK 32(22Q12.1) MUTATED                                  2
  DEL PEAK 32(22Q12.1) WILD-TYPE                                5
D59V9, multiclass
                                  clus
vv                                 DEL PEAK 32(22Q12.1) MUTATED
  FIBROLAMELLAR CARCINOMA                                     3
  HEPATOCELLULAR CARCINOMA                                   74
  HEPATOCHOLANGIOCARCINOMA (MIXED)                            2
                                  clus
vv                                 DEL PEAK 32(22Q12.1) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                       0
  HEPATOCELLULAR CARCINOMA                                    286
  HEPATOCHOLANGIOCARCINOMA (MIXED)                              5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 32(22Q12.1) MUTATED    64   6   0   8
  DEL PEAK 32(22Q12.1) WILD-TYPE 260  11   1  13
D59V10, multiclass
    clus
vv   DEL PEAK 32(22Q12.1) MUTATED DEL PEAK 32(22Q12.1) WILD-TYPE
  R0                           64                            260
  R1                            6                             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 32(22Q12.1) MUTATED                                  1    25
  DEL PEAK 32(22Q12.1) WILD-TYPE                                1   133
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 32(22Q12.1) MUTATED                           8    44
  DEL PEAK 32(22Q12.1) WILD-TYPE                         9   139
D59V11, multiclass
                                  clus
vv                                 DEL PEAK 32(22Q12.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                      25
  BLACK OR AFRICAN AMERICAN                                   8
  WHITE                                                      44
                                  clus
vv                                 DEL PEAK 32(22Q12.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                       133
  BLACK OR AFRICAN AMERICAN                                     9
  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"
D59V12, binary
                                cls
clus                               0   1
  DEL PEAK 32(22Q12.1) MUTATED     6  65
  DEL PEAK 32(22Q12.1) WILD-TYPE  10 270
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 32(22Q12.1) MUTATED      6   65
  DEL PEAK 32(22Q12.1) WILD-TYPE   10  270
                        clus
vv                       DEL PEAK 32(22Q12.1) MUTATED
  HISPANIC OR LATINO                                6
  NOT HISPANIC OR LATINO                           65
                        clus
vv                       DEL PEAK 32(22Q12.1) WILD-TYPE
  HISPANIC OR LATINO                                 10
  NOT HISPANIC OR LATINO                            270
[1] 2 2
[1] FALSE

Clustering(60) Variable = DEL PEAK 33(22Q13.32) MUTATION ANALYSIS
D60V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 33(22Q13.32) MUTATED    47  33
  DEL PEAK 33(22Q13.32) WILD-TYPE 188  96
  DEL PEAK 33(22Q13.32) MUTATED DEL PEAK 33(22Q13.32) WILD-TYPE 
                             80                             284 
  DEL PEAK 33(22Q13.32) MUTATED DEL PEAK 33(22Q13.32) WILD-TYPE 
                             33                              96 
$`DEL PEAK 33(22Q13.32) MUTATED`
TCGA-BC-A5W4 TCGA-DD-A4NI TCGA-DD-AADV TCGA-FV-A4ZP TCGA-G3-A7M9 TCGA-KR-A7K7 
       17.98        26.83        18.87        81.73         1.84        31.27 
TCGA-T1-A6J8 TCGA-2Y-A9GS TCGA-2Y-A9H0 TCGA-2Y-A9H3 TCGA-2Y-A9H4 TCGA-5C-A9VG 
        0.76        23.80       120.82        49.84        47.74        10.78 
TCGA-5R-AA1D TCGA-BC-A10Q TCGA-BC-A10T TCGA-BC-A10Y TCGA-BC-A217 TCGA-BC-A3KF 
       14.76        37.32        27.52        23.38        45.93         0.26 
TCGA-BC-A3KG TCGA-BC-A8YO TCGA-BD-A3EP TCGA-CC-5260 TCGA-CC-5264 TCGA-CC-A1HT 
       22.36        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-A4NJ TCGA-DD-A4NO TCGA-DD-A4NP 
       13.78        33.14        32.52        30.51        73.81       108.76 
TCGA-DD-A73B TCGA-DD-AAC8 TCGA-DD-AACZ TCGA-DD-AADD TCGA-DD-AADF TCGA-DD-AADQ 
        9.30         0.53         5.62        40.47         3.78        14.33 
TCGA-DD-AADS TCGA-DD-AAE3 TCGA-DD-AAEE TCGA-ED-A459 TCGA-ED-A66Y TCGA-ED-A7PX 
       15.58        18.61        26.63        29.92         9.73         0.20 
TCGA-ED-A7XO TCGA-ED-A7XP TCGA-EP-A2KB TCGA-FV-A2QR TCGA-G3-A25S TCGA-G3-A25T 
       14.04        13.15        19.59        19.10        13.68        51.06 
TCGA-G3-A3CJ TCGA-G3-A5SI TCGA-G3-A7M5 TCGA-G3-AAV3 TCGA-K7-A5RG TCGA-K7-AAU7 
       19.53        25.25        14.70        13.55        17.06        11.80 
TCGA-KR-A7K2 TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-PD-A5DF 
       27.25        22.95        20.71        10.85        58.88        21.01 
TCGA-QA-A7B7 TCGA-RC-A6M5 TCGA-RC-A6M6 TCGA-RG-A7D4 TCGA-UB-A7MC TCGA-WQ-AB4B 
        3.09         0.49         0.30        36.10        16.44        12.99 
TCGA-XR-A8TD TCGA-ZS-A9CF 
       33.86        79.30 

$`DEL PEAK 33(22Q13.32) WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 
       83.24        11.74        38.40         8.61        69.57         5.03 
TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEA 
       36.66         0.36        90.28        21.17        21.83        18.90 
TCGA-DD-AAEG TCGA-EP-A3JL TCGA-ES-A2HS TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-G3-A25W 
       23.64         9.96        22.62         8.12         6.38        30.74 
TCGA-G3-A3CG TCGA-G3-A6UC TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-LG-A6GG TCGA-MI-A75H 
       22.13        22.06        20.75         2.14        12.72        24.56 
TCGA-UB-A7MF TCGA-UB-AA0V TCGA-XR-A8TG TCGA-ZP-A9D1 TCGA-ZS-A9CE TCGA-2Y-A9GT 
        7.04        10.32        29.52         0.69        40.80        53.39 
TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H1 
       63.75        41.79        80.28        24.89        27.88        40.41 
TCGA-2Y-A9H2 TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB 
       56.91        18.25        20.81        22.92         1.18         8.55 
TCGA-3K-AAZ8 TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AAAM TCGA-BC-4072 
       13.02        10.59         0.66        17.10         1.51        48.99 
TCGA-BC-4073 TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X 
       27.91        10.13        46.78        27.52         2.99        25.32 
TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A69H TCGA-BC-A69I TCGA-BD-A2L6 TCGA-BW-A5NO 
        1.12        44.42        14.60        12.72        44.81         0.66 
TCGA-CC-5258 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A3MA TCGA-CC-A3MB 
        4.24         3.19         3.39         4.24         9.96        10.36 
TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IG 
       11.93        11.41         8.94         7.13        21.34         9.83 
TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IL TCGA-CC-A8HT TCGA-CC-A8HV 
       12.00        13.12        12.56         9.14         4.60         9.17 
TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A 
        6.94         8.15        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-A1EC 
        0.46        21.76        51.29        90.71        79.40        19.79 
TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI 
       75.65        11.47        12.95        45.11        49.15         6.02 
TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39Z 
       33.04        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-A3A9 
       25.81         7.66        70.06        17.59        20.12        30.61 
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        71.80        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-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-AADG TCGA-DD-AADI 
       40.54        40.83        13.97        39.52        37.64        35.67 
TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO 
       35.05        34.49        20.91         0.39        29.52        14.89 
TCGA-DD-AADP TCGA-DD-AADR TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 
       15.06        66.67        18.21        19.30        18.25        18.25 
TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE9 TCGA-DD-AAEB 
       18.15        20.98        19.99         4.64        23.74        15.72 
TCGA-DD-AAED TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ 
       25.08        25.78        50.33        35.08        90.48        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        60.99        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-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S 
       13.41        13.35         1.84         0.20        18.74        19.99 
TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ 
       20.61         0.62        11.93        14.40        60.89        23.97 
TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25U 
       27.88        12.03         0.03         0.33         0.39        53.79 
TCGA-G3-A25V TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI 
       28.27        58.49        14.86        21.53        25.64         5.92 
TCGA-G3-A3CK TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A7M6 TCGA-G3-A7M7 
       19.23        22.95        20.42        17.10        20.78        11.87 
TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV4 
       14.14        15.78        15.65        11.80        12.23         0.89 
TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB 
       11.64         2.14        11.87        28.90         1.02         2.20 
TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A6G5 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD 
        2.99        37.71        16.83        29.79        13.97        12.03 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MR-A520 TCGA-NI-A8LF TCGA-O8-A75V TCGA-RC-A6M4 
        9.57        16.67         7.53        26.27        17.69         0.72 
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        27.88 
TCGA-UB-A7MB TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-A9G7 
       19.76         1.71        15.98        10.75        11.34         0.99 
TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TE TCGA-XR-A8TF TCGA-YA-A8S7 
       20.22        24.85        18.28        30.41        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-A9CG 
       45.57        11.21 

  DEL PEAK 33(22Q13.32) MUTATED DEL PEAK 33(22Q13.32) WILD-TYPE 
                           0.20                            0.03 
  DEL PEAK 33(22Q13.32) MUTATED DEL PEAK 33(22Q13.32) WILD-TYPE 
                         120.82                          114.35 
  DEL PEAK 33(22Q13.32) MUTATED DEL PEAK 33(22Q13.32) WILD-TYPE 
                         18.985                          20.055 
[1] "0.2 - 120.8 (19.0)" "0.0 - 114.3 (20.1)"
[1] "hr=" "1.1"
D60V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE III STAGE IIIA
  DEL PEAK 33(22Q13.32) MUTATED        26       25         1         16
  DEL PEAK 33(22Q13.32) WILD-TYPE     147       62         2         46
                                 vv
clus                              STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 33(22Q13.32) MUTATED            4          3        1         1
  DEL PEAK 33(22Q13.32) WILD-TYPE          5          4        1         0
                                 vv
clus                              STAGE IVB
  DEL PEAK 33(22Q13.32) MUTATED           0
  DEL PEAK 33(22Q13.32) WILD-TYPE         2
D60V3, multiclass
            clus
vv           DEL PEAK 33(22Q13.32) MUTATED DEL PEAK 33(22Q13.32) WILD-TYPE
  STAGE I                               26                             147
  STAGE II                              25                              62
  STAGE III                              1                               2
  STAGE IIIA                            16                              46
  STAGE IIIB                             4                               5
  STAGE IIIC                             3                               4
  STAGE IV                               1                               1
  STAGE IVA                              1                               0
  STAGE IVB                              0                               2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               T1  T2  T3  T4
  DEL PEAK 33(22Q13.32) MUTATED    28  30  20   5
  DEL PEAK 33(22Q13.32) WILD-TYPE 155  65  57   7
D60V4, multiclass
    clus
vv   DEL PEAK 33(22Q13.32) MUTATED DEL PEAK 33(22Q13.32) WILD-TYPE
  T1                            28                             155
  T2                            30                              65
  T3                            20                              57
  T4                             5                               7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V5, binary
                                 cls
clus                                0   1
  DEL PEAK 33(22Q13.32) MUTATED    54   2
  DEL PEAK 33(22Q13.32) WILD-TYPE 200   1
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 33(22Q13.32) MUTATED     54    2
  DEL PEAK 33(22Q13.32) WILD-TYPE  200    1
   clus
vv  DEL PEAK 33(22Q13.32) MUTATED DEL PEAK 33(22Q13.32) WILD-TYPE
  0                            54                             200
  1                             2                               1
[1] 2 2
[1] FALSE
D60V6, binary
                                 cls
clus                                0   1
  DEL PEAK 33(22Q13.32) MUTATED    64   1
  DEL PEAK 33(22Q13.32) WILD-TYPE 202   3
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 33(22Q13.32) MUTATED     64    1
  DEL PEAK 33(22Q13.32) WILD-TYPE  202    3
   clus
vv  DEL PEAK 33(22Q13.32) MUTATED DEL PEAK 33(22Q13.32) WILD-TYPE
  0                            64                             202
  1                             1                               3
[1] 2 2
[1] FALSE
D60V7, binary
                                 cls
clus                                0   1
  DEL PEAK 33(22Q13.32) MUTATED    30  53
  DEL PEAK 33(22Q13.32) WILD-TYPE  88 199
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 33(22Q13.32) MUTATED     30   53
  DEL PEAK 33(22Q13.32) WILD-TYPE   88  199
        clus
vv       DEL PEAK 33(22Q13.32) MUTATED DEL PEAK 33(22Q13.32) WILD-TYPE
  FEMALE                            30                              88
  MALE                              53                             199
[1] 2 2
[1] FALSE
D60V8, binary
                                 cls
clus                                0   1
  DEL PEAK 33(22Q13.32) MUTATED    75   2
  DEL PEAK 33(22Q13.32) WILD-TYPE 263   7
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 33(22Q13.32) MUTATED     75    2
  DEL PEAK 33(22Q13.32) WILD-TYPE  263    7
     clus
vv    DEL PEAK 33(22Q13.32) MUTATED DEL PEAK 33(22Q13.32) WILD-TYPE
  NO                             75                             263
  YES                             2                               7
[1] 2 2
[1] FALSE
                                 vv
clus                              FIBROLAMELLAR CARCINOMA
  DEL PEAK 33(22Q13.32) MUTATED                         3
  DEL PEAK 33(22Q13.32) WILD-TYPE                       0
                                 vv
clus                              HEPATOCELLULAR CARCINOMA
  DEL PEAK 33(22Q13.32) MUTATED                         78
  DEL PEAK 33(22Q13.32) WILD-TYPE                      282
                                 vv
clus                              HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK 33(22Q13.32) MUTATED                                  2
  DEL PEAK 33(22Q13.32) WILD-TYPE                                5
D60V9, multiclass
                                  clus
vv                                 DEL PEAK 33(22Q13.32) MUTATED
  FIBROLAMELLAR CARCINOMA                                      3
  HEPATOCELLULAR CARCINOMA                                    78
  HEPATOCHOLANGIOCARCINOMA (MIXED)                             2
                                  clus
vv                                 DEL PEAK 33(22Q13.32) 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 33(22Q13.32) MUTATED    66   6   0   9
  DEL PEAK 33(22Q13.32) WILD-TYPE 258  11   1  12
D60V10, multiclass
    clus
vv   DEL PEAK 33(22Q13.32) MUTATED DEL PEAK 33(22Q13.32) WILD-TYPE
  R0                            66                             258
  R1                             6                              11
  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 33(22Q13.32) MUTATED                                  2    24
  DEL PEAK 33(22Q13.32) WILD-TYPE                                0   134
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 33(22Q13.32) MUTATED                           7    48
  DEL PEAK 33(22Q13.32) WILD-TYPE                        10   135
D60V11, multiclass
                                  clus
vv                                 DEL PEAK 33(22Q13.32) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             2
  ASIAN                                                       24
  BLACK OR AFRICAN AMERICAN                                    7
  WHITE                                                       48
                                  clus
vv                                 DEL PEAK 33(22Q13.32) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               0
  ASIAN                                                        134
  BLACK OR AFRICAN AMERICAN                                     10
  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"
D60V12, binary
                                 cls
clus                                0   1
  DEL PEAK 33(22Q13.32) MUTATED     6  67
  DEL PEAK 33(22Q13.32) WILD-TYPE  10 268
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 33(22Q13.32) MUTATED      6   67
  DEL PEAK 33(22Q13.32) WILD-TYPE   10  268
                        clus
vv                       DEL PEAK 33(22Q13.32) MUTATED
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                            67
                        clus
vv                       DEL PEAK 33(22Q13.32) WILD-TYPE
  HISPANIC OR LATINO                                  10
  NOT HISPANIC OR LATINO                             268
[1] 2 2
[1] FALSE

Clustering(61) Variable = DEL PEAK 34(XQ26.2) MUTATION ANALYSIS
D61V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 34(XQ26.2) MUTATED    40  27
  DEL PEAK 34(XQ26.2) WILD-TYPE 195 102
  DEL PEAK 34(XQ26.2) MUTATED DEL PEAK 34(XQ26.2) WILD-TYPE 
                           67                           297 
  DEL PEAK 34(XQ26.2) MUTATED DEL PEAK 34(XQ26.2) WILD-TYPE 
                           27                           102 
$`DEL PEAK 34(XQ26.2) MUTATED`
TCGA-BC-A112 TCGA-BC-A5W4 TCGA-DD-AADV TCGA-KR-A7K7 TCGA-T1-A6J8 TCGA-UB-A7MF 
        5.03        17.98        18.87        31.27         0.76         7.04 
TCGA-2Y-A9GS TCGA-5C-AAPD TCGA-BC-A10R TCGA-BC-A10Z TCGA-BC-A217 TCGA-BC-A3KF 
       23.80         0.66        10.13         1.12        45.93         0.26 
TCGA-BC-A3KG TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A5UC 
       22.36         4.24         2.86         9.96        10.36        11.41 
TCGA-CC-A5UD TCGA-CC-A7IE TCGA-CC-A7IJ TCGA-CC-A7IL TCGA-CC-A8HU TCGA-DD-A115 
        9.99         7.13        12.56         9.14        11.31        83.57 
TCGA-DD-A116 TCGA-DD-A11B TCGA-DD-A4NA TCGA-DD-A4NO TCGA-DD-A73B TCGA-DD-A73G 
       53.33         0.46        33.14        73.81         9.30       114.35 
TCGA-DD-AACG TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW 
       15.42        42.81        61.68        51.52        50.33        46.82 
TCGA-DD-AAD5 TCGA-DD-AAD8 TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADL TCGA-DD-AADO 
       44.22        40.08        40.83        13.97        20.91        14.89 
TCGA-DD-AADP TCGA-DD-AADY TCGA-DD-AAE2 TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAVU 
       15.06        18.25        20.98        25.08        26.63        72.39 
TCGA-ED-A459 TCGA-ED-A7PX TCGA-ED-A7PZ TCGA-ED-A97K TCGA-FV-A3I0 TCGA-G3-A7M5 
       29.92         0.20         0.20         0.20        27.88        14.70 
TCGA-G3-AAV4 TCGA-G3-AAV6 TCGA-GJ-A6C0 TCGA-LG-A9QC TCGA-QA-A7B7 TCGA-RC-A6M4 
        0.89         2.14         1.02        13.97         3.09         0.72 
TCGA-RC-A7SB TCGA-RC-A7SH TCGA-RC-A7SK TCGA-UB-A7MC TCGA-WX-AA47 TCGA-ZP-A9D2 
       19.33        15.39        15.52        16.44        18.28        25.15 
TCGA-ZS-A9CF 
       79.30 

$`DEL PEAK 34(XQ26.2) WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BD-A3ER 
       83.24        11.74        38.40         8.61        69.57        36.66 
TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEA 
        0.36        90.28        26.83        21.17        21.83        18.90 
TCGA-DD-AAEG TCGA-EP-A3JL TCGA-ES-A2HS TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A4ZP 
       23.64         9.96        22.62         8.12         6.38        81.73 
TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC TCGA-G3-A7M9 TCGA-K7-A5RF TCGA-KR-A7K0 
       30.74        22.13        22.06         1.84        20.75         2.14 
TCGA-LG-A6GG TCGA-MI-A75H TCGA-UB-AA0V TCGA-XR-A8TG TCGA-ZP-A9D1 TCGA-ZS-A9CE 
       12.72        24.56        10.32        29.52         0.69        40.80 
TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GY TCGA-2Y-A9GZ 
       53.39        63.75        41.79        80.28        24.89        27.88 
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-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-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4072 TCGA-BC-4073 
       10.59        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-A216 TCGA-BC-A69H TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A2L6 
       23.38        44.42        14.60        12.72        18.48        44.81 
TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-5264 
       13.45         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-A3A9 TCGA-DD-A4NB 
       20.12       102.74       107.11        13.78        30.61        32.52 
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-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-AA3A TCGA-DD-AAC8 
       23.05        22.78         1.45        35.67        13.48         0.53 
TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE 
       11.41        75.65        76.41        55.40        12.53        71.80 
TCGA-DD-AACF TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL 
       12.00         6.41        53.19        69.11         0.30         3.52 
TCGA-DD-AACM TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACX 
       58.16        13.64        14.20        59.31        51.35         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-AAD6 TCGA-DD-AADA TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG 
       22.09        40.54        40.47        39.52         3.78        37.64 
TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADQ 
       35.67        35.05        34.49         0.39        29.52        14.33 
TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AAE0 TCGA-DD-AAE1 
       66.67        15.58        18.21        19.30        18.25        18.15 
TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAEH 
       18.61        19.99         4.64        23.74        15.72        25.78 
TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS 
       50.33        35.08        90.48        89.69        82.62        59.93 
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        60.99        53.69        26.93        28.08        13.91 
TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PY TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E 
       13.35         9.73        12.82        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-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR 
        0.62        11.93        14.40        60.89        23.97        19.10 
TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T 
       12.03         0.03         0.33         0.39        13.68        51.06 
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-A5SM TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV0 
       17.10        20.78        11.87        14.14        15.78        15.65 
TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV5 TCGA-G3-AAV7 TCGA-GJ-A3OU 
       11.80        12.23        13.55        11.64        11.87        28.90 
TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 
        2.20         2.99        37.71        17.06        16.83        11.80 
TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G 
       27.25        29.79        12.03         9.57        16.67        22.95 
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-A6M5 TCGA-RC-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SF TCGA-RG-A7D4 
       21.01         0.49         0.30        21.04        19.04        36.10 
TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WJ-A86L 
       27.88        19.76         1.71        15.98        10.75        11.34 
TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-WX-AA46 TCGA-XR-A8TD TCGA-XR-A8TE 
        0.99        12.99        20.22        24.85        33.86        30.41 
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-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CG 
       12.99        45.57        11.21 

  DEL PEAK 34(XQ26.2) MUTATED DEL PEAK 34(XQ26.2) WILD-TYPE 
                         0.20                          0.03 
  DEL PEAK 34(XQ26.2) MUTATED DEL PEAK 34(XQ26.2) WILD-TYPE 
                       114.35                        120.82 
  DEL PEAK 34(XQ26.2) MUTATED DEL PEAK 34(XQ26.2) WILD-TYPE 
                        15.42                         20.71 
[1] "0.2 - 114.3 (15.4)" "0.0 - 120.8 (20.7)"
[1] "hr=" "1.4"
D61V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IIIA
  DEL PEAK 34(XQ26.2) MUTATED        27       17         0         16
  DEL PEAK 34(XQ26.2) WILD-TYPE     146       70         3         46
                               vv
clus                            STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 34(XQ26.2) MUTATED            0          2        0         0
  DEL PEAK 34(XQ26.2) WILD-TYPE          9          5        2         1
                               vv
clus                            STAGE IVB
  DEL PEAK 34(XQ26.2) MUTATED           0
  DEL PEAK 34(XQ26.2) WILD-TYPE         2
D61V3, multiclass
            clus
vv           DEL PEAK 34(XQ26.2) MUTATED DEL PEAK 34(XQ26.2) WILD-TYPE
  STAGE I                             27                           146
  STAGE II                            17                            70
  STAGE III                            0                             3
  STAGE IIIA                          16                            46
  STAGE IIIB                           0                             9
  STAGE IIIC                           2                             5
  STAGE IV                             0                             2
  STAGE IVA                            0                             1
  STAGE IVB                            0                             2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  DEL PEAK 34(XQ26.2) MUTATED    28  20  18   1
  DEL PEAK 34(XQ26.2) WILD-TYPE 155  75  59  11
D61V4, multiclass
    clus
vv   DEL PEAK 34(XQ26.2) MUTATED DEL PEAK 34(XQ26.2) WILD-TYPE
  T1                          28                           155
  T2                          20                            75
  T3                          18                            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"
D61V5, binary
                               cls
clus                              0   1
  DEL PEAK 34(XQ26.2) MUTATED    47   1
  DEL PEAK 34(XQ26.2) WILD-TYPE 207   2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 34(XQ26.2) MUTATED     47    1
  DEL PEAK 34(XQ26.2) WILD-TYPE  207    2
   clus
vv  DEL PEAK 34(XQ26.2) MUTATED DEL PEAK 34(XQ26.2) WILD-TYPE
  0                          47                           207
  1                           1                             2
[1] 2 2
[1] FALSE
D61V6, binary
                               cls
clus                              0   1
  DEL PEAK 34(XQ26.2) MUTATED    54   0
  DEL PEAK 34(XQ26.2) WILD-TYPE 212   4
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 34(XQ26.2) MUTATED     54    0
  DEL PEAK 34(XQ26.2) WILD-TYPE  212    4
   clus
vv  DEL PEAK 34(XQ26.2) MUTATED DEL PEAK 34(XQ26.2) WILD-TYPE
  0                          54                           212
  1                           0                             4
[1] 2 2
[1] FALSE
D61V7, binary
                               cls
clus                              0   1
  DEL PEAK 34(XQ26.2) MUTATED    20  47
  DEL PEAK 34(XQ26.2) WILD-TYPE  98 205
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 34(XQ26.2) MUTATED     20   47
  DEL PEAK 34(XQ26.2) WILD-TYPE   98  205
        clus
vv       DEL PEAK 34(XQ26.2) MUTATED DEL PEAK 34(XQ26.2) WILD-TYPE
  FEMALE                          20                            98
  MALE                            47                           205
[1] 2 2
[1] FALSE
D61V8, binary
                               cls
clus                              0   1
  DEL PEAK 34(XQ26.2) MUTATED    61   3
  DEL PEAK 34(XQ26.2) WILD-TYPE 277   6
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 34(XQ26.2) MUTATED     61    3
  DEL PEAK 34(XQ26.2) WILD-TYPE  277    6
     clus
vv    DEL PEAK 34(XQ26.2) MUTATED DEL PEAK 34(XQ26.2) WILD-TYPE
  NO                           61                           277
  YES                           3                             6
[1] 2 2
[1] FALSE
                               vv
clus                            FIBROLAMELLAR CARCINOMA
  DEL PEAK 34(XQ26.2) MUTATED                         0
  DEL PEAK 34(XQ26.2) WILD-TYPE                       3
                               vv
clus                            HEPATOCELLULAR CARCINOMA
  DEL PEAK 34(XQ26.2) MUTATED                         64
  DEL PEAK 34(XQ26.2) WILD-TYPE                      296
                               vv
clus                            HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK 34(XQ26.2) MUTATED                                  3
  DEL PEAK 34(XQ26.2) WILD-TYPE                                4
D61V9, multiclass
                                  clus
vv                                 DEL PEAK 34(XQ26.2) MUTATED
  FIBROLAMELLAR CARCINOMA                                    0
  HEPATOCELLULAR CARCINOMA                                  64
  HEPATOCHOLANGIOCARCINOMA (MIXED)                           3
                                  clus
vv                                 DEL PEAK 34(XQ26.2) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                      3
  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 34(XQ26.2) MUTATED    59   2   0   6
  DEL PEAK 34(XQ26.2) WILD-TYPE 265  15   1  15
D61V10, multiclass
    clus
vv   DEL PEAK 34(XQ26.2) MUTATED DEL PEAK 34(XQ26.2) WILD-TYPE
  R0                          59                           265
  R1                           2                            15
  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 34(XQ26.2) MUTATED                                  0    39
  DEL PEAK 34(XQ26.2) WILD-TYPE                                2   119
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 34(XQ26.2) MUTATED                           1    27
  DEL PEAK 34(XQ26.2) WILD-TYPE                        16   156
D61V11, multiclass
                                  clus
vv                                 DEL PEAK 34(XQ26.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                     39
  BLACK OR AFRICAN AMERICAN                                  1
  WHITE                                                     27
                                  clus
vv                                 DEL PEAK 34(XQ26.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             2
  ASIAN                                                      119
  BLACK OR AFRICAN AMERICAN                                   16
  WHITE                                                      156
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V12, binary
                               cls
clus                              0   1
  DEL PEAK 34(XQ26.2) MUTATED     2  61
  DEL PEAK 34(XQ26.2) WILD-TYPE  14 274
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 34(XQ26.2) MUTATED      2   61
  DEL PEAK 34(XQ26.2) WILD-TYPE   14  274
                        clus
vv                       DEL PEAK 34(XQ26.2) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          61
                        clus
vv                       DEL PEAK 34(XQ26.2) WILD-TYPE
  HISPANIC OR LATINO                                14
  NOT HISPANIC OR LATINO                           274
[1] 2 2
[1] FALSE
