[1] "terrence_modification_tag"
[1] TRUE
[1] "nver"         "-nVNozzle.R1"
[1] "nfn"                                 "/xchip/tcga/Tools/Nozzle/v1.current"
[1] "Nozzle.R1"
[1] "successfully load Nozzle.R1"
[1] "ofn"        "-oTLIHC-TP"
[1] "opt"       "-OPMUTSIG"
[1] "tl" ""  
[1] "dx" ""  
[1] "opt"    "MUTSIG"
[1] "dx" ""  
[1] "cfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/LIHC-TP/10006007/LIHC-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/LIHC-TP/10013773/transformed.cor.cli.txt"

nPatients in clinical file=176, in cluster file=208, common to both=160
[1]  53 160
[1] "AMP PEAK  1(1P22.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  1(1P22.3) MUTATED AMP PEAK  1(1P22.3) WILD-TYPE 
                           38                           122 
  AMP PEAK  1(1P22.3) MUTATED AMP PEAK  1(1P22.3) WILD-TYPE 
                           38                           122 
[1] "AMP PEAK  2(1Q22) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  2(1Q22) MUTATED AMP PEAK  2(1Q22) WILD-TYPE 
                        119                          41 
  AMP PEAK  2(1Q22) MUTATED AMP PEAK  2(1Q22) WILD-TYPE 
                        119                          41 
[1] "AMP PEAK  3(1Q42.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  3(1Q42.3) MUTATED AMP PEAK  3(1Q42.3) WILD-TYPE 
                          113                            47 
  AMP PEAK  3(1Q42.3) MUTATED AMP PEAK  3(1Q42.3) WILD-TYPE 
                          113                            47 
[1] "AMP PEAK  4(2P24.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  4(2P24.1) MUTATED AMP PEAK  4(2P24.1) WILD-TYPE 
                           34                           126 
  AMP PEAK  4(2P24.1) MUTATED AMP PEAK  4(2P24.1) WILD-TYPE 
                           34                           126 
[1] "AMP PEAK  5(2Q31.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  5(2Q31.2) MUTATED AMP PEAK  5(2Q31.2) WILD-TYPE 
                           31                           129 
  AMP PEAK  5(2Q31.2) MUTATED AMP PEAK  5(2Q31.2) WILD-TYPE 
                           31                           129 
[1] "AMP PEAK  6(3Q26.31) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  6(3Q26.31) MUTATED AMP PEAK  6(3Q26.31) WILD-TYPE 
                            33                            127 
  AMP PEAK  6(3Q26.31) MUTATED AMP PEAK  6(3Q26.31) WILD-TYPE 
                            33                            127 
[1] "AMP PEAK  7(4Q13.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  7(4Q13.3) MUTATED AMP PEAK  7(4Q13.3) WILD-TYPE 
                           15                           145 
  AMP PEAK  7(4Q13.3) MUTATED AMP PEAK  7(4Q13.3) WILD-TYPE 
                           15                           145 
[1] "AMP PEAK  8(5P15.33) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  8(5P15.33) MUTATED AMP PEAK  8(5P15.33) WILD-TYPE 
                            75                             85 
  AMP PEAK  8(5P15.33) MUTATED AMP PEAK  8(5P15.33) WILD-TYPE 
                            75                             85 
[1] "AMP PEAK  9(5Q35.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  9(5Q35.3) MUTATED AMP PEAK  9(5Q35.3) WILD-TYPE 
                           58                           102 
  AMP PEAK  9(5Q35.3) MUTATED AMP PEAK  9(5Q35.3) WILD-TYPE 
                           58                           102 
[1] "AMP PEAK 10(6P25.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 10(6P25.2) MUTATED AMP PEAK 10(6P25.2) WILD-TYPE 
                           67                            93 
  AMP PEAK 10(6P25.2) MUTATED AMP PEAK 10(6P25.2) WILD-TYPE 
                           67                            93 
[1] "AMP PEAK 11(6P21.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 11(6P21.1) MUTATED AMP PEAK 11(6P21.1) WILD-TYPE 
                           67                            93 
  AMP PEAK 11(6P21.1) MUTATED AMP PEAK 11(6P21.1) WILD-TYPE 
                           67                            93 
[1] "AMP PEAK 12(6Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 12(6Q12) MUTATED AMP PEAK 12(6Q12) WILD-TYPE 
                         47                         113 
  AMP PEAK 12(6Q12) MUTATED AMP PEAK 12(6Q12) WILD-TYPE 
                         47                         113 
[1] "AMP PEAK 13(6Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 13(6Q12) MUTATED AMP PEAK 13(6Q12) WILD-TYPE 
                         34                         126 
  AMP PEAK 13(6Q12) MUTATED AMP PEAK 13(6Q12) WILD-TYPE 
                         34                         126 
[1] "AMP PEAK 14(7Q21.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 14(7Q21.2) MUTATED AMP PEAK 14(7Q21.2) WILD-TYPE 
                           59                           101 
  AMP PEAK 14(7Q21.2) MUTATED AMP PEAK 14(7Q21.2) WILD-TYPE 
                           59                           101 
[1] "AMP PEAK 15(7Q31.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 15(7Q31.2) MUTATED AMP PEAK 15(7Q31.2) WILD-TYPE 
                           56                           104 
  AMP PEAK 15(7Q31.2) MUTATED AMP PEAK 15(7Q31.2) WILD-TYPE 
                           56                           104 
[1] "AMP PEAK 16(8Q11.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 16(8Q11.1) MUTATED AMP PEAK 16(8Q11.1) WILD-TYPE 
                           70                            90 
  AMP PEAK 16(8Q11.1) MUTATED AMP PEAK 16(8Q11.1) WILD-TYPE 
                           70                            90 
[1] "AMP PEAK 17(8Q24.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 17(8Q24.21) MUTATED AMP PEAK 17(8Q24.21) WILD-TYPE 
                            96                             64 
  AMP PEAK 17(8Q24.21) MUTATED AMP PEAK 17(8Q24.21) WILD-TYPE 
                            96                             64 
[1] "AMP PEAK 18(9Q34.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 18(9Q34.2) MUTATED AMP PEAK 18(9Q34.2) WILD-TYPE 
                           22                           138 
  AMP PEAK 18(9Q34.2) MUTATED AMP PEAK 18(9Q34.2) WILD-TYPE 
                           22                           138 
[1] "AMP PEAK 19(10P15.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 19(10P15.1) MUTATED AMP PEAK 19(10P15.1) WILD-TYPE 
                            31                            129 
  AMP PEAK 19(10P15.1) MUTATED AMP PEAK 19(10P15.1) WILD-TYPE 
                            31                            129 
[1] "AMP PEAK 20(11Q13.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 20(11Q13.3) MUTATED AMP PEAK 20(11Q13.3) WILD-TYPE 
                            29                            131 
  AMP PEAK 20(11Q13.3) MUTATED AMP PEAK 20(11Q13.3) WILD-TYPE 
                            29                            131 
[1] "AMP PEAK 21(13Q32.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 21(13Q32.3) MUTATED AMP PEAK 21(13Q32.3) WILD-TYPE 
                            25                            135 
  AMP PEAK 21(13Q32.3) MUTATED AMP PEAK 21(13Q32.3) WILD-TYPE 
                            25                            135 
[1] "AMP PEAK 22(15Q26.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 22(15Q26.3) MUTATED AMP PEAK 22(15Q26.3) WILD-TYPE 
                            27                            133 
  AMP PEAK 22(15Q26.3) MUTATED AMP PEAK 22(15Q26.3) WILD-TYPE 
                            27                            133 
[1] "AMP PEAK 23(17P11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 23(17P11.2) MUTATED AMP PEAK 23(17P11.2) WILD-TYPE 
                            26                            134 
  AMP PEAK 23(17P11.2) MUTATED AMP PEAK 23(17P11.2) WILD-TYPE 
                            26                            134 
[1] "AMP PEAK 24(17Q25.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 24(17Q25.3) MUTATED AMP PEAK 24(17Q25.3) WILD-TYPE 
                            72                             88 
  AMP PEAK 24(17Q25.3) MUTATED AMP PEAK 24(17Q25.3) WILD-TYPE 
                            72                             88 
[1] "AMP PEAK 25(19Q13.11) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 25(19Q13.11) MUTATED AMP PEAK 25(19Q13.11) WILD-TYPE 
                             45                             115 
  AMP PEAK 25(19Q13.11) MUTATED AMP PEAK 25(19Q13.11) WILD-TYPE 
                             45                             115 
[1] "AMP PEAK 26(20Q13.13) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 26(20Q13.13) MUTATED AMP PEAK 26(20Q13.13) WILD-TYPE 
                             53                             107 
  AMP PEAK 26(20Q13.13) MUTATED AMP PEAK 26(20Q13.13) WILD-TYPE 
                             53                             107 
[1] "AMP PEAK 27(20Q13.33) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 27(20Q13.33) MUTATED AMP PEAK 27(20Q13.33) WILD-TYPE 
                             55                             105 
  AMP PEAK 27(20Q13.33) MUTATED AMP PEAK 27(20Q13.33) WILD-TYPE 
                             55                             105 
[1] "AMP PEAK 28(XQ28) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 28(XQ28) MUTATED AMP PEAK 28(XQ28) WILD-TYPE 
                         39                         121 
  AMP PEAK 28(XQ28) MUTATED AMP PEAK 28(XQ28) WILD-TYPE 
                         39                         121 
[1] "DEL PEAK  1(1P36.23) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE 
                            76                             84 
  DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE 
                            76                             84 
[1] "DEL PEAK  2(2Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  2(2Q22.1) MUTATED DEL PEAK  2(2Q22.1) WILD-TYPE 
                           17                           143 
  DEL PEAK  2(2Q22.1) MUTATED DEL PEAK  2(2Q22.1) WILD-TYPE 
                           17                           143 
[1] "DEL PEAK  3(2Q37.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE 
                           31                           129 
  DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE 
                           31                           129 
[1] "DEL PEAK  4(3P13) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  4(3P13) MUTATED DEL PEAK  4(3P13) WILD-TYPE 
                         29                         131 
  DEL PEAK  4(3P13) MUTATED DEL PEAK  4(3P13) WILD-TYPE 
                         29                         131 
[1] "DEL PEAK  5(4P16.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  5(4P16.3) MUTATED DEL PEAK  5(4P16.3) WILD-TYPE 
                           29                           131 
  DEL PEAK  5(4P16.3) MUTATED DEL PEAK  5(4P16.3) WILD-TYPE 
                           29                           131 
[1] "DEL PEAK  6(4Q24) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  6(4Q24) MUTATED DEL PEAK  6(4Q24) WILD-TYPE 
                         69                          91 
  DEL PEAK  6(4Q24) MUTATED DEL PEAK  6(4Q24) WILD-TYPE 
                         69                          91 
[1] "DEL PEAK  7(4Q34.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  7(4Q34.1) MUTATED DEL PEAK  7(4Q34.1) WILD-TYPE 
                           65                            95 
  DEL PEAK  7(4Q34.1) MUTATED DEL PEAK  7(4Q34.1) WILD-TYPE 
                           65                            95 
[1] "DEL PEAK  8(4Q34.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  8(4Q34.3) MUTATED DEL PEAK  8(4Q34.3) WILD-TYPE 
                           65                            95 
  DEL PEAK  8(4Q34.3) MUTATED DEL PEAK  8(4Q34.3) WILD-TYPE 
                           65                            95 
[1] "DEL PEAK  9(6Q27) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  9(6Q27) MUTATED DEL PEAK  9(6Q27) WILD-TYPE 
                         62                          98 
  DEL PEAK  9(6Q27) MUTATED DEL PEAK  9(6Q27) WILD-TYPE 
                         62                          98 
[1] "DEL PEAK 10(8P23.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 10(8P23.2) MUTATED DEL PEAK 10(8P23.2) WILD-TYPE 
                          104                            56 
  DEL PEAK 10(8P23.2) MUTATED DEL PEAK 10(8P23.2) WILD-TYPE 
                          104                            56 
[1] "DEL PEAK 11(9P21.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 11(9P21.3) MUTATED DEL PEAK 11(9P21.3) WILD-TYPE 
                           61                            99 
  DEL PEAK 11(9P21.3) MUTATED DEL PEAK 11(9P21.3) WILD-TYPE 
                           61                            99 
[1] "DEL PEAK 12(10Q23.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 12(10Q23.31) MUTATED DEL PEAK 12(10Q23.31) WILD-TYPE 
                             44                             116 
  DEL PEAK 12(10Q23.31) MUTATED DEL PEAK 12(10Q23.31) WILD-TYPE 
                             44                             116 
[1] "DEL PEAK 13(10Q25.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 13(10Q25.2) MUTATED DEL PEAK 13(10Q25.2) WILD-TYPE 
                            43                            117 
  DEL PEAK 13(10Q25.2) MUTATED DEL PEAK 13(10Q25.2) WILD-TYPE 
                            43                            117 
[1] "DEL PEAK 14(11Q14.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 14(11Q14.1) MUTATED DEL PEAK 14(11Q14.1) WILD-TYPE 
                            28                            132 
  DEL PEAK 14(11Q14.1) MUTATED DEL PEAK 14(11Q14.1) WILD-TYPE 
                            28                            132 
[1] "DEL PEAK 15(11Q23.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 15(11Q23.3) MUTATED DEL PEAK 15(11Q23.3) WILD-TYPE 
                            32                            128 
  DEL PEAK 15(11Q23.3) MUTATED DEL PEAK 15(11Q23.3) WILD-TYPE 
                            32                            128 
[1] "DEL PEAK 16(12P12.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 16(12P12.1) MUTATED DEL PEAK 16(12P12.1) WILD-TYPE 
                            34                            126 
  DEL PEAK 16(12P12.1) MUTATED DEL PEAK 16(12P12.1) WILD-TYPE 
                            34                            126 
[1] "DEL PEAK 17(12Q24.33) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 17(12Q24.33) MUTATED DEL PEAK 17(12Q24.33) WILD-TYPE 
                             25                             135 
  DEL PEAK 17(12Q24.33) MUTATED DEL PEAK 17(12Q24.33) WILD-TYPE 
                             25                             135 
[1] "DEL PEAK 18(13Q14.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 18(13Q14.2) MUTATED DEL PEAK 18(13Q14.2) WILD-TYPE 
                            72                             88 
  DEL PEAK 18(13Q14.2) MUTATED DEL PEAK 18(13Q14.2) WILD-TYPE 
                            72                             88 
[1] "DEL PEAK 19(13Q22.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 19(13Q22.2) MUTATED DEL PEAK 19(13Q22.2) WILD-TYPE 
                            57                            103 
  DEL PEAK 19(13Q22.2) MUTATED DEL PEAK 19(13Q22.2) WILD-TYPE 
                            57                            103 
[1] "DEL PEAK 20(14Q23.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 20(14Q23.3) MUTATED DEL PEAK 20(14Q23.3) WILD-TYPE 
                            55                            105 
  DEL PEAK 20(14Q23.3) MUTATED DEL PEAK 20(14Q23.3) WILD-TYPE 
                            55                            105 
[1] "DEL PEAK 21(14Q32.33) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 21(14Q32.33) MUTATED DEL PEAK 21(14Q32.33) WILD-TYPE 
                             56                             104 
  DEL PEAK 21(14Q32.33) MUTATED DEL PEAK 21(14Q32.33) WILD-TYPE 
                             56                             104 
[1] "DEL PEAK 22(16Q23.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 22(16Q23.2) MUTATED DEL PEAK 22(16Q23.2) WILD-TYPE 
                            67                             93 
  DEL PEAK 22(16Q23.2) MUTATED DEL PEAK 22(16Q23.2) WILD-TYPE 
                            67                             93 
[1] "DEL PEAK 23(17P11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 23(17P11.2) MUTATED DEL PEAK 23(17P11.2) WILD-TYPE 
                            84                             76 
  DEL PEAK 23(17P11.2) MUTATED DEL PEAK 23(17P11.2) WILD-TYPE 
                            84                             76 
[1] "DEL PEAK 24(19P13.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 24(19P13.3) MUTATED DEL PEAK 24(19P13.3) WILD-TYPE 
                            34                            126 
  DEL PEAK 24(19P13.3) MUTATED DEL PEAK 24(19P13.3) WILD-TYPE 
                            34                            126 
[1] "DEL PEAK 25(22Q13.32) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 25(22Q13.32) MUTATED DEL PEAK 25(22Q13.32) WILD-TYPE 
                             46                             114 
  DEL PEAK 25(22Q13.32) MUTATED DEL PEAK 25(22Q13.32) WILD-TYPE 
                             46                             114 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "PRIMARYSITEOFDESEASE"                  
 [6] "NEOPLASM.DISEASESTAGE"                 
 [7] "PATHOLOGY.T.STAGE"                     
 [8] "PATHOLOGY.N.STAGE"                     
 [9] "PATHOLOGY.M.STAGE"                     
[10] "DCCUPLOADDATE"                         
[11] "GENDER"                                
[12] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
[13] "DAYSTOLASTKNOWNALIVE"                  
[14] "RADIATIONTHERAPY"                      
[15] "HISTOLOGICALTYPE"                      
[16] "RADIATIONS.RADIATION.REGIMENINDICATION"
[17] "COMPLETENESS.OF.RESECTION"             
[18] "RACE"                                  
[19] "ETHNICITY"                             
[20] "BATCHNUMBER"                           

Input Data has 20 rows and 160 columns.

[1] "Batch" "20"   
[1] "Last Follow UP"
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T 
          NA          849           NA           NA           NA           NA 
TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 
          NA           NA           NA           NA           NA           NA 
TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 
          NA         1351          421            8          680          289 
TCGA-BC-A69H TCGA-BC-A69I TCGA-BW-A5NQ TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 
         444          387           NA            2           NA           12 
TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-5264 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA 
          NA           NA           NA           NA            3            2 
TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 
           3            4         2425           NA           NA           NA 
TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D 
        3437           NA           79           NA          662           NA 
TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE 
          NA         2415         2017          602         2301          204 
TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK 
          NA           NA         1495          183          887           NA 
TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 
          NA           NA           NA           NA           NA           NA 
TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 
          NA           NA           NA           NA           NA           NA 
TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND 
          NA           NA           NA         1008          989         2232 
TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL 
         428          433          561          458           NA         1711 
TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS 
          NA         2245         2849           NA           NA           NA 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E 
        2018          334           NA          230          334           44 
TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 
         843         3071          408          386          482          423 
TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XP 
         406            7            6            6            6            6 
TCGA-ED-A82E TCGA-ED-A8O5 TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB 
           6            6          570          608          357          334 
TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B 
          NA          303          363           NA           NA          987 
TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 
          NA           NA          848           NA           NA            4 
TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T 
           1           10         1836           12           37         1553 
TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z 
        1636          860          935         1779           NA          655 
TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI 
         673          780          180          594          585          447 
TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-A7M9 
         364          243          133          236          182           NA 
TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 
          NA           NA          122           NA          360          407 
TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I 
          15          291          155          433          391          265 
TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V 
          52           NA          498          135 
Variable 1:'AGE':	nDistinctValues=51,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=65,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=87,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'PRIMARY.SITE.OF.DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 6:'NEOPLASM.DISEASESTAGE':	nDistinctValues=9,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY.T.STAGE':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY.N.STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY.M.STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'DCCUPLOADDAY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=18,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 13:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 14:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 15:'HISTOLOGICAL.TYPE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 17:'COMPLETENESS.OF.RESECTION':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 18:'RACE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 19:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 20:'BATCH.NUMBER':	nDistinctValues=15,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
 [1] "AGE"                       "NEOPLASM.DISEASESTAGE"    
 [3] "PATHOLOGY.T.STAGE"         "PATHOLOGY.N.STAGE"        
 [5] "PATHOLOGY.M.STAGE"         "GENDER"                   
 [7] "HISTOLOGICAL.TYPE"         "COMPLETENESS.OF.RESECTION"
 [9] "RACE"                      "ETHNICITY"                
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "3"          
[1] "PATHOLOGY.N" "4"          
Output Data has 160 columns, 1 survival variables, and 10 non-survival variables.
AGE, nv=51, binary=FALSE, numeric=TRUE
NEOPLASM.DISEASESTAGE, 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 
68 41 42  8 
[1] "table(vv)"
vv
T1 T2 T3 T4 
68 41 42  8 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
T1 T2 T3 T4 
68 41 42  8 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


T1 T2 T3 T4 
68 41 42  8 
PATHOLOGY.N.STAGE, nv=2, binary=FALSE, numeric=TRUE
PATHOLOGY.M.STAGE, nv=3, binary=FALSE, numeric=FALSE
GENDER, nv=2, binary=FALSE, numeric=FALSE
HISTOLOGICAL.TYPE, nv=3, binary=FALSE, numeric=FALSE
COMPLETENESS.OF.RESECTION, nv=4, binary=FALSE, numeric=FALSE
RACE, nv=4, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = AMP PEAK  1(1P22.3) MUTATION ANALYSIS
D1V1, survival
                               sevent
clus2                            0  1
  AMP PEAK  1(1P22.3) MUTATED   20 17
  AMP PEAK  1(1P22.3) WILD-TYPE 71 49
  AMP PEAK  1(1P22.3) MUTATED AMP PEAK  1(1P22.3) WILD-TYPE 
                           37                           120 
  AMP PEAK  1(1P22.3) MUTATED AMP PEAK  1(1P22.3) WILD-TYPE 
                           17                            49 
$`AMP PEAK  1(1P22.3) MUTATED`
TCGA-BC-A10Q TCGA-BC-A10S TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A216 TCGA-BC-A217 
       37.32        46.78        27.52         2.99        44.42        13.84 
TCGA-CC-5261 TCGA-CC-5263 TCGA-CC-A3MB TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A119 
        0.39         4.24         0.10        79.73        37.78         7.33 
TCGA-DD-A11A TCGA-DD-A11C TCGA-DD-A1EH TCGA-DD-A1EJ TCGA-DD-A39X TCGA-DD-A39Y 
        2.60        21.76        49.15        29.16        55.69         5.62 
TCGA-DD-A3A1 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NJ TCGA-DD-A73G TCGA-ED-A459 
        7.66        13.78        30.61        15.06       100.96        13.41 
TCGA-ED-A4XI TCGA-ED-A7PY TCGA-ED-A8O5 TCGA-EP-A2KB TCGA-FV-A496 TCGA-FV-A4ZP 
       12.69         0.20         0.20        10.98         0.33        60.36 
TCGA-G3-A25S TCGA-G3-A25W TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A7M9 
        1.22        30.74        19.23        14.70        11.97         1.84 
TCGA-KR-A7K2 
       11.84 

$`AMP PEAK  1(1P22.3) WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10X TCGA-BC-A10Y 
       48.99        27.91        10.13        27.52        25.32        23.34 
TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 
        1.12        69.57         5.03         0.26        22.36         9.50 
TCGA-BC-A69H TCGA-BC-A69I TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5262 TCGA-CC-A1HT 
       14.60        12.72         0.07         2.86         3.39         3.32 
TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MC TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 
        0.10         0.07         0.13        83.57        53.33       113.00 
TCGA-DD-A11B TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC 
        0.46        51.29        90.71        79.40        66.31        19.79 
TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EI TCGA-DD-A1EK 
       75.65         6.71        12.95        45.11         6.02        18.35 
TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A2 TCGA-DD-A3A3 
       13.64        21.14        19.76        25.81        70.06        17.59 
TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A8 TCGA-DD-A4NA TCGA-DD-A4NB 
       20.12       102.74       107.11         0.36        33.14        32.52 
TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NK TCGA-DD-A4NL 
       73.38        14.07        14.24        18.44        39.78        56.25 
TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS 
       29.56        73.81        93.67        12.26         0.30        80.75 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E 
       66.35        10.98         9.30         7.56        10.98         1.45 
TCGA-DD-A73F TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX 
       27.72        15.85        13.91        13.35         0.23         0.20 
TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-ED-A82E TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
        0.20         0.20         0.20        18.74        19.99        11.74 
TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B 
        0.62         9.96        11.93        22.85        14.40        32.45 
TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 
       19.10        27.88         8.12         6.38         0.13         0.03 
TCGA-FV-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-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A5SL 
       21.53        22.13        25.64         5.92        19.53         7.99 
TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 
        4.37         7.76         5.98         1.02         2.66         4.01 
TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G 
        2.14        13.38         0.49         9.57         5.10        14.24 
TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V 
       12.85         8.71         1.71        58.88        16.37         4.44 

  AMP PEAK  1(1P22.3) MUTATED AMP PEAK  1(1P22.3) WILD-TYPE 
                         0.10                          0.03 
  AMP PEAK  1(1P22.3) MUTATED AMP PEAK  1(1P22.3) WILD-TYPE 
                       100.96                        113.00 
  AMP PEAK  1(1P22.3) MUTATED AMP PEAK  1(1P22.3) WILD-TYPE 
                       13.780                        14.155 
[1] "0.1 - 101.0 (13.8)" "0.0 - 113.0 (14.2)"
[1] "hr=" "1.2"
D1V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IIIA
  AMP PEAK  1(1P22.3) MUTATED        12        9         1          6
  AMP PEAK  1(1P22.3) WILD-TYPE      53       28         1         25
                               vv
clus                            STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK  1(1P22.3) MUTATED            3          1        1         0
  AMP PEAK  1(1P22.3) WILD-TYPE          2          4        0         1
                               vv
clus                            STAGE IVB
  AMP PEAK  1(1P22.3) MUTATED           1
  AMP PEAK  1(1P22.3) WILD-TYPE         1
D1V3, multiclass
            clus
vv           AMP PEAK  1(1P22.3) MUTATED AMP PEAK  1(1P22.3) WILD-TYPE
  STAGE I                             12                            53
  STAGE II                             9                            28
  STAGE III                            1                             1
  STAGE IIIA                           6                            25
  STAGE IIIB                           3                             2
  STAGE IIIC                           1                             4
  STAGE IV                             1                             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  1(1P22.3) MUTATED   13 11 12  2
  AMP PEAK  1(1P22.3) WILD-TYPE 55 30 30  6
D1V4, multiclass
    clus
vv   AMP PEAK  1(1P22.3) MUTATED AMP PEAK  1(1P22.3) WILD-TYPE
  T1                          13                            55
  T2                          11                            30
  T3                          12                            30
  T4                           2                             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"
D1V5, binary
                               cls
clus                             0  1
  AMP PEAK  1(1P22.3) MUTATED   21  1
  AMP PEAK  1(1P22.3) WILD-TYPE 81  2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1P22.3) MUTATED     21    1
  AMP PEAK  1(1P22.3) WILD-TYPE   81    2
   clus
vv  AMP PEAK  1(1P22.3) MUTATED AMP PEAK  1(1P22.3) WILD-TYPE
  0                          21                            81
  1                           1                             2
[1] 2 2
[1] FALSE
                               vv
clus                            M0 M1 MX
  AMP PEAK  1(1P22.3) MUTATED   29  2  7
  AMP PEAK  1(1P22.3) WILD-TYPE 91  1 30
D1V6, multiclass
    clus
vv   AMP PEAK  1(1P22.3) MUTATED AMP PEAK  1(1P22.3) WILD-TYPE
  M0                          29                            91
  M1                           2                             1
  MX                           7                            30
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V7, binary
                               cls
clus                             0  1
  AMP PEAK  1(1P22.3) MUTATED   14 24
  AMP PEAK  1(1P22.3) WILD-TYPE 46 76
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1P22.3) MUTATED     14   24
  AMP PEAK  1(1P22.3) WILD-TYPE   46   76
        clus
vv       AMP PEAK  1(1P22.3) MUTATED AMP PEAK  1(1P22.3) WILD-TYPE
  FEMALE                          14                            46
  MALE                            24                            76
[1] 2 2
[1] FALSE
                               vv
clus                            FIBROLAMELLAR CARCINOMA
  AMP PEAK  1(1P22.3) MUTATED                         0
  AMP PEAK  1(1P22.3) WILD-TYPE                       2
                               vv
clus                            HEPATOCELLULAR CARCINOMA
  AMP PEAK  1(1P22.3) MUTATED                         37
  AMP PEAK  1(1P22.3) WILD-TYPE                      119
                               vv
clus                            HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK  1(1P22.3) MUTATED                                  1
  AMP PEAK  1(1P22.3) WILD-TYPE                                1
D1V8, multiclass
                                  clus
vv                                 AMP PEAK  1(1P22.3) MUTATED
  FIBROLAMELLAR CARCINOMA                                    0
  HEPATOCELLULAR CARCINOMA                                  37
  HEPATOCHOLANGIOCARCINOMA (MIXED)                           1
                                  clus
vv                                 AMP PEAK  1(1P22.3) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                      2
  HEPATOCELLULAR CARCINOMA                                   119
  HEPATOCHOLANGIOCARCINOMA (MIXED)                             1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  1(1P22.3) MUTATED    28   5   1   4
  AMP PEAK  1(1P22.3) WILD-TYPE 103   6   0   8
D1V9, multiclass
    clus
vv   AMP PEAK  1(1P22.3) MUTATED AMP PEAK  1(1P22.3) WILD-TYPE
  R0                          28                           103
  R1                           5                             6
  R2                           1                             0
  RX                           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"
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  1(1P22.3) MUTATED                                  0    12
  AMP PEAK  1(1P22.3) WILD-TYPE                                1    24
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  1(1P22.3) MUTATED                           2    22
  AMP PEAK  1(1P22.3) WILD-TYPE                         6    87
D1V10, multiclass
                                  clus
vv                                 AMP PEAK  1(1P22.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                     12
  BLACK OR AFRICAN AMERICAN                                  2
  WHITE                                                     22
                                  clus
vv                                 AMP PEAK  1(1P22.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                       24
  BLACK OR AFRICAN AMERICAN                                    6
  WHITE                                                       87
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V11, binary
                               cls
clus                              0   1
  AMP PEAK  1(1P22.3) MUTATED     0  33
  AMP PEAK  1(1P22.3) WILD-TYPE   3 110
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1P22.3) MUTATED      0   33
  AMP PEAK  1(1P22.3) WILD-TYPE    3  110
                        clus
vv                       AMP PEAK  1(1P22.3) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                          33
                        clus
vv                       AMP PEAK  1(1P22.3) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           110
[1] 2 2
[1] FALSE

Clustering(2) Variable = AMP PEAK  2(1Q22) MUTATION ANALYSIS
D2V1, survival
                             sevent
clus2                          0  1
  AMP PEAK  2(1Q22) MUTATED   65 51
  AMP PEAK  2(1Q22) WILD-TYPE 26 15
  AMP PEAK  2(1Q22) MUTATED AMP PEAK  2(1Q22) WILD-TYPE 
                        116                          41 
  AMP PEAK  2(1Q22) MUTATED AMP PEAK  2(1Q22) WILD-TYPE 
                         51                          15 
$`AMP PEAK  2(1Q22) MUTATED`
TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10Y 
       37.32        10.13        27.52        27.52         2.99        23.34 
TCGA-BC-A10Z TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KG TCGA-BC-A5W4 
        1.12         5.03        44.42        13.84        22.36         9.50 
TCGA-BC-A69H TCGA-BC-A69I TCGA-CC-5258 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 
       14.60        12.72         0.07         0.39         3.39         4.24 
TCGA-CC-A1HT TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 
        3.32         0.07         0.10         0.13        79.73        37.78 
TCGA-DD-A115 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C 
       83.57       113.00         7.33         2.60         0.46        21.76 
TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EE TCGA-DD-A1EF 
       51.29        90.71        79.40        66.31         6.71        12.95 
TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V 
       45.11        49.15        29.16        18.35        13.64        21.14 
TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A3 
       55.69         5.62        19.76        25.81         7.66        17.59 
TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI 
       13.78         0.36        30.61        14.07        14.24        18.44 
TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NR TCGA-DD-A4NV 
       15.06        39.78        29.56        73.81         0.30        66.35 
TCGA-DD-A73B TCGA-DD-A73D TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI 
        9.30        10.98        27.72       100.96        13.41        12.69 
TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-ED-A82E 
       13.35         0.23         0.20         0.20         0.20         0.20 
TCGA-ED-A8O5 TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC 
        0.20        18.74        19.99        11.74        10.98         0.62 
TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I1 
        9.96        11.93        14.40        32.45        19.10         8.12 
TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-G3-A25S TCGA-G3-A25U 
        0.13         0.03         0.33        60.36         1.22        53.79 
TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CJ 
       30.74        58.49        14.86        21.53        22.13        19.53 
TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M9 
       19.23        14.70         7.99         4.37         7.76         1.84 
TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 
        1.02         2.66         4.01         2.14        11.84        13.38 
TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I 
        0.49         9.57         5.10        14.24        12.85         8.71 
TCGA-NI-A8LF TCGA-O8-A75V 
       16.37         4.44 

$`AMP PEAK  2(1Q22) WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10S TCGA-BC-A10X TCGA-BC-A110 TCGA-BC-A3KF 
       48.99        27.91        46.78        25.32        69.57         0.26 
TCGA-CC-5260 TCGA-CC-A3M9 TCGA-DD-A116 TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EI 
        2.86         0.10        53.33        19.79        75.65         6.02 
TCGA-DD-A3A2 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A4NA TCGA-DD-A4NB 
       70.06        20.12       102.74       107.11        33.14        32.52 
TCGA-DD-A4ND TCGA-DD-A4NL TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NS TCGA-DD-A73A 
       73.38        56.25        93.67        12.26        80.75        10.98 
TCGA-DD-A73C TCGA-DD-A73E TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A7PX TCGA-ES-A2HS 
        7.56         1.45        15.85        13.91         0.20        22.85 
TCGA-FV-A3I0 TCGA-FV-A3R2 TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25V TCGA-G3-A3CH 
       27.88         6.38         0.39        51.06        28.27        25.64 
TCGA-G3-A3CI TCGA-G3-A5SJ TCGA-G3-A7M7 TCGA-MR-A8JO TCGA-NI-A4U2 
        5.92        11.97         5.98         1.71        58.88 

  AMP PEAK  2(1Q22) MUTATED AMP PEAK  2(1Q22) WILD-TYPE 
                       0.03                        0.10 
  AMP PEAK  2(1Q22) MUTATED AMP PEAK  2(1Q22) WILD-TYPE 
                     113.00                      107.11 
  AMP PEAK  2(1Q22) MUTATED AMP PEAK  2(1Q22) WILD-TYPE 
                     13.365                      25.320 
[1] "0.0 - 113.0 (13.4)" "0.1 - 107.1 (25.3)"
[1] "hr=" "2"  
D2V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  2(1Q22) MUTATED        44       32         1         21          5
  AMP PEAK  2(1Q22) WILD-TYPE      21        5         1         10          0
                             vv
clus                          STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK  2(1Q22) MUTATED            3        1         1         2
  AMP PEAK  2(1Q22) WILD-TYPE          2        0         0         0
D2V3, multiclass
            clus
vv           AMP PEAK  2(1Q22) MUTATED AMP PEAK  2(1Q22) WILD-TYPE
  STAGE I                           44                          21
  STAGE II                          32                           5
  STAGE III                          1                           1
  STAGE IIIA                        21                          10
  STAGE IIIB                         5                           0
  STAGE IIIC                         3                           2
  STAGE IV                           1                           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
  AMP PEAK  2(1Q22) MUTATED   46 35 30  7
  AMP PEAK  2(1Q22) WILD-TYPE 22  6 12  1
D2V4, multiclass
    clus
vv   AMP PEAK  2(1Q22) MUTATED AMP PEAK  2(1Q22) WILD-TYPE
  T1                        46                          22
  T2                        35                           6
  T3                        30                          12
  T4                         7                           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"
D2V5, binary
                             cls
clus                           0  1
  AMP PEAK  2(1Q22) MUTATED   74  2
  AMP PEAK  2(1Q22) WILD-TYPE 28  1
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  2(1Q22) MUTATED     74    2
  AMP PEAK  2(1Q22) WILD-TYPE   28    1
   clus
vv  AMP PEAK  2(1Q22) MUTATED AMP PEAK  2(1Q22) WILD-TYPE
  0                        74                          28
  1                         2                           1
[1] 2 2
[1] FALSE
                             vv
clus                          M0 M1 MX
  AMP PEAK  2(1Q22) MUTATED   88  3 28
  AMP PEAK  2(1Q22) WILD-TYPE 32  0  9
D2V6, multiclass
    clus
vv   AMP PEAK  2(1Q22) MUTATED AMP PEAK  2(1Q22) WILD-TYPE
  M0                        88                          32
  M1                         3                           0
  MX                        28                           9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V7, binary
                             cls
clus                           0  1
  AMP PEAK  2(1Q22) MUTATED   43 76
  AMP PEAK  2(1Q22) WILD-TYPE 17 24
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  2(1Q22) MUTATED     43   76
  AMP PEAK  2(1Q22) WILD-TYPE   17   24
        clus
vv       AMP PEAK  2(1Q22) MUTATED AMP PEAK  2(1Q22) WILD-TYPE
  FEMALE                        43                          17
  MALE                          76                          24
[1] 2 2
[1] FALSE
                             vv
clus                          FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  AMP PEAK  2(1Q22) MUTATED                         0                      118
  AMP PEAK  2(1Q22) WILD-TYPE                       2                       38
                             vv
clus                          HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK  2(1Q22) MUTATED                                  1
  AMP PEAK  2(1Q22) WILD-TYPE                                1
D2V8, multiclass
                                  clus
vv                                 AMP PEAK  2(1Q22) MUTATED
  FIBROLAMELLAR CARCINOMA                                  0
  HEPATOCELLULAR CARCINOMA                               118
  HEPATOCHOLANGIOCARCINOMA (MIXED)                         1
                                  clus
vv                                 AMP PEAK  2(1Q22) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                    2
  HEPATOCELLULAR CARCINOMA                                  38
  HEPATOCHOLANGIOCARCINOMA (MIXED)                           1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          R0 R1 R2 RX
  AMP PEAK  2(1Q22) MUTATED   94  9  1 10
  AMP PEAK  2(1Q22) WILD-TYPE 37  2  0  2
D2V9, multiclass
    clus
vv   AMP PEAK  2(1Q22) MUTATED AMP PEAK  2(1Q22) WILD-TYPE
  R0                        94                          37
  R1                         9                           2
  R2                         1                           0
  RX                        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"
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  2(1Q22) MUTATED                                  1    29
  AMP PEAK  2(1Q22) WILD-TYPE                                0     7
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  2(1Q22) MUTATED                           7    76
  AMP PEAK  2(1Q22) WILD-TYPE                         1    33
D2V10, multiclass
                                  clus
vv                                 AMP PEAK  2(1Q22) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         1
  ASIAN                                                   29
  BLACK OR AFRICAN AMERICAN                                7
  WHITE                                                   76
                                  clus
vv                                 AMP PEAK  2(1Q22) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      7
  BLACK OR AFRICAN AMERICAN                                  1
  WHITE                                                     33
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V11, binary
                             cls
clus                            0   1
  AMP PEAK  2(1Q22) MUTATED     2 105
  AMP PEAK  2(1Q22) WILD-TYPE   1  38
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  2(1Q22) MUTATED      2  105
  AMP PEAK  2(1Q22) WILD-TYPE    1   38
                        clus
vv                       AMP PEAK  2(1Q22) MUTATED AMP PEAK  2(1Q22) WILD-TYPE
  HISPANIC OR LATINO                             2                           1
  NOT HISPANIC OR LATINO                       105                          38
[1] 2 2
[1] FALSE

Clustering(3) Variable = AMP PEAK  3(1Q42.3) MUTATION ANALYSIS
D3V1, survival
                               sevent
clus2                            0  1
  AMP PEAK  3(1Q42.3) MUTATED   64 46
  AMP PEAK  3(1Q42.3) WILD-TYPE 27 20
  AMP PEAK  3(1Q42.3) MUTATED AMP PEAK  3(1Q42.3) WILD-TYPE 
                          110                            47 
  AMP PEAK  3(1Q42.3) MUTATED AMP PEAK  3(1Q42.3) WILD-TYPE 
                           46                            20 
$`AMP PEAK  3(1Q42.3) MUTATED`
TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10Y TCGA-BC-A112 
       37.32        10.13        27.52        27.52        23.34         5.03 
TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I 
       44.42        13.84        22.36         9.50        14.60        12.72 
TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MC 
        0.39         3.39         4.24         0.10         0.07         0.13 
TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B 
       79.73        37.78       113.00         7.33         2.60         0.46 
TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG 
       51.29        90.71        79.40         6.71        12.95        45.11 
TCGA-DD-A1EH TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39Y 
       49.15        29.16        18.35        13.64        21.14         5.62 
TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A3 TCGA-DD-A3A5 TCGA-DD-A3A7 
       19.76        25.81         7.66        17.59       102.74        13.78 
TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NF TCGA-DD-A4NH 
        0.36        30.61        33.14        32.52        14.07        14.24 
TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NQ 
       18.44        15.06        39.78        29.56        73.81        12.26 
TCGA-DD-A4NR TCGA-DD-A4NV TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G 
        0.30        66.35        10.98         1.45        27.72       100.96 
TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PY 
       13.41        12.69        15.85        13.35         0.23         0.20 
TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-EP-A12J TCGA-EP-A26S 
        0.20         0.20         0.20         0.20        18.74        19.99 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HT 
       11.74        10.98         0.62         9.96        11.93        14.40 
TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I1 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 
       32.45        19.10         8.12         0.13         0.03         0.33 
TCGA-G3-A25S TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG 
        1.22        30.74        58.49        14.86        21.53        22.13 
TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC 
       19.53        19.23        14.70         7.99         4.37         7.76 
TCGA-G3-A7M9 TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 
        1.84         2.66         4.01         2.14        11.84        13.38 
TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I 
        0.49         9.57         5.10        14.24        12.85         8.71 
TCGA-MR-A8JO TCGA-O8-A75V 
        1.71         4.44 

$`AMP PEAK  3(1Q42.3) WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10S TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Z 
       48.99        27.91        46.78         2.99        25.32         1.12 
TCGA-BC-A110 TCGA-BC-A3KF TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-A1HT TCGA-CC-A3MB 
       69.57         0.26         0.07         2.86         3.32         0.10 
TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A11C TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED 
       83.57        53.33        21.76        66.31        19.79        75.65 
TCGA-DD-A1EI TCGA-DD-A39X TCGA-DD-A3A2 TCGA-DD-A3A4 TCGA-DD-A3A6 TCGA-DD-A4ND 
        6.02        55.69        70.06        20.12       107.11        73.38 
TCGA-DD-A4NL TCGA-DD-A4NP TCGA-DD-A4NS TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C 
       56.25        93.67        80.75        10.98         9.30         7.56 
TCGA-ED-A627 TCGA-ED-A7PX TCGA-ES-A2HS TCGA-FV-A3I0 TCGA-FV-A3R2 TCGA-FV-A4ZP 
       13.91         0.20        22.85        27.88         6.38        60.36 
TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A3CH TCGA-G3-A3CI 
        0.39        51.06        53.79        28.27        25.64         5.92 
TCGA-G3-A5SJ TCGA-G3-A7M7 TCGA-GJ-A6C0 TCGA-NI-A4U2 TCGA-NI-A8LF 
       11.97         5.98         1.02        58.88        16.37 

  AMP PEAK  3(1Q42.3) MUTATED AMP PEAK  3(1Q42.3) WILD-TYPE 
                         0.03                          0.07 
  AMP PEAK  3(1Q42.3) MUTATED AMP PEAK  3(1Q42.3) WILD-TYPE 
                       113.00                        107.11 
  AMP PEAK  3(1Q42.3) MUTATED AMP PEAK  3(1Q42.3) WILD-TYPE 
                       13.365                        22.850 
[1] "0.0 - 113.0 (13.4)" "0.1 - 107.1 (22.9)"
[1] "hr=" "1.6"
D3V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IIIA
  AMP PEAK  3(1Q42.3) MUTATED        40       32         2         18
  AMP PEAK  3(1Q42.3) WILD-TYPE      25        5         0         13
                               vv
clus                            STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK  3(1Q42.3) MUTATED            5          4        1         1
  AMP PEAK  3(1Q42.3) WILD-TYPE          0          1        0         0
                               vv
clus                            STAGE IVB
  AMP PEAK  3(1Q42.3) MUTATED           2
  AMP PEAK  3(1Q42.3) WILD-TYPE         0
D3V3, multiclass
            clus
vv           AMP PEAK  3(1Q42.3) MUTATED AMP PEAK  3(1Q42.3) WILD-TYPE
  STAGE I                             40                            25
  STAGE II                            32                             5
  STAGE III                            2                             0
  STAGE IIIA                          18                            13
  STAGE IIIB                           5                             0
  STAGE IIIC                           4                             1
  STAGE IV                             1                             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
  AMP PEAK  3(1Q42.3) MUTATED   42 36 28  6
  AMP PEAK  3(1Q42.3) WILD-TYPE 26  5 14  2
D3V4, multiclass
    clus
vv   AMP PEAK  3(1Q42.3) MUTATED AMP PEAK  3(1Q42.3) WILD-TYPE
  T1                          42                            26
  T2                          36                             5
  T3                          28                            14
  T4                           6                             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"
D3V5, binary
                               cls
clus                             0  1
  AMP PEAK  3(1Q42.3) MUTATED   72  3
  AMP PEAK  3(1Q42.3) WILD-TYPE 30  0
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(1Q42.3) MUTATED     72    3
  AMP PEAK  3(1Q42.3) WILD-TYPE   30    0
   clus
vv  AMP PEAK  3(1Q42.3) MUTATED AMP PEAK  3(1Q42.3) WILD-TYPE
  0                          72                            30
  1                           3                             0
[1] 2 2
[1] FALSE
                               vv
clus                            M0 M1 MX
  AMP PEAK  3(1Q42.3) MUTATED   85  3 25
  AMP PEAK  3(1Q42.3) WILD-TYPE 35  0 12
D3V6, multiclass
    clus
vv   AMP PEAK  3(1Q42.3) MUTATED AMP PEAK  3(1Q42.3) WILD-TYPE
  M0                          85                            35
  M1                           3                             0
  MX                          25                            12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V7, binary
                               cls
clus                             0  1
  AMP PEAK  3(1Q42.3) MUTATED   40 73
  AMP PEAK  3(1Q42.3) WILD-TYPE 20 27
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(1Q42.3) MUTATED     40   73
  AMP PEAK  3(1Q42.3) WILD-TYPE   20   27
        clus
vv       AMP PEAK  3(1Q42.3) MUTATED AMP PEAK  3(1Q42.3) WILD-TYPE
  FEMALE                          40                            20
  MALE                            73                            27
[1] 2 2
[1] FALSE
                               vv
clus                            FIBROLAMELLAR CARCINOMA
  AMP PEAK  3(1Q42.3) MUTATED                         2
  AMP PEAK  3(1Q42.3) WILD-TYPE                       0
                               vv
clus                            HEPATOCELLULAR CARCINOMA
  AMP PEAK  3(1Q42.3) MUTATED                        110
  AMP PEAK  3(1Q42.3) WILD-TYPE                       46
                               vv
clus                            HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK  3(1Q42.3) MUTATED                                  1
  AMP PEAK  3(1Q42.3) WILD-TYPE                                1
D3V8, multiclass
                                  clus
vv                                 AMP PEAK  3(1Q42.3) MUTATED
  FIBROLAMELLAR CARCINOMA                                    2
  HEPATOCELLULAR CARCINOMA                                 110
  HEPATOCHOLANGIOCARCINOMA (MIXED)                           1
                                  clus
vv                                 AMP PEAK  3(1Q42.3) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                      0
  HEPATOCELLULAR CARCINOMA                                    46
  HEPATOCHOLANGIOCARCINOMA (MIXED)                             1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            R0 R1 R2 RX
  AMP PEAK  3(1Q42.3) MUTATED   93  7  1  8
  AMP PEAK  3(1Q42.3) WILD-TYPE 38  4  0  4
D3V9, multiclass
    clus
vv   AMP PEAK  3(1Q42.3) MUTATED AMP PEAK  3(1Q42.3) WILD-TYPE
  R0                          93                            38
  R1                           7                             4
  R2                           1                             0
  RX                           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"
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  3(1Q42.3) MUTATED                                  1    26
  AMP PEAK  3(1Q42.3) WILD-TYPE                                0    10
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  3(1Q42.3) MUTATED                           7    74
  AMP PEAK  3(1Q42.3) WILD-TYPE                         1    35
D3V10, multiclass
                                  clus
vv                                 AMP PEAK  3(1Q42.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                     26
  BLACK OR AFRICAN AMERICAN                                  7
  WHITE                                                     74
                                  clus
vv                                 AMP PEAK  3(1Q42.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                       10
  BLACK OR AFRICAN AMERICAN                                    1
  WHITE                                                       35
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V11, binary
                               cls
clus                              0   1
  AMP PEAK  3(1Q42.3) MUTATED     2 100
  AMP PEAK  3(1Q42.3) WILD-TYPE   1  43
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(1Q42.3) MUTATED      2  100
  AMP PEAK  3(1Q42.3) WILD-TYPE    1   43
                        clus
vv                       AMP PEAK  3(1Q42.3) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                         100
                        clus
vv                       AMP PEAK  3(1Q42.3) WILD-TYPE
  HISPANIC OR LATINO                                 1
  NOT HISPANIC OR LATINO                            43
[1] 2 2
[1] FALSE

Clustering(4) Variable = AMP PEAK  4(2P24.1) MUTATION ANALYSIS
D4V1, survival
                               sevent
clus2                            0  1
  AMP PEAK  4(2P24.1) MUTATED   15 18
  AMP PEAK  4(2P24.1) WILD-TYPE 76 48
  AMP PEAK  4(2P24.1) MUTATED AMP PEAK  4(2P24.1) WILD-TYPE 
                           33                           124 
  AMP PEAK  4(2P24.1) MUTATED AMP PEAK  4(2P24.1) WILD-TYPE 
                           18                            48 
$`AMP PEAK  4(2P24.1) MUTATED`
TCGA-BC-4072 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10Y TCGA-BC-A112 
       48.99        37.32        10.13        27.52        23.34         5.03 
TCGA-BC-A5W4 TCGA-CC-5263 TCGA-CC-A3M9 TCGA-DD-A113 TCGA-DD-A115 TCGA-DD-A11A 
        9.50         4.24         0.10        79.73        83.57         2.60 
TCGA-DD-A1E9 TCGA-DD-A1EG TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39X TCGA-DD-A3A9 
       90.71        45.11        29.16        13.64        55.69        30.61 
TCGA-DD-A4NA TCGA-DD-A4NO TCGA-DD-A73B TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F 
       33.14        73.81         9.30        10.98         1.45        27.72 
TCGA-ED-A7PY TCGA-ED-A82E TCGA-EP-A2KA TCGA-ES-A2HS TCGA-G3-A25T TCGA-G3-A25W 
        0.20         0.20        11.74        22.85        51.06        30.74 
TCGA-G3-A25Z TCGA-G3-A7M9 TCGA-LG-A6GG 
       21.53         1.84         0.49 

$`AMP PEAK  4(2P24.1) WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10S TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Z 
       27.91        46.78        27.52         2.99        25.32         1.12 
TCGA-BC-A110 TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A69H 
       69.57        44.42        13.84         0.26        22.36        14.60 
TCGA-BC-A69I TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-A1HT 
       12.72         0.07         2.86         0.39         3.39         3.32 
TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A114 TCGA-DD-A116 TCGA-DD-A118 
        0.07         0.10         0.13        37.78        53.33       113.00 
TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-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-A1EH TCGA-DD-A1EI 
       19.79        75.65         6.71        12.95        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-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 
       70.06        17.59        20.12       102.74       107.11        13.78 
TCGA-DD-A3A8 TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI 
        0.36        32.52        73.38        14.07        14.24        18.44 
TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NP TCGA-DD-A4NQ 
       15.06        39.78        56.25        29.56        93.67        12.26 
TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73C TCGA-DD-A73G 
        0.30        80.75        66.35        10.98         7.56       100.96 
TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y 
       13.41        12.69        15.85        13.91        13.35         0.23 
TCGA-ED-A7PX TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-ED-A8O5 TCGA-EP-A12J TCGA-EP-A26S 
        0.20         0.20         0.20         0.20        18.74        19.99 
TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B 
       10.98         0.62         9.96        11.93        14.40        32.45 
TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 
       19.10        27.88         8.12         6.38         0.13         0.03 
TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25V 
        0.33        60.36         0.39         1.22        53.79        28.27 
TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ 
       58.49        14.86        22.13        25.64         5.92        19.53 
TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC 
       19.23        14.70        11.97         7.99         4.37         7.76 
TCGA-G3-A7M7 TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 
        5.98         1.02         2.66         4.01         2.14        11.84 
TCGA-KR-A7K7 TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I 
       13.38         9.57         5.10        14.24        12.85         8.71 
TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V 
        1.71        58.88        16.37         4.44 

  AMP PEAK  4(2P24.1) MUTATED AMP PEAK  4(2P24.1) WILD-TYPE 
                         0.10                          0.03 
  AMP PEAK  4(2P24.1) MUTATED AMP PEAK  4(2P24.1) WILD-TYPE 
                        90.71                        113.00 
  AMP PEAK  4(2P24.1) MUTATED AMP PEAK  4(2P24.1) WILD-TYPE 
                        22.85                         13.81 
[1] "0.1 - 90.7 (22.9)"  "0.0 - 113.0 (13.8)"
[1] "hr=" "1.2"
D4V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IIIA
  AMP PEAK  4(2P24.1) MUTATED        10        5         0          9
  AMP PEAK  4(2P24.1) WILD-TYPE      55       32         2         22
                               vv
clus                            STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK  4(2P24.1) MUTATED            2          2        0         0
  AMP PEAK  4(2P24.1) WILD-TYPE          3          3        1         1
                               vv
clus                            STAGE IVB
  AMP PEAK  4(2P24.1) MUTATED           1
  AMP PEAK  4(2P24.1) WILD-TYPE         1
D4V3, multiclass
            clus
vv           AMP PEAK  4(2P24.1) MUTATED AMP PEAK  4(2P24.1) WILD-TYPE
  STAGE I                             10                            55
  STAGE II                             5                            32
  STAGE III                            0                             2
  STAGE IIIA                           9                            22
  STAGE IIIB                           2                             3
  STAGE IIIC                           2                             3
  STAGE IV                             0                             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(2P24.1) MUTATED   11  7 13  3
  AMP PEAK  4(2P24.1) WILD-TYPE 57 34 29  5
D4V4, multiclass
    clus
vv   AMP PEAK  4(2P24.1) MUTATED AMP PEAK  4(2P24.1) WILD-TYPE
  T1                          11                            57
  T2                           7                            34
  T3                          13                            29
  T4                           3                             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"
D4V5, binary
                               cls
clus                             0  1
  AMP PEAK  4(2P24.1) MUTATED   19  2
  AMP PEAK  4(2P24.1) WILD-TYPE 83  1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(2P24.1) MUTATED     19    2
  AMP PEAK  4(2P24.1) WILD-TYPE   83    1
   clus
vv  AMP PEAK  4(2P24.1) MUTATED AMP PEAK  4(2P24.1) WILD-TYPE
  0                          19                            83
  1                           2                             1
[1] 2 2
[1] FALSE
                               vv
clus                            M0 M1 MX
  AMP PEAK  4(2P24.1) MUTATED   24  1  9
  AMP PEAK  4(2P24.1) WILD-TYPE 96  2 28
D4V6, multiclass
    clus
vv   AMP PEAK  4(2P24.1) MUTATED AMP PEAK  4(2P24.1) WILD-TYPE
  M0                          24                            96
  M1                           1                             2
  MX                           9                            28
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V7, binary
                               cls
clus                             0  1
  AMP PEAK  4(2P24.1) MUTATED   17 17
  AMP PEAK  4(2P24.1) WILD-TYPE 43 83
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(2P24.1) MUTATED     17   17
  AMP PEAK  4(2P24.1) WILD-TYPE   43   83
        clus
vv       AMP PEAK  4(2P24.1) MUTATED AMP PEAK  4(2P24.1) WILD-TYPE
  FEMALE                          17                            43
  MALE                            17                            83
[1] 2 2
[1] FALSE
                               vv
clus                            FIBROLAMELLAR CARCINOMA
  AMP PEAK  4(2P24.1) MUTATED                         0
  AMP PEAK  4(2P24.1) WILD-TYPE                       2
                               vv
clus                            HEPATOCELLULAR CARCINOMA
  AMP PEAK  4(2P24.1) MUTATED                         34
  AMP PEAK  4(2P24.1) WILD-TYPE                      122
                               vv
clus                            HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK  4(2P24.1) MUTATED                                  0
  AMP PEAK  4(2P24.1) WILD-TYPE                                2
D4V8, multiclass
                                  clus
vv                                 AMP PEAK  4(2P24.1) MUTATED
  FIBROLAMELLAR CARCINOMA                                    0
  HEPATOCELLULAR CARCINOMA                                  34
  HEPATOCHOLANGIOCARCINOMA (MIXED)                           0
                                  clus
vv                                 AMP PEAK  4(2P24.1) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                      2
  HEPATOCELLULAR CARCINOMA                                   122
  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  4(2P24.1) MUTATED    28   4   0   2
  AMP PEAK  4(2P24.1) WILD-TYPE 103   7   1  10
D4V9, multiclass
    clus
vv   AMP PEAK  4(2P24.1) MUTATED AMP PEAK  4(2P24.1) WILD-TYPE
  R0                          28                           103
  R1                           4                             7
  R2                           0                             1
  RX                           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"
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  4(2P24.1) MUTATED                                  0     6
  AMP PEAK  4(2P24.1) WILD-TYPE                                1    30
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  4(2P24.1) MUTATED                           2    26
  AMP PEAK  4(2P24.1) WILD-TYPE                         6    83
D4V10, multiclass
                                  clus
vv                                 AMP PEAK  4(2P24.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      6
  BLACK OR AFRICAN AMERICAN                                  2
  WHITE                                                     26
                                  clus
vv                                 AMP PEAK  4(2P24.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                       30
  BLACK OR AFRICAN AMERICAN                                    6
  WHITE                                                       83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V11, binary
                               cls
clus                              0   1
  AMP PEAK  4(2P24.1) MUTATED     1  32
  AMP PEAK  4(2P24.1) WILD-TYPE   2 111
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(2P24.1) MUTATED      1   32
  AMP PEAK  4(2P24.1) WILD-TYPE    2  111
                        clus
vv                       AMP PEAK  4(2P24.1) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          32
                        clus
vv                       AMP PEAK  4(2P24.1) WILD-TYPE
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                           111
[1] 2 2
[1] FALSE

Clustering(5) Variable = AMP PEAK  5(2Q31.2) MUTATION ANALYSIS
D5V1, survival
                               sevent
clus2                            0  1
  AMP PEAK  5(2Q31.2) MUTATED   14 17
  AMP PEAK  5(2Q31.2) WILD-TYPE 77 49
  AMP PEAK  5(2Q31.2) MUTATED AMP PEAK  5(2Q31.2) WILD-TYPE 
                           31                           126 
  AMP PEAK  5(2Q31.2) MUTATED AMP PEAK  5(2Q31.2) WILD-TYPE 
                           17                            49 
$`AMP PEAK  5(2Q31.2) MUTATED`
TCGA-BC-4072 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A3KG TCGA-CC-5263 
       48.99        37.32        10.13        27.52        22.36         4.24 
TCGA-DD-A113 TCGA-DD-A11C TCGA-DD-A1E9 TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39X 
       79.73        21.76        90.71        29.16        13.64        55.69 
TCGA-DD-A3A0 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NQ TCGA-DD-A73D TCGA-DD-A73E 
       25.81        13.78        30.61        12.26        10.98         1.45 
TCGA-ED-A7PY TCGA-ED-A82E TCGA-EP-A2KA TCGA-ES-A2HS TCGA-FV-A3I1 TCGA-FV-A495 
        0.20         0.20        11.74        22.85         8.12         0.03 
TCGA-FV-A496 TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25W TCGA-G3-A25Z TCGA-G3-A5SM 
        0.33         1.22        51.06        30.74        21.53         4.37 
TCGA-LG-A6GG 
        0.49 

$`AMP PEAK  5(2Q31.2) WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10S TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y 
       27.91        46.78        27.52         2.99        25.32        23.34 
TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF 
        1.12        69.57         5.03        44.42        13.84         0.26 
TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 
        9.50        14.60        12.72         0.07         2.86         0.39 
TCGA-CC-5262 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC 
        3.39         3.32         0.10         0.07         0.10         0.13 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A 
       37.78        83.57        53.33       113.00         7.33         2.60 
TCGA-DD-A11B TCGA-DD-A11D TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED 
        0.46        51.29        79.40        66.31        19.79        75.65 
TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EK 
        6.71        12.95        45.11        49.15         6.02        18.35 
TCGA-DD-A39V TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 
       21.14         5.62        19.76         7.66        70.06        17.59 
TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A8 TCGA-DD-A4NA TCGA-DD-A4NB 
       20.12       102.74       107.11         0.36        33.14        32.52 
TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK 
       73.38        14.07        14.24        18.44        15.06        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        93.67         0.30        80.75 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73F TCGA-DD-A73G 
       66.35        10.98         9.30         7.56        27.72       100.96 
TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y 
       13.41        12.69        15.85        13.91        13.35         0.23 
TCGA-ED-A7PX TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-ED-A8O5 TCGA-EP-A12J TCGA-EP-A26S 
        0.20         0.20         0.20         0.20        18.74        19.99 
TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B 
       10.98         0.62         9.96        11.93        14.40        32.45 
TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A4ZP TCGA-FV-A4ZQ 
       19.10        27.88         6.38         0.13        60.36         0.39 
TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A3CG TCGA-G3-A3CH 
       53.79        28.27        58.49        14.86        22.13        25.64 
TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL 
        5.92        19.53        19.23        14.70        11.97         7.99 
TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 
        7.76         5.98         1.84         1.02         2.66         4.01 
TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G 
        2.14        11.84        13.38         9.57         5.10        14.24 
TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V 
       12.85         8.71         1.71        58.88        16.37         4.44 

  AMP PEAK  5(2Q31.2) MUTATED AMP PEAK  5(2Q31.2) WILD-TYPE 
                         0.03                          0.07 
  AMP PEAK  5(2Q31.2) MUTATED AMP PEAK  5(2Q31.2) WILD-TYPE 
                        90.71                        113.00 
  AMP PEAK  5(2Q31.2) MUTATED AMP PEAK  5(2Q31.2) WILD-TYPE 
                        13.78                         13.99 
[1] "0.0 - 90.7 (13.8)"  "0.1 - 113.0 (14.0)"
[1] "hr=" "1.5"
D5V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IIIA
  AMP PEAK  5(2Q31.2) MUTATED         9       10         0          5
  AMP PEAK  5(2Q31.2) WILD-TYPE      56       27         2         26
                               vv
clus                            STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK  5(2Q31.2) MUTATED            2          1        0         0
  AMP PEAK  5(2Q31.2) WILD-TYPE          3          4        1         1
                               vv
clus                            STAGE IVB
  AMP PEAK  5(2Q31.2) MUTATED           1
  AMP PEAK  5(2Q31.2) WILD-TYPE         1
D5V3, multiclass
            clus
vv           AMP PEAK  5(2Q31.2) MUTATED AMP PEAK  5(2Q31.2) WILD-TYPE
  STAGE I                              9                            56
  STAGE II                            10                            27
  STAGE III                            0                             2
  STAGE IIIA                           5                            26
  STAGE IIIB                           2                             3
  STAGE IIIC                           1                             4
  STAGE IV                             0                             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  5(2Q31.2) MUTATED   10 11  8  2
  AMP PEAK  5(2Q31.2) WILD-TYPE 58 30 34  6
D5V4, multiclass
    clus
vv   AMP PEAK  5(2Q31.2) MUTATED AMP PEAK  5(2Q31.2) WILD-TYPE
  T1                          10                            58
  T2                          11                            30
  T3                           8                            34
  T4                           2                             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"
D5V5, binary
                               cls
clus                             0  1
  AMP PEAK  5(2Q31.2) MUTATED   17  1
  AMP PEAK  5(2Q31.2) WILD-TYPE 85  2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(2Q31.2) MUTATED     17    1
  AMP PEAK  5(2Q31.2) WILD-TYPE   85    2
   clus
vv  AMP PEAK  5(2Q31.2) MUTATED AMP PEAK  5(2Q31.2) WILD-TYPE
  0                          17                            85
  1                           1                             2
[1] 2 2
[1] FALSE
                               vv
clus                            M0 M1 MX
  AMP PEAK  5(2Q31.2) MUTATED   23  1  7
  AMP PEAK  5(2Q31.2) WILD-TYPE 97  2 30
D5V6, multiclass
    clus
vv   AMP PEAK  5(2Q31.2) MUTATED AMP PEAK  5(2Q31.2) WILD-TYPE
  M0                          23                            97
  M1                           1                             2
  MX                           7                            30
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V7, binary
                               cls
clus                             0  1
  AMP PEAK  5(2Q31.2) MUTATED   18 13
  AMP PEAK  5(2Q31.2) WILD-TYPE 42 87
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(2Q31.2) MUTATED     18   13
  AMP PEAK  5(2Q31.2) WILD-TYPE   42   87
        clus
vv       AMP PEAK  5(2Q31.2) MUTATED AMP PEAK  5(2Q31.2) WILD-TYPE
  FEMALE                          18                            42
  MALE                            13                            87
[1] 2 2
[1] FALSE
                               vv
clus                            FIBROLAMELLAR CARCINOMA
  AMP PEAK  5(2Q31.2) MUTATED                         0
  AMP PEAK  5(2Q31.2) WILD-TYPE                       2
                               vv
clus                            HEPATOCELLULAR CARCINOMA
  AMP PEAK  5(2Q31.2) MUTATED                         31
  AMP PEAK  5(2Q31.2) WILD-TYPE                      125
                               vv
clus                            HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK  5(2Q31.2) MUTATED                                  0
  AMP PEAK  5(2Q31.2) WILD-TYPE                                2
D5V8, multiclass
                                  clus
vv                                 AMP PEAK  5(2Q31.2) MUTATED
  FIBROLAMELLAR CARCINOMA                                    0
  HEPATOCELLULAR CARCINOMA                                  31
  HEPATOCHOLANGIOCARCINOMA (MIXED)                           0
                                  clus
vv                                 AMP PEAK  5(2Q31.2) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                      2
  HEPATOCELLULAR CARCINOMA                                   125
  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  5(2Q31.2) MUTATED    25   4   0   2
  AMP PEAK  5(2Q31.2) WILD-TYPE 106   7   1  10
D5V9, multiclass
    clus
vv   AMP PEAK  5(2Q31.2) MUTATED AMP PEAK  5(2Q31.2) WILD-TYPE
  R0                          25                           106
  R1                           4                             7
  R2                           0                             1
  RX                           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"
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  5(2Q31.2) MUTATED                                  0     4
  AMP PEAK  5(2Q31.2) WILD-TYPE                                1    32
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  5(2Q31.2) MUTATED                           1    25
  AMP PEAK  5(2Q31.2) WILD-TYPE                         7    84
D5V10, multiclass
                                  clus
vv                                 AMP PEAK  5(2Q31.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      4
  BLACK OR AFRICAN AMERICAN                                  1
  WHITE                                                     25
                                  clus
vv                                 AMP PEAK  5(2Q31.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                       32
  BLACK OR AFRICAN AMERICAN                                    7
  WHITE                                                       84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V11, binary
                               cls
clus                              0   1
  AMP PEAK  5(2Q31.2) MUTATED     1  29
  AMP PEAK  5(2Q31.2) WILD-TYPE   2 114
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(2Q31.2) MUTATED      1   29
  AMP PEAK  5(2Q31.2) WILD-TYPE    2  114
                        clus
vv                       AMP PEAK  5(2Q31.2) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          29
                        clus
vv                       AMP PEAK  5(2Q31.2) WILD-TYPE
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                           114
[1] 2 2
[1] FALSE

Clustering(6) Variable = AMP PEAK  6(3Q26.31) MUTATION ANALYSIS
D6V1, survival
                                sevent
clus2                             0  1
  AMP PEAK  6(3Q26.31) MUTATED   16 16
  AMP PEAK  6(3Q26.31) WILD-TYPE 75 50
  AMP PEAK  6(3Q26.31) MUTATED AMP PEAK  6(3Q26.31) WILD-TYPE 
                            32                            125 
  AMP PEAK  6(3Q26.31) MUTATED AMP PEAK  6(3Q26.31) WILD-TYPE 
                            16                             50 
$`AMP PEAK  6(3Q26.31) MUTATED`
TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A217 TCGA-BC-A3KG 
       10.13        27.52        23.34         1.12        13.84        22.36 
TCGA-BC-A5W4 TCGA-BC-A69H TCGA-CC-A3MA TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A11C 
        9.50        14.60         0.07        37.78        83.57        21.76 
TCGA-DD-A1EF TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39Y TCGA-DD-A3A5 TCGA-DD-A4NI 
       12.95        29.16        13.64         5.62       102.74        18.44 
TCGA-DD-A4NV TCGA-DD-A73E TCGA-DD-A73G TCGA-ED-A7PX TCGA-ED-A7PZ TCGA-ED-A82E 
       66.35         1.45       100.96         0.20         0.20         0.20 
TCGA-EP-A2KA TCGA-ES-A2HS TCGA-FV-A3R2 TCGA-FV-A495 TCGA-G3-A25X TCGA-G3-A7M9 
       11.74        22.85         6.38         0.03        58.49         1.84 
TCGA-GJ-A6C0 TCGA-MI-A75G 
        1.02        14.24 

$`AMP PEAK  6(3Q26.31) WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10S TCGA-BC-A10U TCGA-BC-A10W 
       48.99        27.91        37.32        46.78        27.52         2.99 
TCGA-BC-A10X TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A3KF TCGA-BC-A69I 
       25.32        69.57         5.03        44.42         0.26        12.72 
TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT 
        0.07         2.86         0.39         3.39         4.24         3.32 
TCGA-CC-A3M9 TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A116 TCGA-DD-A118 
        0.10         0.10         0.13        79.73        53.33       113.00 
TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA 
        7.33         2.60         0.46        51.29        90.71        79.40 
TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EG TCGA-DD-A1EH 
       66.31        19.79        75.65         6.71        45.11        49.15 
TCGA-DD-A1EI TCGA-DD-A1EK TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Z TCGA-DD-A3A0 
        6.02        18.35        21.14        55.69        19.76        25.81 
TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A6 TCGA-DD-A3A7 
        7.66        70.06        17.59        20.12       107.11        13.78 
TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NF 
        0.36        30.61        33.14        32.52        73.38        14.07 
TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO 
       14.24        15.06        39.78        56.25        29.56        73.81 
TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A73A TCGA-DD-A73B 
       93.67        12.26         0.30        80.75        10.98         9.30 
TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73F TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG 
        7.56        10.98        27.72        13.41        12.69        15.85 
TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PY TCGA-ED-A7XP TCGA-ED-A8O5 
       13.91        13.35         0.23         0.20         0.20         0.20 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK 
       18.74        19.99        10.98         0.62         9.96        11.93 
TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R3 
       14.40        32.45        19.10        27.88         8.12         0.13 
TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U 
        0.33        60.36         0.39         1.22        51.06        53.79 
TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH 
       28.27        30.74        14.86        21.53        22.13        25.64 
TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL 
        5.92        19.53        19.23        14.70        11.97         7.99 
TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 
        4.37         7.76         5.98         2.66         4.01         2.14 
TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75H 
       11.84        13.38         0.49         9.57         5.10        12.85 
TCGA-MI-A75I TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V 
        8.71         1.71        58.88        16.37         4.44 

  AMP PEAK  6(3Q26.31) MUTATED AMP PEAK  6(3Q26.31) WILD-TYPE 
                          0.03                           0.07 
  AMP PEAK  6(3Q26.31) MUTATED AMP PEAK  6(3Q26.31) WILD-TYPE 
                        102.74                         113.00 
  AMP PEAK  6(3Q26.31) MUTATED AMP PEAK  6(3Q26.31) WILD-TYPE 
                         13.74                          14.07 
[1] "0.0 - 102.7 (13.7)" "0.1 - 113.0 (14.1)"
[1] "hr=" "1.3"
D6V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IIIA
  AMP PEAK  6(3Q26.31) MUTATED         9       12         1          6
  AMP PEAK  6(3Q26.31) WILD-TYPE      56       25         1         25
                                vv
clus                             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK  6(3Q26.31) MUTATED            1          1        0         0
  AMP PEAK  6(3Q26.31) WILD-TYPE          4          4        1         1
                                vv
clus                             STAGE IVB
  AMP PEAK  6(3Q26.31) MUTATED           0
  AMP PEAK  6(3Q26.31) WILD-TYPE         2
D6V3, multiclass
            clus
vv           AMP PEAK  6(3Q26.31) MUTATED AMP PEAK  6(3Q26.31) WILD-TYPE
  STAGE I                               9                             56
  STAGE II                             12                             25
  STAGE III                             1                              1
  STAGE IIIA                            6                             25
  STAGE IIIB                            1                              4
  STAGE IIIC                            1                              4
  STAGE IV                              0                              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  6(3Q26.31) MUTATED   10 12  9  2
  AMP PEAK  6(3Q26.31) WILD-TYPE 58 29 33  6
D6V4, multiclass
    clus
vv   AMP PEAK  6(3Q26.31) MUTATED AMP PEAK  6(3Q26.31) WILD-TYPE
  T1                           10                             58
  T2                           12                             29
  T3                            9                             33
  T4                            2                              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"
D6V5, binary
                                cls
clus                              0  1
  AMP PEAK  6(3Q26.31) MUTATED   14  1
  AMP PEAK  6(3Q26.31) WILD-TYPE 88  2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  6(3Q26.31) MUTATED     14    1
  AMP PEAK  6(3Q26.31) WILD-TYPE   88    2
   clus
vv  AMP PEAK  6(3Q26.31) MUTATED AMP PEAK  6(3Q26.31) WILD-TYPE
  0                           14                             88
  1                            1                              2
[1] 2 2
[1] FALSE
                                vv
clus                             M0 M1 MX
  AMP PEAK  6(3Q26.31) MUTATED   23  0 10
  AMP PEAK  6(3Q26.31) WILD-TYPE 97  3 27
D6V6, multiclass
    clus
vv   AMP PEAK  6(3Q26.31) MUTATED AMP PEAK  6(3Q26.31) WILD-TYPE
  M0                           23                             97
  M1                            0                              3
  MX                           10                             27
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V7, binary
                                cls
clus                              0  1
  AMP PEAK  6(3Q26.31) MUTATED   13 20
  AMP PEAK  6(3Q26.31) WILD-TYPE 47 80
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  6(3Q26.31) MUTATED     13   20
  AMP PEAK  6(3Q26.31) WILD-TYPE   47   80
        clus
vv       AMP PEAK  6(3Q26.31) MUTATED AMP PEAK  6(3Q26.31) WILD-TYPE
  FEMALE                           13                             47
  MALE                             20                             80
[1] 2 2
[1] FALSE
                                vv
clus                             FIBROLAMELLAR CARCINOMA
  AMP PEAK  6(3Q26.31) MUTATED                         0
  AMP PEAK  6(3Q26.31) WILD-TYPE                       2
                                vv
clus                             HEPATOCELLULAR CARCINOMA
  AMP PEAK  6(3Q26.31) MUTATED                         33
  AMP PEAK  6(3Q26.31) WILD-TYPE                      123
                                vv
clus                             HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK  6(3Q26.31) MUTATED                                  0
  AMP PEAK  6(3Q26.31) WILD-TYPE                                2
D6V8, multiclass
                                  clus
vv                                 AMP PEAK  6(3Q26.31) MUTATED
  FIBROLAMELLAR CARCINOMA                                     0
  HEPATOCELLULAR CARCINOMA                                   33
  HEPATOCHOLANGIOCARCINOMA (MIXED)                            0
                                  clus
vv                                 AMP PEAK  6(3Q26.31) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                       2
  HEPATOCELLULAR CARCINOMA                                    123
  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  6(3Q26.31) MUTATED    28   2   0   3
  AMP PEAK  6(3Q26.31) WILD-TYPE 103   9   1   9
D6V9, multiclass
    clus
vv   AMP PEAK  6(3Q26.31) MUTATED AMP PEAK  6(3Q26.31) WILD-TYPE
  R0                           28                            103
  R1                            2                              9
  R2                            0                              1
  RX                            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"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  6(3Q26.31) MUTATED                                  0     6
  AMP PEAK  6(3Q26.31) WILD-TYPE                                1    30
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  6(3Q26.31) MUTATED                           2    25
  AMP PEAK  6(3Q26.31) WILD-TYPE                         6    84
D6V10, multiclass
                                  clus
vv                                 AMP PEAK  6(3Q26.31) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       6
  BLACK OR AFRICAN AMERICAN                                   2
  WHITE                                                      25
                                  clus
vv                                 AMP PEAK  6(3Q26.31) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        30
  BLACK OR AFRICAN AMERICAN                                     6
  WHITE                                                        84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V11, binary
                                cls
clus                               0   1
  AMP PEAK  6(3Q26.31) MUTATED     0  31
  AMP PEAK  6(3Q26.31) WILD-TYPE   3 112
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  6(3Q26.31) MUTATED      0   31
  AMP PEAK  6(3Q26.31) WILD-TYPE    3  112
                        clus
vv                       AMP PEAK  6(3Q26.31) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           31
                        clus
vv                       AMP PEAK  6(3Q26.31) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            112
[1] 2 2
[1] FALSE

Clustering(7) Variable = AMP PEAK  7(4Q13.3) MUTATION ANALYSIS
D7V1, survival
                               sevent
clus2                            0  1
  AMP PEAK  7(4Q13.3) MUTATED   10  5
  AMP PEAK  7(4Q13.3) WILD-TYPE 81 61
  AMP PEAK  7(4Q13.3) MUTATED AMP PEAK  7(4Q13.3) WILD-TYPE 
                           15                           142 
  AMP PEAK  7(4Q13.3) MUTATED AMP PEAK  7(4Q13.3) WILD-TYPE 
                            5                            61 
$`AMP PEAK  7(4Q13.3) MUTATED`
TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A217 TCGA-CC-5258 TCGA-CC-5261 TCGA-DD-A113 
       10.13        27.52        13.84         0.07         0.39        79.73 
TCGA-DD-A11C TCGA-DD-A1EC TCGA-DD-A1EH TCGA-DD-A73F TCGA-ED-A82E TCGA-EP-A12J 
       21.76        19.79        49.15        27.72         0.20        18.74 
TCGA-EP-A2KA TCGA-G3-A3CG TCGA-GJ-A6C0 
       11.74        22.13         1.02 

$`AMP PEAK  7(4Q13.3) WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10S TCGA-BC-A10U TCGA-BC-A10W 
       48.99        27.91        37.32        46.78        27.52         2.99 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 
       25.32        23.34         1.12        69.57         5.03        44.42 
TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I TCGA-CC-5260 
        0.26        22.36         9.50        14.60        12.72         2.86 
TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB 
        3.39         4.24         3.32         0.10         0.07         0.10 
TCGA-CC-A3MC TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 
        0.13        37.78        83.57        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-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EI TCGA-DD-A1EJ 
       75.65         6.71        12.95        45.11         6.02        29.16 
TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z 
       18.35        13.64        21.14        55.69         5.62        19.76 
TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 
       25.81         7.66        70.06        17.59        20.12       102.74 
TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB 
      107.11        13.78         0.36        30.61        33.14        32.52 
TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK 
       73.38        14.07        14.24        18.44        15.06        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        93.67        12.26         0.30 
TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D 
       80.75        66.35        10.98         9.30         7.56        10.98 
TCGA-DD-A73E TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 
        1.45       100.96        13.41        12.69        15.85        13.91 
TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XP 
       13.35         0.23         0.20         0.20         0.20         0.20 
TCGA-ED-A8O5 TCGA-EP-A26S TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK 
        0.20        19.99        10.98         0.62         9.96        11.93 
TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 
       22.85        14.40        32.45        19.10        27.88         8.12 
TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ 
        6.38         0.13         0.03         0.33        60.36         0.39 
TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X 
        1.22        51.06        53.79        28.27        30.74        58.49 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
       14.86        21.53        25.64         5.92        19.53        19.23 
TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M7 
       14.70        11.97         7.99         4.37         7.76         5.98 
TCGA-G3-A7M9 TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 
        1.84         2.66         4.01         2.14        11.84        13.38 
TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I 
        0.49         9.57         5.10        14.24        12.85         8.71 
TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V 
        1.71        58.88        16.37         4.44 

  AMP PEAK  7(4Q13.3) MUTATED AMP PEAK  7(4Q13.3) WILD-TYPE 
                         0.07                          0.03 
  AMP PEAK  7(4Q13.3) MUTATED AMP PEAK  7(4Q13.3) WILD-TYPE 
                        79.73                        113.00 
  AMP PEAK  7(4Q13.3) MUTATED AMP PEAK  7(4Q13.3) WILD-TYPE 
                       18.740                        13.845 
[1] "0.1 - 79.7 (18.7)"  "0.0 - 113.0 (13.8)"
[1] "hr=" "1.1"
D7V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IIIA
  AMP PEAK  7(4Q13.3) MUTATED         5        5         1          2
  AMP PEAK  7(4Q13.3) WILD-TYPE      60       32         1         29
                               vv
clus                            STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK  7(4Q13.3) MUTATED            0          0        0         0
  AMP PEAK  7(4Q13.3) WILD-TYPE          5          5        1         1
                               vv
clus                            STAGE IVB
  AMP PEAK  7(4Q13.3) MUTATED           0
  AMP PEAK  7(4Q13.3) WILD-TYPE         2
D7V3, multiclass
            clus
vv           AMP PEAK  7(4Q13.3) MUTATED AMP PEAK  7(4Q13.3) WILD-TYPE
  STAGE I                              5                            60
  STAGE II                             5                            32
  STAGE III                            1                             1
  STAGE IIIA                           2                            29
  STAGE IIIB                           0                             5
  STAGE IIIC                           0                             5
  STAGE IV                             0                             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(4Q13.3) MUTATED    5  5  4  1
  AMP PEAK  7(4Q13.3) WILD-TYPE 63 36 38  7
D7V4, multiclass
    clus
vv   AMP PEAK  7(4Q13.3) MUTATED AMP PEAK  7(4Q13.3) WILD-TYPE
  T1                           5                            63
  T2                           5                            36
  T3                           4                            38
  T4                           1                             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"
D7V5, binary
                               cls
clus                             0  1
  AMP PEAK  7(4Q13.3) MUTATED    9  0
  AMP PEAK  7(4Q13.3) WILD-TYPE 93  3
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  7(4Q13.3) MUTATED      9    0
  AMP PEAK  7(4Q13.3) WILD-TYPE   93    3
   clus
vv  AMP PEAK  7(4Q13.3) MUTATED AMP PEAK  7(4Q13.3) WILD-TYPE
  0                           9                            93
  1                           0                             3
[1] 2 2
[1] FALSE
                               vv
clus                             M0  M1  MX
  AMP PEAK  7(4Q13.3) MUTATED    10   0   5
  AMP PEAK  7(4Q13.3) WILD-TYPE 110   3  32
D7V6, multiclass
    clus
vv   AMP PEAK  7(4Q13.3) MUTATED AMP PEAK  7(4Q13.3) WILD-TYPE
  M0                          10                           110
  M1                           0                             3
  MX                           5                            32
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V7, binary
                               cls
clus                             0  1
  AMP PEAK  7(4Q13.3) MUTATED    8  7
  AMP PEAK  7(4Q13.3) WILD-TYPE 52 93
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  7(4Q13.3) MUTATED      8    7
  AMP PEAK  7(4Q13.3) WILD-TYPE   52   93
        clus
vv       AMP PEAK  7(4Q13.3) MUTATED AMP PEAK  7(4Q13.3) WILD-TYPE
  FEMALE                           8                            52
  MALE                             7                            93
[1] 2 2
[1] FALSE
                               vv
clus                            FIBROLAMELLAR CARCINOMA
  AMP PEAK  7(4Q13.3) MUTATED                         0
  AMP PEAK  7(4Q13.3) WILD-TYPE                       2
                               vv
clus                            HEPATOCELLULAR CARCINOMA
  AMP PEAK  7(4Q13.3) MUTATED                         15
  AMP PEAK  7(4Q13.3) WILD-TYPE                      141
                               vv
clus                            HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK  7(4Q13.3) MUTATED                                  0
  AMP PEAK  7(4Q13.3) WILD-TYPE                                2
D7V8, multiclass
                                  clus
vv                                 AMP PEAK  7(4Q13.3) MUTATED
  FIBROLAMELLAR CARCINOMA                                    0
  HEPATOCELLULAR CARCINOMA                                  15
  HEPATOCHOLANGIOCARCINOMA (MIXED)                           0
                                  clus
vv                                 AMP PEAK  7(4Q13.3) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                      2
  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
  AMP PEAK  7(4Q13.3) MUTATED     9   2   0   4
  AMP PEAK  7(4Q13.3) WILD-TYPE 122   9   1   8
D7V9, multiclass
    clus
vv   AMP PEAK  7(4Q13.3) MUTATED AMP PEAK  7(4Q13.3) WILD-TYPE
  R0                           9                           122
  R1                           2                             9
  R2                           0                             1
  RX                           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"
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  7(4Q13.3) MUTATED                                  0     3
  AMP PEAK  7(4Q13.3) WILD-TYPE                                1    33
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  7(4Q13.3) MUTATED                           1    11
  AMP PEAK  7(4Q13.3) WILD-TYPE                         7    98
D7V10, multiclass
                                  clus
vv                                 AMP PEAK  7(4Q13.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      3
  BLACK OR AFRICAN AMERICAN                                  1
  WHITE                                                     11
                                  clus
vv                                 AMP PEAK  7(4Q13.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                       33
  BLACK OR AFRICAN AMERICAN                                    7
  WHITE                                                       98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V11, binary
                               cls
clus                              0   1
  AMP PEAK  7(4Q13.3) MUTATED     0  14
  AMP PEAK  7(4Q13.3) WILD-TYPE   3 129
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  7(4Q13.3) MUTATED      0   14
  AMP PEAK  7(4Q13.3) WILD-TYPE    3  129
                        clus
vv                       AMP PEAK  7(4Q13.3) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                          14
                        clus
vv                       AMP PEAK  7(4Q13.3) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           129
[1] 2 2
[1] FALSE

Clustering(8) Variable = AMP PEAK  8(5P15.33) MUTATION ANALYSIS
D8V1, survival
                                sevent
clus2                             0  1
  AMP PEAK  8(5P15.33) MUTATED   40 32
  AMP PEAK  8(5P15.33) WILD-TYPE 51 34
  AMP PEAK  8(5P15.33) MUTATED AMP PEAK  8(5P15.33) WILD-TYPE 
                            72                             85 
  AMP PEAK  8(5P15.33) MUTATED AMP PEAK  8(5P15.33) WILD-TYPE 
                            32                             34 
$`AMP PEAK  8(5P15.33) MUTATED`
TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10W TCGA-BC-A10Z TCGA-BC-A112 TCGA-BC-A216 
       37.32        10.13         2.99         1.12         5.03        44.42 
TCGA-BC-A217 TCGA-BC-A3KG TCGA-CC-5258 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 
       13.84        22.36         0.07         4.24         3.32         0.10 
TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A11A 
        0.10         0.13        83.57        53.33       113.00         2.60 
TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EI 
       51.29        90.71        79.40         6.71        12.95         6.02 
TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A3A1 TCGA-DD-A3A3 
       13.64        21.14        55.69         5.62         7.66        17.59 
TCGA-DD-A3A5 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NJ TCGA-DD-A4NK 
      102.74        13.78         0.36        73.38        15.06        39.78 
TCGA-DD-A4NO TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73C TCGA-DD-A73G TCGA-ED-A459 
       73.81        66.35        10.98         7.56       100.96        13.41 
TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7XP TCGA-ED-A82E TCGA-EP-A2KB TCGA-EP-A2KC 
       13.35         0.23         0.20         0.20        10.98         0.62 
TCGA-EP-A3JL TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A495 
        9.96        14.40        32.45        19.10        27.88         0.03 
TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A3CG 
       60.36         0.39        51.06        30.74        58.49        22.13 
TCGA-G3-A3CJ TCGA-G3-A5SI TCGA-G3-A5SM TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ 
       19.53        14.70         4.37         1.84         1.02         2.66 
TCGA-KR-A7K2 TCGA-LG-A6GG TCGA-MI-A75G TCGA-MI-A75I TCGA-NI-A4U2 TCGA-O8-A75V 
       11.84         0.49        14.24         8.71        58.88         4.44 

$`AMP PEAK  8(5P15.33) WILD-TYPE`
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-A110 TCGA-BC-A3KF TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I 
       23.34        69.57         0.26         9.50        14.60        12.72 
TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-A3MA TCGA-DD-A113 TCGA-DD-A114 
        2.86         0.39         3.39         0.07        79.73        37.78 
TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED 
        7.33         0.46        21.76        66.31        19.79        75.65 
TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A39Z TCGA-DD-A3A0 
       45.11        49.15        29.16        18.35        19.76        25.81 
TCGA-DD-A3A2 TCGA-DD-A3A4 TCGA-DD-A3A6 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB 
       70.06        20.12       107.11        30.61        33.14        32.52 
TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NP 
       14.07        14.24        18.44        56.25        29.56        93.67 
TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A73B TCGA-DD-A73D TCGA-DD-A73E 
       12.26         0.30        80.75         9.30        10.98         1.45 
TCGA-DD-A73F TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A7PX TCGA-ED-A7PY 
       27.72        12.69        15.85        13.91         0.20         0.20 
TCGA-ED-A7PZ TCGA-ED-A8O5 TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A3RK 
        0.20         0.20        18.74        19.99        11.74        11.93 
TCGA-ES-A2HS TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A496 TCGA-G3-A25S 
       22.85         8.12         6.38         0.13         0.33         1.22 
TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI 
       53.79        28.27        14.86        21.53        25.64         5.92 
TCGA-G3-A3CK TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-K7-A6G5 
       19.23        11.97         7.99         7.76         5.98         4.01 
TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75H TCGA-MR-A8JO 
        2.14        13.38         9.57         5.10        12.85         1.71 
TCGA-NI-A8LF 
       16.37 

  AMP PEAK  8(5P15.33) MUTATED AMP PEAK  8(5P15.33) WILD-TYPE 
                          0.03                           0.07 
  AMP PEAK  8(5P15.33) MUTATED AMP PEAK  8(5P15.33) WILD-TYPE 
                        113.00                         107.11 
  AMP PEAK  8(5P15.33) MUTATED AMP PEAK  8(5P15.33) WILD-TYPE 
                         13.38                          14.86 
[1] "0.0 - 113.0 (13.4)" "0.1 - 107.1 (14.9)"
[1] "hr=" "1"  
D8V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IIIA
  AMP PEAK  8(5P15.33) MUTATED        24       21         1         20
  AMP PEAK  8(5P15.33) WILD-TYPE      41       16         1         11
                                vv
clus                             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK  8(5P15.33) MUTATED            3          0        0         1
  AMP PEAK  8(5P15.33) WILD-TYPE          2          5        1         0
                                vv
clus                             STAGE IVB
  AMP PEAK  8(5P15.33) MUTATED           0
  AMP PEAK  8(5P15.33) WILD-TYPE         2
D8V3, multiclass
            clus
vv           AMP PEAK  8(5P15.33) MUTATED AMP PEAK  8(5P15.33) WILD-TYPE
  STAGE I                              24                             41
  STAGE II                             21                             16
  STAGE III                             1                              1
  STAGE IIIA                           20                             11
  STAGE IIIB                            3                              2
  STAGE IIIC                            0                              5
  STAGE IV                              0                              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
  AMP PEAK  8(5P15.33) MUTATED   25 23 26  1
  AMP PEAK  8(5P15.33) WILD-TYPE 43 18 16  7
D8V4, multiclass
    clus
vv   AMP PEAK  8(5P15.33) MUTATED AMP PEAK  8(5P15.33) WILD-TYPE
  T1                           25                             43
  T2                           23                             18
  T3                           26                             16
  T4                            1                              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"
D8V5, binary
                                cls
clus                              0  1
  AMP PEAK  8(5P15.33) MUTATED   48  1
  AMP PEAK  8(5P15.33) WILD-TYPE 54  2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  8(5P15.33) MUTATED     48    1
  AMP PEAK  8(5P15.33) WILD-TYPE   54    2
   clus
vv  AMP PEAK  8(5P15.33) MUTATED AMP PEAK  8(5P15.33) WILD-TYPE
  0                           48                             54
  1                            1                              2
[1] 2 2
[1] FALSE
                                vv
clus                             M0 M1 MX
  AMP PEAK  8(5P15.33) MUTATED   59  0 16
  AMP PEAK  8(5P15.33) WILD-TYPE 61  3 21
D8V6, multiclass
    clus
vv   AMP PEAK  8(5P15.33) MUTATED AMP PEAK  8(5P15.33) WILD-TYPE
  M0                           59                             61
  M1                            0                              3
  MX                           16                             21
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V7, binary
                                cls
clus                              0  1
  AMP PEAK  8(5P15.33) MUTATED   27 48
  AMP PEAK  8(5P15.33) WILD-TYPE 33 52
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  8(5P15.33) MUTATED     27   48
  AMP PEAK  8(5P15.33) WILD-TYPE   33   52
        clus
vv       AMP PEAK  8(5P15.33) MUTATED AMP PEAK  8(5P15.33) WILD-TYPE
  FEMALE                           27                             33
  MALE                             48                             52
[1] 2 2
[1] FALSE
                                vv
clus                             FIBROLAMELLAR CARCINOMA
  AMP PEAK  8(5P15.33) MUTATED                         0
  AMP PEAK  8(5P15.33) WILD-TYPE                       2
                                vv
clus                             HEPATOCELLULAR CARCINOMA
  AMP PEAK  8(5P15.33) MUTATED                         73
  AMP PEAK  8(5P15.33) WILD-TYPE                       83
                                vv
clus                             HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK  8(5P15.33) MUTATED                                  2
  AMP PEAK  8(5P15.33) WILD-TYPE                                0
D8V8, multiclass
                                  clus
vv                                 AMP PEAK  8(5P15.33) MUTATED
  FIBROLAMELLAR CARCINOMA                                     0
  HEPATOCELLULAR CARCINOMA                                   73
  HEPATOCHOLANGIOCARCINOMA (MIXED)                            2
                                  clus
vv                                 AMP PEAK  8(5P15.33) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                       2
  HEPATOCELLULAR CARCINOMA                                     83
  HEPATOCHOLANGIOCARCINOMA (MIXED)                              0
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             R0 R1 R2 RX
  AMP PEAK  8(5P15.33) MUTATED   62  5  0  6
  AMP PEAK  8(5P15.33) WILD-TYPE 69  6  1  6
D8V9, multiclass
    clus
vv   AMP PEAK  8(5P15.33) MUTATED AMP PEAK  8(5P15.33) WILD-TYPE
  R0                           62                             69
  R1                            5                              6
  R2                            0                              1
  RX                            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"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  8(5P15.33) MUTATED                                  1    20
  AMP PEAK  8(5P15.33) WILD-TYPE                                0    16
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  8(5P15.33) MUTATED                           5    45
  AMP PEAK  8(5P15.33) WILD-TYPE                         3    64
D8V10, multiclass
                                  clus
vv                                 AMP PEAK  8(5P15.33) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                      20
  BLACK OR AFRICAN AMERICAN                                   5
  WHITE                                                      45
                                  clus
vv                                 AMP PEAK  8(5P15.33) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                        16
  BLACK OR AFRICAN AMERICAN                                     3
  WHITE                                                        64
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V11, binary
                                cls
clus                              0  1
  AMP PEAK  8(5P15.33) MUTATED    1 67
  AMP PEAK  8(5P15.33) WILD-TYPE  2 76
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  8(5P15.33) MUTATED      1   67
  AMP PEAK  8(5P15.33) WILD-TYPE    2   76
                        clus
vv                       AMP PEAK  8(5P15.33) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           67
                        clus
vv                       AMP PEAK  8(5P15.33) WILD-TYPE
  HISPANIC OR LATINO                                  2
  NOT HISPANIC OR LATINO                             76
[1] 2 2
[1] FALSE

Clustering(9) Variable = AMP PEAK  9(5Q35.3) MUTATION ANALYSIS
D9V1, survival
                               sevent
clus2                            0  1
  AMP PEAK  9(5Q35.3) MUTATED   29 28
  AMP PEAK  9(5Q35.3) WILD-TYPE 62 38
  AMP PEAK  9(5Q35.3) MUTATED AMP PEAK  9(5Q35.3) WILD-TYPE 
                           57                           100 
  AMP PEAK  9(5Q35.3) MUTATED AMP PEAK  9(5Q35.3) WILD-TYPE 
                           28                            38 
$`AMP PEAK  9(5Q35.3) MUTATED`
TCGA-BC-A10Q TCGA-BC-A10T TCGA-BC-A10W TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 
       37.32        27.52         2.99         5.03        44.42        13.84 
TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A115 TCGA-DD-A116 
        4.24         3.32         0.10         0.13        83.57        53.33 
TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EE 
      113.00         7.33        51.29        90.71        79.40         6.71 
TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A3A1 TCGA-DD-A3A3 TCGA-DD-A3A5 
       21.14        55.69         5.62         7.66        17.59       102.74 
TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NK TCGA-DD-A4NO TCGA-DD-A4NR 
       13.78         0.36        73.38        39.78        73.81         0.30 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73G TCGA-ED-A66Y TCGA-ED-A7XP TCGA-EP-A2KB 
       66.35        10.98       100.96         0.23         0.20        10.98 
TCGA-EP-A2KC TCGA-EP-A3JL TCGA-ES-A2HT TCGA-FV-A3I0 TCGA-FV-A3R2 TCGA-FV-A495 
        0.62         9.96        14.40        27.88         6.38         0.03 
TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A3CG 
        0.39         1.22        51.06        30.74        58.49        22.13 
TCGA-G3-A5SM TCGA-HP-A5MZ TCGA-KR-A7K2 TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75G 
        4.37         2.66        11.84         0.49         9.57        14.24 
TCGA-MI-A75I TCGA-NI-A8LF TCGA-O8-A75V 
        8.71        16.37         4.44 

$`AMP PEAK  9(5Q35.3) WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10U TCGA-BC-A10X 
       48.99        27.91        10.13        46.78        27.52        25.32 
TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 
       23.34         1.12        69.57         0.26        22.36         9.50 
TCGA-BC-A69H TCGA-BC-A69I TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
       14.60        12.72         0.07         2.86         0.39         3.39 
TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A11A TCGA-DD-A11B 
        0.10         0.07        79.73        37.78         2.60         0.46 
TCGA-DD-A11C TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EF TCGA-DD-A1EG 
       21.76        66.31        19.79        75.65        12.95        45.11 
TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39Z 
       49.15         6.02        29.16        18.35        13.64        19.76 
TCGA-DD-A3A0 TCGA-DD-A3A2 TCGA-DD-A3A4 TCGA-DD-A3A6 TCGA-DD-A3A9 TCGA-DD-A4NA 
       25.81        70.06        20.12       107.11        30.61        33.14 
TCGA-DD-A4NB TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NL 
       32.52        14.07        14.24        18.44        15.06        56.25 
TCGA-DD-A4NN TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NS TCGA-DD-A73B TCGA-DD-A73C 
       29.56        93.67        12.26        80.75         9.30         7.56 
TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG 
       10.98         1.45        27.72        13.41        12.69        15.85 
TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A82E 
       13.91        13.35         0.20         0.20         0.20         0.20 
TCGA-ED-A8O5 TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A3RK TCGA-ES-A2HS 
        0.20        18.74        19.99        11.74        11.93        22.85 
TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I1 TCGA-FV-A3R3 TCGA-FV-A496 TCGA-FV-A4ZP 
       32.45        19.10         8.12         0.13         0.33        60.36 
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-A6UC 
       19.53        19.23        14.70        11.97         7.99         7.76 
TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K7 
        5.98         1.84         1.02         4.01         2.14        13.38 
TCGA-MI-A75E TCGA-MI-A75H TCGA-MR-A8JO TCGA-NI-A4U2 
        5.10        12.85         1.71        58.88 

  AMP PEAK  9(5Q35.3) MUTATED AMP PEAK  9(5Q35.3) WILD-TYPE 
                         0.03                          0.07 
  AMP PEAK  9(5Q35.3) MUTATED AMP PEAK  9(5Q35.3) WILD-TYPE 
                       113.00                        107.11 
  AMP PEAK  9(5Q35.3) MUTATED AMP PEAK  9(5Q35.3) WILD-TYPE 
                        11.84                         14.42 
[1] "0.0 - 113.0 (11.8)" "0.1 - 107.1 (14.4)"
[1] "hr=" "1.1"
D9V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IIIA
  AMP PEAK  9(5Q35.3) MUTATED        24       12         1         13
  AMP PEAK  9(5Q35.3) WILD-TYPE      41       25         1         18
                               vv
clus                            STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK  9(5Q35.3) MUTATED            2          0        1         0
  AMP PEAK  9(5Q35.3) WILD-TYPE          3          5        0         1
                               vv
clus                            STAGE IVB
  AMP PEAK  9(5Q35.3) MUTATED           0
  AMP PEAK  9(5Q35.3) WILD-TYPE         2
D9V3, multiclass
            clus
vv           AMP PEAK  9(5Q35.3) MUTATED AMP PEAK  9(5Q35.3) WILD-TYPE
  STAGE I                             24                            41
  STAGE II                            12                            25
  STAGE III                            1                             1
  STAGE IIIA                          13                            18
  STAGE IIIB                           2                             3
  STAGE IIIC                           0                             5
  STAGE IV                             1                             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  9(5Q35.3) MUTATED   24 14 18  2
  AMP PEAK  9(5Q35.3) WILD-TYPE 44 27 24  6
D9V4, multiclass
    clus
vv   AMP PEAK  9(5Q35.3) MUTATED AMP PEAK  9(5Q35.3) WILD-TYPE
  T1                          24                            44
  T2                          14                            27
  T3                          18                            24
  T4                           2                             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"
D9V5, binary
                               cls
clus                             0  1
  AMP PEAK  9(5Q35.3) MUTATED   34  0
  AMP PEAK  9(5Q35.3) WILD-TYPE 68  3
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  9(5Q35.3) MUTATED     34    0
  AMP PEAK  9(5Q35.3) WILD-TYPE   68    3
   clus
vv  AMP PEAK  9(5Q35.3) MUTATED AMP PEAK  9(5Q35.3) WILD-TYPE
  0                          34                            68
  1                           0                             3
[1] 2 2
[1] FALSE
                               vv
clus                            M0 M1 MX
  AMP PEAK  9(5Q35.3) MUTATED   44  1 13
  AMP PEAK  9(5Q35.3) WILD-TYPE 76  2 24
D9V6, multiclass
    clus
vv   AMP PEAK  9(5Q35.3) MUTATED AMP PEAK  9(5Q35.3) WILD-TYPE
  M0                          44                            76
  M1                           1                             2
  MX                          13                            24
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V7, binary
                               cls
clus                             0  1
  AMP PEAK  9(5Q35.3) MUTATED   19 39
  AMP PEAK  9(5Q35.3) WILD-TYPE 41 61
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  9(5Q35.3) MUTATED     19   39
  AMP PEAK  9(5Q35.3) WILD-TYPE   41   61
        clus
vv       AMP PEAK  9(5Q35.3) MUTATED AMP PEAK  9(5Q35.3) WILD-TYPE
  FEMALE                          19                            41
  MALE                            39                            61
[1] 2 2
[1] FALSE
                               vv
clus                            FIBROLAMELLAR CARCINOMA
  AMP PEAK  9(5Q35.3) MUTATED                         0
  AMP PEAK  9(5Q35.3) WILD-TYPE                       2
                               vv
clus                            HEPATOCELLULAR CARCINOMA
  AMP PEAK  9(5Q35.3) MUTATED                         56
  AMP PEAK  9(5Q35.3) WILD-TYPE                      100
                               vv
clus                            HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK  9(5Q35.3) MUTATED                                  2
  AMP PEAK  9(5Q35.3) WILD-TYPE                                0
D9V8, multiclass
                                  clus
vv                                 AMP PEAK  9(5Q35.3) MUTATED
  FIBROLAMELLAR CARCINOMA                                    0
  HEPATOCELLULAR CARCINOMA                                  56
  HEPATOCHOLANGIOCARCINOMA (MIXED)                           2
                                  clus
vv                                 AMP PEAK  9(5Q35.3) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                      2
  HEPATOCELLULAR CARCINOMA                                   100
  HEPATOCHOLANGIOCARCINOMA (MIXED)                             0
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            R0 R1 R2 RX
  AMP PEAK  9(5Q35.3) MUTATED   47  6  1  2
  AMP PEAK  9(5Q35.3) WILD-TYPE 84  5  0 10
D9V9, multiclass
    clus
vv   AMP PEAK  9(5Q35.3) MUTATED AMP PEAK  9(5Q35.3) WILD-TYPE
  R0                          47                            84
  R1                           6                             5
  R2                           1                             0
  RX                           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"
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  9(5Q35.3) MUTATED                                  0    13
  AMP PEAK  9(5Q35.3) WILD-TYPE                                1    23
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  9(5Q35.3) MUTATED                           3    38
  AMP PEAK  9(5Q35.3) WILD-TYPE                         5    71
D9V10, multiclass
                                  clus
vv                                 AMP PEAK  9(5Q35.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                     13
  BLACK OR AFRICAN AMERICAN                                  3
  WHITE                                                     38
                                  clus
vv                                 AMP PEAK  9(5Q35.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                       23
  BLACK OR AFRICAN AMERICAN                                    5
  WHITE                                                       71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V11, binary
                               cls
clus                             0  1
  AMP PEAK  9(5Q35.3) MUTATED    1 50
  AMP PEAK  9(5Q35.3) WILD-TYPE  2 93
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  9(5Q35.3) MUTATED      1   50
  AMP PEAK  9(5Q35.3) WILD-TYPE    2   93
                        clus
vv                       AMP PEAK  9(5Q35.3) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          50
                        clus
vv                       AMP PEAK  9(5Q35.3) WILD-TYPE
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                            93
[1] 2 2
[1] FALSE

Clustering(10) Variable = AMP PEAK 10(6P25.2) MUTATION ANALYSIS
D10V1, survival
                               sevent
clus2                            0  1
  AMP PEAK 10(6P25.2) MUTATED   38 28
  AMP PEAK 10(6P25.2) WILD-TYPE 53 38
  AMP PEAK 10(6P25.2) MUTATED AMP PEAK 10(6P25.2) WILD-TYPE 
                           66                            91 
  AMP PEAK 10(6P25.2) MUTATED AMP PEAK 10(6P25.2) WILD-TYPE 
                           28                            38 
$`AMP PEAK 10(6P25.2) MUTATED`
TCGA-BC-4073 TCGA-BC-A10R TCGA-BC-A10U TCGA-BC-A112 TCGA-BC-A217 TCGA-BC-A3KG 
       27.91        10.13        27.52         5.03        13.84        22.36 
TCGA-BC-A69H TCGA-BC-A69I TCGA-CC-5261 TCGA-CC-5263 TCGA-CC-A3MB TCGA-CC-A3MC 
       14.60        12.72         0.39         4.24         0.10         0.13 
TCGA-DD-A114 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11C TCGA-DD-A1EE 
       37.78       113.00         7.33         2.60        21.76         6.71 
TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EJ TCGA-DD-A39X TCGA-DD-A39Y 
       12.95        45.11        49.15        29.16        55.69         5.62 
TCGA-DD-A39Z TCGA-DD-A3A5 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NH 
       19.76       102.74        13.78         0.36        30.61        14.24 
TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NN TCGA-DD-A4NS TCGA-DD-A73C TCGA-DD-A73D 
       15.06        39.78        29.56        80.75         7.56        10.98 
TCGA-DD-A73E TCGA-ED-A66X TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A82E TCGA-ED-A8O5 
        1.45        13.35         0.20         0.20         0.20         0.20 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-ES-A2HS TCGA-FV-A3I0 TCGA-FV-A3R2 
       11.74        10.98         0.62        22.85        27.88         6.38 
TCGA-FV-A3R3 TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25X TCGA-G3-A25Y 
        0.13         0.39         1.22        53.79        58.49        14.86 
TCGA-G3-A3CG TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SL TCGA-G3-A6UC TCGA-KR-A7K2 
       22.13        19.23        14.70         7.99         7.76        11.84 
TCGA-LG-A6GG TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-NI-A8LF TCGA-O8-A75V 
        0.49        14.24        12.85         8.71        16.37         4.44 

$`AMP PEAK 10(6P25.2) WILD-TYPE`
TCGA-BC-4072 TCGA-BC-A10Q TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10W TCGA-BC-A10X 
       48.99        37.32        46.78        27.52         2.99        25.32 
TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A216 TCGA-BC-A3KF TCGA-BC-A5W4 
       23.34         1.12        69.57        44.42         0.26         9.50 
TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5262 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA 
        0.07         2.86         3.39         3.32         0.10         0.07 
TCGA-DD-A113 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A11B TCGA-DD-A11D TCGA-DD-A1E9 
       79.73        83.57        53.33         0.46        51.29        90.71 
TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EI TCGA-DD-A1EK 
       79.40        66.31        19.79        75.65         6.02        18.35 
TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 
       13.64        21.14        25.81         7.66        70.06        17.59 
TCGA-DD-A3A4 TCGA-DD-A3A6 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NF 
       20.12       107.11        33.14        32.52        73.38        14.07 
TCGA-DD-A4NI TCGA-DD-A4NL TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR 
       18.44        56.25        73.81        93.67        12.26         0.30 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 
       66.35        10.98         9.30        27.72       100.96        13.41 
TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7XP 
       12.69        15.85        13.91         0.23         0.20         0.20 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B 
       18.74        19.99         9.96        11.93        14.40        32.45 
TCGA-FV-A2QR TCGA-FV-A3I1 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-G3-A25T 
       19.10         8.12         0.03         0.33        60.36        51.06 
TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ 
       28.27        30.74        21.53        25.64         5.92        19.53 
TCGA-G3-A5SJ TCGA-G3-A5SM TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ 
       11.97         4.37         5.98         1.84         1.02         2.66 
TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-MI-A75C TCGA-MI-A75E TCGA-MR-A8JO 
        4.01         2.14        13.38         9.57         5.10         1.71 
TCGA-NI-A4U2 
       58.88 

  AMP PEAK 10(6P25.2) MUTATED AMP PEAK 10(6P25.2) WILD-TYPE 
                         0.10                          0.03 
  AMP PEAK 10(6P25.2) MUTATED AMP PEAK 10(6P25.2) WILD-TYPE 
                       113.00                        107.11 
  AMP PEAK 10(6P25.2) MUTATED AMP PEAK 10(6P25.2) WILD-TYPE 
                        12.90                         17.59 
[1] "0.1 - 113.0 (12.9)" "0.0 - 107.1 (17.6)"
[1] "hr=" "1.3"
D10V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IIIA
  AMP PEAK 10(6P25.2) MUTATED        25       17         2         12
  AMP PEAK 10(6P25.2) WILD-TYPE      40       20         0         19
                               vv
clus                            STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 10(6P25.2) MUTATED            3          1        1         0
  AMP PEAK 10(6P25.2) WILD-TYPE          2          4        0         1
                               vv
clus                            STAGE IVB
  AMP PEAK 10(6P25.2) MUTATED           1
  AMP PEAK 10(6P25.2) WILD-TYPE         1
D10V3, multiclass
            clus
vv           AMP PEAK 10(6P25.2) MUTATED AMP PEAK 10(6P25.2) WILD-TYPE
  STAGE I                             25                            40
  STAGE II                            17                            20
  STAGE III                            2                             0
  STAGE IIIA                          12                            19
  STAGE IIIB                           3                             2
  STAGE IIIC                           1                             4
  STAGE IV                             1                             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(6P25.2) MUTATED   26 19 20  1
  AMP PEAK 10(6P25.2) WILD-TYPE 42 22 22  7
D10V4, multiclass
    clus
vv   AMP PEAK 10(6P25.2) MUTATED AMP PEAK 10(6P25.2) WILD-TYPE
  T1                          26                            42
  T2                          19                            22
  T3                          20                            22
  T4                           1                             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(6P25.2) MUTATED   39  1
  AMP PEAK 10(6P25.2) WILD-TYPE 63  2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(6P25.2) MUTATED     39    1
  AMP PEAK 10(6P25.2) WILD-TYPE   63    2
   clus
vv  AMP PEAK 10(6P25.2) MUTATED AMP PEAK 10(6P25.2) WILD-TYPE
  0                          39                            63
  1                           1                             2
[1] 2 2
[1] FALSE
                               vv
clus                            M0 M1 MX
  AMP PEAK 10(6P25.2) MUTATED   49  2 16
  AMP PEAK 10(6P25.2) WILD-TYPE 71  1 21
D10V6, multiclass
    clus
vv   AMP PEAK 10(6P25.2) MUTATED AMP PEAK 10(6P25.2) WILD-TYPE
  M0                          49                            71
  M1                           2                             1
  MX                          16                            21
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V7, binary
                               cls
clus                             0  1
  AMP PEAK 10(6P25.2) MUTATED   27 40
  AMP PEAK 10(6P25.2) WILD-TYPE 33 60
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(6P25.2) MUTATED     27   40
  AMP PEAK 10(6P25.2) WILD-TYPE   33   60
        clus
vv       AMP PEAK 10(6P25.2) MUTATED AMP PEAK 10(6P25.2) WILD-TYPE
  FEMALE                          27                            33
  MALE                            40                            60
[1] 2 2
[1] FALSE
                               vv
clus                            FIBROLAMELLAR CARCINOMA
  AMP PEAK 10(6P25.2) MUTATED                         0
  AMP PEAK 10(6P25.2) WILD-TYPE                       2
                               vv
clus                            HEPATOCELLULAR CARCINOMA
  AMP PEAK 10(6P25.2) MUTATED                         65
  AMP PEAK 10(6P25.2) WILD-TYPE                       91
                               vv
clus                            HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK 10(6P25.2) MUTATED                                  2
  AMP PEAK 10(6P25.2) WILD-TYPE                                0
D10V8, multiclass
                                  clus
vv                                 AMP PEAK 10(6P25.2) MUTATED
  FIBROLAMELLAR CARCINOMA                                    0
  HEPATOCELLULAR CARCINOMA                                  65
  HEPATOCHOLANGIOCARCINOMA (MIXED)                           2
                                  clus
vv                                 AMP PEAK 10(6P25.2) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                      2
  HEPATOCELLULAR CARCINOMA                                    91
  HEPATOCHOLANGIOCARCINOMA (MIXED)                             0
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            R0 R1 R2 RX
  AMP PEAK 10(6P25.2) MUTATED   57  5  1  4
  AMP PEAK 10(6P25.2) WILD-TYPE 74  6  0  8
D10V9, multiclass
    clus
vv   AMP PEAK 10(6P25.2) MUTATED AMP PEAK 10(6P25.2) WILD-TYPE
  R0                          57                            74
  R1                           5                             6
  R2                           1                             0
  RX                           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"
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 10(6P25.2) MUTATED                                  0    16
  AMP PEAK 10(6P25.2) WILD-TYPE                                1    20
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 10(6P25.2) MUTATED                           4    44
  AMP PEAK 10(6P25.2) WILD-TYPE                         4    65
D10V10, multiclass
                                  clus
vv                                 AMP PEAK 10(6P25.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                     16
  BLACK OR AFRICAN AMERICAN                                  4
  WHITE                                                     44
                                  clus
vv                                 AMP PEAK 10(6P25.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                       20
  BLACK OR AFRICAN AMERICAN                                    4
  WHITE                                                       65
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V11, binary
                               cls
clus                             0  1
  AMP PEAK 10(6P25.2) MUTATED    1 61
  AMP PEAK 10(6P25.2) WILD-TYPE  2 82
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(6P25.2) MUTATED      1   61
  AMP PEAK 10(6P25.2) WILD-TYPE    2   82
                        clus
vv                       AMP PEAK 10(6P25.2) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          61
                        clus
vv                       AMP PEAK 10(6P25.2) WILD-TYPE
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                            82
[1] 2 2
[1] FALSE

Clustering(11) Variable = AMP PEAK 11(6P21.1) MUTATION ANALYSIS
D11V1, survival
                               sevent
clus2                            0  1
  AMP PEAK 11(6P21.1) MUTATED   37 29
  AMP PEAK 11(6P21.1) WILD-TYPE 54 37
  AMP PEAK 11(6P21.1) MUTATED AMP PEAK 11(6P21.1) WILD-TYPE 
                           66                            91 
  AMP PEAK 11(6P21.1) MUTATED AMP PEAK 11(6P21.1) WILD-TYPE 
                           29                            37 
$`AMP PEAK 11(6P21.1) MUTATED`
TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A217 
       27.52        27.52        23.34         1.12        44.42        13.84 
TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A69I TCGA-CC-5261 TCGA-CC-5263 
        0.26        22.36        14.60        12.72         0.39         4.24 
TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A118 TCGA-DD-A119 
        0.10         0.13        37.78        83.57       113.00         7.33 
TCGA-DD-A11A TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1EB TCGA-DD-A1EE TCGA-DD-A1EF 
        2.60        21.76        51.29        66.31         6.71        12.95 
TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A5 
       45.11        49.15        55.69         5.62        19.76       102.74 
TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NH TCGA-DD-A4NK TCGA-DD-A4NN TCGA-DD-A4NS 
        0.36        30.61        14.24        39.78        29.56        80.75 
TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A66X TCGA-ED-A7PZ 
       10.98         1.45        27.72       100.96        13.35         0.20 
TCGA-ED-A82E TCGA-ED-A8O5 TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-ES-A2HS 
        0.20         0.20        11.74        10.98         0.62        22.85 
TCGA-FV-A23B TCGA-FV-A3I0 TCGA-FV-A3R2 TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25U 
       32.45        27.88         6.38         0.39         1.22        53.79 
TCGA-G3-A25X TCGA-G3-A3CG TCGA-G3-A3CK TCGA-G3-A5SL TCGA-G3-A6UC TCGA-KR-A7K2 
       58.49        22.13        19.23         7.99         7.76        11.84 
TCGA-LG-A6GG TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-NI-A8LF TCGA-O8-A75V 
        0.49        14.24        12.85         8.71        16.37         4.44 

$`AMP PEAK 11(6P21.1) WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10W 
       48.99        27.91        37.32        10.13        46.78         2.99 
TCGA-BC-A10X TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A5W4 TCGA-CC-5258 TCGA-CC-5260 
       25.32        69.57         5.03         9.50         0.07         2.86 
TCGA-CC-5262 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-DD-A113 TCGA-DD-A116 
        3.39         3.32         0.10         0.07        79.73        53.33 
TCGA-DD-A11B TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EI 
        0.46        90.71        79.40        19.79        75.65         6.02 
TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A3A0 TCGA-DD-A3A1 
       29.16        18.35        13.64        21.14        25.81         7.66 
TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A4NA 
       70.06        17.59        20.12       107.11        13.78        33.14 
TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NL 
       32.52        73.38        14.07        18.44        15.06        56.25 
TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NV TCGA-DD-A73A 
       73.81        93.67        12.26         0.30        66.35        10.98 
TCGA-DD-A73B TCGA-DD-A73C TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 
        9.30         7.56        13.41        12.69        15.85        13.91 
TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7XP TCGA-EP-A12J TCGA-EP-A26S 
        0.23         0.20         0.20         0.20        18.74        19.99 
TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A2QR TCGA-FV-A3I1 TCGA-FV-A3R3 
        9.96        11.93        14.40        19.10         8.12         0.13 
TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-G3-A25T TCGA-G3-A25V TCGA-G3-A25W 
        0.03         0.33        60.36        51.06        28.27        30.74 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A5SI 
       14.86        21.53        25.64         5.92        19.53        14.70 
TCGA-G3-A5SJ TCGA-G3-A5SM TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ 
       11.97         4.37         5.98         1.84         1.02         2.66 
TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-MI-A75C TCGA-MI-A75E TCGA-MR-A8JO 
        4.01         2.14        13.38         9.57         5.10         1.71 
TCGA-NI-A4U2 
       58.88 

  AMP PEAK 11(6P21.1) MUTATED AMP PEAK 11(6P21.1) WILD-TYPE 
                         0.10                          0.03 
  AMP PEAK 11(6P21.1) MUTATED AMP PEAK 11(6P21.1) WILD-TYPE 
                       113.00                        107.11 
  AMP PEAK 11(6P21.1) MUTATED AMP PEAK 11(6P21.1) WILD-TYPE 
                        14.04                         13.91 
[1] "0.1 - 113.0 (14.0)" "0.0 - 107.1 (13.9)"
[1] "hr=" "1"  
D11V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IIIA
  AMP PEAK 11(6P21.1) MUTATED        29       15         2         12
  AMP PEAK 11(6P21.1) WILD-TYPE      36       22         0         19
                               vv
clus                            STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 11(6P21.1) MUTATED            2          0        1         0
  AMP PEAK 11(6P21.1) WILD-TYPE          3          5        0         1
                               vv
clus                            STAGE IVB
  AMP PEAK 11(6P21.1) MUTATED           1
  AMP PEAK 11(6P21.1) WILD-TYPE         1
D11V3, multiclass
            clus
vv           AMP PEAK 11(6P21.1) MUTATED AMP PEAK 11(6P21.1) WILD-TYPE
  STAGE I                             29                            36
  STAGE II                            15                            22
  STAGE III                            2                             0
  STAGE IIIA                          12                            19
  STAGE IIIB                           2                             3
  STAGE IIIC                           0                             5
  STAGE IV                             1                             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 11(6P21.1) MUTATED   29 17 17  3
  AMP PEAK 11(6P21.1) WILD-TYPE 39 24 25  5
D11V4, multiclass
    clus
vv   AMP PEAK 11(6P21.1) MUTATED AMP PEAK 11(6P21.1) WILD-TYPE
  T1                          29                            39
  T2                          17                            24
  T3                          17                            25
  T4                           3                             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"
D11V5, binary
                               cls
clus                             0  1
  AMP PEAK 11(6P21.1) MUTATED   40  0
  AMP PEAK 11(6P21.1) WILD-TYPE 62  3
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 11(6P21.1) MUTATED     40    0
  AMP PEAK 11(6P21.1) WILD-TYPE   62    3
   clus
vv  AMP PEAK 11(6P21.1) MUTATED AMP PEAK 11(6P21.1) WILD-TYPE
  0                          40                            62
  1                           0                             3
[1] 2 2
[1] FALSE
                               vv
clus                            M0 M1 MX
  AMP PEAK 11(6P21.1) MUTATED   50  2 15
  AMP PEAK 11(6P21.1) WILD-TYPE 70  1 22
D11V6, multiclass
    clus
vv   AMP PEAK 11(6P21.1) MUTATED AMP PEAK 11(6P21.1) WILD-TYPE
  M0                          50                            70
  M1                           2                             1
  MX                          15                            22
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V7, binary
                               cls
clus                             0  1
  AMP PEAK 11(6P21.1) MUTATED   28 39
  AMP PEAK 11(6P21.1) WILD-TYPE 32 61
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 11(6P21.1) MUTATED     28   39
  AMP PEAK 11(6P21.1) WILD-TYPE   32   61
        clus
vv       AMP PEAK 11(6P21.1) MUTATED AMP PEAK 11(6P21.1) WILD-TYPE
  FEMALE                          28                            32
  MALE                            39                            61
[1] 2 2
[1] FALSE
                               vv
clus                            FIBROLAMELLAR CARCINOMA
  AMP PEAK 11(6P21.1) MUTATED                         0
  AMP PEAK 11(6P21.1) WILD-TYPE                       2
                               vv
clus                            HEPATOCELLULAR CARCINOMA
  AMP PEAK 11(6P21.1) MUTATED                         65
  AMP PEAK 11(6P21.1) WILD-TYPE                       91
                               vv
clus                            HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK 11(6P21.1) MUTATED                                  2
  AMP PEAK 11(6P21.1) WILD-TYPE                                0
D11V8, multiclass
                                  clus
vv                                 AMP PEAK 11(6P21.1) MUTATED
  FIBROLAMELLAR CARCINOMA                                    0
  HEPATOCELLULAR CARCINOMA                                  65
  HEPATOCHOLANGIOCARCINOMA (MIXED)                           2
                                  clus
vv                                 AMP PEAK 11(6P21.1) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                      2
  HEPATOCELLULAR CARCINOMA                                    91
  HEPATOCHOLANGIOCARCINOMA (MIXED)                             0
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            R0 R1 R2 RX
  AMP PEAK 11(6P21.1) MUTATED   57  5  1  4
  AMP PEAK 11(6P21.1) WILD-TYPE 74  6  0  8
D11V9, multiclass
    clus
vv   AMP PEAK 11(6P21.1) MUTATED AMP PEAK 11(6P21.1) WILD-TYPE
  R0                          57                            74
  R1                           5                             6
  R2                           1                             0
  RX                           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"
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 11(6P21.1) MUTATED                                  0    13
  AMP PEAK 11(6P21.1) WILD-TYPE                                1    23
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 11(6P21.1) MUTATED                           4    47
  AMP PEAK 11(6P21.1) WILD-TYPE                         4    62
D11V10, multiclass
                                  clus
vv                                 AMP PEAK 11(6P21.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                     13
  BLACK OR AFRICAN AMERICAN                                  4
  WHITE                                                     47
                                  clus
vv                                 AMP PEAK 11(6P21.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                       23
  BLACK OR AFRICAN AMERICAN                                    4
  WHITE                                                       62
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V11, binary
                               cls
clus                             0  1
  AMP PEAK 11(6P21.1) MUTATED    1 58
  AMP PEAK 11(6P21.1) WILD-TYPE  2 85
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 11(6P21.1) MUTATED      1   58
  AMP PEAK 11(6P21.1) WILD-TYPE    2   85
                        clus
vv                       AMP PEAK 11(6P21.1) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          58
                        clus
vv                       AMP PEAK 11(6P21.1) WILD-TYPE
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                            85
[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   25 21
  AMP PEAK 12(6Q12) WILD-TYPE 66 45
  AMP PEAK 12(6Q12) MUTATED AMP PEAK 12(6Q12) WILD-TYPE 
                         46                         111 
  AMP PEAK 12(6Q12) MUTATED AMP PEAK 12(6Q12) WILD-TYPE 
                         21                          45 
$`AMP PEAK 12(6Q12) MUTATED`
TCGA-BC-A10Q TCGA-BC-A10T TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A69H 
       37.32        27.52        13.84         0.26        22.36        14.60 
TCGA-CC-5263 TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A118 
        4.24         0.10         0.13        37.78        83.57       113.00 
TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11C TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EH 
        7.33         2.60        21.76         6.71        12.95        49.15 
TCGA-DD-A1EJ TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A5 TCGA-DD-A3A7 TCGA-DD-A3A8 
       29.16         5.62        19.76       102.74        13.78         0.36 
TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NH TCGA-DD-A4NK TCGA-DD-A4NN TCGA-DD-A4NS 
       30.61        33.14        14.24        39.78        29.56        80.75 
TCGA-DD-A73E TCGA-DD-A73G TCGA-ED-A66X TCGA-ED-A7PZ TCGA-ED-A8O5 TCGA-EP-A2KB 
        1.45       100.96        13.35         0.20         0.20        10.98 
TCGA-EP-A2KC TCGA-ES-A2HS TCGA-FV-A3I0 TCGA-G3-A25U TCGA-G3-A3CG TCGA-G3-A3CK 
        0.62        22.85        27.88        53.79        22.13        19.23 
TCGA-G3-A6UC TCGA-KR-A7K2 TCGA-LG-A6GG TCGA-O8-A75V 
        7.76        11.84         0.49         4.44 

$`AMP PEAK 12(6Q12) WILD-TYPE`
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-A110 TCGA-BC-A112 TCGA-BC-A216 
       25.32        23.34         1.12        69.57         5.03        44.42 
TCGA-BC-A5W4 TCGA-BC-A69I TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
        9.50        12.72         0.07         2.86         0.39         3.39 
TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-DD-A113 TCGA-DD-A116 TCGA-DD-A11B 
        3.32         0.10         0.07        79.73        53.33         0.46 
TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED 
       51.29        90.71        79.40        66.31        19.79        75.65 
TCGA-DD-A1EG TCGA-DD-A1EI TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X 
       45.11         6.02        18.35        13.64        21.14        55.69 
TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A6 
       25.81         7.66        70.06        17.59        20.12       107.11 
TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NL 
       32.52        73.38        14.07        18.44        15.06        56.25 
TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NV TCGA-DD-A73A 
       73.81        93.67        12.26         0.30        66.35        10.98 
TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73F TCGA-ED-A459 TCGA-ED-A4XI 
        9.30         7.56        10.98        27.72        13.41        12.69 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7XP 
       15.85        13.91         0.23         0.20         0.20         0.20 
TCGA-ED-A82E TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A3JL TCGA-EP-A3RK 
        0.20        18.74        19.99        11.74         9.96        11.93 
TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 
       14.40        32.45        19.10         8.12         6.38         0.13 
TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T 
        0.03         0.33        60.36         0.39         1.22        51.06 
TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH 
       28.27        30.74        58.49        14.86        21.53        25.64 
TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM 
        5.92        19.53        14.70        11.97         7.99         4.37 
TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 
        5.98         1.84         1.02         2.66         4.01         2.14 
TCGA-KR-A7K7 TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I 
       13.38         9.57         5.10        14.24        12.85         8.71 
TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF 
        1.71        58.88        16.37 

  AMP PEAK 12(6Q12) MUTATED AMP PEAK 12(6Q12) WILD-TYPE 
                       0.10                        0.03 
  AMP PEAK 12(6Q12) MUTATED AMP PEAK 12(6Q12) WILD-TYPE 
                     113.00                      107.11 
  AMP PEAK 12(6Q12) MUTATED AMP PEAK 12(6Q12) WILD-TYPE 
                      14.42                       13.64 
[1] "0.1 - 113.0 (14.4)" "0.0 - 107.1 (13.6)"
[1] "hr=" "1"  
D12V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 12(6Q12) MUTATED        18       10         2          8          3
  AMP PEAK 12(6Q12) WILD-TYPE      47       27         0         23          2
                             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          3        0         1         1
D12V3, multiclass
            clus
vv           AMP PEAK 12(6Q12) MUTATED AMP PEAK 12(6Q12) WILD-TYPE
  STAGE I                           18                          47
  STAGE II                          10                          27
  STAGE III                          2                           0
  STAGE IIIA                         8                          23
  STAGE IIIB                         3                           2
  STAGE IIIC                         2                           3
  STAGE IV                           1                           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 12(6Q12) MUTATED   19 12 14  2
  AMP PEAK 12(6Q12) WILD-TYPE 49 29 28  6
D12V4, multiclass
    clus
vv   AMP PEAK 12(6Q12) MUTATED AMP PEAK 12(6Q12) WILD-TYPE
  T1                        19                          49
  T2                        12                          29
  T3                        14                          28
  T4                         2                           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"
D12V5, binary
                             cls
clus                           0  1
  AMP PEAK 12(6Q12) MUTATED   29  2
  AMP PEAK 12(6Q12) WILD-TYPE 73  1
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 12(6Q12) MUTATED     29    2
  AMP PEAK 12(6Q12) WILD-TYPE   73    1
   clus
vv  AMP PEAK 12(6Q12) MUTATED AMP PEAK 12(6Q12) WILD-TYPE
  0                        29                          73
  1                         2                           1
[1] 2 2
[1] FALSE
                             vv
clus                          M0 M1 MX
  AMP PEAK 12(6Q12) MUTATED   38  2  7
  AMP PEAK 12(6Q12) WILD-TYPE 82  1 30
D12V6, multiclass
    clus
vv   AMP PEAK 12(6Q12) MUTATED AMP PEAK 12(6Q12) WILD-TYPE
  M0                        38                          82
  M1                         2                           1
  MX                         7                          30
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V7, binary
                             cls
clus                           0  1
  AMP PEAK 12(6Q12) MUTATED   21 26
  AMP PEAK 12(6Q12) WILD-TYPE 39 74
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 12(6Q12) MUTATED     21   26
  AMP PEAK 12(6Q12) WILD-TYPE   39   74
        clus
vv       AMP PEAK 12(6Q12) MUTATED AMP PEAK 12(6Q12) WILD-TYPE
  FEMALE                        21                          39
  MALE                          26                          74
[1] 2 2
[1] FALSE
                             vv
clus                          FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  AMP PEAK 12(6Q12) MUTATED                         0                       45
  AMP PEAK 12(6Q12) WILD-TYPE                       2                      111
                             vv
clus                          HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK 12(6Q12) MUTATED                                  2
  AMP PEAK 12(6Q12) WILD-TYPE                                0
D12V8, multiclass
                                  clus
vv                                 AMP PEAK 12(6Q12) MUTATED
  FIBROLAMELLAR CARCINOMA                                  0
  HEPATOCELLULAR CARCINOMA                                45
  HEPATOCHOLANGIOCARCINOMA (MIXED)                         2
                                  clus
vv                                 AMP PEAK 12(6Q12) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                    2
  HEPATOCELLULAR CARCINOMA                                 111
  HEPATOCHOLANGIOCARCINOMA (MIXED)                           0
[1] 3 2
[1] 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   39  4  1  3
  AMP PEAK 12(6Q12) WILD-TYPE 92  7  0  9
D12V9, multiclass
    clus
vv   AMP PEAK 12(6Q12) MUTATED AMP PEAK 12(6Q12) WILD-TYPE
  R0                        39                          92
  R1                         4                           7
  R2                         1                           0
  RX                         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"
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 12(6Q12) MUTATED                                  0    10
  AMP PEAK 12(6Q12) WILD-TYPE                                1    26
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 12(6Q12) MUTATED                           3    31
  AMP PEAK 12(6Q12) WILD-TYPE                         5    78
D12V10, multiclass
                                  clus
vv                                 AMP PEAK 12(6Q12) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         0
  ASIAN                                                   10
  BLACK OR AFRICAN AMERICAN                                3
  WHITE                                                   31
                                  clus
vv                                 AMP PEAK 12(6Q12) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                     26
  BLACK OR AFRICAN AMERICAN                                  5
  WHITE                                                     78
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V11, binary
                             cls
clus                            0   1
  AMP PEAK 12(6Q12) MUTATED     1  40
  AMP PEAK 12(6Q12) WILD-TYPE   2 103
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 12(6Q12) MUTATED      1   40
  AMP PEAK 12(6Q12) WILD-TYPE    2  103
                        clus
vv                       AMP PEAK 12(6Q12) MUTATED AMP PEAK 12(6Q12) WILD-TYPE
  HISPANIC OR LATINO                             1                           2
  NOT HISPANIC OR LATINO                        40                         103
[1] 2 2
[1] FALSE

Clustering(13) Variable = AMP PEAK 13(6Q12) MUTATION ANALYSIS
D13V1, survival
                             sevent
clus2                          0  1
  AMP PEAK 13(6Q12) MUTATED   20 13
  AMP PEAK 13(6Q12) WILD-TYPE 71 53
  AMP PEAK 13(6Q12) MUTATED AMP PEAK 13(6Q12) WILD-TYPE 
                         33                         124 
  AMP PEAK 13(6Q12) MUTATED AMP PEAK 13(6Q12) WILD-TYPE 
                         13                          53 
$`AMP PEAK 13(6Q12) MUTATED`
TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A69H TCGA-CC-5260 TCGA-CC-5263 
       13.84         0.26        22.36        14.60         2.86         4.24 
TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A115 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A 
        0.10         0.13        83.57       113.00         7.33         2.60 
TCGA-DD-A11D TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A39Y TCGA-DD-A3A8 TCGA-DD-A3A9 
       51.29        12.95        49.15         5.62         0.36        30.61 
TCGA-DD-A73G TCGA-ED-A66X TCGA-ED-A7PZ TCGA-ED-A8O5 TCGA-EP-A12J TCGA-EP-A2KA 
      100.96        13.35         0.20         0.20        18.74        11.74 
TCGA-EP-A2KB TCGA-EP-A2KC TCGA-ES-A2HS TCGA-FV-A3I0 TCGA-G3-A25U TCGA-G3-A3CK 
       10.98         0.62        22.85        27.88        53.79        19.23 
TCGA-KR-A7K2 TCGA-LG-A6GG TCGA-O8-A75V 
       11.84         0.49         4.44 

$`AMP PEAK 13(6Q12) WILD-TYPE`
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-A110 
       27.52         2.99        25.32        23.34         1.12        69.57 
TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A5W4 TCGA-BC-A69I TCGA-CC-5258 TCGA-CC-5261 
        5.03        44.42         9.50        12.72         0.07         0.39 
TCGA-CC-5262 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-DD-A113 TCGA-DD-A114 
        3.39         3.32         0.10         0.07        79.73        37.78 
TCGA-DD-A116 TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB 
       53.33         0.46        21.76        90.71        79.40        66.31 
TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EG TCGA-DD-A1EI TCGA-DD-A1EJ 
       19.79        75.65         6.71        45.11         6.02        29.16 
TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Z TCGA-DD-A3A0 
       18.35        13.64        21.14        55.69        19.76        25.81 
TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 
        7.66        70.06        17.59        20.12       102.74       107.11 
TCGA-DD-A3A7 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH 
       13.78        33.14        32.52        73.38        14.07        14.24 
TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO 
       18.44        15.06        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 
       93.67        12.26         0.30        80.75        66.35        10.98 
TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-ED-A459 
        9.30         7.56        10.98         1.45        27.72        13.41 
TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY 
       12.69        15.85        13.91         0.23         0.20         0.20 
TCGA-ED-A7XP TCGA-ED-A82E TCGA-EP-A26S TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HT 
        0.20         0.20        19.99         9.96        11.93        14.40 
TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 
       32.45        19.10         8.12         6.38         0.13         0.03 
TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25V 
        0.33        60.36         0.39         1.22        51.06        28.27 
TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH 
       30.74        58.49        14.86        21.53        22.13        25.64 
TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM 
        5.92        19.53        14.70        11.97         7.99         4.37 
TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 
        7.76         5.98         1.84         1.02         2.66         4.01 
TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H 
        2.14        13.38         9.57         5.10        14.24        12.85 
TCGA-MI-A75I TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF 
        8.71         1.71        58.88        16.37 

  AMP PEAK 13(6Q12) MUTATED AMP PEAK 13(6Q12) WILD-TYPE 
                       0.10                        0.03 
  AMP PEAK 13(6Q12) MUTATED AMP PEAK 13(6Q12) WILD-TYPE 
                     113.00                      107.11 
  AMP PEAK 13(6Q12) MUTATED AMP PEAK 13(6Q12) WILD-TYPE 
                      11.84                       14.32 
[1] "0.1 - 113.0 (11.8)" "0.0 - 107.1 (14.3)"
[1] "hr=" "1"  
D13V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 13(6Q12) MUTATED        15        8         1          7          0
  AMP PEAK 13(6Q12) WILD-TYPE      50       29         1         24          5
                             vv
clus                          STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 13(6Q12) MUTATED            1        1         0         1
  AMP PEAK 13(6Q12) WILD-TYPE          4        0         1         1
D13V3, multiclass
            clus
vv           AMP PEAK 13(6Q12) MUTATED AMP PEAK 13(6Q12) WILD-TYPE
  STAGE I                           15                          50
  STAGE II                           8                          29
  STAGE III                          1                           1
  STAGE IIIA                         7                          24
  STAGE IIIB                         0                           5
  STAGE IIIC                         1                           4
  STAGE IV                           1                           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 13(6Q12) MUTATED   15  8  9  2
  AMP PEAK 13(6Q12) WILD-TYPE 53 33 33  6
D13V4, multiclass
    clus
vv   AMP PEAK 13(6Q12) MUTATED AMP PEAK 13(6Q12) WILD-TYPE
  T1                        15                          53
  T2                         8                          33
  T3                         9                          33
  T4                         2                           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"
D13V5, binary
                             cls
clus                           0  1
  AMP PEAK 13(6Q12) MUTATED   20  0
  AMP PEAK 13(6Q12) WILD-TYPE 82  3
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 13(6Q12) MUTATED     20    0
  AMP PEAK 13(6Q12) WILD-TYPE   82    3
   clus
vv  AMP PEAK 13(6Q12) MUTATED AMP PEAK 13(6Q12) WILD-TYPE
  0                        20                          82
  1                         0                           3
[1] 2 2
[1] FALSE
                             vv
clus                          M0 M1 MX
  AMP PEAK 13(6Q12) MUTATED   25  2  7
  AMP PEAK 13(6Q12) WILD-TYPE 95  1 30
D13V6, multiclass
    clus
vv   AMP PEAK 13(6Q12) MUTATED AMP PEAK 13(6Q12) WILD-TYPE
  M0                        25                          95
  M1                         2                           1
  MX                         7                          30
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V7, binary
                             cls
clus                           0  1
  AMP PEAK 13(6Q12) MUTATED   15 19
  AMP PEAK 13(6Q12) WILD-TYPE 45 81
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 13(6Q12) MUTATED     15   19
  AMP PEAK 13(6Q12) WILD-TYPE   45   81
        clus
vv       AMP PEAK 13(6Q12) MUTATED AMP PEAK 13(6Q12) WILD-TYPE
  FEMALE                        15                          45
  MALE                          19                          81
[1] 2 2
[1] FALSE
                             vv
clus                          FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  AMP PEAK 13(6Q12) MUTATED                         0                       32
  AMP PEAK 13(6Q12) WILD-TYPE                       2                      124
                             vv
clus                          HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK 13(6Q12) MUTATED                                  2
  AMP PEAK 13(6Q12) WILD-TYPE                                0
D13V8, multiclass
                                  clus
vv                                 AMP PEAK 13(6Q12) MUTATED
  FIBROLAMELLAR CARCINOMA                                  0
  HEPATOCELLULAR CARCINOMA                                32
  HEPATOCHOLANGIOCARCINOMA (MIXED)                         2
                                  clus
vv                                 AMP PEAK 13(6Q12) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                    2
  HEPATOCELLULAR CARCINOMA                                 124
  HEPATOCHOLANGIOCARCINOMA (MIXED)                           0
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           R0  R1  R2  RX
  AMP PEAK 13(6Q12) MUTATED    29   1   1   3
  AMP PEAK 13(6Q12) WILD-TYPE 102  10   0   9
D13V9, multiclass
    clus
vv   AMP PEAK 13(6Q12) MUTATED AMP PEAK 13(6Q12) WILD-TYPE
  R0                        29                         102
  R1                         1                          10
  R2                         1                           0
  RX                         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"
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 13(6Q12) MUTATED                                  0    11
  AMP PEAK 13(6Q12) WILD-TYPE                                1    25
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 13(6Q12) MUTATED                           3    19
  AMP PEAK 13(6Q12) WILD-TYPE                         5    90
D13V10, multiclass
                                  clus
vv                                 AMP PEAK 13(6Q12) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         0
  ASIAN                                                   11
  BLACK OR AFRICAN AMERICAN                                3
  WHITE                                                   19
                                  clus
vv                                 AMP PEAK 13(6Q12) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                     25
  BLACK OR AFRICAN AMERICAN                                  5
  WHITE                                                     90
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V11, binary
                             cls
clus                            0   1
  AMP PEAK 13(6Q12) MUTATED     1  29
  AMP PEAK 13(6Q12) WILD-TYPE   2 114
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 13(6Q12) MUTATED      1   29
  AMP PEAK 13(6Q12) WILD-TYPE    2  114
                        clus
vv                       AMP PEAK 13(6Q12) MUTATED AMP PEAK 13(6Q12) WILD-TYPE
  HISPANIC OR LATINO                             1                           2
  NOT HISPANIC OR LATINO                        29                         114
[1] 2 2
[1] FALSE

Clustering(14) Variable = AMP PEAK 14(7Q21.2) MUTATION ANALYSIS
D14V1, survival
                               sevent
clus2                            0  1
  AMP PEAK 14(7Q21.2) MUTATED   33 24
  AMP PEAK 14(7Q21.2) WILD-TYPE 58 42
  AMP PEAK 14(7Q21.2) MUTATED AMP PEAK 14(7Q21.2) WILD-TYPE 
                           57                           100 
  AMP PEAK 14(7Q21.2) MUTATED AMP PEAK 14(7Q21.2) WILD-TYPE 
                           24                            42 
$`AMP PEAK 14(7Q21.2) MUTATED`
TCGA-BC-4072 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10U TCGA-BC-A5W4 TCGA-BC-A69H 
       48.99        37.32        10.13        27.52         9.50        14.60 
TCGA-CC-5260 TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-DD-A118 TCGA-DD-A11A 
        2.86         0.10         0.07         0.10       113.00         2.60 
TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EC TCGA-DD-A1EE TCGA-DD-A1EJ TCGA-DD-A39V 
       51.29        90.71        19.79         6.71        29.16        21.14 
TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A2 TCGA-DD-A3A7 TCGA-DD-A4NA 
        5.62        19.76        25.81        70.06        13.78        33.14 
TCGA-DD-A4NI TCGA-DD-A4NK TCGA-DD-A4NQ TCGA-DD-A4NV TCGA-DD-A73C TCGA-DD-A73E 
       18.44        39.78        12.26        66.35         7.56         1.45 
TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A66Y TCGA-ED-A7PY TCGA-EP-A26S TCGA-EP-A2KA 
      100.96        13.41         0.23         0.20        19.99        11.74 
TCGA-EP-A2KC TCGA-EP-A3JL TCGA-ES-A2HS TCGA-FV-A2QR TCGA-FV-A3I1 TCGA-FV-A3R2 
        0.62         9.96        22.85        19.10         8.12         6.38 
TCGA-FV-A4ZP TCGA-G3-A25T TCGA-G3-A25V TCGA-G3-A25X TCGA-G3-A3CG TCGA-G3-A3CJ 
       60.36        51.06        28.27        58.49        22.13        19.53 
TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-KR-A7K2 TCGA-LG-A6GG TCGA-MI-A75E 
        7.99         4.37         7.76        11.84         0.49         5.10 
TCGA-MI-A75G TCGA-NI-A4U2 TCGA-NI-A8LF 
       14.24        58.88        16.37 

$`AMP PEAK 14(7Q21.2) WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y 
       27.91        46.78        27.52         2.99        25.32        23.34 
TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF 
        1.12        69.57         5.03        44.42        13.84         0.26 
TCGA-BC-A3KG TCGA-BC-A69I TCGA-CC-5258 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 
       22.36        12.72         0.07         0.39         3.39         4.24 
TCGA-CC-A1HT TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 
        3.32         0.13        79.73        37.78        83.57        53.33 
TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1ED 
        7.33         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-A39X TCGA-DD-A3A1 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 
       55.69         7.66        17.59        20.12       102.74       107.11 
TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH 
        0.36        30.61        32.52        73.38        14.07        14.24 
TCGA-DD-A4NJ TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NR 
       15.06        56.25        29.56        73.81        93.67         0.30 
TCGA-DD-A4NS TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73D TCGA-DD-A73F TCGA-ED-A4XI 
       80.75        10.98         9.30        10.98        27.72        12.69 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A7PX TCGA-ED-A7PZ TCGA-ED-A7XP 
       15.85        13.91        13.35         0.20         0.20         0.20 
TCGA-ED-A82E TCGA-ED-A8O5 TCGA-EP-A12J TCGA-EP-A2KB TCGA-EP-A3RK TCGA-ES-A2HT 
        0.20         0.20        18.74        10.98        11.93        14.40 
TCGA-FV-A23B TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ 
       32.45        27.88         0.13         0.03         0.33         0.39 
TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH 
        1.22        53.79        30.74        14.86        21.53        25.64 
TCGA-G3-A3CI TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A7M7 TCGA-G3-A7M9 
        5.92        19.23        14.70        11.97         5.98         1.84 
TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-MI-A75C 
        1.02         2.66         4.01         2.14        13.38         9.57 
TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A8JO TCGA-O8-A75V 
       12.85         8.71         1.71         4.44 

  AMP PEAK 14(7Q21.2) MUTATED AMP PEAK 14(7Q21.2) WILD-TYPE 
                         0.07                          0.03 
  AMP PEAK 14(7Q21.2) MUTATED AMP PEAK 14(7Q21.2) WILD-TYPE 
                       113.00                        107.11 
  AMP PEAK 14(7Q21.2) MUTATED AMP PEAK 14(7Q21.2) WILD-TYPE 
                        14.60                         13.74 
[1] "0.1 - 113.0 (14.6)" "0.0 - 107.1 (13.7)"
[1] "hr=" "1.1"
D14V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IIIA
  AMP PEAK 14(7Q21.2) MUTATED        20       14         0         16
  AMP PEAK 14(7Q21.2) WILD-TYPE      45       23         2         15
                               vv
clus                            STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 14(7Q21.2) MUTATED            2          4        0         0
  AMP PEAK 14(7Q21.2) WILD-TYPE          3          1        1         1
                               vv
clus                            STAGE IVB
  AMP PEAK 14(7Q21.2) MUTATED           0
  AMP PEAK 14(7Q21.2) WILD-TYPE         2
D14V3, multiclass
            clus
vv           AMP PEAK 14(7Q21.2) MUTATED AMP PEAK 14(7Q21.2) WILD-TYPE
  STAGE I                             20                            45
  STAGE II                            14                            23
  STAGE III                            0                             2
  STAGE IIIA                          16                            15
  STAGE IIIB                           2                             3
  STAGE IIIC                           4                             1
  STAGE IV                             0                             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 14(7Q21.2) MUTATED   21 17 19  2
  AMP PEAK 14(7Q21.2) WILD-TYPE 47 24 23  6
D14V4, multiclass
    clus
vv   AMP PEAK 14(7Q21.2) MUTATED AMP PEAK 14(7Q21.2) WILD-TYPE
  T1                          21                            47
  T2                          17                            24
  T3                          19                            23
  T4                           2                             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(7Q21.2) MUTATED   34  2
  AMP PEAK 14(7Q21.2) WILD-TYPE 68  1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 14(7Q21.2) MUTATED     34    2
  AMP PEAK 14(7Q21.2) WILD-TYPE   68    1
   clus
vv  AMP PEAK 14(7Q21.2) MUTATED AMP PEAK 14(7Q21.2) WILD-TYPE
  0                          34                            68
  1                           2                             1
[1] 2 2
[1] FALSE
                               vv
clus                            M0 M1 MX
  AMP PEAK 14(7Q21.2) MUTATED   46  0 13
  AMP PEAK 14(7Q21.2) WILD-TYPE 74  3 24
D14V6, multiclass
    clus
vv   AMP PEAK 14(7Q21.2) MUTATED AMP PEAK 14(7Q21.2) WILD-TYPE
  M0                          46                            74
  M1                           0                             3
  MX                          13                            24
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V7, binary
                               cls
clus                             0  1
  AMP PEAK 14(7Q21.2) MUTATED   20 39
  AMP PEAK 14(7Q21.2) WILD-TYPE 40 61
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 14(7Q21.2) MUTATED     20   39
  AMP PEAK 14(7Q21.2) WILD-TYPE   40   61
        clus
vv       AMP PEAK 14(7Q21.2) MUTATED AMP PEAK 14(7Q21.2) WILD-TYPE
  FEMALE                          20                            40
  MALE                            39                            61
[1] 2 2
[1] FALSE
                               vv
clus                            FIBROLAMELLAR CARCINOMA
  AMP PEAK 14(7Q21.2) MUTATED                         0
  AMP PEAK 14(7Q21.2) WILD-TYPE                       2
                               vv
clus                            HEPATOCELLULAR CARCINOMA
  AMP PEAK 14(7Q21.2) MUTATED                         58
  AMP PEAK 14(7Q21.2) WILD-TYPE                       98
                               vv
clus                            HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK 14(7Q21.2) MUTATED                                  1
  AMP PEAK 14(7Q21.2) WILD-TYPE                                1
D14V8, multiclass
                                  clus
vv                                 AMP PEAK 14(7Q21.2) MUTATED
  FIBROLAMELLAR CARCINOMA                                    0
  HEPATOCELLULAR CARCINOMA                                  58
  HEPATOCHOLANGIOCARCINOMA (MIXED)                           1
                                  clus
vv                                 AMP PEAK 14(7Q21.2) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                      2
  HEPATOCELLULAR CARCINOMA                                    98
  HEPATOCHOLANGIOCARCINOMA (MIXED)                             1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            R0 R1 R2 RX
  AMP PEAK 14(7Q21.2) MUTATED   47  6  0  4
  AMP PEAK 14(7Q21.2) WILD-TYPE 84  5  1  8
D14V9, multiclass
    clus
vv   AMP PEAK 14(7Q21.2) MUTATED AMP PEAK 14(7Q21.2) WILD-TYPE
  R0                          47                            84
  R1                           6                             5
  R2                           0                             1
  RX                           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"
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 14(7Q21.2) MUTATED                                  1    10
  AMP PEAK 14(7Q21.2) WILD-TYPE                                0    26
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 14(7Q21.2) MUTATED                           2    44
  AMP PEAK 14(7Q21.2) WILD-TYPE                         6    65
D14V10, multiclass
                                  clus
vv                                 AMP PEAK 14(7Q21.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                     10
  BLACK OR AFRICAN AMERICAN                                  2
  WHITE                                                     44
                                  clus
vv                                 AMP PEAK 14(7Q21.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                       26
  BLACK OR AFRICAN AMERICAN                                    6
  WHITE                                                       65
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V11, binary
                               cls
clus                             0  1
  AMP PEAK 14(7Q21.2) MUTATED    1 55
  AMP PEAK 14(7Q21.2) WILD-TYPE  2 88
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 14(7Q21.2) MUTATED      1   55
  AMP PEAK 14(7Q21.2) WILD-TYPE    2   88
                        clus
vv                       AMP PEAK 14(7Q21.2) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          55
                        clus
vv                       AMP PEAK 14(7Q21.2) WILD-TYPE
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                            88
[1] 2 2
[1] FALSE

Clustering(15) Variable = AMP PEAK 15(7Q31.2) MUTATION ANALYSIS
D15V1, survival
                               sevent
clus2                            0  1
  AMP PEAK 15(7Q31.2) MUTATED   33 21
  AMP PEAK 15(7Q31.2) WILD-TYPE 58 45
  AMP PEAK 15(7Q31.2) MUTATED AMP PEAK 15(7Q31.2) WILD-TYPE 
                           54                           103 
  AMP PEAK 15(7Q31.2) MUTATED AMP PEAK 15(7Q31.2) WILD-TYPE 
                           21                            45 
$`AMP PEAK 15(7Q31.2) MUTATED`
TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10U TCGA-BC-A216 TCGA-BC-A3KF TCGA-BC-A5W4 
       37.32        10.13        27.52        44.42         0.26         9.50 
TCGA-BC-A69H TCGA-CC-5260 TCGA-CC-A3M9 TCGA-CC-A3MB TCGA-DD-A118 TCGA-DD-A11D 
       14.60         2.86         0.10         0.10       113.00        51.29 
TCGA-DD-A1E9 TCGA-DD-A1EC TCGA-DD-A1EE TCGA-DD-A1EJ TCGA-DD-A39V TCGA-DD-A39Y 
       90.71        19.79         6.71        29.16        21.14         5.62 
TCGA-DD-A39Z TCGA-DD-A3A2 TCGA-DD-A4NA TCGA-DD-A4NI TCGA-DD-A4NK TCGA-DD-A4NQ 
       19.76        70.06        33.14        18.44        39.78        12.26 
TCGA-DD-A4NV TCGA-DD-A73C TCGA-DD-A73E TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A66Y 
       66.35         7.56         1.45       100.96        13.41         0.23 
TCGA-ED-A7PY TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3JL TCGA-ES-A2HS 
        0.20        19.99        11.74         0.62         9.96        22.85 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25T TCGA-G3-A25V TCGA-G3-A25X 
        8.12         6.38        60.36        51.06        28.27        58.49 
TCGA-G3-A25Y TCGA-G3-A3CG TCGA-G3-A3CJ TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC 
       14.86        22.13        19.53         7.99         4.37         7.76 
TCGA-KR-A7K2 TCGA-LG-A6GG TCGA-MI-A75E TCGA-MI-A75G TCGA-NI-A4U2 TCGA-NI-A8LF 
       11.84         0.49         5.10        14.24        58.88        16.37 

$`AMP PEAK 15(7Q31.2) WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10W TCGA-BC-A10X 
       48.99        27.91        46.78        27.52         2.99        25.32 
TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A217 TCGA-BC-A3KG 
       23.34         1.12        69.57         5.03        13.84        22.36 
TCGA-BC-A69I TCGA-CC-5258 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT 
       12.72         0.07         0.39         3.39         4.24         3.32 
TCGA-CC-A3MA TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 
        0.07         0.13        79.73        37.78        83.57        53.33 
TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A1EA TCGA-DD-A1EB 
        7.33         2.60         0.46        21.76        79.40        66.31 
TCGA-DD-A1ED TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EK 
       75.65        12.95        45.11        49.15         6.02        18.35 
TCGA-DD-A1EL TCGA-DD-A39X TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A3 TCGA-DD-A3A4 
       13.64        55.69        25.81         7.66        17.59        20.12 
TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NB 
      102.74       107.11        13.78         0.36        30.61        32.52 
TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NL TCGA-DD-A4NN 
       73.38        14.07        14.24        15.06        56.25        29.56 
TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A73A TCGA-DD-A73B 
       73.81        93.67         0.30        80.75        10.98         9.30 
TCGA-DD-A73D TCGA-DD-A73F TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X 
       10.98        27.72        12.69        15.85        13.91        13.35 
TCGA-ED-A7PX TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-EP-A12J 
        0.20         0.20         0.20         0.20         0.20        18.74 
TCGA-EP-A2KB TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 
       10.98        11.93        14.40        32.45        19.10        27.88 
TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25U 
        0.13         0.03         0.33         0.39         1.22        53.79 
TCGA-G3-A25W TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CK TCGA-G3-A5SI 
       30.74        21.53        25.64         5.92        19.23        14.70 
TCGA-G3-A5SJ TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 
       11.97         5.98         1.84         1.02         2.66         4.01 
TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-MI-A75C TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A8JO 
        2.14        13.38         9.57        12.85         8.71         1.71 
TCGA-O8-A75V 
        4.44 

  AMP PEAK 15(7Q31.2) MUTATED AMP PEAK 15(7Q31.2) WILD-TYPE 
                         0.10                          0.03 
  AMP PEAK 15(7Q31.2) MUTATED AMP PEAK 15(7Q31.2) WILD-TYPE 
                       113.00                        107.11 
  AMP PEAK 15(7Q31.2) MUTATED AMP PEAK 15(7Q31.2) WILD-TYPE 
                        14.73                         13.78 
[1] "0.1 - 113.0 (14.7)" "0.0 - 107.1 (13.8)"
[1] "hr=" "1.2"
D15V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IIIA
  AMP PEAK 15(7Q31.2) MUTATED        19       14         0         15
  AMP PEAK 15(7Q31.2) WILD-TYPE      46       23         2         16
                               vv
clus                            STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 15(7Q31.2) MUTATED            1          4        0         0
  AMP PEAK 15(7Q31.2) WILD-TYPE          4          1        1         1
                               vv
clus                            STAGE IVB
  AMP PEAK 15(7Q31.2) MUTATED           0
  AMP PEAK 15(7Q31.2) WILD-TYPE         2
D15V3, multiclass
            clus
vv           AMP PEAK 15(7Q31.2) MUTATED AMP PEAK 15(7Q31.2) WILD-TYPE
  STAGE I                             19                            46
  STAGE II                            14                            23
  STAGE III                            0                             2
  STAGE IIIA                          15                            16
  STAGE IIIB                           1                             4
  STAGE IIIC                           4                             1
  STAGE IV                             0                             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(7Q31.2) MUTATED   20 17 17  2
  AMP PEAK 15(7Q31.2) WILD-TYPE 48 24 25  6
D15V4, multiclass
    clus
vv   AMP PEAK 15(7Q31.2) MUTATED AMP PEAK 15(7Q31.2) WILD-TYPE
  T1                          20                            48
  T2                          17                            24
  T3                          17                            25
  T4                           2                             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"
D15V5, binary
                               cls
clus                             0  1
  AMP PEAK 15(7Q31.2) MUTATED   30  2
  AMP PEAK 15(7Q31.2) WILD-TYPE 72  1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 15(7Q31.2) MUTATED     30    2
  AMP PEAK 15(7Q31.2) WILD-TYPE   72    1
   clus
vv  AMP PEAK 15(7Q31.2) MUTATED AMP PEAK 15(7Q31.2) WILD-TYPE
  0                          30                            72
  1                           2                             1
[1] 2 2
[1] FALSE
                               vv
clus                            M0 M1 MX
  AMP PEAK 15(7Q31.2) MUTATED   43  0 13
  AMP PEAK 15(7Q31.2) WILD-TYPE 77  3 24
D15V6, multiclass
    clus
vv   AMP PEAK 15(7Q31.2) MUTATED AMP PEAK 15(7Q31.2) WILD-TYPE
  M0                          43                            77
  M1                           0                             3
  MX                          13                            24
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V7, binary
                               cls
clus                             0  1
  AMP PEAK 15(7Q31.2) MUTATED   22 34
  AMP PEAK 15(7Q31.2) WILD-TYPE 38 66
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 15(7Q31.2) MUTATED     22   34
  AMP PEAK 15(7Q31.2) WILD-TYPE   38   66
        clus
vv       AMP PEAK 15(7Q31.2) MUTATED AMP PEAK 15(7Q31.2) WILD-TYPE
  FEMALE                          22                            38
  MALE                            34                            66
[1] 2 2
[1] FALSE
                               vv
clus                            FIBROLAMELLAR CARCINOMA
  AMP PEAK 15(7Q31.2) MUTATED                         0
  AMP PEAK 15(7Q31.2) WILD-TYPE                       2
                               vv
clus                            HEPATOCELLULAR CARCINOMA
  AMP PEAK 15(7Q31.2) MUTATED                         55
  AMP PEAK 15(7Q31.2) WILD-TYPE                      101
                               vv
clus                            HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK 15(7Q31.2) MUTATED                                  1
  AMP PEAK 15(7Q31.2) WILD-TYPE                                1
D15V8, multiclass
                                  clus
vv                                 AMP PEAK 15(7Q31.2) MUTATED
  FIBROLAMELLAR CARCINOMA                                    0
  HEPATOCELLULAR CARCINOMA                                  55
  HEPATOCHOLANGIOCARCINOMA (MIXED)                           1
                                  clus
vv                                 AMP PEAK 15(7Q31.2) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                      2
  HEPATOCELLULAR CARCINOMA                                   101
  HEPATOCHOLANGIOCARCINOMA (MIXED)                             1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            R0 R1 R2 RX
  AMP PEAK 15(7Q31.2) MUTATED   46  5  0  3
  AMP PEAK 15(7Q31.2) WILD-TYPE 85  6  1  9
D15V9, multiclass
    clus
vv   AMP PEAK 15(7Q31.2) MUTATED AMP PEAK 15(7Q31.2) WILD-TYPE
  R0                          46                            85
  R1                           5                             6
  R2                           0                             1
  RX                           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"
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 15(7Q31.2) MUTATED                                  1    10
  AMP PEAK 15(7Q31.2) WILD-TYPE                                0    26
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 15(7Q31.2) MUTATED                           1    43
  AMP PEAK 15(7Q31.2) WILD-TYPE                         7    66
D15V10, multiclass
                                  clus
vv                                 AMP PEAK 15(7Q31.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                     10
  BLACK OR AFRICAN AMERICAN                                  1
  WHITE                                                     43
                                  clus
vv                                 AMP PEAK 15(7Q31.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                       26
  BLACK OR AFRICAN AMERICAN                                    7
  WHITE                                                       66
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V11, binary
                               cls
clus                             0  1
  AMP PEAK 15(7Q31.2) MUTATED    1 51
  AMP PEAK 15(7Q31.2) WILD-TYPE  2 92
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 15(7Q31.2) MUTATED      1   51
  AMP PEAK 15(7Q31.2) WILD-TYPE    2   92
                        clus
vv                       AMP PEAK 15(7Q31.2) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          51
                        clus
vv                       AMP PEAK 15(7Q31.2) WILD-TYPE
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                            92
[1] 2 2
[1] FALSE

Clustering(16) Variable = AMP PEAK 16(8Q11.1) MUTATION ANALYSIS
D16V1, survival
                               sevent
clus2                            0  1
  AMP PEAK 16(8Q11.1) MUTATED   40 28
  AMP PEAK 16(8Q11.1) WILD-TYPE 51 38
  AMP PEAK 16(8Q11.1) MUTATED AMP PEAK 16(8Q11.1) WILD-TYPE 
                           68                            89 
  AMP PEAK 16(8Q11.1) MUTATED AMP PEAK 16(8Q11.1) WILD-TYPE 
                           28                            38 
$`AMP PEAK 16(8Q11.1) MUTATED`
TCGA-BC-4072 TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10U TCGA-BC-A3KF TCGA-BC-A69H 
       48.99        10.13        46.78        27.52         0.26        14.60 
TCGA-CC-5258 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC 
        0.07         3.32         0.10         0.07         0.10         0.13 
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         6.71 
TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EI TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39Y 
       12.95        45.11         6.02        13.64        21.14         5.62 
TCGA-DD-A39Z TCGA-DD-A3A1 TCGA-DD-A3A3 TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI 
       19.76         7.66        17.59         0.36        73.38        18.44 
TCGA-DD-A4NK TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NQ TCGA-DD-A4NS TCGA-DD-A73G 
       39.78        29.56        73.81        12.26        80.75       100.96 
TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PZ TCGA-EP-A12J TCGA-EP-A2KA TCGA-EP-A2KB 
       13.35         0.23         0.20        18.74        11.74        10.98 
TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A4ZP 
        0.62         9.96        11.93        22.85        14.40        60.36 
TCGA-FV-A4ZQ TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CJ 
        0.39        28.27        30.74        21.53        22.13        19.53 
TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-HP-A5MZ TCGA-K7-A6G5 
       11.97         7.99         5.98         1.84         2.66         4.01 
TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-MI-A75E TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A8JO 
       11.84        13.38         5.10        12.85         8.71         1.71 
TCGA-NI-A8LF TCGA-O8-A75V 
       16.37         4.44 

$`AMP PEAK 16(8Q11.1) WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10T TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y 
       27.91        37.32        27.52         2.99        25.32        23.34 
TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KG 
        1.12        69.57         5.03        44.42        13.84        22.36 
TCGA-BC-A5W4 TCGA-BC-A69I TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 
        9.50        12.72         2.86         0.39         3.39         4.24 
TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A11B 
       79.73        37.78        83.57        53.33       113.00         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        29.16 
TCGA-DD-A1EK TCGA-DD-A39X TCGA-DD-A3A0 TCGA-DD-A3A2 TCGA-DD-A3A4 TCGA-DD-A3A5 
       18.35        55.69        25.81        70.06        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        14.07 
TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NL TCGA-DD-A4NP TCGA-DD-A4NR TCGA-DD-A4NV 
       14.24        15.06        56.25        93.67         0.30        66.35 
TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F 
       10.98         9.30         7.56        10.98         1.45        27.72 
TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A7PX TCGA-ED-A7PY 
       13.41        12.69        15.85        13.91         0.20         0.20 
TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-EP-A26S TCGA-FV-A23B TCGA-FV-A2QR 
        0.20         0.20         0.20        19.99        32.45        19.10 
TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 
       27.88         8.12         6.38         0.13         0.03         0.33 
TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A3CH 
        1.22        51.06        53.79        58.49        14.86        25.64 
TCGA-G3-A3CI TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SM TCGA-G3-A6UC TCGA-GJ-A6C0 
        5.92        19.23        14.70         4.37         7.76         1.02 
TCGA-KR-A7K0 TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75G TCGA-NI-A4U2 
        2.14         0.49         9.57        14.24        58.88 

  AMP PEAK 16(8Q11.1) MUTATED AMP PEAK 16(8Q11.1) WILD-TYPE 
                         0.07                          0.03 
  AMP PEAK 16(8Q11.1) MUTATED AMP PEAK 16(8Q11.1) WILD-TYPE 
                       100.96                        113.00 
  AMP PEAK 16(8Q11.1) MUTATED AMP PEAK 16(8Q11.1) WILD-TYPE 
                       12.115                        15.060 
[1] "0.1 - 101.0 (12.1)" "0.0 - 113.0 (15.1)"
[1] "hr=" "1.4"
D16V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IIIA
  AMP PEAK 16(8Q11.1) MUTATED        34       11         0         16
  AMP PEAK 16(8Q11.1) WILD-TYPE      31       26         2         15
                               vv
clus                            STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 16(8Q11.1) MUTATED            2          1        1         0
  AMP PEAK 16(8Q11.1) WILD-TYPE          3          4        0         1
                               vv
clus                            STAGE IVB
  AMP PEAK 16(8Q11.1) MUTATED           0
  AMP PEAK 16(8Q11.1) WILD-TYPE         2
D16V3, multiclass
            clus
vv           AMP PEAK 16(8Q11.1) MUTATED AMP PEAK 16(8Q11.1) WILD-TYPE
  STAGE I                             34                            31
  STAGE II                            11                            26
  STAGE III                            0                             2
  STAGE IIIA                          16                            15
  STAGE IIIB                           2                             3
  STAGE IIIC                           1                             4
  STAGE IV                             1                             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 16(8Q11.1) MUTATED   34 13 21  1
  AMP PEAK 16(8Q11.1) WILD-TYPE 34 28 21  7
D16V4, multiclass
    clus
vv   AMP PEAK 16(8Q11.1) MUTATED AMP PEAK 16(8Q11.1) WILD-TYPE
  T1                          34                            34
  T2                          13                            28
  T3                          21                            21
  T4                           1                             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"
D16V5, binary
                               cls
clus                             0  1
  AMP PEAK 16(8Q11.1) MUTATED   40  0
  AMP PEAK 16(8Q11.1) WILD-TYPE 62  3
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 16(8Q11.1) MUTATED     40    0
  AMP PEAK 16(8Q11.1) WILD-TYPE   62    3
   clus
vv  AMP PEAK 16(8Q11.1) MUTATED AMP PEAK 16(8Q11.1) WILD-TYPE
  0                          40                            62
  1                           0                             3
[1] 2 2
[1] FALSE
                               vv
clus                            M0 M1 MX
  AMP PEAK 16(8Q11.1) MUTATED   49  1 20
  AMP PEAK 16(8Q11.1) WILD-TYPE 71  2 17
D16V6, multiclass
    clus
vv   AMP PEAK 16(8Q11.1) MUTATED AMP PEAK 16(8Q11.1) WILD-TYPE
  M0                          49                            71
  M1                           1                             2
  MX                          20                            17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V7, binary
                               cls
clus                             0  1
  AMP PEAK 16(8Q11.1) MUTATED   16 54
  AMP PEAK 16(8Q11.1) WILD-TYPE 44 46
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 16(8Q11.1) MUTATED     16   54
  AMP PEAK 16(8Q11.1) WILD-TYPE   44   46
        clus
vv       AMP PEAK 16(8Q11.1) MUTATED AMP PEAK 16(8Q11.1) WILD-TYPE
  FEMALE                          16                            44
  MALE                            54                            46
[1] 2 2
[1] FALSE
                               vv
clus                            FIBROLAMELLAR CARCINOMA
  AMP PEAK 16(8Q11.1) MUTATED                         1
  AMP PEAK 16(8Q11.1) WILD-TYPE                       1
                               vv
clus                            HEPATOCELLULAR CARCINOMA
  AMP PEAK 16(8Q11.1) MUTATED                         68
  AMP PEAK 16(8Q11.1) WILD-TYPE                       88
                               vv
clus                            HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK 16(8Q11.1) MUTATED                                  1
  AMP PEAK 16(8Q11.1) WILD-TYPE                                1
D16V8, multiclass
                                  clus
vv                                 AMP PEAK 16(8Q11.1) MUTATED
  FIBROLAMELLAR CARCINOMA                                    1
  HEPATOCELLULAR CARCINOMA                                  68
  HEPATOCHOLANGIOCARCINOMA (MIXED)                           1
                                  clus
vv                                 AMP PEAK 16(8Q11.1) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                      1
  HEPATOCELLULAR CARCINOMA                                    88
  HEPATOCHOLANGIOCARCINOMA (MIXED)                             1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            R0 R1 R2 RX
  AMP PEAK 16(8Q11.1) MUTATED   55  5  1  6
  AMP PEAK 16(8Q11.1) WILD-TYPE 76  6  0  6
D16V9, multiclass
    clus
vv   AMP PEAK 16(8Q11.1) MUTATED AMP PEAK 16(8Q11.1) WILD-TYPE
  R0                          55                            76
  R1                           5                             6
  R2                           1                             0
  RX                           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"
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 16(8Q11.1) MUTATED                                  1    15
  AMP PEAK 16(8Q11.1) WILD-TYPE                                0    21
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 16(8Q11.1) MUTATED                           6    44
  AMP PEAK 16(8Q11.1) WILD-TYPE                         2    65
D16V10, multiclass
                                  clus
vv                                 AMP PEAK 16(8Q11.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                     15
  BLACK OR AFRICAN AMERICAN                                  6
  WHITE                                                     44
                                  clus
vv                                 AMP PEAK 16(8Q11.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                       21
  BLACK OR AFRICAN AMERICAN                                    2
  WHITE                                                       65
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V11, binary
                               cls
clus                             0  1
  AMP PEAK 16(8Q11.1) MUTATED    2 61
  AMP PEAK 16(8Q11.1) WILD-TYPE  1 82
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 16(8Q11.1) MUTATED      2   61
  AMP PEAK 16(8Q11.1) WILD-TYPE    1   82
                        clus
vv                       AMP PEAK 16(8Q11.1) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          61
                        clus
vv                       AMP PEAK 16(8Q11.1) WILD-TYPE
  HISPANIC OR LATINO                                 1
  NOT HISPANIC OR LATINO                            82
[1] 2 2
[1] FALSE

Clustering(17) Variable = AMP PEAK 17(8Q24.21) MUTATION ANALYSIS
D17V1, survival
                                sevent
clus2                             0  1
  AMP PEAK 17(8Q24.21) MUTATED   57 36
  AMP PEAK 17(8Q24.21) WILD-TYPE 34 30
  AMP PEAK 17(8Q24.21) MUTATED AMP PEAK 17(8Q24.21) WILD-TYPE 
                            93                             64 
  AMP PEAK 17(8Q24.21) MUTATED AMP PEAK 17(8Q24.21) WILD-TYPE 
                            36                             30 
$`AMP PEAK 17(8Q24.21) MUTATED`
TCGA-BC-4072 TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A3KF 
       48.99        46.78        27.52        27.52         2.99         0.26 
TCGA-BC-A69H TCGA-CC-5258 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-A1HT TCGA-CC-A3M9 
       14.60         0.07         0.39         3.39         3.32         0.10 
TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A116 TCGA-DD-A118 
        0.07         0.10         0.13        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         6.71 
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-A3A8 
        5.62        19.76         7.66        17.59        13.78         0.36 
TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NN 
       73.38        14.07        18.44        15.06        39.78        29.56 
TCGA-DD-A4NO TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A73A TCGA-DD-A73D 
       73.81        12.26         0.30        80.75        10.98        10.98 
TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PY TCGA-ED-A7PZ 
      100.96        13.41        13.35         0.23         0.20         0.20 
TCGA-ED-A7XP TCGA-ED-A82E TCGA-EP-A12J TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC 
        0.20         0.20        18.74        11.74        10.98         0.62 
TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A3I0 TCGA-FV-A3I1 
        9.96        11.93        22.85        14.40        27.88         8.12 
TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V 
        6.38        60.36         0.39        51.06        53.79        28.27 
TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CJ 
       30.74        58.49        21.53        22.13        25.64        19.53 
TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A7M7 TCGA-HP-A5MZ TCGA-K7-A6G5 
       14.70        11.97         7.99         5.98         2.66         4.01 
TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75H TCGA-MI-A75I 
       11.84        13.38         9.57         5.10        12.85         8.71 
TCGA-MR-A8JO TCGA-NI-A8LF TCGA-O8-A75V 
        1.71        16.37         4.44 

$`AMP PEAK 17(8Q24.21) WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z 
       27.91        37.32        10.13        25.32        23.34         1.12 
TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KG TCGA-BC-A5W4 
       69.57         5.03        44.42        13.84        22.36         9.50 
TCGA-BC-A69I TCGA-CC-5260 TCGA-CC-5263 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A11B 
       12.72         2.86         4.24        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        29.16 
TCGA-DD-A1EK TCGA-DD-A3A0 TCGA-DD-A3A2 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 
       18.35        25.81        70.06        20.12       102.74       107.11 
TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NH TCGA-DD-A4NL TCGA-DD-A4NP 
       30.61        33.14        32.52        14.24        56.25        93.67 
TCGA-DD-A4NV TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73E TCGA-DD-A73F TCGA-ED-A4XI 
       66.35         9.30         7.56         1.45        27.72        12.69 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A7PX TCGA-ED-A8O5 TCGA-EP-A26S TCGA-FV-A23B 
       15.85        13.91         0.20         0.20        19.99        32.45 
TCGA-FV-A2QR TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-G3-A25S TCGA-G3-A25Y 
       19.10         0.13         0.03         0.33         1.22        14.86 
TCGA-G3-A3CI TCGA-G3-A3CK TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M9 TCGA-GJ-A6C0 
        5.92        19.23         4.37         7.76         1.84         1.02 
TCGA-KR-A7K0 TCGA-LG-A6GG TCGA-MI-A75G TCGA-NI-A4U2 
        2.14         0.49        14.24        58.88 

  AMP PEAK 17(8Q24.21) MUTATED AMP PEAK 17(8Q24.21) WILD-TYPE 
                          0.07                           0.03 
  AMP PEAK 17(8Q24.21) MUTATED AMP PEAK 17(8Q24.21) WILD-TYPE 
                        113.00                         107.11 
  AMP PEAK 17(8Q24.21) MUTATED AMP PEAK 17(8Q24.21) WILD-TYPE 
                        12.950                         18.725 
[1] "0.1 - 113.0 (12.9)" "0.0 - 107.1 (18.7)"
[1] "hr=" "1.1"
D17V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IIIA
  AMP PEAK 17(8Q24.21) MUTATED        41       23         0         20
  AMP PEAK 17(8Q24.21) WILD-TYPE      24       14         2         11
                                vv
clus                             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 17(8Q24.21) MUTATED            2          2        1         1
  AMP PEAK 17(8Q24.21) WILD-TYPE          3          3        0         0
                                vv
clus                             STAGE IVB
  AMP PEAK 17(8Q24.21) MUTATED           0
  AMP PEAK 17(8Q24.21) WILD-TYPE         2
D17V3, multiclass
            clus
vv           AMP PEAK 17(8Q24.21) MUTATED AMP PEAK 17(8Q24.21) WILD-TYPE
  STAGE I                              41                             24
  STAGE II                             23                             14
  STAGE III                             0                              2
  STAGE IIIA                           20                             11
  STAGE IIIB                            2                              3
  STAGE IIIC                            2                              3
  STAGE IV                              1                              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
  AMP PEAK 17(8Q24.21) MUTATED   42 25 24  4
  AMP PEAK 17(8Q24.21) WILD-TYPE 26 16 18  4
D17V4, multiclass
    clus
vv   AMP PEAK 17(8Q24.21) MUTATED AMP PEAK 17(8Q24.21) WILD-TYPE
  T1                           42                             26
  T2                           25                             16
  T3                           24                             18
  T4                            4                              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"
D17V5, binary
                                cls
clus                              0  1
  AMP PEAK 17(8Q24.21) MUTATED   60  1
  AMP PEAK 17(8Q24.21) WILD-TYPE 42  2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(8Q24.21) MUTATED     60    1
  AMP PEAK 17(8Q24.21) WILD-TYPE   42    2
   clus
vv  AMP PEAK 17(8Q24.21) MUTATED AMP PEAK 17(8Q24.21) WILD-TYPE
  0                           60                             42
  1                            1                              2
[1] 2 2
[1] FALSE
                                vv
clus                             M0 M1 MX
  AMP PEAK 17(8Q24.21) MUTATED   71  1 24
  AMP PEAK 17(8Q24.21) WILD-TYPE 49  2 13
D17V6, multiclass
    clus
vv   AMP PEAK 17(8Q24.21) MUTATED AMP PEAK 17(8Q24.21) WILD-TYPE
  M0                           71                             49
  M1                            1                              2
  MX                           24                             13
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V7, binary
                                cls
clus                              0  1
  AMP PEAK 17(8Q24.21) MUTATED   28 68
  AMP PEAK 17(8Q24.21) WILD-TYPE 32 32
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(8Q24.21) MUTATED     28   68
  AMP PEAK 17(8Q24.21) WILD-TYPE   32   32
        clus
vv       AMP PEAK 17(8Q24.21) MUTATED AMP PEAK 17(8Q24.21) WILD-TYPE
  FEMALE                           28                             32
  MALE                             68                             32
[1] 2 2
[1] FALSE
                                vv
clus                             FIBROLAMELLAR CARCINOMA
  AMP PEAK 17(8Q24.21) MUTATED                         1
  AMP PEAK 17(8Q24.21) WILD-TYPE                       1
                                vv
clus                             HEPATOCELLULAR CARCINOMA
  AMP PEAK 17(8Q24.21) MUTATED                         93
  AMP PEAK 17(8Q24.21) WILD-TYPE                       63
                                vv
clus                             HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK 17(8Q24.21) MUTATED                                  2
  AMP PEAK 17(8Q24.21) WILD-TYPE                                0
D17V8, multiclass
                                  clus
vv                                 AMP PEAK 17(8Q24.21) MUTATED
  FIBROLAMELLAR CARCINOMA                                     1
  HEPATOCELLULAR CARCINOMA                                   93
  HEPATOCHOLANGIOCARCINOMA (MIXED)                            2
                                  clus
vv                                 AMP PEAK 17(8Q24.21) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                       1
  HEPATOCELLULAR CARCINOMA                                     63
  HEPATOCHOLANGIOCARCINOMA (MIXED)                              0
[1] 3 2
[1] 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(8Q24.21) MUTATED   77  7  1  7
  AMP PEAK 17(8Q24.21) WILD-TYPE 54  4  0  5
D17V9, multiclass
    clus
vv   AMP PEAK 17(8Q24.21) MUTATED AMP PEAK 17(8Q24.21) WILD-TYPE
  R0                           77                             54
  R1                            7                              4
  R2                            1                              0
  RX                            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"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 17(8Q24.21) MUTATED                                  1    27
  AMP PEAK 17(8Q24.21) WILD-TYPE                                0     9
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 17(8Q24.21) MUTATED                           6    57
  AMP PEAK 17(8Q24.21) WILD-TYPE                         2    52
D17V10, multiclass
                                  clus
vv                                 AMP PEAK 17(8Q24.21) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                      27
  BLACK OR AFRICAN AMERICAN                                   6
  WHITE                                                      57
                                  clus
vv                                 AMP PEAK 17(8Q24.21) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         9
  BLACK OR AFRICAN AMERICAN                                     2
  WHITE                                                        52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V11, binary
                                cls
clus                              0  1
  AMP PEAK 17(8Q24.21) MUTATED    2 86
  AMP PEAK 17(8Q24.21) WILD-TYPE  1 57
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(8Q24.21) MUTATED      2   86
  AMP PEAK 17(8Q24.21) WILD-TYPE    1   57
                        clus
vv                       AMP PEAK 17(8Q24.21) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           86
                        clus
vv                       AMP PEAK 17(8Q24.21) WILD-TYPE
  HISPANIC OR LATINO                                  1
  NOT HISPANIC OR LATINO                             57
[1] 2 2
[1] FALSE

Clustering(18) Variable = AMP PEAK 18(9Q34.2) MUTATION ANALYSIS
D18V1, survival
                               sevent
clus2                            0  1
  AMP PEAK 18(9Q34.2) MUTATED    9 11
  AMP PEAK 18(9Q34.2) WILD-TYPE 82 55
  AMP PEAK 18(9Q34.2) MUTATED AMP PEAK 18(9Q34.2) WILD-TYPE 
                           20                           137 
  AMP PEAK 18(9Q34.2) MUTATED AMP PEAK 18(9Q34.2) WILD-TYPE 
                           11                            55 
$`AMP PEAK 18(9Q34.2) MUTATED`
TCGA-BC-A10T TCGA-BC-A10Y TCGA-CC-5261 TCGA-CC-5263 TCGA-DD-A1EG TCGA-DD-A3A0 
       27.52        23.34         0.39         4.24        45.11        25.81 
TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A4NV TCGA-DD-A73G TCGA-ED-A66Y TCGA-ED-A82E 
      102.74       107.11        66.35       100.96         0.23         0.20 
TCGA-EP-A2KB TCGA-ES-A2HS TCGA-FV-A495 TCGA-FV-A4ZP TCGA-G3-A25U TCGA-G3-A3CG 
       10.98        22.85         0.03        60.36        53.79        22.13 
TCGA-G3-A7M9 TCGA-KR-A7K2 
        1.84        11.84 

$`AMP PEAK 18(9Q34.2) WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10U 
       48.99        27.91        37.32        10.13        46.78        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 
        2.99        25.32         1.12        69.57         5.03        44.42 
TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I 
       13.84         0.26        22.36         9.50        14.60        12.72 
TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5262 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA 
        0.07         2.86         3.39         3.32         0.10         0.07 
TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 
        0.10         0.13        79.73        37.78        83.57        53.33 
TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D 
      113.00         7.33         2.60         0.46        21.76        51.29 
TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE 
       90.71        79.40        66.31        19.79        75.65         6.71 
TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL 
       12.95        49.15         6.02        29.16        18.35        13.64 
TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A1 TCGA-DD-A3A2 
       21.14        55.69         5.62        19.76         7.66        70.06 
TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA 
       17.59        20.12        13.78         0.36        30.61        33.14 
TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ 
       32.52        73.38        14.07        14.24        18.44        15.06 
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        93.67        12.26 
TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D 
        0.30        80.75        10.98         9.30         7.56        10.98 
TCGA-DD-A73E TCGA-DD-A73F TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 
        1.45        27.72        13.41        12.69        15.85        13.91 
TCGA-ED-A66X TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-ED-A8O5 
       13.35         0.20         0.20         0.20         0.20         0.20 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK 
       18.74        19.99        11.74         0.62         9.96        11.93 
TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 
       14.40        32.45        19.10        27.88         8.12         6.38 
TCGA-FV-A3R3 TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25V 
        0.13         0.33         0.39         1.22        51.06        28.27 
TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI 
       30.74        58.49        14.86        21.53        25.64         5.92 
TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM 
       19.53        19.23        14.70        11.97         7.99         4.37 
TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 
        7.76         5.98         1.02         2.66         4.01         2.14 
TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H 
       13.38         0.49         9.57         5.10        14.24        12.85 
TCGA-MI-A75I TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V 
        8.71         1.71        58.88        16.37         4.44 

  AMP PEAK 18(9Q34.2) MUTATED AMP PEAK 18(9Q34.2) WILD-TYPE 
                         0.03                          0.07 
  AMP PEAK 18(9Q34.2) MUTATED AMP PEAK 18(9Q34.2) WILD-TYPE 
                       107.11                        113.00 
  AMP PEAK 18(9Q34.2) MUTATED AMP PEAK 18(9Q34.2) WILD-TYPE 
                       23.095                        13.780 
[1] "0.0 - 107.1 (23.1)" "0.1 - 113.0 (13.8)"
[1] "hr=" "1.2"
D18V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IIIA
  AMP PEAK 18(9Q34.2) MUTATED         8        3         1          6
  AMP PEAK 18(9Q34.2) WILD-TYPE      57       34         1         25
                               vv
clus                            STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 18(9Q34.2) MUTATED            1          0        0         1
  AMP PEAK 18(9Q34.2) WILD-TYPE          4          5        1         0
                               vv
clus                            STAGE IVB
  AMP PEAK 18(9Q34.2) MUTATED           0
  AMP PEAK 18(9Q34.2) WILD-TYPE         2
D18V3, multiclass
            clus
vv           AMP PEAK 18(9Q34.2) MUTATED AMP PEAK 18(9Q34.2) WILD-TYPE
  STAGE I                              8                            57
  STAGE II                             3                            34
  STAGE III                            1                             1
  STAGE IIIA                           6                            25
  STAGE IIIB                           1                             4
  STAGE IIIC                           0                             5
  STAGE IV                             0                             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
  AMP PEAK 18(9Q34.2) MUTATED    9  3  8  2
  AMP PEAK 18(9Q34.2) WILD-TYPE 59 38 34  6
D18V4, multiclass
    clus
vv   AMP PEAK 18(9Q34.2) MUTATED AMP PEAK 18(9Q34.2) WILD-TYPE
  T1                           9                            59
  T2                           3                            38
  T3                           8                            34
  T4                           2                             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"
D18V5, binary
                               cls
clus                             0  1
  AMP PEAK 18(9Q34.2) MUTATED   13  1
  AMP PEAK 18(9Q34.2) WILD-TYPE 89  2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 18(9Q34.2) MUTATED     13    1
  AMP PEAK 18(9Q34.2) WILD-TYPE   89    2
   clus
vv  AMP PEAK 18(9Q34.2) MUTATED AMP PEAK 18(9Q34.2) WILD-TYPE
  0                          13                            89
  1                           1                             2
[1] 2 2
[1] FALSE
                               vv
clus                             M0  M1  MX
  AMP PEAK 18(9Q34.2) MUTATED    16   0   6
  AMP PEAK 18(9Q34.2) WILD-TYPE 104   3  31
D18V6, multiclass
    clus
vv   AMP PEAK 18(9Q34.2) MUTATED AMP PEAK 18(9Q34.2) WILD-TYPE
  M0                          16                           104
  M1                           0                             3
  MX                           6                            31
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V7, binary
                               cls
clus                             0  1
  AMP PEAK 18(9Q34.2) MUTATED    8 14
  AMP PEAK 18(9Q34.2) WILD-TYPE 52 86
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 18(9Q34.2) MUTATED      8   14
  AMP PEAK 18(9Q34.2) WILD-TYPE   52   86
        clus
vv       AMP PEAK 18(9Q34.2) MUTATED AMP PEAK 18(9Q34.2) WILD-TYPE
  FEMALE                           8                            52
  MALE                            14                            86
[1] 2 2
[1] FALSE
                               vv
clus                            FIBROLAMELLAR CARCINOMA
  AMP PEAK 18(9Q34.2) MUTATED                         0
  AMP PEAK 18(9Q34.2) WILD-TYPE                       2
                               vv
clus                            HEPATOCELLULAR CARCINOMA
  AMP PEAK 18(9Q34.2) MUTATED                         21
  AMP PEAK 18(9Q34.2) WILD-TYPE                      135
                               vv
clus                            HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK 18(9Q34.2) MUTATED                                  1
  AMP PEAK 18(9Q34.2) WILD-TYPE                                1
D18V8, multiclass
                                  clus
vv                                 AMP PEAK 18(9Q34.2) MUTATED
  FIBROLAMELLAR CARCINOMA                                    0
  HEPATOCELLULAR CARCINOMA                                  21
  HEPATOCHOLANGIOCARCINOMA (MIXED)                           1
                                  clus
vv                                 AMP PEAK 18(9Q34.2) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                      2
  HEPATOCELLULAR CARCINOMA                                   135
  HEPATOCHOLANGIOCARCINOMA (MIXED)                             1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK 18(9Q34.2) MUTATED    16   3   0   3
  AMP PEAK 18(9Q34.2) WILD-TYPE 115   8   1   9
D18V9, multiclass
    clus
vv   AMP PEAK 18(9Q34.2) MUTATED AMP PEAK 18(9Q34.2) WILD-TYPE
  R0                          16                           115
  R1                           3                             8
  R2                           0                             1
  RX                           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"
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 18(9Q34.2) MUTATED                                  0     6
  AMP PEAK 18(9Q34.2) WILD-TYPE                                1    30
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 18(9Q34.2) MUTATED                           0    16
  AMP PEAK 18(9Q34.2) WILD-TYPE                         8    93
D18V10, multiclass
                                  clus
vv                                 AMP PEAK 18(9Q34.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      6
  BLACK OR AFRICAN AMERICAN                                  0
  WHITE                                                     16
                                  clus
vv                                 AMP PEAK 18(9Q34.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                       30
  BLACK OR AFRICAN AMERICAN                                    8
  WHITE                                                       93
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V11, binary
                               cls
clus                              0   1
  AMP PEAK 18(9Q34.2) MUTATED     0  21
  AMP PEAK 18(9Q34.2) WILD-TYPE   3 122
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 18(9Q34.2) MUTATED      0   21
  AMP PEAK 18(9Q34.2) WILD-TYPE    3  122
                        clus
vv                       AMP PEAK 18(9Q34.2) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                          21
                        clus
vv                       AMP PEAK 18(9Q34.2) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           122
[1] 2 2
[1] FALSE

Clustering(19) Variable = AMP PEAK 19(10P15.1) MUTATION ANALYSIS
D19V1, survival
                                sevent
clus2                             0  1
  AMP PEAK 19(10P15.1) MUTATED   17 13
  AMP PEAK 19(10P15.1) WILD-TYPE 74 53
  AMP PEAK 19(10P15.1) MUTATED AMP PEAK 19(10P15.1) WILD-TYPE 
                            30                            127 
  AMP PEAK 19(10P15.1) MUTATED AMP PEAK 19(10P15.1) WILD-TYPE 
                            13                             53 
$`AMP PEAK 19(10P15.1) MUTATED`
TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A217 TCGA-CC-A3MA TCGA-CC-A3MB 
       37.32        10.13        27.52        13.84         0.07         0.10 
TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A3A7 TCGA-DD-A3A9 
       79.73        37.78        18.35        13.64        13.78        30.61 
TCGA-DD-A4NQ TCGA-DD-A4NV TCGA-DD-A73D TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A66X 
       12.26        66.35        10.98       100.96        13.41        13.35 
TCGA-ED-A66Y TCGA-ED-A82E TCGA-EP-A2KA TCGA-EP-A2KB TCGA-ES-A2HS TCGA-FV-A4ZQ 
        0.23         0.20        11.74        10.98        22.85         0.39 
TCGA-G3-A25X TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM TCGA-GJ-A6C0 TCGA-MR-A8JO 
       58.49        11.97         7.99         4.37         1.02         1.71 

$`AMP PEAK 19(10P15.1) WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10S TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X 
       48.99        27.91        46.78        27.52         2.99        25.32 
TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A3KF 
       23.34         1.12        69.57         5.03        44.42         0.26 
TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I TCGA-CC-5258 TCGA-CC-5260 
       22.36         9.50        14.60        12.72         0.07         2.86 
TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MC 
        0.39         3.39         4.24         3.32         0.10         0.13 
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-A1EG TCGA-DD-A1EH TCGA-DD-A1EI 
       75.65         6.71        12.95        45.11        49.15         6.02 
TCGA-DD-A1EJ TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 
       29.16        21.14        55.69         5.62        19.76        25.81 
TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 
        7.66        70.06        17.59        20.12       102.74       107.11 
TCGA-DD-A3A8 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH 
        0.36        33.14        32.52        73.38        14.07        14.24 
TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO 
       18.44        15.06        39.78        56.25        29.56        73.81 
TCGA-DD-A4NP TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C 
       93.67         0.30        80.75        10.98         9.30         7.56 
TCGA-DD-A73E TCGA-DD-A73F TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A7PX 
        1.45        27.72        12.69        15.85        13.91         0.20 
TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-ED-A8O5 TCGA-EP-A12J TCGA-EP-A26S 
        0.20         0.20         0.20         0.20        18.74        19.99 
TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR 
        0.62         9.96        11.93        14.40        32.45        19.10 
TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 
       27.88         8.12         6.38         0.13         0.03         0.33 
TCGA-FV-A4ZP TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W 
       60.36         1.22        51.06        53.79        28.27        30.74 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ 
       14.86        21.53        22.13        25.64         5.92        19.53 
TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-HP-A5MZ 
       19.23        14.70         7.76         5.98         1.84         2.66 
TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75C 
        4.01         2.14        11.84        13.38         0.49         9.57 
TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-NI-A4U2 TCGA-NI-A8LF 
        5.10        14.24        12.85         8.71        58.88        16.37 
TCGA-O8-A75V 
        4.44 

  AMP PEAK 19(10P15.1) MUTATED AMP PEAK 19(10P15.1) WILD-TYPE 
                          0.07                           0.03 
  AMP PEAK 19(10P15.1) MUTATED AMP PEAK 19(10P15.1) WILD-TYPE 
                        100.96                         113.00 
  AMP PEAK 19(10P15.1) MUTATED AMP PEAK 19(10P15.1) WILD-TYPE 
                        12.805                         14.600 
[1] "0.1 - 101.0 (12.8)" "0.0 - 113.0 (14.6)"
[1] "hr=" "1.2"
D19V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IIIA
  AMP PEAK 19(10P15.1) MUTATED         6       10         0          9
  AMP PEAK 19(10P15.1) WILD-TYPE      59       27         2         22
                                vv
clus                             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 19(10P15.1) MUTATED            1          0        0         0
  AMP PEAK 19(10P15.1) WILD-TYPE          4          5        1         1
                                vv
clus                             STAGE IVB
  AMP PEAK 19(10P15.1) MUTATED           2
  AMP PEAK 19(10P15.1) WILD-TYPE         0
D19V3, multiclass
            clus
vv           AMP PEAK 19(10P15.1) MUTATED AMP PEAK 19(10P15.1) WILD-TYPE
  STAGE I                               6                             59
  STAGE II                             10                             27
  STAGE III                             0                              2
  STAGE IIIA                            9                             22
  STAGE IIIB                            1                              4
  STAGE IIIC                            0                              5
  STAGE IV                              0                              1
  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 19(10P15.1) MUTATED    6 11 11  3
  AMP PEAK 19(10P15.1) WILD-TYPE 62 30 31  5
D19V4, multiclass
    clus
vv   AMP PEAK 19(10P15.1) MUTATED AMP PEAK 19(10P15.1) WILD-TYPE
  T1                            6                             62
  T2                           11                             30
  T3                           11                             31
  T4                            3                              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"
D19V5, binary
                                cls
clus                              0  1
  AMP PEAK 19(10P15.1) MUTATED   17  0
  AMP PEAK 19(10P15.1) WILD-TYPE 85  3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 19(10P15.1) MUTATED     17    0
  AMP PEAK 19(10P15.1) WILD-TYPE   85    3
   clus
vv  AMP PEAK 19(10P15.1) MUTATED AMP PEAK 19(10P15.1) WILD-TYPE
  0                           17                             85
  1                            0                              3
[1] 2 2
[1] FALSE
                                vv
clus                              M0  M1  MX
  AMP PEAK 19(10P15.1) MUTATED    20   2   9
  AMP PEAK 19(10P15.1) WILD-TYPE 100   1  28
D19V6, multiclass
    clus
vv   AMP PEAK 19(10P15.1) MUTATED AMP PEAK 19(10P15.1) WILD-TYPE
  M0                           20                            100
  M1                            2                              1
  MX                            9                             28
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V7, binary
                                cls
clus                              0  1
  AMP PEAK 19(10P15.1) MUTATED   13 18
  AMP PEAK 19(10P15.1) WILD-TYPE 47 82
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 19(10P15.1) MUTATED     13   18
  AMP PEAK 19(10P15.1) WILD-TYPE   47   82
        clus
vv       AMP PEAK 19(10P15.1) MUTATED AMP PEAK 19(10P15.1) WILD-TYPE
  FEMALE                           13                             47
  MALE                             18                             82
[1] 2 2
[1] FALSE
                                vv
clus                             FIBROLAMELLAR CARCINOMA
  AMP PEAK 19(10P15.1) MUTATED                         1
  AMP PEAK 19(10P15.1) WILD-TYPE                       1
                                vv
clus                             HEPATOCELLULAR CARCINOMA
  AMP PEAK 19(10P15.1) MUTATED                         30
  AMP PEAK 19(10P15.1) WILD-TYPE                      126
                                vv
clus                             HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK 19(10P15.1) MUTATED                                  0
  AMP PEAK 19(10P15.1) WILD-TYPE                                2
D19V8, multiclass
                                  clus
vv                                 AMP PEAK 19(10P15.1) MUTATED
  FIBROLAMELLAR CARCINOMA                                     1
  HEPATOCELLULAR CARCINOMA                                   30
  HEPATOCHOLANGIOCARCINOMA (MIXED)                            0
                                  clus
vv                                 AMP PEAK 19(10P15.1) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                       1
  HEPATOCELLULAR CARCINOMA                                    126
  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 19(10P15.1) MUTATED    26   2   0   3
  AMP PEAK 19(10P15.1) WILD-TYPE 105   9   1   9
D19V9, multiclass
    clus
vv   AMP PEAK 19(10P15.1) MUTATED AMP PEAK 19(10P15.1) WILD-TYPE
  R0                           26                            105
  R1                            2                              9
  R2                            0                              1
  RX                            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"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 19(10P15.1) MUTATED                                  0     8
  AMP PEAK 19(10P15.1) WILD-TYPE                                1    28
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 19(10P15.1) MUTATED                           2    20
  AMP PEAK 19(10P15.1) WILD-TYPE                         6    89
D19V10, multiclass
                                  clus
vv                                 AMP PEAK 19(10P15.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       8
  BLACK OR AFRICAN AMERICAN                                   2
  WHITE                                                      20
                                  clus
vv                                 AMP PEAK 19(10P15.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        28
  BLACK OR AFRICAN AMERICAN                                     6
  WHITE                                                        89
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V11, binary
                                cls
clus                               0   1
  AMP PEAK 19(10P15.1) MUTATED     1  27
  AMP PEAK 19(10P15.1) WILD-TYPE   2 116
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 19(10P15.1) MUTATED      1   27
  AMP PEAK 19(10P15.1) WILD-TYPE    2  116
                        clus
vv                       AMP PEAK 19(10P15.1) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           27
                        clus
vv                       AMP PEAK 19(10P15.1) WILD-TYPE
  HISPANIC OR LATINO                                  2
  NOT HISPANIC OR LATINO                            116
[1] 2 2
[1] FALSE

Clustering(20) Variable = AMP PEAK 20(11Q13.3) MUTATION ANALYSIS
D20V1, survival
                                sevent
clus2                             0  1
  AMP PEAK 20(11Q13.3) MUTATED   19  8
  AMP PEAK 20(11Q13.3) WILD-TYPE 72 58
  AMP PEAK 20(11Q13.3) MUTATED AMP PEAK 20(11Q13.3) WILD-TYPE 
                            27                            130 
  AMP PEAK 20(11Q13.3) MUTATED AMP PEAK 20(11Q13.3) WILD-TYPE 
                             8                             58 
$`AMP PEAK 20(11Q13.3) MUTATED`
TCGA-BC-4073 TCGA-BC-A10T TCGA-BC-A3KG TCGA-BC-A69I TCGA-CC-A3M9 TCGA-CC-A3MB 
       27.91        27.52        22.36        12.72         0.10         0.10 
TCGA-DD-A115 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A1EB TCGA-DD-A39Y TCGA-DD-A3A0 
       83.57         7.33         2.60        66.31         5.62        25.81 
TCGA-DD-A4ND TCGA-DD-A4NN TCGA-DD-A4NV TCGA-DD-A73E TCGA-DD-A73G TCGA-ED-A66Y 
       73.38        29.56        66.35         1.45       100.96         0.23 
TCGA-ED-A82E TCGA-EP-A2KA TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25W 
        0.20        11.74         0.33         0.39         1.22        30.74 
TCGA-G3-A3CG TCGA-G3-A5SJ TCGA-LG-A6GG 
       22.13        11.97         0.49 

$`AMP PEAK 20(11Q13.3) WILD-TYPE`
TCGA-BC-4072 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10U TCGA-BC-A10W 
       48.99        37.32        10.13        46.78        27.52         2.99 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 
       25.32        23.34         1.12        69.57         5.03        44.42 
TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A5W4 TCGA-BC-A69H TCGA-CC-5258 TCGA-CC-5260 
       13.84         0.26         9.50        14.60         0.07         2.86 
TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3MA TCGA-CC-A3MC 
        0.39         3.39         4.24         3.32         0.07         0.13 
TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A11B TCGA-DD-A11C 
       79.73        37.78        53.33       113.00         0.46        21.76 
TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE 
       51.29        90.71        79.40        19.79        75.65         6.71 
TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK 
       12.95        45.11        49.15         6.02        29.16        18.35 
TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Z TCGA-DD-A3A1 TCGA-DD-A3A2 
       13.64        21.14        55.69        19.76         7.66        70.06 
TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 
       17.59        20.12       102.74       107.11        13.78         0.36 
TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI 
       30.61        33.14        32.52        14.07        14.24        18.44 
TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ 
       15.06        39.78        56.25        73.81        93.67        12.26 
TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D 
        0.30        80.75        10.98         9.30         7.56        10.98 
TCGA-DD-A73F TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X 
       27.72        13.41        12.69        15.85        13.91        13.35 
TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-ED-A8O5 TCGA-EP-A12J 
        0.20         0.20         0.20         0.20         0.20        18.74 
TCGA-EP-A26S TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS 
       19.99        10.98         0.62         9.96        11.93        22.85 
TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 
       14.40        32.45        19.10        27.88         8.12         6.38 
TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A4ZP TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V 
        0.13         0.03        60.36        51.06        53.79        28.27 
TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ 
       58.49        14.86        21.53        25.64         5.92        19.53 
TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M7 
       19.23        14.70         7.99         4.37         7.76         5.98 
TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 
        1.84         1.02         2.66         4.01         2.14        11.84 
TCGA-KR-A7K7 TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I 
       13.38         9.57         5.10        14.24        12.85         8.71 
TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V 
        1.71        58.88        16.37         4.44 

  AMP PEAK 20(11Q13.3) MUTATED AMP PEAK 20(11Q13.3) WILD-TYPE 
                          0.10                           0.03 
  AMP PEAK 20(11Q13.3) MUTATED AMP PEAK 20(11Q13.3) WILD-TYPE 
                        100.96                         113.00 
  AMP PEAK 20(11Q13.3) MUTATED AMP PEAK 20(11Q13.3) WILD-TYPE 
                        11.970                         14.155 
[1] "0.1 - 101.0 (12.0)" "0.0 - 113.0 (14.2)"
[1] "hr=" "1.4"
D20V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IIIA
  AMP PEAK 20(11Q13.3) MUTATED        15        2         0          9
  AMP PEAK 20(11Q13.3) WILD-TYPE      50       35         2         22
                                vv
clus                             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 20(11Q13.3) MUTATED            1          0        1         0
  AMP PEAK 20(11Q13.3) WILD-TYPE          4          5        0         1
                                vv
clus                             STAGE IVB
  AMP PEAK 20(11Q13.3) MUTATED           0
  AMP PEAK 20(11Q13.3) WILD-TYPE         2
D20V3, multiclass
            clus
vv           AMP PEAK 20(11Q13.3) MUTATED AMP PEAK 20(11Q13.3) WILD-TYPE
  STAGE I                              15                             50
  STAGE II                              2                             35
  STAGE III                             0                              2
  STAGE IIIA                            9                             22
  STAGE IIIB                            1                              4
  STAGE IIIC                            0                              5
  STAGE IV                              1                              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 20(11Q13.3) MUTATED   15  2 11  1
  AMP PEAK 20(11Q13.3) WILD-TYPE 53 39 31  7
D20V4, multiclass
    clus
vv   AMP PEAK 20(11Q13.3) MUTATED AMP PEAK 20(11Q13.3) WILD-TYPE
  T1                           15                             53
  T2                            2                             39
  T3                           11                             31
  T4                            1                              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"
D20V5, binary
                                cls
clus                              0  1
  AMP PEAK 20(11Q13.3) MUTATED   20  0
  AMP PEAK 20(11Q13.3) WILD-TYPE 82  3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(11Q13.3) MUTATED     20    0
  AMP PEAK 20(11Q13.3) WILD-TYPE   82    3
   clus
vv  AMP PEAK 20(11Q13.3) MUTATED AMP PEAK 20(11Q13.3) WILD-TYPE
  0                           20                             82
  1                            0                              3
[1] 2 2
[1] FALSE
                                vv
clus                             M0 M1 MX
  AMP PEAK 20(11Q13.3) MUTATED   24  1  4
  AMP PEAK 20(11Q13.3) WILD-TYPE 96  2 33
D20V6, multiclass
    clus
vv   AMP PEAK 20(11Q13.3) MUTATED AMP PEAK 20(11Q13.3) WILD-TYPE
  M0                           24                             96
  M1                            1                              2
  MX                            4                             33
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V7, binary
                                cls
clus                              0  1
  AMP PEAK 20(11Q13.3) MUTATED   11 18
  AMP PEAK 20(11Q13.3) WILD-TYPE 49 82
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(11Q13.3) MUTATED     11   18
  AMP PEAK 20(11Q13.3) WILD-TYPE   49   82
        clus
vv       AMP PEAK 20(11Q13.3) MUTATED AMP PEAK 20(11Q13.3) WILD-TYPE
  FEMALE                           11                             49
  MALE                             18                             82
[1] 2 2
[1] FALSE
                                vv
clus                             FIBROLAMELLAR CARCINOMA
  AMP PEAK 20(11Q13.3) MUTATED                         0
  AMP PEAK 20(11Q13.3) WILD-TYPE                       2
                                vv
clus                             HEPATOCELLULAR CARCINOMA
  AMP PEAK 20(11Q13.3) MUTATED                         29
  AMP PEAK 20(11Q13.3) WILD-TYPE                      127
                                vv
clus                             HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK 20(11Q13.3) MUTATED                                  0
  AMP PEAK 20(11Q13.3) WILD-TYPE                                2
D20V8, multiclass
                                  clus
vv                                 AMP PEAK 20(11Q13.3) MUTATED
  FIBROLAMELLAR CARCINOMA                                     0
  HEPATOCELLULAR CARCINOMA                                   29
  HEPATOCHOLANGIOCARCINOMA (MIXED)                            0
                                  clus
vv                                 AMP PEAK 20(11Q13.3) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                       2
  HEPATOCELLULAR CARCINOMA                                    127
  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 20(11Q13.3) MUTATED    22   4   1   2
  AMP PEAK 20(11Q13.3) WILD-TYPE 109   7   0  10
D20V9, multiclass
    clus
vv   AMP PEAK 20(11Q13.3) MUTATED AMP PEAK 20(11Q13.3) WILD-TYPE
  R0                           22                            109
  R1                            4                              7
  R2                            1                              0
  RX                            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"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 20(11Q13.3) MUTATED                                  0     7
  AMP PEAK 20(11Q13.3) WILD-TYPE                                1    29
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 20(11Q13.3) MUTATED                           1    20
  AMP PEAK 20(11Q13.3) WILD-TYPE                         7    89
D20V10, multiclass
                                  clus
vv                                 AMP PEAK 20(11Q13.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       7
  BLACK OR AFRICAN AMERICAN                                   1
  WHITE                                                      20
                                  clus
vv                                 AMP PEAK 20(11Q13.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        29
  BLACK OR AFRICAN AMERICAN                                     7
  WHITE                                                        89
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V11, binary
                                cls
clus                               0   1
  AMP PEAK 20(11Q13.3) MUTATED     0  26
  AMP PEAK 20(11Q13.3) WILD-TYPE   3 117
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(11Q13.3) MUTATED      0   26
  AMP PEAK 20(11Q13.3) WILD-TYPE    3  117
                        clus
vv                       AMP PEAK 20(11Q13.3) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           26
                        clus
vv                       AMP PEAK 20(11Q13.3) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            117
[1] 2 2
[1] FALSE

Clustering(21) Variable = AMP PEAK 21(13Q32.3) MUTATION ANALYSIS
D21V1, survival
                                sevent
clus2                             0  1
  AMP PEAK 21(13Q32.3) MUTATED   13 12
  AMP PEAK 21(13Q32.3) WILD-TYPE 78 54
  AMP PEAK 21(13Q32.3) MUTATED AMP PEAK 21(13Q32.3) WILD-TYPE 
                            25                            132 
  AMP PEAK 21(13Q32.3) MUTATED AMP PEAK 21(13Q32.3) WILD-TYPE 
                            12                             54 
$`AMP PEAK 21(13Q32.3) MUTATED`
TCGA-BC-A10W TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A3KF TCGA-CC-5258 TCGA-CC-5261 
        2.99         1.12        44.42         0.26         0.07         0.39 
TCGA-CC-5263 TCGA-CC-A3MA TCGA-DD-A113 TCGA-DD-A11A TCGA-DD-A11C TCGA-DD-A1EG 
        4.24         0.07        79.73         2.60        21.76        45.11 
TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A3A7 TCGA-ED-A7PY 
       29.16        13.64        55.69         5.62        13.78         0.20 
TCGA-EP-A2KA TCGA-EP-A3JL TCGA-FV-A23B TCGA-FV-A3I0 TCGA-FV-A496 TCGA-KR-A7K2 
       11.74         9.96        32.45        27.88         0.33        11.84 
TCGA-NI-A8LF 
       16.37 

$`AMP PEAK 21(13Q32.3) WILD-TYPE`
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-A10X TCGA-BC-A10Y TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A217 
       27.52        25.32        23.34        69.57         5.03        13.84 
TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I TCGA-CC-5260 TCGA-CC-5262 
       22.36         9.50        14.60        12.72         2.86         3.39 
TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A114 TCGA-DD-A115 
        3.32         0.10         0.10         0.13        37.78        83.57 
TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11D TCGA-DD-A1E9 
       53.33       113.00         7.33         0.46        51.29        90.71 
TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF 
       79.40        66.31        19.79        75.65         6.71        12.95 
TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EK TCGA-DD-A39V TCGA-DD-A39Z TCGA-DD-A3A0 
       49.15         6.02        18.35        21.14        19.76        25.81 
TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 
        7.66        70.06        17.59        20.12       102.74       107.11 
TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NF 
        0.36        30.61        33.14        32.52        73.38        14.07 
TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN 
       14.24        18.44        15.06        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        93.67        12.26         0.30        80.75        66.35 
TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F 
       10.98         9.30         7.56        10.98         1.45        27.72 
TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X 
      100.96        13.41        12.69        15.85        13.91        13.35 
TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 
        0.23         0.20         0.20         0.20         0.20         0.20 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HS 
       18.74        19.99        10.98         0.62        11.93        22.85 
TCGA-ES-A2HT TCGA-FV-A2QR TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 
       14.40        19.10         8.12         6.38         0.13         0.03 
TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V 
       60.36         0.39         1.22        51.06        53.79        28.27 
TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH 
       30.74        58.49        14.86        21.53        22.13        25.64 
TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL 
        5.92        19.53        19.23        14.70        11.97         7.99 
TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ 
        4.37         7.76         5.98         1.84         1.02         2.66 
TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E 
        4.01         2.14        13.38         0.49         9.57         5.10 
TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-O8-A75V 
       14.24        12.85         8.71         1.71        58.88         4.44 

  AMP PEAK 21(13Q32.3) MUTATED AMP PEAK 21(13Q32.3) WILD-TYPE 
                          0.07                           0.03 
  AMP PEAK 21(13Q32.3) MUTATED AMP PEAK 21(13Q32.3) WILD-TYPE 
                         79.73                         113.00 
  AMP PEAK 21(13Q32.3) MUTATED AMP PEAK 21(13Q32.3) WILD-TYPE 
                         11.74                          14.32 
[1] "0.1 - 79.7 (11.7)"  "0.0 - 113.0 (14.3)"
[1] "hr=" "1.7"
D21V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IIIA
  AMP PEAK 21(13Q32.3) MUTATED        11        7         0          4
  AMP PEAK 21(13Q32.3) WILD-TYPE      54       30         2         27
                                vv
clus                             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 21(13Q32.3) MUTATED            1          1        0         0
  AMP PEAK 21(13Q32.3) WILD-TYPE          4          4        1         1
                                vv
clus                             STAGE IVB
  AMP PEAK 21(13Q32.3) MUTATED           0
  AMP PEAK 21(13Q32.3) WILD-TYPE         2
D21V3, multiclass
            clus
vv           AMP PEAK 21(13Q32.3) MUTATED AMP PEAK 21(13Q32.3) WILD-TYPE
  STAGE I                              11                             54
  STAGE II                              7                             30
  STAGE III                             0                              2
  STAGE IIIA                            4                             27
  STAGE IIIB                            1                              4
  STAGE IIIC                            1                              4
  STAGE IV                              0                              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(13Q32.3) MUTATED   12  7  5  1
  AMP PEAK 21(13Q32.3) WILD-TYPE 56 34 37  7
D21V4, multiclass
    clus
vv   AMP PEAK 21(13Q32.3) MUTATED AMP PEAK 21(13Q32.3) WILD-TYPE
  T1                           12                             56
  T2                            7                             34
  T3                            5                             37
  T4                            1                              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"
D21V5, binary
                                cls
clus                              0  1
  AMP PEAK 21(13Q32.3) MUTATED   13  1
  AMP PEAK 21(13Q32.3) WILD-TYPE 89  2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 21(13Q32.3) MUTATED     13    1
  AMP PEAK 21(13Q32.3) WILD-TYPE   89    2
   clus
vv  AMP PEAK 21(13Q32.3) MUTATED AMP PEAK 21(13Q32.3) WILD-TYPE
  0                           13                             89
  1                            1                              2
[1] 2 2
[1] FALSE
                                vv
clus                              M0  M1  MX
  AMP PEAK 21(13Q32.3) MUTATED    20   0   5
  AMP PEAK 21(13Q32.3) WILD-TYPE 100   3  32
D21V6, multiclass
    clus
vv   AMP PEAK 21(13Q32.3) MUTATED AMP PEAK 21(13Q32.3) WILD-TYPE
  M0                           20                            100
  M1                            0                              3
  MX                            5                             32
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V7, binary
                                cls
clus                              0  1
  AMP PEAK 21(13Q32.3) MUTATED   11 14
  AMP PEAK 21(13Q32.3) WILD-TYPE 49 86
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 21(13Q32.3) MUTATED     11   14
  AMP PEAK 21(13Q32.3) WILD-TYPE   49   86
        clus
vv       AMP PEAK 21(13Q32.3) MUTATED AMP PEAK 21(13Q32.3) WILD-TYPE
  FEMALE                           11                             49
  MALE                             14                             86
[1] 2 2
[1] FALSE
                                vv
clus                             FIBROLAMELLAR CARCINOMA
  AMP PEAK 21(13Q32.3) MUTATED                         0
  AMP PEAK 21(13Q32.3) WILD-TYPE                       2
                                vv
clus                             HEPATOCELLULAR CARCINOMA
  AMP PEAK 21(13Q32.3) MUTATED                         23
  AMP PEAK 21(13Q32.3) WILD-TYPE                      133
                                vv
clus                             HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK 21(13Q32.3) MUTATED                                  2
  AMP PEAK 21(13Q32.3) WILD-TYPE                                0
D21V8, multiclass
                                  clus
vv                                 AMP PEAK 21(13Q32.3) MUTATED
  FIBROLAMELLAR CARCINOMA                                     0
  HEPATOCELLULAR CARCINOMA                                   23
  HEPATOCHOLANGIOCARCINOMA (MIXED)                            2
                                  clus
vv                                 AMP PEAK 21(13Q32.3) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                       2
  HEPATOCELLULAR CARCINOMA                                    133
  HEPATOCHOLANGIOCARCINOMA (MIXED)                              0
[1] 3 2
[1] 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(13Q32.3) MUTATED    19   1   0   4
  AMP PEAK 21(13Q32.3) WILD-TYPE 112  10   1   8
D21V9, multiclass
    clus
vv   AMP PEAK 21(13Q32.3) MUTATED AMP PEAK 21(13Q32.3) WILD-TYPE
  R0                           19                            112
  R1                            1                             10
  R2                            0                              1
  RX                            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"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 21(13Q32.3) MUTATED                                  0     7
  AMP PEAK 21(13Q32.3) WILD-TYPE                                1    29
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 21(13Q32.3) MUTATED                           2    15
  AMP PEAK 21(13Q32.3) WILD-TYPE                         6    94
D21V10, multiclass
                                  clus
vv                                 AMP PEAK 21(13Q32.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       7
  BLACK OR AFRICAN AMERICAN                                   2
  WHITE                                                      15
                                  clus
vv                                 AMP PEAK 21(13Q32.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        29
  BLACK OR AFRICAN AMERICAN                                     6
  WHITE                                                        94
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V11, binary
                                cls
clus                               0   1
  AMP PEAK 21(13Q32.3) MUTATED     0  21
  AMP PEAK 21(13Q32.3) WILD-TYPE   3 122
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 21(13Q32.3) MUTATED      0   21
  AMP PEAK 21(13Q32.3) WILD-TYPE    3  122
                        clus
vv                       AMP PEAK 21(13Q32.3) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           21
                        clus
vv                       AMP PEAK 21(13Q32.3) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            122
[1] 2 2
[1] FALSE

Clustering(22) Variable = AMP PEAK 22(15Q26.3) MUTATION ANALYSIS
D22V1, survival
                                sevent
clus2                             0  1
  AMP PEAK 22(15Q26.3) MUTATED   18  9
  AMP PEAK 22(15Q26.3) WILD-TYPE 73 57
  AMP PEAK 22(15Q26.3) MUTATED AMP PEAK 22(15Q26.3) WILD-TYPE 
                            27                            130 
  AMP PEAK 22(15Q26.3) MUTATED AMP PEAK 22(15Q26.3) WILD-TYPE 
                             9                             57 
$`AMP PEAK 22(15Q26.3) MUTATED`
TCGA-BC-A10Q TCGA-BC-A10Y TCGA-BC-A217 TCGA-BC-A3KF TCGA-CC-5262 TCGA-CC-5263 
       37.32        23.34        13.84         0.26         3.39         4.24 
TCGA-CC-A3M9 TCGA-DD-A11A TCGA-DD-A39Z TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NV 
        0.10         2.60        19.76        18.44        15.06        66.35 
TCGA-DD-A73G TCGA-ED-A5KG TCGA-ED-A66X TCGA-ED-A7PZ TCGA-EP-A2KA TCGA-ES-A2HS 
      100.96        15.85        13.35         0.20        11.74        22.85 
TCGA-FV-A23B TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25Y TCGA-G3-A3CH TCGA-G3-A6UC 
       32.45         0.39        51.06        14.86        25.64         7.76 
TCGA-MI-A75G TCGA-MR-A8JO TCGA-O8-A75V 
       14.24         1.71         4.44 

$`AMP PEAK 22(15Q26.3) WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
       48.99        27.91        10.13        46.78        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 
        2.99        25.32         1.12        69.57         5.03        44.42 
TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I TCGA-CC-5258 TCGA-CC-5260 
       22.36         9.50        14.60        12.72         0.07         2.86 
TCGA-CC-5261 TCGA-CC-A1HT TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 
        0.39         3.32         0.07         0.10         0.13        79.73 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11B 
       37.78        83.57        53.33       113.00         7.33         0.46 
TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC 
       21.76        51.29        90.71        79.40        66.31        19.79 
TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI 
       75.65         6.71        12.95        45.11        49.15         6.02 
TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y 
       29.16        18.35        13.64        21.14        55.69         5.62 
TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 
       25.81         7.66        70.06        17.59        20.12       102.74 
TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB 
      107.11        13.78         0.36        30.61        33.14        32.52 
TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN 
       73.38        14.07        14.24        39.78        56.25        29.56 
TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A73A 
       73.81        93.67        12.26         0.30        80.75        10.98 
TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-ED-A459 
        9.30         7.56        10.98         1.45        27.72        13.41 
TCGA-ED-A4XI TCGA-ED-A627 TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7XP 
       12.69        13.91         0.23         0.20         0.20         0.20 
TCGA-ED-A82E TCGA-ED-A8O5 TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KB TCGA-EP-A2KC 
        0.20         0.20        18.74        19.99        10.98         0.62 
TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 
        9.96        11.93        14.40        19.10        27.88         8.12 
TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-G3-A25S 
        6.38         0.13         0.03         0.33        60.36         1.22 
TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Z TCGA-G3-A3CG 
       53.79        28.27        30.74        58.49        21.53        22.13 
TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL 
        5.92        19.53        19.23        14.70        11.97         7.99 
TCGA-G3-A5SM TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 
        4.37         5.98         1.84         1.02         2.66         4.01 
TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E 
        2.14        11.84        13.38         0.49         9.57         5.10 
TCGA-MI-A75H TCGA-MI-A75I TCGA-NI-A4U2 TCGA-NI-A8LF 
       12.85         8.71        58.88        16.37 

  AMP PEAK 22(15Q26.3) MUTATED AMP PEAK 22(15Q26.3) WILD-TYPE 
                          0.10                           0.03 
  AMP PEAK 22(15Q26.3) MUTATED AMP PEAK 22(15Q26.3) WILD-TYPE 
                        100.96                         113.00 
  AMP PEAK 22(15Q26.3) MUTATED AMP PEAK 22(15Q26.3) WILD-TYPE 
                        14.240                         13.845 
[1] "0.1 - 101.0 (14.2)" "0.0 - 113.0 (13.8)"
[1] "hr=" "1"  
D22V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IIIA
  AMP PEAK 22(15Q26.3) MUTATED         8        8         0          7
  AMP PEAK 22(15Q26.3) WILD-TYPE      57       29         2         24
                                vv
clus                             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 22(15Q26.3) MUTATED            1          1        0         0
  AMP PEAK 22(15Q26.3) WILD-TYPE          4          4        1         1
                                vv
clus                             STAGE IVB
  AMP PEAK 22(15Q26.3) MUTATED           0
  AMP PEAK 22(15Q26.3) WILD-TYPE         2
D22V3, multiclass
            clus
vv           AMP PEAK 22(15Q26.3) MUTATED AMP PEAK 22(15Q26.3) WILD-TYPE
  STAGE I                               8                             57
  STAGE II                              8                             29
  STAGE III                             0                              2
  STAGE IIIA                            7                             24
  STAGE IIIB                            1                              4
  STAGE IIIC                            1                              4
  STAGE IV                              0                              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 22(15Q26.3) MUTATED    8  9  8  2
  AMP PEAK 22(15Q26.3) WILD-TYPE 60 32 34  6
D22V4, multiclass
    clus
vv   AMP PEAK 22(15Q26.3) MUTATED AMP PEAK 22(15Q26.3) WILD-TYPE
  T1                            8                             60
  T2                            9                             32
  T3                            8                             34
  T4                            2                              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"
D22V5, binary
                                cls
clus                              0  1
  AMP PEAK 22(15Q26.3) MUTATED   16  0
  AMP PEAK 22(15Q26.3) WILD-TYPE 86  3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 22(15Q26.3) MUTATED     16    0
  AMP PEAK 22(15Q26.3) WILD-TYPE   86    3
   clus
vv  AMP PEAK 22(15Q26.3) MUTATED AMP PEAK 22(15Q26.3) WILD-TYPE
  0                           16                             86
  1                            0                              3
[1] 2 2
[1] FALSE
                                vv
clus                             M0 M1 MX
  AMP PEAK 22(15Q26.3) MUTATED   21  0  6
  AMP PEAK 22(15Q26.3) WILD-TYPE 99  3 31
D22V6, multiclass
    clus
vv   AMP PEAK 22(15Q26.3) MUTATED AMP PEAK 22(15Q26.3) WILD-TYPE
  M0                           21                             99
  M1                            0                              3
  MX                            6                             31
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V7, binary
                                cls
clus                              0  1
  AMP PEAK 22(15Q26.3) MUTATED   11 16
  AMP PEAK 22(15Q26.3) WILD-TYPE 49 84
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 22(15Q26.3) MUTATED     11   16
  AMP PEAK 22(15Q26.3) WILD-TYPE   49   84
        clus
vv       AMP PEAK 22(15Q26.3) MUTATED AMP PEAK 22(15Q26.3) WILD-TYPE
  FEMALE                           11                             49
  MALE                             16                             84
[1] 2 2
[1] FALSE
                                vv
clus                             FIBROLAMELLAR CARCINOMA
  AMP PEAK 22(15Q26.3) MUTATED                         1
  AMP PEAK 22(15Q26.3) WILD-TYPE                       1
                                vv
clus                             HEPATOCELLULAR CARCINOMA
  AMP PEAK 22(15Q26.3) MUTATED                         26
  AMP PEAK 22(15Q26.3) WILD-TYPE                      130
                                vv
clus                             HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK 22(15Q26.3) MUTATED                                  0
  AMP PEAK 22(15Q26.3) WILD-TYPE                                2
D22V8, multiclass
                                  clus
vv                                 AMP PEAK 22(15Q26.3) MUTATED
  FIBROLAMELLAR CARCINOMA                                     1
  HEPATOCELLULAR CARCINOMA                                   26
  HEPATOCHOLANGIOCARCINOMA (MIXED)                            0
                                  clus
vv                                 AMP PEAK 22(15Q26.3) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                       1
  HEPATOCELLULAR CARCINOMA                                    130
  HEPATOCHOLANGIOCARCINOMA (MIXED)                              2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 22(15Q26.3) MUTATED    22   2   0   2
  AMP PEAK 22(15Q26.3) WILD-TYPE 109   9   1  10
D22V9, multiclass
    clus
vv   AMP PEAK 22(15Q26.3) MUTATED AMP PEAK 22(15Q26.3) WILD-TYPE
  R0                           22                            109
  R1                            2                              9
  R2                            0                              1
  RX                            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"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 22(15Q26.3) MUTATED                                  0     8
  AMP PEAK 22(15Q26.3) WILD-TYPE                                1    28
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 22(15Q26.3) MUTATED                           1    16
  AMP PEAK 22(15Q26.3) WILD-TYPE                         7    93
D22V10, multiclass
                                  clus
vv                                 AMP PEAK 22(15Q26.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       8
  BLACK OR AFRICAN AMERICAN                                   1
  WHITE                                                      16
                                  clus
vv                                 AMP PEAK 22(15Q26.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        28
  BLACK OR AFRICAN AMERICAN                                     7
  WHITE                                                        93
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V11, binary
                                cls
clus                               0   1
  AMP PEAK 22(15Q26.3) MUTATED     1  22
  AMP PEAK 22(15Q26.3) WILD-TYPE   2 121
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 22(15Q26.3) MUTATED      1   22
  AMP PEAK 22(15Q26.3) WILD-TYPE    2  121
                        clus
vv                       AMP PEAK 22(15Q26.3) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           22
                        clus
vv                       AMP PEAK 22(15Q26.3) WILD-TYPE
  HISPANIC OR LATINO                                  2
  NOT HISPANIC OR LATINO                            121
[1] 2 2
[1] FALSE

Clustering(23) Variable = AMP PEAK 23(17P11.2) MUTATION ANALYSIS
D23V1, survival
                                sevent
clus2                             0  1
  AMP PEAK 23(17P11.2) MUTATED   13 12
  AMP PEAK 23(17P11.2) WILD-TYPE 78 54
  AMP PEAK 23(17P11.2) MUTATED AMP PEAK 23(17P11.2) WILD-TYPE 
                            25                            132 
  AMP PEAK 23(17P11.2) MUTATED AMP PEAK 23(17P11.2) WILD-TYPE 
                            12                             54 
$`AMP PEAK 23(17P11.2) MUTATED`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A112 TCGA-BC-A217 TCGA-CC-5260 TCGA-CC-A3M9 
       27.91        37.32         5.03        13.84         2.86         0.10 
TCGA-DD-A115 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A3A3 TCGA-DD-A3A5 TCGA-DD-A3A7 
       83.57         7.33         2.60        17.59       102.74        13.78 
TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A73E TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PZ 
       73.81        93.67         1.45        13.35         0.23         0.20 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-ES-A2HS TCGA-FV-A4ZP TCGA-GJ-A6C0 TCGA-MI-A75G 
       11.74        10.98        22.85        60.36         1.02        14.24 
TCGA-O8-A75V 
        4.44 

$`AMP PEAK 23(17P11.2) WILD-TYPE`
TCGA-BC-4072 TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W 
       48.99        10.13        46.78        27.52        27.52         2.99 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A216 TCGA-BC-A3KF 
       25.32        23.34         1.12        69.57        44.42         0.26 
TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I TCGA-CC-5258 TCGA-CC-5261 
       22.36         9.50        14.60        12.72         0.07         0.39 
TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC 
        3.39         4.24         3.32         0.07         0.10         0.13 
TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A11B TCGA-DD-A11C 
       79.73        37.78        53.33       113.00         0.46        21.76 
TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED 
       51.29        90.71        79.40        66.31        19.79        75.65 
TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ 
        6.71        12.95        45.11        49.15         6.02        29.16 
TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z 
       18.35        13.64        21.14        55.69         5.62        19.76 
TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A4 TCGA-DD-A3A6 TCGA-DD-A3A8 
       25.81         7.66        70.06        20.12       107.11         0.36 
TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH 
       30.61        33.14        32.52        73.38        14.07        14.24 
TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NQ 
       18.44        15.06        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        66.35        10.98         9.30         7.56 
TCGA-DD-A73D TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG 
       10.98        27.72       100.96        13.41        12.69        15.85 
TCGA-ED-A627 TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 
       13.91         0.20         0.20         0.20         0.20         0.20 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HT 
       18.74        19.99         0.62         9.96        11.93        14.40 
TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 
       32.45        19.10        27.88         8.12         6.38         0.13 
TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U 
        0.03         0.33         0.39         1.22        51.06        53.79 
TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG 
       28.27        30.74        58.49        14.86        21.53        22.13 
TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ 
       25.64         5.92        19.53        19.23        14.70        11.97 
TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-HP-A5MZ 
        7.99         4.37         7.76         5.98         1.84         2.66 
TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75C 
        4.01         2.14        11.84        13.38         0.49         9.57 
TCGA-MI-A75E TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF 
        5.10        12.85         8.71         1.71        58.88        16.37 

  AMP PEAK 23(17P11.2) MUTATED AMP PEAK 23(17P11.2) WILD-TYPE 
                          0.10                           0.03 
  AMP PEAK 23(17P11.2) MUTATED AMP PEAK 23(17P11.2) WILD-TYPE 
                        102.74                         113.00 
  AMP PEAK 23(17P11.2) MUTATED AMP PEAK 23(17P11.2) WILD-TYPE 
                         13.35                          14.32 
[1] "0.1 - 102.7 (13.3)" "0.0 - 113.0 (14.3)"
[1] "hr=" "1.1"
D23V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IIIA
  AMP PEAK 23(17P11.2) MUTATED         8        4         1          8
  AMP PEAK 23(17P11.2) WILD-TYPE      57       33         1         23
                                vv
clus                             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 23(17P11.2) MUTATED            1          1        1         0
  AMP PEAK 23(17P11.2) WILD-TYPE          4          4        0         1
                                vv
clus                             STAGE IVB
  AMP PEAK 23(17P11.2) MUTATED           0
  AMP PEAK 23(17P11.2) WILD-TYPE         2
D23V3, multiclass
            clus
vv           AMP PEAK 23(17P11.2) MUTATED AMP PEAK 23(17P11.2) WILD-TYPE
  STAGE I                               8                             57
  STAGE II                              4                             33
  STAGE III                             1                              1
  STAGE IIIA                            8                             23
  STAGE IIIB                            1                              4
  STAGE IIIC                            1                              4
  STAGE IV                              1                              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 23(17P11.2) MUTATED    8  5 12  1
  AMP PEAK 23(17P11.2) WILD-TYPE 60 36 30  7
D23V4, multiclass
    clus
vv   AMP PEAK 23(17P11.2) MUTATED AMP PEAK 23(17P11.2) WILD-TYPE
  T1                            8                             60
  T2                            5                             36
  T3                           12                             30
  T4                            1                              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"
D23V5, binary
                                cls
clus                              0  1
  AMP PEAK 23(17P11.2) MUTATED   16  0
  AMP PEAK 23(17P11.2) WILD-TYPE 86  3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 23(17P11.2) MUTATED     16    0
  AMP PEAK 23(17P11.2) WILD-TYPE   86    3
   clus
vv  AMP PEAK 23(17P11.2) MUTATED AMP PEAK 23(17P11.2) WILD-TYPE
  0                           16                             86
  1                            0                              3
[1] 2 2
[1] FALSE
                                vv
clus                              M0  M1  MX
  AMP PEAK 23(17P11.2) MUTATED    17   1   8
  AMP PEAK 23(17P11.2) WILD-TYPE 103   2  29
D23V6, multiclass
    clus
vv   AMP PEAK 23(17P11.2) MUTATED AMP PEAK 23(17P11.2) WILD-TYPE
  M0                           17                            103
  M1                            1                              2
  MX                            8                             29
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V7, binary
                                cls
clus                              0  1
  AMP PEAK 23(17P11.2) MUTATED    8 18
  AMP PEAK 23(17P11.2) WILD-TYPE 52 82
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 23(17P11.2) MUTATED      8   18
  AMP PEAK 23(17P11.2) WILD-TYPE   52   82
        clus
vv       AMP PEAK 23(17P11.2) MUTATED AMP PEAK 23(17P11.2) WILD-TYPE
  FEMALE                            8                             52
  MALE                             18                             82
[1] 2 2
[1] FALSE
                                vv
clus                             FIBROLAMELLAR CARCINOMA
  AMP PEAK 23(17P11.2) MUTATED                         0
  AMP PEAK 23(17P11.2) WILD-TYPE                       2
                                vv
clus                             HEPATOCELLULAR CARCINOMA
  AMP PEAK 23(17P11.2) MUTATED                         26
  AMP PEAK 23(17P11.2) WILD-TYPE                      130
                                vv
clus                             HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK 23(17P11.2) MUTATED                                  0
  AMP PEAK 23(17P11.2) WILD-TYPE                                2
D23V8, multiclass
                                  clus
vv                                 AMP PEAK 23(17P11.2) MUTATED
  FIBROLAMELLAR CARCINOMA                                     0
  HEPATOCELLULAR CARCINOMA                                   26
  HEPATOCHOLANGIOCARCINOMA (MIXED)                            0
                                  clus
vv                                 AMP PEAK 23(17P11.2) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                       2
  HEPATOCELLULAR CARCINOMA                                    130
  HEPATOCHOLANGIOCARCINOMA (MIXED)                              2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 23(17P11.2) MUTATED    18   4   1   3
  AMP PEAK 23(17P11.2) WILD-TYPE 113   7   0   9
D23V9, multiclass
    clus
vv   AMP PEAK 23(17P11.2) MUTATED AMP PEAK 23(17P11.2) WILD-TYPE
  R0                           18                            113
  R1                            4                              7
  R2                            1                              0
  RX                            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"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 23(17P11.2) MUTATED                                  0     8
  AMP PEAK 23(17P11.2) WILD-TYPE                                1    28
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 23(17P11.2) MUTATED                           1    15
  AMP PEAK 23(17P11.2) WILD-TYPE                         7    94
D23V10, multiclass
                                  clus
vv                                 AMP PEAK 23(17P11.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       8
  BLACK OR AFRICAN AMERICAN                                   1
  WHITE                                                      15
                                  clus
vv                                 AMP PEAK 23(17P11.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        28
  BLACK OR AFRICAN AMERICAN                                     7
  WHITE                                                        94
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V11, binary
                                cls
clus                               0   1
  AMP PEAK 23(17P11.2) MUTATED     1  22
  AMP PEAK 23(17P11.2) WILD-TYPE   2 121
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 23(17P11.2) MUTATED      1   22
  AMP PEAK 23(17P11.2) WILD-TYPE    2  121
                        clus
vv                       AMP PEAK 23(17P11.2) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           22
                        clus
vv                       AMP PEAK 23(17P11.2) WILD-TYPE
  HISPANIC OR LATINO                                  2
  NOT HISPANIC OR LATINO                            121
[1] 2 2
[1] FALSE

Clustering(24) Variable = AMP PEAK 24(17Q25.3) MUTATION ANALYSIS
D24V1, survival
                                sevent
clus2                             0  1
  AMP PEAK 24(17Q25.3) MUTATED   40 30
  AMP PEAK 24(17Q25.3) WILD-TYPE 51 36
  AMP PEAK 24(17Q25.3) MUTATED AMP PEAK 24(17Q25.3) WILD-TYPE 
                            70                             87 
  AMP PEAK 24(17Q25.3) MUTATED AMP PEAK 24(17Q25.3) WILD-TYPE 
                            30                             36 
$`AMP PEAK 24(17Q25.3) MUTATED`
TCGA-BC-4072 TCGA-BC-A10Q TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10Y 
       48.99        37.32        27.52        27.52         2.99        23.34 
TCGA-BC-A10Z TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A69H TCGA-CC-5260 
        1.12         5.03        44.42        13.84        14.60         2.86 
TCGA-CC-5261 TCGA-CC-5263 TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A114 TCGA-DD-A115 
        0.39         4.24         0.10         0.13        37.78        83.57 
TCGA-DD-A116 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11C TCGA-DD-A1EA TCGA-DD-A1EB 
       53.33         7.33         2.60        21.76        79.40        66.31 
TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A39Y TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A3 
        6.02        29.16         5.62        25.81         7.66        17.59 
TCGA-DD-A3A4 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ 
       20.12        13.78        30.61        14.24        18.44        15.06 
TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A73A TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F 
       73.81        93.67        10.98        10.98         1.45        27.72 
TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-EP-A2KB TCGA-EP-A2KC 
       13.35         0.23         0.20         0.20        10.98         0.62 
TCGA-ES-A2HS TCGA-FV-A2QR TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-G3-A25S 
       22.85        19.10         0.03         0.33        60.36         1.22 
TCGA-G3-A25U TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Z TCGA-G3-A3CJ TCGA-G3-A3CK 
       53.79        30.74        58.49        21.53        19.53        19.23 
TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-GJ-A6C0 TCGA-LG-A6GG TCGA-MI-A75G 
       14.70        11.97         7.99         1.02         0.49        14.24 
TCGA-MI-A75I TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V 
        8.71        58.88        16.37         4.44 

$`AMP PEAK 24(17Q25.3) WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10X TCGA-BC-A110 TCGA-BC-A3KF 
       27.91        10.13        46.78        25.32        69.57         0.26 
TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69I TCGA-CC-5258 TCGA-CC-5262 TCGA-CC-A1HT 
       22.36         9.50        12.72         0.07         3.39         3.32 
TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-DD-A113 TCGA-DD-A118 TCGA-DD-A11B TCGA-DD-A11D 
        0.10         0.07        79.73       113.00         0.46        51.29 
TCGA-DD-A1E9 TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG 
       90.71        19.79        75.65         6.71        12.95        45.11 
TCGA-DD-A1EH TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Z 
       49.15        18.35        13.64        21.14        55.69        19.76 
TCGA-DD-A3A2 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A8 TCGA-DD-A4NA TCGA-DD-A4NB 
       70.06       102.74       107.11         0.36        33.14        32.52 
TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NQ 
       73.38        14.07        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        66.35         9.30         7.56       100.96 
TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A7PX TCGA-ED-A7PY 
       13.41        12.69        15.85        13.91         0.20         0.20 
TCGA-ED-A82E TCGA-ED-A8O5 TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A3JL 
        0.20         0.20        18.74        19.99        11.74         9.96 
TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 
       11.93        14.40        32.45        27.88         8.12         6.38 
TCGA-FV-A3R3 TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25V TCGA-G3-A25Y TCGA-G3-A3CG 
        0.13         0.39        51.06        28.27        14.86        22.13 
TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-A7M9 
       25.64         5.92         4.37         7.76         5.98         1.84 
TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-MI-A75C 
        2.66         4.01         2.14        11.84        13.38         9.57 
TCGA-MI-A75E TCGA-MI-A75H TCGA-MR-A8JO 
        5.10        12.85         1.71 

  AMP PEAK 24(17Q25.3) MUTATED AMP PEAK 24(17Q25.3) WILD-TYPE 
                          0.03                           0.07 
  AMP PEAK 24(17Q25.3) MUTATED AMP PEAK 24(17Q25.3) WILD-TYPE 
                         93.67                         113.00 
  AMP PEAK 24(17Q25.3) MUTATED AMP PEAK 24(17Q25.3) WILD-TYPE 
                         14.42                          13.41 
[1] "0.0 - 93.7 (14.4)"  "0.1 - 113.0 (13.4)"
[1] "hr=" "1.2"
D24V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IIIA
  AMP PEAK 24(17Q25.3) MUTATED        26       17         0         15
  AMP PEAK 24(17Q25.3) WILD-TYPE      39       20         2         16
                                vv
clus                             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 24(17Q25.3) MUTATED            3          2        1         0
  AMP PEAK 24(17Q25.3) WILD-TYPE          2          3        0         1
                                vv
clus                             STAGE IVB
  AMP PEAK 24(17Q25.3) MUTATED           1
  AMP PEAK 24(17Q25.3) WILD-TYPE         1
D24V3, multiclass
            clus
vv           AMP PEAK 24(17Q25.3) MUTATED AMP PEAK 24(17Q25.3) WILD-TYPE
  STAGE I                              26                             39
  STAGE II                             17                             20
  STAGE III                             0                              2
  STAGE IIIA                           15                             16
  STAGE IIIB                            3                              2
  STAGE IIIC                            2                              3
  STAGE IV                              1                              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(17Q25.3) MUTATED   27 20 20  5
  AMP PEAK 24(17Q25.3) WILD-TYPE 41 21 22  3
D24V4, multiclass
    clus
vv   AMP PEAK 24(17Q25.3) MUTATED AMP PEAK 24(17Q25.3) WILD-TYPE
  T1                           27                             41
  T2                           20                             21
  T3                           20                             22
  T4                            5                              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"
D24V5, binary
                                cls
clus                              0  1
  AMP PEAK 24(17Q25.3) MUTATED   41  1
  AMP PEAK 24(17Q25.3) WILD-TYPE 61  2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 24(17Q25.3) MUTATED     41    1
  AMP PEAK 24(17Q25.3) WILD-TYPE   61    2
   clus
vv  AMP PEAK 24(17Q25.3) MUTATED AMP PEAK 24(17Q25.3) WILD-TYPE
  0                           41                             61
  1                            1                              2
[1] 2 2
[1] FALSE
                                vv
clus                             M0 M1 MX
  AMP PEAK 24(17Q25.3) MUTATED   53  2 17
  AMP PEAK 24(17Q25.3) WILD-TYPE 67  1 20
D24V6, multiclass
    clus
vv   AMP PEAK 24(17Q25.3) MUTATED AMP PEAK 24(17Q25.3) WILD-TYPE
  M0                           53                             67
  M1                            2                              1
  MX                           17                             20
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V7, binary
                                cls
clus                              0  1
  AMP PEAK 24(17Q25.3) MUTATED   22 50
  AMP PEAK 24(17Q25.3) WILD-TYPE 38 50
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 24(17Q25.3) MUTATED     22   50
  AMP PEAK 24(17Q25.3) WILD-TYPE   38   50
        clus
vv       AMP PEAK 24(17Q25.3) MUTATED AMP PEAK 24(17Q25.3) WILD-TYPE
  FEMALE                           22                             38
  MALE                             50                             50
[1] 2 2
[1] FALSE
                                vv
clus                             FIBROLAMELLAR CARCINOMA
  AMP PEAK 24(17Q25.3) MUTATED                         0
  AMP PEAK 24(17Q25.3) WILD-TYPE                       2
                                vv
clus                             HEPATOCELLULAR CARCINOMA
  AMP PEAK 24(17Q25.3) MUTATED                         72
  AMP PEAK 24(17Q25.3) WILD-TYPE                       84
                                vv
clus                             HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK 24(17Q25.3) MUTATED                                  0
  AMP PEAK 24(17Q25.3) WILD-TYPE                                2
D24V8, multiclass
                                  clus
vv                                 AMP PEAK 24(17Q25.3) MUTATED
  FIBROLAMELLAR CARCINOMA                                     0
  HEPATOCELLULAR CARCINOMA                                   72
  HEPATOCHOLANGIOCARCINOMA (MIXED)                            0
                                  clus
vv                                 AMP PEAK 24(17Q25.3) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                       2
  HEPATOCELLULAR CARCINOMA                                     84
  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 24(17Q25.3) MUTATED   55  8  1  8
  AMP PEAK 24(17Q25.3) WILD-TYPE 76  3  0  4
D24V9, multiclass
    clus
vv   AMP PEAK 24(17Q25.3) MUTATED AMP PEAK 24(17Q25.3) WILD-TYPE
  R0                           55                             76
  R1                            8                              3
  R2                            1                              0
  RX                            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"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 24(17Q25.3) MUTATED                                  1    22
  AMP PEAK 24(17Q25.3) WILD-TYPE                                0    14
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 24(17Q25.3) MUTATED                           4    41
  AMP PEAK 24(17Q25.3) WILD-TYPE                         4    68
D24V10, multiclass
                                  clus
vv                                 AMP PEAK 24(17Q25.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                      22
  BLACK OR AFRICAN AMERICAN                                   4
  WHITE                                                      41
                                  clus
vv                                 AMP PEAK 24(17Q25.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                        14
  BLACK OR AFRICAN AMERICAN                                     4
  WHITE                                                        68
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V11, binary
                                cls
clus                              0  1
  AMP PEAK 24(17Q25.3) MUTATED    1 65
  AMP PEAK 24(17Q25.3) WILD-TYPE  2 78
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 24(17Q25.3) MUTATED      1   65
  AMP PEAK 24(17Q25.3) WILD-TYPE    2   78
                        clus
vv                       AMP PEAK 24(17Q25.3) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           65
                        clus
vv                       AMP PEAK 24(17Q25.3) WILD-TYPE
  HISPANIC OR LATINO                                  2
  NOT HISPANIC OR LATINO                             78
[1] 2 2
[1] FALSE

Clustering(25) Variable = AMP PEAK 25(19Q13.11) MUTATION ANALYSIS
D25V1, survival
                                 sevent
clus2                              0  1
  AMP PEAK 25(19Q13.11) MUTATED   24 20
  AMP PEAK 25(19Q13.11) WILD-TYPE 67 46
  AMP PEAK 25(19Q13.11) MUTATED AMP PEAK 25(19Q13.11) WILD-TYPE 
                             44                             113 
  AMP PEAK 25(19Q13.11) MUTATED AMP PEAK 25(19Q13.11) WILD-TYPE 
                             20                              46 
$`AMP PEAK 25(19Q13.11) MUTATED`
TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A112 TCGA-BC-A3KG TCGA-CC-5261 TCGA-CC-A3M9 
       37.32        10.13         5.03        22.36         0.39         0.10 
TCGA-DD-A113 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11C TCGA-DD-A1E9 TCGA-DD-A1EC 
       79.73       113.00         7.33        21.76        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-A4ND TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NQ TCGA-DD-A4NV 
       30.61        73.38        29.56        73.81        12.26        66.35 
TCGA-DD-A73G TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PZ TCGA-ED-A82E TCGA-EP-A2KA 
      100.96        13.35         0.23         0.20         0.20        11.74 
TCGA-EP-A2KB TCGA-EP-A2KC TCGA-ES-A2HS TCGA-FV-A3I0 TCGA-FV-A4ZQ TCGA-G3-A25T 
       10.98         0.62        22.85        27.88         0.39        51.06 
TCGA-G3-A25X TCGA-G3-A5SM TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-KR-A7K2 
       58.49         4.37         5.98         1.84         1.02        11.84 
TCGA-MI-A75G TCGA-NI-A8LF 
       14.24        16.37 

$`AMP PEAK 25(19Q13.11) WILD-TYPE`
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-A110 TCGA-BC-A216 TCGA-BC-A217 
       25.32        23.34         1.12        69.57        44.42        13.84 
TCGA-BC-A3KF TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I TCGA-CC-5258 TCGA-CC-5260 
        0.26         9.50        14.60        12.72         0.07         2.86 
TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC 
        3.39         4.24         3.32         0.07         0.10         0.13 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11D 
       37.78        83.57        53.33         2.60         0.46        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         6.71        49.15        29.16 
TCGA-DD-A1EK TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 
       18.35        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-A3A8 
       70.06        17.59        20.12       102.74       107.11         0.36 
TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ 
       33.14        32.52        14.07        14.24        18.44        15.06 
TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NP TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A73A 
       39.78        56.25        93.67         0.30        80.75        10.98 
TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-ED-A459 
        9.30         7.56        10.98         1.45        27.72        13.41 
TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7XP 
       12.69        15.85        13.91         0.20         0.20         0.20 
TCGA-ED-A8O5 TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HT 
        0.20        18.74        19.99         9.96        11.93        14.40 
TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 
       32.45        19.10         8.12         6.38         0.13         0.03 
TCGA-FV-A496 TCGA-FV-A4ZP TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W 
        0.33        60.36         1.22        53.79        28.27        30.74 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ 
       14.86        21.53        22.13        25.64         5.92        19.53 
TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A6UC TCGA-HP-A5MZ 
       19.23        14.70        11.97         7.99         7.76         2.66 
TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E 
        4.01         2.14        13.38         0.49         9.57         5.10 
TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-O8-A75V 
       12.85         8.71         1.71        58.88         4.44 

  AMP PEAK 25(19Q13.11) MUTATED AMP PEAK 25(19Q13.11) WILD-TYPE 
                           0.10                            0.03 
  AMP PEAK 25(19Q13.11) MUTATED AMP PEAK 25(19Q13.11) WILD-TYPE 
                         113.00                          107.11 
  AMP PEAK 25(19Q13.11) MUTATED AMP PEAK 25(19Q13.11) WILD-TYPE 
                          13.71                           14.07 
[1] "0.1 - 113.0 (13.7)" "0.0 - 107.1 (14.1)"
[1] "hr=" "1"  
D25V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE III STAGE IIIA
  AMP PEAK 25(19Q13.11) MUTATED        17       13         0          7
  AMP PEAK 25(19Q13.11) WILD-TYPE      48       24         2         24
                                 vv
clus                              STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 25(19Q13.11) MUTATED            2          0        1         1
  AMP PEAK 25(19Q13.11) WILD-TYPE          3          5        0         0
                                 vv
clus                              STAGE IVB
  AMP PEAK 25(19Q13.11) MUTATED           1
  AMP PEAK 25(19Q13.11) WILD-TYPE         1
D25V3, multiclass
            clus
vv           AMP PEAK 25(19Q13.11) MUTATED AMP PEAK 25(19Q13.11) WILD-TYPE
  STAGE I                               17                              48
  STAGE II                              13                              24
  STAGE III                              0                               2
  STAGE IIIA                             7                              24
  STAGE IIIB                             2                               3
  STAGE IIIC                             0                               5
  STAGE IV                               1                               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
  AMP PEAK 25(19Q13.11) MUTATED   18 14 12  1
  AMP PEAK 25(19Q13.11) WILD-TYPE 50 27 30  7
D25V4, multiclass
    clus
vv   AMP PEAK 25(19Q13.11) MUTATED AMP PEAK 25(19Q13.11) WILD-TYPE
  T1                            18                              50
  T2                            14                              27
  T3                            12                              30
  T4                             1                               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"
D25V5, binary
                                 cls
clus                               0  1
  AMP PEAK 25(19Q13.11) MUTATED   28  1
  AMP PEAK 25(19Q13.11) WILD-TYPE 74  2
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 25(19Q13.11) MUTATED     28    1
  AMP PEAK 25(19Q13.11) WILD-TYPE   74    2
   clus
vv  AMP PEAK 25(19Q13.11) MUTATED AMP PEAK 25(19Q13.11) WILD-TYPE
  0                            28                              74
  1                             1                               2
[1] 2 2
[1] FALSE
                                 vv
clus                              M0 M1 MX
  AMP PEAK 25(19Q13.11) MUTATED   31  2 12
  AMP PEAK 25(19Q13.11) WILD-TYPE 89  1 25
D25V6, multiclass
    clus
vv   AMP PEAK 25(19Q13.11) MUTATED AMP PEAK 25(19Q13.11) WILD-TYPE
  M0                            31                              89
  M1                             2                               1
  MX                            12                              25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V7, binary
                                 cls
clus                               0  1
  AMP PEAK 25(19Q13.11) MUTATED   18 27
  AMP PEAK 25(19Q13.11) WILD-TYPE 42 73
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 25(19Q13.11) MUTATED     18   27
  AMP PEAK 25(19Q13.11) WILD-TYPE   42   73
        clus
vv       AMP PEAK 25(19Q13.11) MUTATED AMP PEAK 25(19Q13.11) WILD-TYPE
  FEMALE                            18                              42
  MALE                              27                              73
[1] 2 2
[1] FALSE
                                 vv
clus                              FIBROLAMELLAR CARCINOMA
  AMP PEAK 25(19Q13.11) MUTATED                         0
  AMP PEAK 25(19Q13.11) WILD-TYPE                       2
                                 vv
clus                              HEPATOCELLULAR CARCINOMA
  AMP PEAK 25(19Q13.11) MUTATED                         43
  AMP PEAK 25(19Q13.11) WILD-TYPE                      113
                                 vv
clus                              HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK 25(19Q13.11) MUTATED                                  2
  AMP PEAK 25(19Q13.11) WILD-TYPE                                0
D25V8, multiclass
                                  clus
vv                                 AMP PEAK 25(19Q13.11) MUTATED
  FIBROLAMELLAR CARCINOMA                                      0
  HEPATOCELLULAR CARCINOMA                                    43
  HEPATOCHOLANGIOCARCINOMA (MIXED)                             2
                                  clus
vv                                 AMP PEAK 25(19Q13.11) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                        2
  HEPATOCELLULAR CARCINOMA                                     113
  HEPATOCHOLANGIOCARCINOMA (MIXED)                               0
[1] 3 2
[1] 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(19Q13.11) MUTATED   40  1  1  3
  AMP PEAK 25(19Q13.11) WILD-TYPE 91 10  0  9
D25V9, multiclass
    clus
vv   AMP PEAK 25(19Q13.11) MUTATED AMP PEAK 25(19Q13.11) WILD-TYPE
  R0                            40                              91
  R1                             1                              10
  R2                             1                               0
  RX                             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"
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 25(19Q13.11) MUTATED                                  0     9
  AMP PEAK 25(19Q13.11) WILD-TYPE                                1    27
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 25(19Q13.11) MUTATED                           2    33
  AMP PEAK 25(19Q13.11) WILD-TYPE                         6    76
D25V10, multiclass
                                  clus
vv                                 AMP PEAK 25(19Q13.11) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        9
  BLACK OR AFRICAN AMERICAN                                    2
  WHITE                                                       33
                                  clus
vv                                 AMP PEAK 25(19Q13.11) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               1
  ASIAN                                                         27
  BLACK OR AFRICAN AMERICAN                                      6
  WHITE                                                         76
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V11, binary
                                 cls
clus                                0   1
  AMP PEAK 25(19Q13.11) MUTATED     1  42
  AMP PEAK 25(19Q13.11) WILD-TYPE   2 101
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 25(19Q13.11) MUTATED      1   42
  AMP PEAK 25(19Q13.11) WILD-TYPE    2  101
                        clus
vv                       AMP PEAK 25(19Q13.11) MUTATED
  HISPANIC OR LATINO                                 1
  NOT HISPANIC OR LATINO                            42
                        clus
vv                       AMP PEAK 25(19Q13.11) WILD-TYPE
  HISPANIC OR LATINO                                   2
  NOT HISPANIC OR LATINO                             101
[1] 2 2
[1] FALSE

Clustering(26) Variable = AMP PEAK 26(20Q13.13) MUTATION ANALYSIS
D26V1, survival
                                 sevent
clus2                              0  1
  AMP PEAK 26(20Q13.13) MUTATED   26 25
  AMP PEAK 26(20Q13.13) WILD-TYPE 65 41
  AMP PEAK 26(20Q13.13) MUTATED AMP PEAK 26(20Q13.13) WILD-TYPE 
                             51                             106 
  AMP PEAK 26(20Q13.13) MUTATED AMP PEAK 26(20Q13.13) WILD-TYPE 
                             25                              41 
$`AMP PEAK 26(20Q13.13) MUTATED`
TCGA-BC-4072 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10Y TCGA-BC-A217 
       48.99        37.32        10.13        27.52        23.34        13.84 
TCGA-BC-A3KF TCGA-BC-A69H TCGA-CC-5261 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MB 
        0.26        14.60         0.39         3.32         0.10         0.10 
TCGA-CC-A3MC TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C 
        0.13       113.00         7.33         2.60         0.46        21.76 
TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EJ TCGA-DD-A39V TCGA-DD-A3A5 
       12.95        45.11        49.15        29.16        21.14       102.74 
TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4ND TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NR 
       13.78        30.61        73.38        29.56        73.81         0.30 
TCGA-DD-A4NV TCGA-DD-A73G TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A82E TCGA-EP-A2KB 
       66.35       100.96        13.35         0.23         0.20        10.98 
TCGA-EP-A3JL TCGA-ES-A2HS TCGA-FV-A23B TCGA-FV-A3R2 TCGA-FV-A4ZQ TCGA-G3-A25S 
        9.96        22.85        32.45         6.38         0.39         1.22 
TCGA-G3-A25W TCGA-G3-A5SM TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-HP-A5MZ TCGA-KR-A7K2 
       30.74         4.37         5.98         1.84         2.66        11.84 
TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75G 
       13.38         0.49        14.24 

$`AMP PEAK 26(20Q13.13) WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10S TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Z 
       27.91        46.78        27.52         2.99        25.32         1.12 
TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69I 
       69.57         5.03        44.42        22.36         9.50        12.72 
TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A3MA TCGA-DD-A113 
        0.07         2.86         3.39         4.24         0.07        79.73 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA 
       37.78        83.57        53.33        51.29        90.71        79.40 
TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EI TCGA-DD-A1EK 
       66.31        19.79        75.65         6.71         6.02        18.35 
TCGA-DD-A1EL TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 
       13.64        55.69         5.62        19.76        25.81         7.66 
TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A6 TCGA-DD-A3A8 TCGA-DD-A4NA 
       70.06        17.59        20.12       107.11         0.36        33.14 
TCGA-DD-A4NB TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK 
       32.52        14.07        14.24        18.44        15.06        39.78 
TCGA-DD-A4NL TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NS TCGA-DD-A73A TCGA-DD-A73B 
       56.25        93.67        12.26        80.75        10.98         9.30 
TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-ED-A459 TCGA-ED-A4XI 
        7.56        10.98         1.45        27.72        13.41        12.69 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XP 
       15.85        13.91         0.20         0.20         0.20         0.20 
TCGA-ED-A8O5 TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3RK 
        0.20        18.74        19.99        11.74         0.62        11.93 
TCGA-ES-A2HT TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R3 TCGA-FV-A495 
       14.40        19.10        27.88         8.12         0.13         0.03 
TCGA-FV-A496 TCGA-FV-A4ZP TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25X 
        0.33        60.36        51.06        53.79        28.27        58.49 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ 
       14.86        21.53        22.13        25.64         5.92        19.53 
TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A6UC TCGA-GJ-A6C0 
       19.23        14.70        11.97         7.99         7.76         1.02 
TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75H TCGA-MI-A75I 
        4.01         2.14         9.57         5.10        12.85         8.71 
TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V 
        1.71        58.88        16.37         4.44 

  AMP PEAK 26(20Q13.13) MUTATED AMP PEAK 26(20Q13.13) WILD-TYPE 
                           0.10                            0.03 
  AMP PEAK 26(20Q13.13) MUTATED AMP PEAK 26(20Q13.13) WILD-TYPE 
                         113.00                          107.11 
  AMP PEAK 26(20Q13.13) MUTATED AMP PEAK 26(20Q13.13) WILD-TYPE 
                          13.35                           14.55 
[1] "0.1 - 113.0 (13.3)" "0.0 - 107.1 (14.6)"
[1] "hr=" "1.3"
D26V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE III STAGE IIIA
  AMP PEAK 26(20Q13.13) MUTATED        20       10         2         10
  AMP PEAK 26(20Q13.13) WILD-TYPE      45       27         0         21
                                 vv
clus                              STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 26(20Q13.13) MUTATED            3          1        1         1
  AMP PEAK 26(20Q13.13) WILD-TYPE          2          4        0         0
                                 vv
clus                              STAGE IVB
  AMP PEAK 26(20Q13.13) MUTATED           1
  AMP PEAK 26(20Q13.13) WILD-TYPE         1
D26V3, multiclass
            clus
vv           AMP PEAK 26(20Q13.13) MUTATED AMP PEAK 26(20Q13.13) WILD-TYPE
  STAGE I                               20                              45
  STAGE II                              10                              27
  STAGE III                              2                               0
  STAGE IIIA                            10                              21
  STAGE IIIB                             3                               2
  STAGE IIIC                             1                               4
  STAGE IV                               1                               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
  AMP PEAK 26(20Q13.13) MUTATED   22 11 17  3
  AMP PEAK 26(20Q13.13) WILD-TYPE 46 30 25  5
D26V4, multiclass
    clus
vv   AMP PEAK 26(20Q13.13) MUTATED AMP PEAK 26(20Q13.13) WILD-TYPE
  T1                            22                              46
  T2                            11                              30
  T3                            17                              25
  T4                             3                               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"
D26V5, binary
                                 cls
clus                               0  1
  AMP PEAK 26(20Q13.13) MUTATED   33  2
  AMP PEAK 26(20Q13.13) WILD-TYPE 69  1
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 26(20Q13.13) MUTATED     33    2
  AMP PEAK 26(20Q13.13) WILD-TYPE   69    1
   clus
vv  AMP PEAK 26(20Q13.13) MUTATED AMP PEAK 26(20Q13.13) WILD-TYPE
  0                            33                              69
  1                             2                               1
[1] 2 2
[1] FALSE
                                 vv
clus                              M0 M1 MX
  AMP PEAK 26(20Q13.13) MUTATED   40  2 11
  AMP PEAK 26(20Q13.13) WILD-TYPE 80  1 26
D26V6, multiclass
    clus
vv   AMP PEAK 26(20Q13.13) MUTATED AMP PEAK 26(20Q13.13) WILD-TYPE
  M0                            40                              80
  M1                             2                               1
  MX                            11                              26
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V7, binary
                                 cls
clus                               0  1
  AMP PEAK 26(20Q13.13) MUTATED   21 32
  AMP PEAK 26(20Q13.13) WILD-TYPE 39 68
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 26(20Q13.13) MUTATED     21   32
  AMP PEAK 26(20Q13.13) WILD-TYPE   39   68
        clus
vv       AMP PEAK 26(20Q13.13) MUTATED AMP PEAK 26(20Q13.13) WILD-TYPE
  FEMALE                            21                              39
  MALE                              32                              68
[1] 2 2
[1] FALSE
                                 vv
clus                              FIBROLAMELLAR CARCINOMA
  AMP PEAK 26(20Q13.13) MUTATED                         0
  AMP PEAK 26(20Q13.13) WILD-TYPE                       2
                                 vv
clus                              HEPATOCELLULAR CARCINOMA
  AMP PEAK 26(20Q13.13) MUTATED                         52
  AMP PEAK 26(20Q13.13) WILD-TYPE                      104
                                 vv
clus                              HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK 26(20Q13.13) MUTATED                                  1
  AMP PEAK 26(20Q13.13) WILD-TYPE                                1
D26V8, multiclass
                                  clus
vv                                 AMP PEAK 26(20Q13.13) MUTATED
  FIBROLAMELLAR CARCINOMA                                      0
  HEPATOCELLULAR CARCINOMA                                    52
  HEPATOCHOLANGIOCARCINOMA (MIXED)                             1
                                  clus
vv                                 AMP PEAK 26(20Q13.13) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                        2
  HEPATOCELLULAR CARCINOMA                                     104
  HEPATOCHOLANGIOCARCINOMA (MIXED)                               1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              R0 R1 R2 RX
  AMP PEAK 26(20Q13.13) MUTATED   42  4  1  4
  AMP PEAK 26(20Q13.13) WILD-TYPE 89  7  0  8
D26V9, multiclass
    clus
vv   AMP PEAK 26(20Q13.13) MUTATED AMP PEAK 26(20Q13.13) WILD-TYPE
  R0                            42                              89
  R1                             4                               7
  R2                             1                               0
  RX                             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"
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 26(20Q13.13) MUTATED                                  0    10
  AMP PEAK 26(20Q13.13) WILD-TYPE                                1    26
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 26(20Q13.13) MUTATED                           1    40
  AMP PEAK 26(20Q13.13) WILD-TYPE                         7    69
D26V10, multiclass
                                  clus
vv                                 AMP PEAK 26(20Q13.13) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                       10
  BLACK OR AFRICAN AMERICAN                                    1
  WHITE                                                       40
                                  clus
vv                                 AMP PEAK 26(20Q13.13) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               1
  ASIAN                                                         26
  BLACK OR AFRICAN AMERICAN                                      7
  WHITE                                                         69
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V11, binary
                                 cls
clus                               0  1
  AMP PEAK 26(20Q13.13) MUTATED    0 47
  AMP PEAK 26(20Q13.13) WILD-TYPE  3 96
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 26(20Q13.13) MUTATED      0   47
  AMP PEAK 26(20Q13.13) WILD-TYPE    3   96
                        clus
vv                       AMP PEAK 26(20Q13.13) MUTATED
  HISPANIC OR LATINO                                 0
  NOT HISPANIC OR LATINO                            47
                        clus
vv                       AMP PEAK 26(20Q13.13) WILD-TYPE
  HISPANIC OR LATINO                                   3
  NOT HISPANIC OR LATINO                              96
[1] 2 2
[1] FALSE

Clustering(27) Variable = AMP PEAK 27(20Q13.33) MUTATION ANALYSIS
D27V1, survival
                                 sevent
clus2                              0  1
  AMP PEAK 27(20Q13.33) MUTATED   29 24
  AMP PEAK 27(20Q13.33) WILD-TYPE 62 42
  AMP PEAK 27(20Q13.33) MUTATED AMP PEAK 27(20Q13.33) WILD-TYPE 
                             53                             104 
  AMP PEAK 27(20Q13.33) MUTATED AMP PEAK 27(20Q13.33) WILD-TYPE 
                             24                              42 
$`AMP PEAK 27(20Q13.33) MUTATED`
TCGA-BC-4072 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10Y TCGA-BC-A217 TCGA-BC-A3KF 
       48.99        37.32        10.13        23.34        13.84         0.26 
TCGA-BC-A69H TCGA-CC-5261 TCGA-CC-A3M9 TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 
       14.60         0.39         0.10         0.10         0.13        79.73 
TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A1EF 
      113.00         7.33         2.60         0.46        21.76        12.95 
TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EJ TCGA-DD-A39V TCGA-DD-A3A5 TCGA-DD-A3A7 
       45.11        49.15        29.16        21.14       102.74        13.78 
TCGA-DD-A3A9 TCGA-DD-A4ND TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NR TCGA-DD-A4NV 
       30.61        73.38        29.56        73.81         0.30        66.35 
TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A82E TCGA-ED-A8O5 
       27.72       100.96        13.35         0.23         0.20         0.20 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A3JL TCGA-ES-A2HS TCGA-FV-A23B TCGA-FV-A3R2 
       11.74        10.98         9.96        22.85        32.45         6.38 
TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A5SM TCGA-G3-A7M9 
        0.39         1.22        30.74        58.49         4.37         1.84 
TCGA-HP-A5MZ TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75G 
        2.66        11.84        13.38         0.49        14.24 

$`AMP PEAK 27(20Q13.33) WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X 
       27.91        46.78        27.52        27.52         2.99        25.32 
TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A3KG TCGA-BC-A5W4 
        1.12        69.57         5.03        44.42        22.36         9.50 
TCGA-BC-A69I TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT 
       12.72         0.07         2.86         3.39         4.24         3.32 
TCGA-CC-A3MA TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A11D TCGA-DD-A1E9 
        0.07        37.78        83.57        53.33        51.29        90.71 
TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EI 
       79.40        66.31        19.79        75.65         6.71         6.02 
TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 
       18.35        13.64        55.69         5.62        19.76        25.81 
TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A6 TCGA-DD-A3A8 
        7.66        70.06        17.59        20.12       107.11         0.36 
TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ 
       33.14        32.52        14.07        14.24        18.44        15.06 
TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NS TCGA-DD-A73A 
       39.78        56.25        93.67        12.26        80.75        10.98 
TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-ED-A459 TCGA-ED-A4XI 
        9.30         7.56        10.98         1.45        13.41        12.69 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XP 
       15.85        13.91         0.20         0.20         0.20         0.20 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A2QR 
       18.74        19.99         0.62        11.93        14.40        19.10 
TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP 
       27.88         8.12         0.13         0.03         0.33        60.36 
TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG 
       51.06        53.79        28.27        14.86        21.53        22.13 
TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ 
       25.64         5.92        19.53        19.23        14.70        11.97 
TCGA-G3-A5SL TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-GJ-A6C0 TCGA-K7-A6G5 TCGA-KR-A7K0 
        7.99         7.76         5.98         1.02         4.01         2.14 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A8JO TCGA-NI-A4U2 
        9.57         5.10        12.85         8.71         1.71        58.88 
TCGA-NI-A8LF TCGA-O8-A75V 
       16.37         4.44 

  AMP PEAK 27(20Q13.33) MUTATED AMP PEAK 27(20Q13.33) WILD-TYPE 
                           0.10                            0.03 
  AMP PEAK 27(20Q13.33) MUTATED AMP PEAK 27(20Q13.33) WILD-TYPE 
                         113.00                          107.11 
  AMP PEAK 27(20Q13.33) MUTATED AMP PEAK 27(20Q13.33) WILD-TYPE 
                          13.38                           14.32 
[1] "0.1 - 113.0 (13.4)" "0.0 - 107.1 (14.3)"
[1] "hr=" "1.1"
D27V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE III STAGE IIIA
  AMP PEAK 27(20Q13.33) MUTATED        20       12         2         11
  AMP PEAK 27(20Q13.33) WILD-TYPE      45       25         0         20
                                 vv
clus                              STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 27(20Q13.33) MUTATED            3          1        1         1
  AMP PEAK 27(20Q13.33) WILD-TYPE          2          4        0         0
                                 vv
clus                              STAGE IVB
  AMP PEAK 27(20Q13.33) MUTATED           1
  AMP PEAK 27(20Q13.33) WILD-TYPE         1
D27V3, multiclass
            clus
vv           AMP PEAK 27(20Q13.33) MUTATED AMP PEAK 27(20Q13.33) WILD-TYPE
  STAGE I                               20                              45
  STAGE II                              12                              25
  STAGE III                              2                               0
  STAGE IIIA                            11                              20
  STAGE IIIB                             3                               2
  STAGE IIIC                             1                               4
  STAGE IV                               1                               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
  AMP PEAK 27(20Q13.33) MUTATED   22 13 18  2
  AMP PEAK 27(20Q13.33) WILD-TYPE 46 28 24  6
D27V4, multiclass
    clus
vv   AMP PEAK 27(20Q13.33) MUTATED AMP PEAK 27(20Q13.33) WILD-TYPE
  T1                            22                              46
  T2                            13                              28
  T3                            18                              24
  T4                             2                               6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V5, binary
                                 cls
clus                               0  1
  AMP PEAK 27(20Q13.33) MUTATED   36  2
  AMP PEAK 27(20Q13.33) WILD-TYPE 66  1
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 27(20Q13.33) MUTATED     36    2
  AMP PEAK 27(20Q13.33) WILD-TYPE   66    1
   clus
vv  AMP PEAK 27(20Q13.33) MUTATED AMP PEAK 27(20Q13.33) WILD-TYPE
  0                            36                              66
  1                             2                               1
[1] 2 2
[1] FALSE
                                 vv
clus                              M0 M1 MX
  AMP PEAK 27(20Q13.33) MUTATED   43  2 10
  AMP PEAK 27(20Q13.33) WILD-TYPE 77  1 27
D27V6, multiclass
    clus
vv   AMP PEAK 27(20Q13.33) MUTATED AMP PEAK 27(20Q13.33) WILD-TYPE
  M0                            43                              77
  M1                             2                               1
  MX                            10                              27
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V7, binary
                                 cls
clus                               0  1
  AMP PEAK 27(20Q13.33) MUTATED   25 30
  AMP PEAK 27(20Q13.33) WILD-TYPE 35 70
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 27(20Q13.33) MUTATED     25   30
  AMP PEAK 27(20Q13.33) WILD-TYPE   35   70
        clus
vv       AMP PEAK 27(20Q13.33) MUTATED AMP PEAK 27(20Q13.33) WILD-TYPE
  FEMALE                            25                              35
  MALE                              30                              70
[1] 2 2
[1] FALSE
                                 vv
clus                              FIBROLAMELLAR CARCINOMA
  AMP PEAK 27(20Q13.33) MUTATED                         0
  AMP PEAK 27(20Q13.33) WILD-TYPE                       2
                                 vv
clus                              HEPATOCELLULAR CARCINOMA
  AMP PEAK 27(20Q13.33) MUTATED                         54
  AMP PEAK 27(20Q13.33) WILD-TYPE                      102
                                 vv
clus                              HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK 27(20Q13.33) MUTATED                                  1
  AMP PEAK 27(20Q13.33) WILD-TYPE                                1
D27V8, multiclass
                                  clus
vv                                 AMP PEAK 27(20Q13.33) MUTATED
  FIBROLAMELLAR CARCINOMA                                      0
  HEPATOCELLULAR CARCINOMA                                    54
  HEPATOCHOLANGIOCARCINOMA (MIXED)                             1
                                  clus
vv                                 AMP PEAK 27(20Q13.33) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                        2
  HEPATOCELLULAR CARCINOMA                                     102
  HEPATOCHOLANGIOCARCINOMA (MIXED)                               1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              R0 R1 R2 RX
  AMP PEAK 27(20Q13.33) MUTATED   46  3  1  4
  AMP PEAK 27(20Q13.33) WILD-TYPE 85  8  0  8
D27V9, multiclass
    clus
vv   AMP PEAK 27(20Q13.33) MUTATED AMP PEAK 27(20Q13.33) WILD-TYPE
  R0                            46                              85
  R1                             3                               8
  R2                             1                               0
  RX                             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"
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 27(20Q13.33) MUTATED                                  0    11
  AMP PEAK 27(20Q13.33) WILD-TYPE                                1    25
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 27(20Q13.33) MUTATED                           1    41
  AMP PEAK 27(20Q13.33) WILD-TYPE                         7    68
D27V10, multiclass
                                  clus
vv                                 AMP PEAK 27(20Q13.33) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                       11
  BLACK OR AFRICAN AMERICAN                                    1
  WHITE                                                       41
                                  clus
vv                                 AMP PEAK 27(20Q13.33) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               1
  ASIAN                                                         25
  BLACK OR AFRICAN AMERICAN                                      7
  WHITE                                                         68
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V11, binary
                                 cls
clus                               0  1
  AMP PEAK 27(20Q13.33) MUTATED    0 49
  AMP PEAK 27(20Q13.33) WILD-TYPE  3 94
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 27(20Q13.33) MUTATED      0   49
  AMP PEAK 27(20Q13.33) WILD-TYPE    3   94
                        clus
vv                       AMP PEAK 27(20Q13.33) MUTATED
  HISPANIC OR LATINO                                 0
  NOT HISPANIC OR LATINO                            49
                        clus
vv                       AMP PEAK 27(20Q13.33) WILD-TYPE
  HISPANIC OR LATINO                                   3
  NOT HISPANIC OR LATINO                              94
[1] 2 2
[1] FALSE

Clustering(28) Variable = AMP PEAK 28(XQ28) MUTATION ANALYSIS
D28V1, survival
                             sevent
clus2                          0  1
  AMP PEAK 28(XQ28) MUTATED   25 13
  AMP PEAK 28(XQ28) WILD-TYPE 66 53
  AMP PEAK 28(XQ28) MUTATED AMP PEAK 28(XQ28) WILD-TYPE 
                         38                         119 
  AMP PEAK 28(XQ28) MUTATED AMP PEAK 28(XQ28) WILD-TYPE 
                         13                          53 
$`AMP PEAK 28(XQ28) MUTATED`
TCGA-BC-A10U TCGA-BC-A69I TCGA-CC-A3MA TCGA-DD-A114 TCGA-DD-A11A TCGA-DD-A1E9 
       27.52        12.72         0.07        37.78         2.60        90.71 
TCGA-DD-A39V TCGA-DD-A39Y TCGA-DD-A3A3 TCGA-DD-A3A7 TCGA-DD-A4NF TCGA-DD-A4NK 
       21.14         5.62        17.59        13.78        14.07        39.78 
TCGA-DD-A4NV TCGA-DD-A73D TCGA-DD-A73G TCGA-ED-A66Y TCGA-ED-A7PZ TCGA-EP-A12J 
       66.35        10.98       100.96         0.23         0.20        18.74 
TCGA-EP-A2KA TCGA-EP-A3JL TCGA-ES-A2HS TCGA-FV-A2QR TCGA-FV-A496 TCGA-FV-A4ZQ 
       11.74         9.96        22.85        19.10         0.33         0.39 
TCGA-G3-A25U TCGA-G3-A3CG TCGA-G3-A3CJ TCGA-G3-A5SI TCGA-G3-A5SL TCGA-G3-A6UC 
       53.79        22.13        19.53        14.70         7.99         7.76 
TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G 
        2.66         4.01         0.49         9.57         5.10        14.24 
TCGA-NI-A4U2 TCGA-O8-A75V 
       58.88         4.44 

$`AMP PEAK 28(XQ28) WILD-TYPE`
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-A110 TCGA-BC-A112 
        2.99        25.32        23.34         1.12        69.57         5.03 
TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H 
       44.42        13.84         0.26        22.36         9.50        14.60 
TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT 
        0.07         2.86         0.39         3.39         4.24         3.32 
TCGA-CC-A3M9 TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A115 TCGA-DD-A116 
        0.10         0.10         0.13        79.73        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         6.71        12.95        45.11 
TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39X 
       49.15         6.02        29.16        18.35        13.64        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-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND 
      107.11         0.36        30.61        33.14        32.52        73.38 
TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO 
       14.24        18.44        15.06        56.25        29.56        73.81 
TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A73A TCGA-DD-A73B 
       93.67        12.26         0.30        80.75        10.98         9.30 
TCGA-DD-A73C TCGA-DD-A73E TCGA-DD-A73F TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG 
        7.56         1.45        27.72        13.41        12.69        15.85 
TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7XP TCGA-ED-A82E 
       13.91        13.35         0.20         0.20         0.20         0.20 
TCGA-ED-A8O5 TCGA-EP-A26S TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HT 
        0.20        19.99        10.98         0.62        11.93        14.40 
TCGA-FV-A23B TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 
       32.45        27.88         8.12         6.38         0.13         0.03 
TCGA-FV-A4ZP TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X 
       60.36         1.22        51.06        28.27        30.74        58.49 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CK TCGA-G3-A5SJ 
       14.86        21.53        25.64         5.92        19.23        11.97 
TCGA-G3-A5SM TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-KR-A7K0 TCGA-KR-A7K2 
        4.37         5.98         1.84         1.02         2.14        11.84 
TCGA-KR-A7K7 TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A8JO TCGA-NI-A8LF 
       13.38        12.85         8.71         1.71        16.37 

  AMP PEAK 28(XQ28) MUTATED AMP PEAK 28(XQ28) WILD-TYPE 
                       0.07                        0.03 
  AMP PEAK 28(XQ28) MUTATED AMP PEAK 28(XQ28) WILD-TYPE 
                     100.96                      113.00 
  AMP PEAK 28(XQ28) MUTATED AMP PEAK 28(XQ28) WILD-TYPE 
                      13.25                       14.24 
[1] "0.1 - 101.0 (13.2)" "0.0 - 113.0 (14.2)"
[1] "hr=" "1.1"
D28V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 28(XQ28) MUTATED        19        8         0          8          2
  AMP PEAK 28(XQ28) WILD-TYPE      46       29         2         23          3
                             vv
clus                          STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 28(XQ28) MUTATED            1        0         0         0
  AMP PEAK 28(XQ28) WILD-TYPE          4        1         1         2
D28V3, multiclass
            clus
vv           AMP PEAK 28(XQ28) MUTATED AMP PEAK 28(XQ28) WILD-TYPE
  STAGE I                           19                          46
  STAGE II                           8                          29
  STAGE III                          0                           2
  STAGE IIIA                         8                          23
  STAGE IIIB                         2                           3
  STAGE IIIC                         1                           4
  STAGE IV                           0                           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 28(XQ28) MUTATED   19  9 10  1
  AMP PEAK 28(XQ28) WILD-TYPE 49 32 32  7
D28V4, multiclass
    clus
vv   AMP PEAK 28(XQ28) MUTATED AMP PEAK 28(XQ28) WILD-TYPE
  T1                        19                          49
  T2                         9                          32
  T3                        10                          32
  T4                         1                           7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V5, binary
                             cls
clus                           0  1
  AMP PEAK 28(XQ28) MUTATED   22  0
  AMP PEAK 28(XQ28) WILD-TYPE 80  3
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 28(XQ28) MUTATED     22    0
  AMP PEAK 28(XQ28) WILD-TYPE   80    3
   clus
vv  AMP PEAK 28(XQ28) MUTATED AMP PEAK 28(XQ28) WILD-TYPE
  0                        22                          80
  1                         0                           3
[1] 2 2
[1] FALSE
                             vv
clus                          M0 M1 MX
  AMP PEAK 28(XQ28) MUTATED   30  0  9
  AMP PEAK 28(XQ28) WILD-TYPE 90  3 28
D28V6, multiclass
    clus
vv   AMP PEAK 28(XQ28) MUTATED AMP PEAK 28(XQ28) WILD-TYPE
  M0                        30                          90
  M1                         0                           3
  MX                         9                          28
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V7, binary
                             cls
clus                           0  1
  AMP PEAK 28(XQ28) MUTATED    8 31
  AMP PEAK 28(XQ28) WILD-TYPE 52 69
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 28(XQ28) MUTATED      8   31
  AMP PEAK 28(XQ28) WILD-TYPE   52   69
        clus
vv       AMP PEAK 28(XQ28) MUTATED AMP PEAK 28(XQ28) WILD-TYPE
  FEMALE                         8                          52
  MALE                          31                          69
[1] 2 2
[1] FALSE
                             vv
clus                          FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  AMP PEAK 28(XQ28) MUTATED                         0                       39
  AMP PEAK 28(XQ28) WILD-TYPE                       2                      117
                             vv
clus                          HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK 28(XQ28) MUTATED                                  0
  AMP PEAK 28(XQ28) WILD-TYPE                                2
D28V8, multiclass
                                  clus
vv                                 AMP PEAK 28(XQ28) MUTATED
  FIBROLAMELLAR CARCINOMA                                  0
  HEPATOCELLULAR CARCINOMA                                39
  HEPATOCHOLANGIOCARCINOMA (MIXED)                         0
                                  clus
vv                                 AMP PEAK 28(XQ28) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                    2
  HEPATOCELLULAR CARCINOMA                                 117
  HEPATOCHOLANGIOCARCINOMA (MIXED)                           2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          R0 R1 R2 RX
  AMP PEAK 28(XQ28) MUTATED   32  3  0  3
  AMP PEAK 28(XQ28) WILD-TYPE 99  8  1  9
D28V9, multiclass
    clus
vv   AMP PEAK 28(XQ28) MUTATED AMP PEAK 28(XQ28) WILD-TYPE
  R0                        32                          99
  R1                         3                           8
  R2                         0                           1
  RX                         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"
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 28(XQ28) MUTATED                                  1     8
  AMP PEAK 28(XQ28) WILD-TYPE                                0    28
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 28(XQ28) MUTATED                           3    24
  AMP PEAK 28(XQ28) WILD-TYPE                         5    85
D28V10, multiclass
                                  clus
vv                                 AMP PEAK 28(XQ28) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         1
  ASIAN                                                    8
  BLACK OR AFRICAN AMERICAN                                3
  WHITE                                                   24
                                  clus
vv                                 AMP PEAK 28(XQ28) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                     28
  BLACK OR AFRICAN AMERICAN                                  5
  WHITE                                                     85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V11, binary
                             cls
clus                            0   1
  AMP PEAK 28(XQ28) MUTATED     1  35
  AMP PEAK 28(XQ28) WILD-TYPE   2 108
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 28(XQ28) MUTATED      1   35
  AMP PEAK 28(XQ28) WILD-TYPE    2  108
                        clus
vv                       AMP PEAK 28(XQ28) MUTATED AMP PEAK 28(XQ28) WILD-TYPE
  HISPANIC OR LATINO                             1                           2
  NOT HISPANIC OR LATINO                        35                         108
[1] 2 2
[1] FALSE

Clustering(29) Variable = DEL PEAK  1(1P36.23) MUTATION ANALYSIS
D29V1, survival
                                sevent
clus2                             0  1
  DEL PEAK  1(1P36.23) MUTATED   41 34
  DEL PEAK  1(1P36.23) WILD-TYPE 50 32
  DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE 
                            75                             82 
  DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE 
                            34                             32 
$`DEL PEAK  1(1P36.23) MUTATED`
TCGA-BC-A10Q TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10W TCGA-BC-A10Y TCGA-BC-A112 
       37.32        46.78        27.52         2.99        23.34         5.03 
TCGA-BC-A217 TCGA-BC-A69H TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 
       13.84        14.60         2.86         0.39         3.39         4.24 
TCGA-CC-A3MA TCGA-CC-A3MB TCGA-DD-A113 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 
        0.07         0.10        79.73        53.33       113.00         7.33 
TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EB 
        2.60         0.46        21.76        51.29        90.71        66.31 
TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EJ TCGA-DD-A39X TCGA-DD-A39Z 
       12.95        45.11        49.15        29.16        55.69        19.76 
TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A9 TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ 
       25.81         7.66        30.61        14.24        18.44        15.06 
TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NR TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73F 
       29.56        73.81         0.30        10.98         9.30        27.72 
TCGA-DD-A73G TCGA-ED-A4XI TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY 
      100.96        12.69        13.35         0.23         0.20         0.20 
TCGA-ED-A82E TCGA-ED-A8O5 TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HS 
        0.20         0.20        10.98         0.62        11.93        22.85 
TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A4ZP 
       32.45        19.10        27.88         0.13         0.03        60.36 
TCGA-G3-A25S TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A5SI 
        1.22        28.27        30.74        58.49        14.86        14.70 
TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A7M9 TCGA-KR-A7K2 TCGA-KR-A7K7 
       11.97         7.99         4.37         1.84        11.84        13.38 
TCGA-MI-A75G TCGA-MI-A75H TCGA-O8-A75V 
       14.24        12.85         4.44 

$`DEL PEAK  1(1P36.23) WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10R TCGA-BC-A10U TCGA-BC-A10X TCGA-BC-A10Z 
       48.99        27.91        10.13        27.52        25.32         1.12 
TCGA-BC-A110 TCGA-BC-A216 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69I 
       69.57        44.42         0.26        22.36         9.50        12.72 
TCGA-CC-5258 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MC TCGA-DD-A114 TCGA-DD-A115 
        0.07         3.32         0.10         0.13        37.78        83.57 
TCGA-DD-A1EA TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EI TCGA-DD-A1EK 
       79.40        19.79        75.65         6.71         6.02        18.35 
TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39Y TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 
       13.64        21.14         5.62        70.06        17.59        20.12 
TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A4NA TCGA-DD-A4NB 
      102.74       107.11        13.78         0.36        33.14        32.52 
TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NP TCGA-DD-A4NQ 
       73.38        14.07        39.78        56.25        93.67        12.26 
TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-ED-A459 
       80.75        66.35         7.56        10.98         1.45        13.41 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-EP-A12J TCGA-EP-A26S 
       15.85        13.91         0.20         0.20        18.74        19.99 
TCGA-EP-A2KA TCGA-EP-A3JL TCGA-ES-A2HT TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A496 
       11.74         9.96        14.40         8.12         6.38         0.33 
TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH 
        0.39        51.06        53.79        21.53        22.13        25.64 
TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-GJ-A6C0 
        5.92        19.53        19.23         7.76         5.98         1.02 
TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E 
        2.66         4.01         2.14         0.49         9.57         5.10 
TCGA-MI-A75I TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF 
        8.71         1.71        58.88        16.37 

  DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE 
                          0.03                           0.07 
  DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE 
                        113.00                         107.11 
  DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE 
                         13.84                          13.99 
[1] "0.0 - 113.0 (13.8)" "0.1 - 107.1 (14.0)"
[1] "hr=" "1.2"
D29V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IIIA
  DEL PEAK  1(1P36.23) MUTATED        28       19         1         12
  DEL PEAK  1(1P36.23) WILD-TYPE      37       18         1         19
                                vv
clus                             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK  1(1P36.23) MUTATED            3          3        1         1
  DEL PEAK  1(1P36.23) WILD-TYPE          2          2        0         0
                                vv
clus                             STAGE IVB
  DEL PEAK  1(1P36.23) MUTATED           1
  DEL PEAK  1(1P36.23) WILD-TYPE         1
D29V3, multiclass
            clus
vv           DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE
  STAGE I                              28                             37
  STAGE II                             19                             18
  STAGE III                             1                              1
  STAGE IIIA                           12                             19
  STAGE IIIB                            3                              2
  STAGE IIIC                            3                              2
  STAGE IV                              1                              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  1(1P36.23) MUTATED   30 20 19  6
  DEL PEAK  1(1P36.23) WILD-TYPE 38 21 23  2
D29V4, multiclass
    clus
vv   DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE
  T1                           30                             38
  T2                           20                             21
  T3                           19                             23
  T4                            6                              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"
D29V5, binary
                                cls
clus                              0  1
  DEL PEAK  1(1P36.23) MUTATED   46  2
  DEL PEAK  1(1P36.23) WILD-TYPE 56  1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.23) MUTATED     46    2
  DEL PEAK  1(1P36.23) WILD-TYPE   56    1
   clus
vv  DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE
  0                           46                             56
  1                            2                              1
[1] 2 2
[1] FALSE
                                vv
clus                             M0 M1 MX
  DEL PEAK  1(1P36.23) MUTATED   59  2 15
  DEL PEAK  1(1P36.23) WILD-TYPE 61  1 22
D29V6, multiclass
    clus
vv   DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE
  M0                           59                             61
  M1                            2                              1
  MX                           15                             22
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V7, binary
                                cls
clus                              0  1
  DEL PEAK  1(1P36.23) MUTATED   32 44
  DEL PEAK  1(1P36.23) WILD-TYPE 28 56
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.23) MUTATED     32   44
  DEL PEAK  1(1P36.23) WILD-TYPE   28   56
        clus
vv       DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE
  FEMALE                           32                             28
  MALE                             44                             56
[1] 2 2
[1] FALSE
                                vv
clus                             FIBROLAMELLAR CARCINOMA
  DEL PEAK  1(1P36.23) MUTATED                         0
  DEL PEAK  1(1P36.23) WILD-TYPE                       2
                                vv
clus                             HEPATOCELLULAR CARCINOMA
  DEL PEAK  1(1P36.23) MUTATED                         74
  DEL PEAK  1(1P36.23) WILD-TYPE                       82
                                vv
clus                             HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK  1(1P36.23) MUTATED                                  2
  DEL PEAK  1(1P36.23) WILD-TYPE                                0
D29V8, multiclass
                                  clus
vv                                 DEL PEAK  1(1P36.23) MUTATED
  FIBROLAMELLAR CARCINOMA                                     0
  HEPATOCELLULAR CARCINOMA                                   74
  HEPATOCHOLANGIOCARCINOMA (MIXED)                            2
                                  clus
vv                                 DEL PEAK  1(1P36.23) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                       2
  HEPATOCELLULAR CARCINOMA                                     82
  HEPATOCHOLANGIOCARCINOMA (MIXED)                              0
[1] 3 2
[1] 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(1P36.23) MUTATED   61  6  1  6
  DEL PEAK  1(1P36.23) WILD-TYPE 70  5  0  6
D29V9, multiclass
    clus
vv   DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE
  R0                           61                             70
  R1                            6                              5
  R2                            1                              0
  RX                            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"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  1(1P36.23) MUTATED                                  0    19
  DEL PEAK  1(1P36.23) WILD-TYPE                                1    17
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  1(1P36.23) MUTATED                           2    51
  DEL PEAK  1(1P36.23) WILD-TYPE                         6    58
D29V10, multiclass
                                  clus
vv                                 DEL PEAK  1(1P36.23) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                      19
  BLACK OR AFRICAN AMERICAN                                   2
  WHITE                                                      51
                                  clus
vv                                 DEL PEAK  1(1P36.23) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        17
  BLACK OR AFRICAN AMERICAN                                     6
  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"
D29V11, binary
                                cls
clus                              0  1
  DEL PEAK  1(1P36.23) MUTATED    2 68
  DEL PEAK  1(1P36.23) WILD-TYPE  1 75
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.23) MUTATED      2   68
  DEL PEAK  1(1P36.23) WILD-TYPE    1   75
                        clus
vv                       DEL PEAK  1(1P36.23) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           68
                        clus
vv                       DEL PEAK  1(1P36.23) WILD-TYPE
  HISPANIC OR LATINO                                  1
  NOT HISPANIC OR LATINO                             75
[1] 2 2
[1] FALSE

Clustering(30) Variable = DEL PEAK  2(2Q22.1) MUTATION ANALYSIS
D30V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  2(2Q22.1) MUTATED    6  9
  DEL PEAK  2(2Q22.1) WILD-TYPE 85 57
  DEL PEAK  2(2Q22.1) MUTATED DEL PEAK  2(2Q22.1) WILD-TYPE 
                           15                           142 
  DEL PEAK  2(2Q22.1) MUTATED DEL PEAK  2(2Q22.1) WILD-TYPE 
                            9                            57 
$`DEL PEAK  2(2Q22.1) MUTATED`
TCGA-BC-A10R TCGA-BC-A10Y TCGA-BC-A3KF TCGA-DD-A115 TCGA-DD-A1EL TCGA-DD-A39V 
       10.13        23.34         0.26        83.57        13.64        21.14 
TCGA-DD-A39Y TCGA-DD-A3A1 TCGA-DD-A4NJ TCGA-DD-A73B TCGA-ED-A459 TCGA-ED-A66Y 
        5.62         7.66        15.06         9.30        13.41         0.23 
TCGA-ED-A7PZ TCGA-FV-A3I1 TCGA-KR-A7K2 
        0.20         8.12        11.84 

$`DEL PEAK  2(2Q22.1) WILD-TYPE`
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-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 
        2.99        25.32         1.12        69.57         5.03        44.42 
TCGA-BC-A217 TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I TCGA-CC-5258 
       13.84        22.36         9.50        14.60        12.72         0.07 
TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 
        2.86         0.39         3.39         4.24         3.32         0.10 
TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A116 
        0.07         0.10         0.13        79.73        37.78        53.33 
TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D 
      113.00         7.33         2.60         0.46        21.76        51.29 
TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE 
       90.71        79.40        66.31        19.79        75.65         6.71 
TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK 
       12.95        45.11        49.15         6.02        29.16        18.35 
TCGA-DD-A39X TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 
       55.69        19.76        25.81        70.06        17.59        20.12 
TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA 
      102.74       107.11        13.78         0.36        30.61        33.14 
TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NK 
       32.52        73.38        14.07        14.24        18.44        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        93.67        12.26         0.30 
TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E 
       80.75        66.35        10.98         7.56        10.98         1.45 
TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X 
       27.72       100.96        12.69        15.85        13.91        13.35 
TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-EP-A12J 
        0.20         0.20         0.20         0.20         0.20        18.74 
TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK 
       19.99        11.74        10.98         0.62         9.96        11.93 
TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R2 
       22.85        14.40        32.45        19.10        27.88         6.38 
TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S 
        0.13         0.03         0.33        60.36         0.39         1.22 
TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y 
       51.06        53.79        28.27        30.74        58.49        14.86 
TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
       21.53        22.13        25.64         5.92        19.53        19.23 
TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M7 
       14.70        11.97         7.99         4.37         7.76         5.98 
TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K7 
        1.84         1.02         2.66         4.01         2.14        13.38 
TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I 
        0.49         9.57         5.10        14.24        12.85         8.71 
TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V 
        1.71        58.88        16.37         4.44 

  DEL PEAK  2(2Q22.1) MUTATED DEL PEAK  2(2Q22.1) WILD-TYPE 
                         0.20                          0.03 
  DEL PEAK  2(2Q22.1) MUTATED DEL PEAK  2(2Q22.1) WILD-TYPE 
                        83.57                        113.00 
  DEL PEAK  2(2Q22.1) MUTATED DEL PEAK  2(2Q22.1) WILD-TYPE 
                        10.13                         14.32 
[1] "0.2 - 83.6 (10.1)"  "0.0 - 113.0 (14.3)"
[1] "hr=" "2.4"
D30V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IIIA
  DEL PEAK  2(2Q22.1) MUTATED         5        6         0          4
  DEL PEAK  2(2Q22.1) WILD-TYPE      60       31         2         27
                               vv
clus                            STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK  2(2Q22.1) MUTATED            0          0        0         0
  DEL PEAK  2(2Q22.1) WILD-TYPE          5          5        1         1
                               vv
clus                            STAGE IVB
  DEL PEAK  2(2Q22.1) MUTATED           0
  DEL PEAK  2(2Q22.1) WILD-TYPE         2
D30V3, multiclass
            clus
vv           DEL PEAK  2(2Q22.1) MUTATED DEL PEAK  2(2Q22.1) WILD-TYPE
  STAGE I                              5                            60
  STAGE II                             6                            31
  STAGE III                            0                             2
  STAGE IIIA                           4                            27
  STAGE IIIB                           0                             5
  STAGE IIIC                           0                             5
  STAGE IV                             0                             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
  DEL PEAK  2(2Q22.1) MUTATED    5  6  5  1
  DEL PEAK  2(2Q22.1) WILD-TYPE 63 35 37  7
D30V4, multiclass
    clus
vv   DEL PEAK  2(2Q22.1) MUTATED DEL PEAK  2(2Q22.1) WILD-TYPE
  T1                           5                            63
  T2                           6                            35
  T3                           5                            37
  T4                           1                             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"
D30V5, binary
                               cls
clus                             0  1
  DEL PEAK  2(2Q22.1) MUTATED   10  0
  DEL PEAK  2(2Q22.1) WILD-TYPE 92  3
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(2Q22.1) MUTATED     10    0
  DEL PEAK  2(2Q22.1) WILD-TYPE   92    3
   clus
vv  DEL PEAK  2(2Q22.1) MUTATED DEL PEAK  2(2Q22.1) WILD-TYPE
  0                          10                            92
  1                           0                             3
[1] 2 2
[1] FALSE
                               vv
clus                             M0  M1  MX
  DEL PEAK  2(2Q22.1) MUTATED    13   0   4
  DEL PEAK  2(2Q22.1) WILD-TYPE 107   3  33
D30V6, multiclass
    clus
vv   DEL PEAK  2(2Q22.1) MUTATED DEL PEAK  2(2Q22.1) WILD-TYPE
  M0                          13                           107
  M1                           0                             3
  MX                           4                            33
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V7, binary
                               cls
clus                             0  1
  DEL PEAK  2(2Q22.1) MUTATED    6 11
  DEL PEAK  2(2Q22.1) WILD-TYPE 54 89
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(2Q22.1) MUTATED      6   11
  DEL PEAK  2(2Q22.1) WILD-TYPE   54   89
        clus
vv       DEL PEAK  2(2Q22.1) MUTATED DEL PEAK  2(2Q22.1) WILD-TYPE
  FEMALE                           6                            54
  MALE                            11                            89
[1] 2 2
[1] FALSE
                               vv
clus                            FIBROLAMELLAR CARCINOMA
  DEL PEAK  2(2Q22.1) MUTATED                         0
  DEL PEAK  2(2Q22.1) WILD-TYPE                       2
                               vv
clus                            HEPATOCELLULAR CARCINOMA
  DEL PEAK  2(2Q22.1) MUTATED                         16
  DEL PEAK  2(2Q22.1) WILD-TYPE                      140
                               vv
clus                            HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK  2(2Q22.1) MUTATED                                  1
  DEL PEAK  2(2Q22.1) WILD-TYPE                                1
D30V8, multiclass
                                  clus
vv                                 DEL PEAK  2(2Q22.1) MUTATED
  FIBROLAMELLAR CARCINOMA                                    0
  HEPATOCELLULAR CARCINOMA                                  16
  HEPATOCHOLANGIOCARCINOMA (MIXED)                           1
                                  clus
vv                                 DEL PEAK  2(2Q22.1) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                      2
  HEPATOCELLULAR CARCINOMA                                   140
  HEPATOCHOLANGIOCARCINOMA (MIXED)                             1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  2(2Q22.1) MUTATED    15   0   0   2
  DEL PEAK  2(2Q22.1) WILD-TYPE 116  11   1  10
D30V9, multiclass
    clus
vv   DEL PEAK  2(2Q22.1) MUTATED DEL PEAK  2(2Q22.1) WILD-TYPE
  R0                          15                           116
  R1                           0                            11
  R2                           0                             1
  RX                           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"
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  2(2Q22.1) MUTATED                                  0     5
  DEL PEAK  2(2Q22.1) WILD-TYPE                                1    31
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  2(2Q22.1) MUTATED                           1    10
  DEL PEAK  2(2Q22.1) WILD-TYPE                         7    99
D30V10, multiclass
                                  clus
vv                                 DEL PEAK  2(2Q22.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      5
  BLACK OR AFRICAN AMERICAN                                  1
  WHITE                                                     10
                                  clus
vv                                 DEL PEAK  2(2Q22.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                       31
  BLACK OR AFRICAN AMERICAN                                    7
  WHITE                                                       99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V11, binary
                               cls
clus                              0   1
  DEL PEAK  2(2Q22.1) MUTATED     1  12
  DEL PEAK  2(2Q22.1) WILD-TYPE   2 131
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(2Q22.1) MUTATED      1   12
  DEL PEAK  2(2Q22.1) WILD-TYPE    2  131
                        clus
vv                       DEL PEAK  2(2Q22.1) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          12
                        clus
vv                       DEL PEAK  2(2Q22.1) WILD-TYPE
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                           131
[1] 2 2
[1] FALSE

Clustering(31) Variable = DEL PEAK  3(2Q37.3) MUTATION ANALYSIS
D31V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  3(2Q37.3) MUTATED   20  9
  DEL PEAK  3(2Q37.3) WILD-TYPE 71 57
  DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE 
                           29                           128 
  DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE 
                            9                            57 
$`DEL PEAK  3(2Q37.3) MUTATED`
TCGA-BC-A10Y TCGA-BC-A216 TCGA-BC-A3KF TCGA-BC-A5W4 TCGA-BC-A69H TCGA-CC-A3M9 
       23.34        44.42         0.26         9.50        14.60         0.10 
TCGA-DD-A113 TCGA-DD-A115 TCGA-DD-A11A TCGA-DD-A11C TCGA-DD-A1EB TCGA-DD-A1EL 
       79.73        83.57         2.60        21.76        66.31        13.64 
TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A4NA TCGA-DD-A4NJ TCGA-DD-A4NQ TCGA-DD-A73B 
        5.62        19.76        33.14        15.06        12.26         9.30 
TCGA-ED-A459 TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PZ TCGA-FV-A3I0 TCGA-FV-A3I1 
       13.41         0.23         0.20         0.20        27.88         8.12 
TCGA-FV-A496 TCGA-G3-A5SI TCGA-G3-A7M9 TCGA-KR-A7K2 TCGA-MI-A75I 
        0.33        14.70         1.84        11.84         8.71 

$`DEL PEAK  3(2Q37.3) WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T 
       48.99        27.91        37.32        10.13        46.78        27.52 
TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 
       27.52         2.99        25.32         1.12        69.57         5.03 
TCGA-BC-A217 TCGA-BC-A3KG TCGA-BC-A69I TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 
       13.84        22.36        12.72         0.07         2.86         0.39 
TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC 
        3.39         4.24         3.32         0.07         0.10         0.13 
TCGA-DD-A114 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11D 
       37.78        53.33       113.00         7.33         0.46        51.29 
TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF 
       90.71        79.40        19.79        75.65         6.71        12.95 
TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A39V 
       45.11        49.15         6.02        29.16        18.35        21.14 
TCGA-DD-A39X TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 
       55.69        25.81         7.66        70.06        17.59        20.12 
TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NB 
      102.74       107.11        13.78         0.36        30.61        32.52 
TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NK TCGA-DD-A4NL 
       73.38        14.07        14.24        18.44        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        93.67         0.30        80.75        66.35 
TCGA-DD-A73A TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G 
       10.98         7.56        10.98         1.45        27.72       100.96 
TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A7PY TCGA-ED-A7XP 
       12.69        15.85        13.91        13.35         0.20         0.20 
TCGA-ED-A82E TCGA-ED-A8O5 TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB 
        0.20         0.20        18.74        19.99        11.74        10.98 
TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B 
        0.62         9.96        11.93        22.85        14.40        32.45 
TCGA-FV-A2QR TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A4ZP TCGA-FV-A4ZQ 
       19.10         6.38         0.13         0.03        60.36         0.39 
TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X 
        1.22        51.06        53.79        28.27        30.74        58.49 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ 
       14.86        21.53        22.13        25.64         5.92        19.53 
TCGA-G3-A3CK TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M7 
       19.23        11.97         7.99         4.37         7.76         5.98 
TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG 
        1.02         2.66         4.01         2.14        13.38         0.49 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MR-A8JO TCGA-NI-A4U2 
        9.57         5.10        14.24        12.85         1.71        58.88 
TCGA-NI-A8LF TCGA-O8-A75V 
       16.37         4.44 

  DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE 
                         0.10                          0.03 
  DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE 
                        83.57                        113.00 
  DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE 
                        12.26                         14.24 
[1] "0.1 - 83.6 (12.3)"  "0.0 - 113.0 (14.2)"
[1] "hr=" "1.1"
D31V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IIIA
  DEL PEAK  3(2Q37.3) MUTATED         9       12         0          6
  DEL PEAK  3(2Q37.3) WILD-TYPE      56       25         2         25
                               vv
clus                            STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK  3(2Q37.3) MUTATED            1          1        0         0
  DEL PEAK  3(2Q37.3) WILD-TYPE          4          4        1         1
                               vv
clus                            STAGE IVB
  DEL PEAK  3(2Q37.3) MUTATED           0
  DEL PEAK  3(2Q37.3) WILD-TYPE         2
D31V3, multiclass
            clus
vv           DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE
  STAGE I                              9                            56
  STAGE II                            12                            25
  STAGE III                            0                             2
  STAGE IIIA                           6                            25
  STAGE IIIB                           1                             4
  STAGE IIIC                           1                             4
  STAGE IV                             0                             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
  DEL PEAK  3(2Q37.3) MUTATED    9 14  7  1
  DEL PEAK  3(2Q37.3) WILD-TYPE 59 27 35  7
D31V4, multiclass
    clus
vv   DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE
  T1                           9                            59
  T2                          14                            27
  T3                           7                            35
  T4                           1                             7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V5, binary
                               cls
clus                             0  1
  DEL PEAK  3(2Q37.3) MUTATED   16  1
  DEL PEAK  3(2Q37.3) WILD-TYPE 86  2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2Q37.3) MUTATED     16    1
  DEL PEAK  3(2Q37.3) WILD-TYPE   86    2
   clus
vv  DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE
  0                          16                            86
  1                           1                             2
[1] 2 2
[1] FALSE
                               vv
clus                            M0 M1 MX
  DEL PEAK  3(2Q37.3) MUTATED   26  0  5
  DEL PEAK  3(2Q37.3) WILD-TYPE 94  3 32
D31V6, multiclass
    clus
vv   DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE
  M0                          26                            94
  M1                           0                             3
  MX                           5                            32
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V7, binary
                               cls
clus                             0  1
  DEL PEAK  3(2Q37.3) MUTATED   13 18
  DEL PEAK  3(2Q37.3) WILD-TYPE 47 82
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2Q37.3) MUTATED     13   18
  DEL PEAK  3(2Q37.3) WILD-TYPE   47   82
        clus
vv       DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE
  FEMALE                          13                            47
  MALE                            18                            82
[1] 2 2
[1] FALSE
                               vv
clus                            FIBROLAMELLAR CARCINOMA
  DEL PEAK  3(2Q37.3) MUTATED                         0
  DEL PEAK  3(2Q37.3) WILD-TYPE                       2
                               vv
clus                            HEPATOCELLULAR CARCINOMA
  DEL PEAK  3(2Q37.3) MUTATED                         29
  DEL PEAK  3(2Q37.3) WILD-TYPE                      127
                               vv
clus                            HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK  3(2Q37.3) MUTATED                                  2
  DEL PEAK  3(2Q37.3) WILD-TYPE                                0
D31V8, multiclass
                                  clus
vv                                 DEL PEAK  3(2Q37.3) MUTATED
  FIBROLAMELLAR CARCINOMA                                    0
  HEPATOCELLULAR CARCINOMA                                  29
  HEPATOCHOLANGIOCARCINOMA (MIXED)                           2
                                  clus
vv                                 DEL PEAK  3(2Q37.3) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                      2
  HEPATOCELLULAR CARCINOMA                                   127
  HEPATOCHOLANGIOCARCINOMA (MIXED)                             0
[1] 3 2
[1] 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(2Q37.3) MUTATED    27   1   0   3
  DEL PEAK  3(2Q37.3) WILD-TYPE 104  10   1   9
D31V9, multiclass
    clus
vv   DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE
  R0                          27                           104
  R1                           1                            10
  R2                           0                             1
  RX                           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"
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  3(2Q37.3) MUTATED                                  0     8
  DEL PEAK  3(2Q37.3) WILD-TYPE                                1    28
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  3(2Q37.3) MUTATED                           3    18
  DEL PEAK  3(2Q37.3) WILD-TYPE                         5    91
D31V10, multiclass
                                  clus
vv                                 DEL PEAK  3(2Q37.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      8
  BLACK OR AFRICAN AMERICAN                                  3
  WHITE                                                     18
                                  clus
vv                                 DEL PEAK  3(2Q37.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                       28
  BLACK OR AFRICAN AMERICAN                                    5
  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"
D31V11, binary
                               cls
clus                              0   1
  DEL PEAK  3(2Q37.3) MUTATED     2  23
  DEL PEAK  3(2Q37.3) WILD-TYPE   1 120
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2Q37.3) MUTATED      2   23
  DEL PEAK  3(2Q37.3) WILD-TYPE    1  120
                        clus
vv                       DEL PEAK  3(2Q37.3) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          23
                        clus
vv                       DEL PEAK  3(2Q37.3) WILD-TYPE
  HISPANIC OR LATINO                                 1
  NOT HISPANIC OR LATINO                           120
[1] 2 2
[1] FALSE

Clustering(32) Variable = DEL PEAK  4(3P13) MUTATION ANALYSIS
D32V1, survival
                             sevent
clus2                          0  1
  DEL PEAK  4(3P13) MUTATED   21  8
  DEL PEAK  4(3P13) WILD-TYPE 70 58
  DEL PEAK  4(3P13) MUTATED DEL PEAK  4(3P13) WILD-TYPE 
                         29                         128 
  DEL PEAK  4(3P13) MUTATED DEL PEAK  4(3P13) WILD-TYPE 
                          8                          58 
$`DEL PEAK  4(3P13) MUTATED`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A112 TCGA-BC-A217 TCGA-CC-5260 
       27.91        37.32        10.13         5.03        13.84         2.86 
TCGA-CC-5263 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-DD-A113 TCGA-DD-A11A TCGA-DD-A1E9 
        4.24         0.07         0.10        79.73         2.60        90.71 
TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NO TCGA-DD-A73G 
       30.61        33.14        14.24        18.44        73.81       100.96 
TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PZ TCGA-ED-A82E TCGA-FV-A3I0 TCGA-FV-A3R3 
        0.23         0.20         0.20         0.20        27.88         0.13 
TCGA-G3-A25T TCGA-G3-A25X TCGA-G3-A7M9 TCGA-KR-A7K2 TCGA-KR-A7K7 
       51.06        58.49         1.84        11.84        13.38 

$`DEL PEAK  4(3P13) WILD-TYPE`
TCGA-BC-4072 TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X 
       48.99        46.78        27.52        27.52         2.99        25.32 
TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A216 TCGA-BC-A3KF TCGA-BC-A3KG 
       23.34         1.12        69.57        44.42         0.26        22.36 
TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I TCGA-CC-5258 TCGA-CC-5261 TCGA-CC-5262 
        9.50        14.60        12.72         0.07         0.39         3.39 
TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MC TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 
        3.32         0.10         0.13        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         6.71        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        29.16        18.35        13.64        21.14 
TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 
       55.69         5.62        19.76        25.81         7.66        70.06 
TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 
       17.59        20.12       102.74       107.11        13.78         0.36 
TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL 
       32.52        73.38        14.07        15.06        39.78        56.25 
TCGA-DD-A4NN TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV 
       29.56        93.67        12.26         0.30        80.75        66.35 
TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F 
       10.98         9.30         7.56        10.98         1.45        27.72 
TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A7PY 
       13.41        12.69        15.85        13.91        13.35         0.20 
TCGA-ED-A7XP TCGA-ED-A8O5 TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB 
        0.20         0.20        18.74        19.99        11.74        10.98 
TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B 
        0.62         9.96        11.93        22.85        14.40        32.45 
TCGA-FV-A2QR TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP 
       19.10         8.12         6.38         0.03         0.33        60.36 
TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y 
        0.39         1.22        53.79        28.27        30.74        14.86 
TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
       21.53        22.13        25.64         5.92        19.53        19.23 
TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M7 
       14.70        11.97         7.99         4.37         7.76         5.98 
TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-LG-A6GG TCGA-MI-A75C 
        1.02         2.66         4.01         2.14         0.49         9.57 
TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A8JO TCGA-NI-A4U2 
        5.10        14.24        12.85         8.71         1.71        58.88 
TCGA-NI-A8LF TCGA-O8-A75V 
       16.37         4.44 

  DEL PEAK  4(3P13) MUTATED DEL PEAK  4(3P13) WILD-TYPE 
                       0.07                        0.03 
  DEL PEAK  4(3P13) MUTATED DEL PEAK  4(3P13) WILD-TYPE 
                     100.96                      113.00 
  DEL PEAK  4(3P13) MUTATED DEL PEAK  4(3P13) WILD-TYPE 
                     13.380                      14.155 
[1] "0.1 - 101.0 (13.4)" "0.0 - 113.0 (14.2)"
[1] "hr=" "1.6"
D32V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  4(3P13) MUTATED         6        8         0          7          2
  DEL PEAK  4(3P13) WILD-TYPE      59       29         2         24          3
                             vv
clus                          STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK  4(3P13) MUTATED            2        0         0         1
  DEL PEAK  4(3P13) WILD-TYPE          3        1         1         1
D32V3, multiclass
            clus
vv           DEL PEAK  4(3P13) MUTATED DEL PEAK  4(3P13) WILD-TYPE
  STAGE I                            6                          59
  STAGE II                           8                          29
  STAGE III                          0                           2
  STAGE IIIA                         7                          24
  STAGE IIIB                         2                           3
  STAGE IIIC                         2                           3
  STAGE IV                           0                           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  4(3P13) MUTATED    6 10 11  2
  DEL PEAK  4(3P13) WILD-TYPE 62 31 31  6
D32V4, multiclass
    clus
vv   DEL PEAK  4(3P13) MUTATED DEL PEAK  4(3P13) WILD-TYPE
  T1                         6                          62
  T2                        10                          31
  T3                        11                          31
  T4                         2                           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"
D32V5, binary
                             cls
clus                           0  1
  DEL PEAK  4(3P13) MUTATED   18  1
  DEL PEAK  4(3P13) WILD-TYPE 84  2
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  4(3P13) MUTATED     18    1
  DEL PEAK  4(3P13) WILD-TYPE   84    2
   clus
vv  DEL PEAK  4(3P13) MUTATED DEL PEAK  4(3P13) WILD-TYPE
  0                        18                          84
  1                         1                           2
[1] 2 2
[1] FALSE
                             vv
clus                          M0 M1 MX
  DEL PEAK  4(3P13) MUTATED   22  1  6
  DEL PEAK  4(3P13) WILD-TYPE 98  2 31
D32V6, multiclass
    clus
vv   DEL PEAK  4(3P13) MUTATED DEL PEAK  4(3P13) WILD-TYPE
  M0                        22                          98
  M1                         1                           2
  MX                         6                          31
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V7, binary
                             cls
clus                           0  1
  DEL PEAK  4(3P13) MUTATED   16 13
  DEL PEAK  4(3P13) WILD-TYPE 44 87
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  4(3P13) MUTATED     16   13
  DEL PEAK  4(3P13) WILD-TYPE   44   87
        clus
vv       DEL PEAK  4(3P13) MUTATED DEL PEAK  4(3P13) WILD-TYPE
  FEMALE                        16                          44
  MALE                          13                          87
[1] 2 2
[1] FALSE
                             vv
clus                          FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  DEL PEAK  4(3P13) MUTATED                         0                       27
  DEL PEAK  4(3P13) WILD-TYPE                       2                      129
                             vv
clus                          HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK  4(3P13) MUTATED                                  2
  DEL PEAK  4(3P13) WILD-TYPE                                0
D32V8, multiclass
                                  clus
vv                                 DEL PEAK  4(3P13) MUTATED
  FIBROLAMELLAR CARCINOMA                                  0
  HEPATOCELLULAR CARCINOMA                                27
  HEPATOCHOLANGIOCARCINOMA (MIXED)                         2
                                  clus
vv                                 DEL PEAK  4(3P13) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                    2
  HEPATOCELLULAR CARCINOMA                                 129
  HEPATOCHOLANGIOCARCINOMA (MIXED)                           0
[1] 3 2
[1] 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(3P13) MUTATED    25   2   0   2
  DEL PEAK  4(3P13) WILD-TYPE 106   9   1  10
D32V9, multiclass
    clus
vv   DEL PEAK  4(3P13) MUTATED DEL PEAK  4(3P13) WILD-TYPE
  R0                        25                         106
  R1                         2                           9
  R2                         0                           1
  RX                         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"
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  4(3P13) MUTATED                                  0     9
  DEL PEAK  4(3P13) WILD-TYPE                                1    27
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  4(3P13) MUTATED                           1    19
  DEL PEAK  4(3P13) WILD-TYPE                         7    90
D32V10, multiclass
                                  clus
vv                                 DEL PEAK  4(3P13) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         0
  ASIAN                                                    9
  BLACK OR AFRICAN AMERICAN                                1
  WHITE                                                   19
                                  clus
vv                                 DEL PEAK  4(3P13) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                     27
  BLACK OR AFRICAN AMERICAN                                  7
  WHITE                                                     90
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V11, binary
                             cls
clus                            0   1
  DEL PEAK  4(3P13) MUTATED     0  26
  DEL PEAK  4(3P13) WILD-TYPE   3 117
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  4(3P13) MUTATED      0   26
  DEL PEAK  4(3P13) WILD-TYPE    3  117
                        clus
vv                       DEL PEAK  4(3P13) MUTATED DEL PEAK  4(3P13) WILD-TYPE
  HISPANIC OR LATINO                             0                           3
  NOT HISPANIC OR LATINO                        26                         117
[1] 2 2
[1] FALSE

Clustering(33) Variable = DEL PEAK  5(4P16.3) MUTATION ANALYSIS
D33V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  5(4P16.3) MUTATED   15 11
  DEL PEAK  5(4P16.3) WILD-TYPE 76 55
  DEL PEAK  5(4P16.3) MUTATED DEL PEAK  5(4P16.3) WILD-TYPE 
                           26                           131 
  DEL PEAK  5(4P16.3) MUTATED DEL PEAK  5(4P16.3) WILD-TYPE 
                           11                            55 
$`DEL PEAK  5(4P16.3) MUTATED`
TCGA-BC-A10Y TCGA-BC-A112 TCGA-BC-A5W4 TCGA-BC-A69H TCGA-CC-A3MC TCGA-DD-A114 
       23.34         5.03         9.50        14.60         0.13        37.78 
TCGA-DD-A119 TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A4NI 
        7.33         6.02        29.16        55.69         5.62        18.44 
TCGA-DD-A4NJ TCGA-DD-A4NN TCGA-DD-A73A TCGA-ED-A459 TCGA-EP-A2KB TCGA-EP-A2KC 
       15.06        29.56        10.98        13.41        10.98         0.62 
TCGA-FV-A4ZP TCGA-G3-A25U TCGA-G3-A25X TCGA-G3-A3CH TCGA-GJ-A6C0 TCGA-KR-A7K2 
       60.36        53.79        58.49        25.64         1.02        11.84 
TCGA-KR-A7K7 TCGA-MI-A75G 
       13.38        14.24 

$`DEL PEAK  5(4P16.3) WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T 
       48.99        27.91        37.32        10.13        46.78        27.52 
TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A216 
       27.52         2.99        25.32         1.12        69.57        44.42 
TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A69I TCGA-CC-5258 TCGA-CC-5260 
       13.84         0.26        22.36        12.72         0.07         2.86 
TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA 
        0.39         3.39         4.24         3.32         0.10         0.07 
TCGA-CC-A3MB TCGA-DD-A113 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A11A 
        0.10        79.73        83.57        53.33       113.00         2.60 
TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB 
        0.46        21.76        51.29        90.71        79.40        66.31 
TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH 
       19.79        75.65         6.71        12.95        45.11        49.15 
TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 
       18.35        13.64        21.14        19.76        25.81         7.66 
TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 
       70.06        17.59        20.12       102.74       107.11        13.78 
TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NF 
        0.36        30.61        33.14        32.52        73.38        14.07 
TCGA-DD-A4NH TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ 
       14.24        39.78        56.25        73.81        93.67        12.26 
TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D 
        0.30        80.75        66.35         9.30         7.56        10.98 
TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 
        1.45        27.72       100.96        12.69        15.85        13.91 
TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XP 
       13.35         0.23         0.20         0.20         0.20         0.20 
TCGA-ED-A82E TCGA-ED-A8O5 TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A3JL 
        0.20         0.20        18.74        19.99        11.74         9.96 
TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 
       11.93        22.85        14.40        32.45        19.10        27.88 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ 
        8.12         6.38         0.13         0.03         0.33         0.39 
TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z 
        1.22        51.06        28.27        30.74        14.86        21.53 
TCGA-G3-A3CG TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ 
       22.13         5.92        19.53        19.23        14.70        11.97 
TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-HP-A5MZ 
        7.99         4.37         7.76         5.98         1.84         2.66 
TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75H 
        4.01         2.14         0.49         9.57         5.10        12.85 
TCGA-MI-A75I TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V 
        8.71         1.71        58.88        16.37         4.44 

  DEL PEAK  5(4P16.3) MUTATED DEL PEAK  5(4P16.3) WILD-TYPE 
                         0.13                          0.03 
  DEL PEAK  5(4P16.3) MUTATED DEL PEAK  5(4P16.3) WILD-TYPE 
                        60.36                        113.00 
  DEL PEAK  5(4P16.3) MUTATED DEL PEAK  5(4P16.3) WILD-TYPE 
                       13.825                        13.910 
[1] "0.1 - 60.4 (13.8)"  "0.0 - 113.0 (13.9)"
[1] "hr=" "1.2"
D33V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IIIA
  DEL PEAK  5(4P16.3) MUTATED        10        9         0          5
  DEL PEAK  5(4P16.3) WILD-TYPE      55       28         2         26
                               vv
clus                            STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK  5(4P16.3) MUTATED            0          1        1         1
  DEL PEAK  5(4P16.3) WILD-TYPE          5          4        0         0
                               vv
clus                            STAGE IVB
  DEL PEAK  5(4P16.3) MUTATED           0
  DEL PEAK  5(4P16.3) WILD-TYPE         2
D33V3, multiclass
            clus
vv           DEL PEAK  5(4P16.3) MUTATED DEL PEAK  5(4P16.3) WILD-TYPE
  STAGE I                             10                            55
  STAGE II                             9                            28
  STAGE III                            0                             2
  STAGE IIIA                           5                            26
  STAGE IIIB                           0                             5
  STAGE IIIC                           1                             4
  STAGE IV                             1                             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  5(4P16.3) MUTATED   12  9  7  1
  DEL PEAK  5(4P16.3) WILD-TYPE 56 32 35  7
D33V4, multiclass
    clus
vv   DEL PEAK  5(4P16.3) MUTATED DEL PEAK  5(4P16.3) WILD-TYPE
  T1                          12                            56
  T2                           9                            32
  T3                           7                            35
  T4                           1                             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"
D33V5, binary
                               cls
clus                             0  1
  DEL PEAK  5(4P16.3) MUTATED   14  2
  DEL PEAK  5(4P16.3) WILD-TYPE 88  1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(4P16.3) MUTATED     14    2
  DEL PEAK  5(4P16.3) WILD-TYPE   88    1
   clus
vv  DEL PEAK  5(4P16.3) MUTATED DEL PEAK  5(4P16.3) WILD-TYPE
  0                          14                            88
  1                           2                             1
[1] 2 2
[1] FALSE
                               vv
clus                            M0 M1 MX
  DEL PEAK  5(4P16.3) MUTATED   21  1  7
  DEL PEAK  5(4P16.3) WILD-TYPE 99  2 30
D33V6, multiclass
    clus
vv   DEL PEAK  5(4P16.3) MUTATED DEL PEAK  5(4P16.3) WILD-TYPE
  M0                          21                            99
  M1                           1                             2
  MX                           7                            30
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V7, binary
                               cls
clus                             0  1
  DEL PEAK  5(4P16.3) MUTATED    8 21
  DEL PEAK  5(4P16.3) WILD-TYPE 52 79
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(4P16.3) MUTATED      8   21
  DEL PEAK  5(4P16.3) WILD-TYPE   52   79
        clus
vv       DEL PEAK  5(4P16.3) MUTATED DEL PEAK  5(4P16.3) WILD-TYPE
  FEMALE                           8                            52
  MALE                            21                            79
[1] 2 2
[1] FALSE
                               vv
clus                            FIBROLAMELLAR CARCINOMA
  DEL PEAK  5(4P16.3) MUTATED                         0
  DEL PEAK  5(4P16.3) WILD-TYPE                       2
                               vv
clus                            HEPATOCELLULAR CARCINOMA
  DEL PEAK  5(4P16.3) MUTATED                         28
  DEL PEAK  5(4P16.3) WILD-TYPE                      128
                               vv
clus                            HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK  5(4P16.3) MUTATED                                  1
  DEL PEAK  5(4P16.3) WILD-TYPE                                1
D33V8, multiclass
                                  clus
vv                                 DEL PEAK  5(4P16.3) MUTATED
  FIBROLAMELLAR CARCINOMA                                    0
  HEPATOCELLULAR CARCINOMA                                  28
  HEPATOCHOLANGIOCARCINOMA (MIXED)                           1
                                  clus
vv                                 DEL PEAK  5(4P16.3) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                      2
  HEPATOCELLULAR CARCINOMA                                   128
  HEPATOCHOLANGIOCARCINOMA (MIXED)                             1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  5(4P16.3) MUTATED    23   2   1   3
  DEL PEAK  5(4P16.3) WILD-TYPE 108   9   0   9
D33V9, multiclass
    clus
vv   DEL PEAK  5(4P16.3) MUTATED DEL PEAK  5(4P16.3) WILD-TYPE
  R0                          23                           108
  R1                           2                             9
  R2                           1                             0
  RX                           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"
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  5(4P16.3) MUTATED                                  0     9
  DEL PEAK  5(4P16.3) WILD-TYPE                                1    27
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  5(4P16.3) MUTATED                           2    18
  DEL PEAK  5(4P16.3) WILD-TYPE                         6    91
D33V10, multiclass
                                  clus
vv                                 DEL PEAK  5(4P16.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      9
  BLACK OR AFRICAN AMERICAN                                  2
  WHITE                                                     18
                                  clus
vv                                 DEL PEAK  5(4P16.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                       27
  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"
D33V11, binary
                               cls
clus                              0   1
  DEL PEAK  5(4P16.3) MUTATED     0  27
  DEL PEAK  5(4P16.3) WILD-TYPE   3 116
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(4P16.3) MUTATED      0   27
  DEL PEAK  5(4P16.3) WILD-TYPE    3  116
                        clus
vv                       DEL PEAK  5(4P16.3) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                          27
                        clus
vv                       DEL PEAK  5(4P16.3) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           116
[1] 2 2
[1] FALSE

Clustering(34) Variable = DEL PEAK  6(4Q24) MUTATION ANALYSIS
D34V1, survival
                             sevent
clus2                          0  1
  DEL PEAK  6(4Q24) MUTATED   38 28
  DEL PEAK  6(4Q24) WILD-TYPE 53 38
  DEL PEAK  6(4Q24) MUTATED DEL PEAK  6(4Q24) WILD-TYPE 
                         66                          91 
  DEL PEAK  6(4Q24) MUTATED DEL PEAK  6(4Q24) WILD-TYPE 
                         28                          38 
$`DEL PEAK  6(4Q24) MUTATED`
TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A112 TCGA-BC-A217 
       27.52        27.52        23.34         1.12         5.03        13.84 
TCGA-BC-A3KF TCGA-BC-A5W4 TCGA-BC-A69H TCGA-CC-5258 TCGA-CC-5261 TCGA-CC-5263 
        0.26         9.50        14.60         0.07         0.39         4.24 
TCGA-CC-A3M9 TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A114 TCGA-DD-A116 TCGA-DD-A119 
        0.10         0.10         0.13        37.78        53.33         7.33 
TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A1EB TCGA-DD-A1EF TCGA-DD-A1EG 
        2.60         0.46        21.76        66.31        12.95        45.11 
TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EL TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A3A0 
       49.15         6.02        13.64        55.69         5.62        25.81 
TCGA-DD-A3A5 TCGA-DD-A3A9 TCGA-DD-A4ND TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ 
      102.74        30.61        73.38        14.24        18.44        15.06 
TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NQ TCGA-DD-A73B TCGA-DD-A73G TCGA-ED-A459 
       29.56        73.81        12.26         9.30       100.96        13.41 
TCGA-ED-A66X TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-ED-A8O5 
       13.35         0.20         0.20         0.20         0.20         0.20 
TCGA-EP-A2KB TCGA-EP-A2KC TCGA-FV-A3I1 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP 
       10.98         0.62         8.12         0.03         0.33        60.36 
TCGA-G3-A25S TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A5SI TCGA-G3-A5SM 
        1.22        58.49        14.86        21.53        14.70         4.37 
TCGA-G3-A7M9 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75G TCGA-O8-A75V 
        1.84        11.84        13.38         0.49        14.24         4.44 

$`DEL PEAK  6(4Q24) WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10W 
       48.99        27.91        37.32        10.13        46.78         2.99 
TCGA-BC-A10X TCGA-BC-A110 TCGA-BC-A216 TCGA-BC-A3KG TCGA-BC-A69I TCGA-CC-5260 
       25.32        69.57        44.42        22.36        12.72         2.86 
TCGA-CC-5262 TCGA-CC-A1HT TCGA-CC-A3MA TCGA-DD-A113 TCGA-DD-A115 TCGA-DD-A118 
        3.39         3.32         0.07        79.73        83.57       113.00 
TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE 
       51.29        90.71        79.40        19.79        75.65         6.71 
TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A39V TCGA-DD-A39Z TCGA-DD-A3A1 TCGA-DD-A3A2 
       29.16        18.35        21.14        19.76         7.66        70.06 
TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A4NA 
       17.59        20.12       107.11        13.78         0.36        33.14 
TCGA-DD-A4NB TCGA-DD-A4NF TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NP TCGA-DD-A4NR 
       32.52        14.07        39.78        56.25        93.67         0.30 
TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E 
       80.75        66.35        10.98         7.56        10.98         1.45 
TCGA-DD-A73F TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66Y TCGA-ED-A82E 
       27.72        12.69        15.85        13.91         0.23         0.20 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS 
       18.74        19.99        11.74         9.96        11.93        22.85 
TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R2 TCGA-FV-A3R3 
       14.40        32.45        19.10        27.88         6.38         0.13 
TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A3CG 
        0.39        51.06        53.79        28.27        30.74        22.13 
TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SJ TCGA-G3-A5SL 
       25.64         5.92        19.53        19.23        11.97         7.99 
TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 
        7.76         5.98         1.02         2.66         4.01         2.14 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A8JO TCGA-NI-A4U2 
        9.57         5.10        12.85         8.71         1.71        58.88 
TCGA-NI-A8LF 
       16.37 

  DEL PEAK  6(4Q24) MUTATED DEL PEAK  6(4Q24) WILD-TYPE 
                       0.03                        0.07 
  DEL PEAK  6(4Q24) MUTATED DEL PEAK  6(4Q24) WILD-TYPE 
                     102.74                      113.00 
  DEL PEAK  6(4Q24) MUTATED DEL PEAK  6(4Q24) WILD-TYPE 
                     12.605                      18.350 
[1] "0.0 - 102.7 (12.6)" "0.1 - 113.0 (18.4)"
[1] "hr=" "1.4"
D34V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  6(4Q24) MUTATED        26       22         2         10          2
  DEL PEAK  6(4Q24) WILD-TYPE      39       15         0         21          3
                             vv
clus                          STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK  6(4Q24) MUTATED            0        1         1         1
  DEL PEAK  6(4Q24) WILD-TYPE          5        0         0         1
D34V3, multiclass
            clus
vv           DEL PEAK  6(4Q24) MUTATED DEL PEAK  6(4Q24) WILD-TYPE
  STAGE I                           26                          39
  STAGE II                          22                          15
  STAGE III                          2                           0
  STAGE IIIA                        10                          21
  STAGE IIIB                         2                           3
  STAGE IIIC                         0                           5
  STAGE IV                           1                           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  6(4Q24) MUTATED   27 23 16  3
  DEL PEAK  6(4Q24) WILD-TYPE 41 18 26  5
D34V4, multiclass
    clus
vv   DEL PEAK  6(4Q24) MUTATED DEL PEAK  6(4Q24) WILD-TYPE
  T1                        27                          41
  T2                        23                          18
  T3                        16                          26
  T4                         3                           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"
D34V5, binary
                             cls
clus                           0  1
  DEL PEAK  6(4Q24) MUTATED   42  1
  DEL PEAK  6(4Q24) WILD-TYPE 60  2
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  6(4Q24) MUTATED     42    1
  DEL PEAK  6(4Q24) WILD-TYPE   60    2
   clus
vv  DEL PEAK  6(4Q24) MUTATED DEL PEAK  6(4Q24) WILD-TYPE
  0                        42                          60
  1                         1                           2
[1] 2 2
[1] FALSE
                             vv
clus                          M0 M1 MX
  DEL PEAK  6(4Q24) MUTATED   55  2 12
  DEL PEAK  6(4Q24) WILD-TYPE 65  1 25
D34V6, multiclass
    clus
vv   DEL PEAK  6(4Q24) MUTATED DEL PEAK  6(4Q24) WILD-TYPE
  M0                        55                          65
  M1                         2                           1
  MX                        12                          25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V7, binary
                             cls
clus                           0  1
  DEL PEAK  6(4Q24) MUTATED   25 44
  DEL PEAK  6(4Q24) WILD-TYPE 35 56
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  6(4Q24) MUTATED     25   44
  DEL PEAK  6(4Q24) WILD-TYPE   35   56
        clus
vv       DEL PEAK  6(4Q24) MUTATED DEL PEAK  6(4Q24) WILD-TYPE
  FEMALE                        25                          35
  MALE                          44                          56
[1] 2 2
[1] FALSE
                             vv
clus                          FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  DEL PEAK  6(4Q24) MUTATED                         0                       68
  DEL PEAK  6(4Q24) WILD-TYPE                       2                       88
                             vv
clus                          HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK  6(4Q24) MUTATED                                  1
  DEL PEAK  6(4Q24) WILD-TYPE                                1
D34V8, multiclass
                                  clus
vv                                 DEL PEAK  6(4Q24) MUTATED
  FIBROLAMELLAR CARCINOMA                                  0
  HEPATOCELLULAR CARCINOMA                                68
  HEPATOCHOLANGIOCARCINOMA (MIXED)                         1
                                  clus
vv                                 DEL PEAK  6(4Q24) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                    2
  HEPATOCELLULAR CARCINOMA                                  88
  HEPATOCHOLANGIOCARCINOMA (MIXED)                           1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          R0 R1 R2 RX
  DEL PEAK  6(4Q24) MUTATED   55  6  1  7
  DEL PEAK  6(4Q24) WILD-TYPE 76  5  0  5
D34V9, multiclass
    clus
vv   DEL PEAK  6(4Q24) MUTATED DEL PEAK  6(4Q24) WILD-TYPE
  R0                        55                          76
  R1                         6                           5
  R2                         1                           0
  RX                         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"
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  6(4Q24) MUTATED                                  0    22
  DEL PEAK  6(4Q24) WILD-TYPE                                1    14
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  6(4Q24) MUTATED                           4    41
  DEL PEAK  6(4Q24) WILD-TYPE                         4    68
D34V10, multiclass
                                  clus
vv                                 DEL PEAK  6(4Q24) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         0
  ASIAN                                                   22
  BLACK OR AFRICAN AMERICAN                                4
  WHITE                                                   41
                                  clus
vv                                 DEL PEAK  6(4Q24) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                     14
  BLACK OR AFRICAN AMERICAN                                  4
  WHITE                                                     68
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V11, binary
                             cls
clus                           0  1
  DEL PEAK  6(4Q24) MUTATED    3 61
  DEL PEAK  6(4Q24) WILD-TYPE  0 82
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  6(4Q24) MUTATED      3   61
  DEL PEAK  6(4Q24) WILD-TYPE    0   82
                        clus
vv                       DEL PEAK  6(4Q24) MUTATED DEL PEAK  6(4Q24) WILD-TYPE
  HISPANIC OR LATINO                             3                           0
  NOT HISPANIC OR LATINO                        61                          82
[1] 2 2
[1] FALSE

Clustering(35) Variable = DEL PEAK  7(4Q34.1) MUTATION ANALYSIS
D35V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  7(4Q34.1) MUTATED   35 27
  DEL PEAK  7(4Q34.1) WILD-TYPE 56 39
  DEL PEAK  7(4Q34.1) MUTATED DEL PEAK  7(4Q34.1) WILD-TYPE 
                           62                            95 
  DEL PEAK  7(4Q34.1) MUTATED DEL PEAK  7(4Q34.1) WILD-TYPE 
                           27                            39 
$`DEL PEAK  7(4Q34.1) MUTATED`
TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10W TCGA-BC-A112 TCGA-BC-A217 TCGA-BC-A3KF 
       10.13        27.52         2.99         5.03        13.84         0.26 
TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-CC-5258 TCGA-CC-5261 TCGA-CC-A1HT 
       22.36         9.50        14.60         0.07         0.39         3.32 
TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 
        0.10         0.07         0.10         0.13        79.73        37.78 
TCGA-DD-A116 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A1EF TCGA-DD-A1EG 
       53.33         7.33         2.60         0.46        12.95        45.11 
TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EL TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A3A0 
       49.15         6.02        13.64        55.69         5.62        25.81 
TCGA-DD-A3A9 TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NN TCGA-DD-A4NO 
       30.61        14.24        18.44        15.06        29.56        73.81 
TCGA-DD-A73B TCGA-ED-A459 TCGA-ED-A66X TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XP 
        9.30        13.41        13.35         0.20         0.20         0.20 
TCGA-ED-A82E TCGA-ED-A8O5 TCGA-EP-A2KB TCGA-EP-A2KC TCGA-FV-A3I1 TCGA-FV-A496 
        0.20         0.20        10.98         0.62         8.12         0.33 
TCGA-FV-A4ZP TCGA-G3-A25S TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A5SI 
       60.36         1.22        58.49        14.86        21.53        14.70 
TCGA-G3-A5SM TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-MI-A75G 
        4.37         1.84         1.02        11.84        13.38        14.24 
TCGA-MI-A75I TCGA-NI-A4U2 
        8.71        58.88 

$`DEL PEAK  7(4Q34.1) WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10S TCGA-BC-A10U TCGA-BC-A10X 
       48.99        27.91        37.32        46.78        27.52        25.32 
TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A216 TCGA-BC-A69I TCGA-CC-5260 
       23.34         1.12        69.57        44.42        12.72         2.86 
TCGA-CC-5262 TCGA-CC-5263 TCGA-DD-A115 TCGA-DD-A118 TCGA-DD-A11C TCGA-DD-A11D 
        3.39         4.24        83.57       113.00        21.76        51.29 
TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE 
       90.71        79.40        66.31        19.79        75.65         6.71 
TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A39V TCGA-DD-A39Z TCGA-DD-A3A1 TCGA-DD-A3A2 
       29.16        18.35        21.14        19.76         7.66        70.06 
TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 
       17.59        20.12       102.74       107.11        13.78         0.36 
TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NK TCGA-DD-A4NL 
       33.14        32.52        73.38        14.07        39.78        56.25 
TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A 
       93.67        12.26         0.30        80.75        66.35        10.98 
TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A4XI 
        7.56        10.98         1.45        27.72       100.96        12.69 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66Y TCGA-ED-A7PX TCGA-EP-A12J TCGA-EP-A26S 
       15.85        13.91         0.23         0.20        18.74        19.99 
TCGA-EP-A2KA TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B 
       11.74         9.96        11.93        22.85        14.40        32.45 
TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A4ZQ 
       19.10        27.88         6.38         0.13         0.03         0.39 
TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A3CH 
       51.06        53.79        28.27        30.74        22.13        25.64 
TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A6UC 
        5.92        19.53        19.23        11.97         7.99         7.76 
TCGA-G3-A7M7 TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-LG-A6GG TCGA-MI-A75C 
        5.98         2.66         4.01         2.14         0.49         9.57 
TCGA-MI-A75E TCGA-MI-A75H TCGA-MR-A8JO TCGA-NI-A8LF TCGA-O8-A75V 
        5.10        12.85         1.71        16.37         4.44 

  DEL PEAK  7(4Q34.1) MUTATED DEL PEAK  7(4Q34.1) WILD-TYPE 
                         0.07                          0.03 
  DEL PEAK  7(4Q34.1) MUTATED DEL PEAK  7(4Q34.1) WILD-TYPE 
                        79.73                        113.00 
  DEL PEAK  7(4Q34.1) MUTATED DEL PEAK  7(4Q34.1) WILD-TYPE 
                       10.555                        19.100 
[1] "0.1 - 79.7 (10.6)"  "0.0 - 113.0 (19.1)"
[1] "hr=" "1.8"
D35V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IIIA
  DEL PEAK  7(4Q34.1) MUTATED        20       21         1         13
  DEL PEAK  7(4Q34.1) WILD-TYPE      45       16         1         18
                               vv
clus                            STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK  7(4Q34.1) MUTATED            2          0        1         1
  DEL PEAK  7(4Q34.1) WILD-TYPE          3          5        0         0
                               vv
clus                            STAGE IVB
  DEL PEAK  7(4Q34.1) MUTATED           1
  DEL PEAK  7(4Q34.1) WILD-TYPE         1
D35V3, multiclass
            clus
vv           DEL PEAK  7(4Q34.1) MUTATED DEL PEAK  7(4Q34.1) WILD-TYPE
  STAGE I                             20                            45
  STAGE II                            21                            16
  STAGE III                            1                             1
  STAGE IIIA                          13                            18
  STAGE IIIB                           2                             3
  STAGE IIIC                           0                             5
  STAGE IV                             1                             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  7(4Q34.1) MUTATED   21 22 19  3
  DEL PEAK  7(4Q34.1) WILD-TYPE 47 19 23  5
D35V4, multiclass
    clus
vv   DEL PEAK  7(4Q34.1) MUTATED DEL PEAK  7(4Q34.1) WILD-TYPE
  T1                          21                            47
  T2                          22                            19
  T3                          19                            23
  T4                           3                             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"
D35V5, binary
                               cls
clus                             0  1
  DEL PEAK  7(4Q34.1) MUTATED   39  1
  DEL PEAK  7(4Q34.1) WILD-TYPE 63  2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(4Q34.1) MUTATED     39    1
  DEL PEAK  7(4Q34.1) WILD-TYPE   63    2
   clus
vv  DEL PEAK  7(4Q34.1) MUTATED DEL PEAK  7(4Q34.1) WILD-TYPE
  0                          39                            63
  1                           1                             2
[1] 2 2
[1] FALSE
                               vv
clus                            M0 M1 MX
  DEL PEAK  7(4Q34.1) MUTATED   50  2 13
  DEL PEAK  7(4Q34.1) WILD-TYPE 70  1 24
D35V6, multiclass
    clus
vv   DEL PEAK  7(4Q34.1) MUTATED DEL PEAK  7(4Q34.1) WILD-TYPE
  M0                          50                            70
  M1                           2                             1
  MX                          13                            24
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V7, binary
                               cls
clus                             0  1
  DEL PEAK  7(4Q34.1) MUTATED   22 43
  DEL PEAK  7(4Q34.1) WILD-TYPE 38 57
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(4Q34.1) MUTATED     22   43
  DEL PEAK  7(4Q34.1) WILD-TYPE   38   57
        clus
vv       DEL PEAK  7(4Q34.1) MUTATED DEL PEAK  7(4Q34.1) WILD-TYPE
  FEMALE                          22                            38
  MALE                            43                            57
[1] 2 2
[1] FALSE
                               vv
clus                            FIBROLAMELLAR CARCINOMA
  DEL PEAK  7(4Q34.1) MUTATED                         0
  DEL PEAK  7(4Q34.1) WILD-TYPE                       2
                               vv
clus                            HEPATOCELLULAR CARCINOMA
  DEL PEAK  7(4Q34.1) MUTATED                         64
  DEL PEAK  7(4Q34.1) WILD-TYPE                       92
                               vv
clus                            HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK  7(4Q34.1) MUTATED                                  1
  DEL PEAK  7(4Q34.1) WILD-TYPE                                1
D35V8, multiclass
                                  clus
vv                                 DEL PEAK  7(4Q34.1) MUTATED
  FIBROLAMELLAR CARCINOMA                                    0
  HEPATOCELLULAR CARCINOMA                                  64
  HEPATOCHOLANGIOCARCINOMA (MIXED)                           1
                                  clus
vv                                 DEL PEAK  7(4Q34.1) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                      2
  HEPATOCELLULAR CARCINOMA                                    92
  HEPATOCHOLANGIOCARCINOMA (MIXED)                             1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            R0 R1 R2 RX
  DEL PEAK  7(4Q34.1) MUTATED   52  5  1  6
  DEL PEAK  7(4Q34.1) WILD-TYPE 79  6  0  6
D35V9, multiclass
    clus
vv   DEL PEAK  7(4Q34.1) MUTATED DEL PEAK  7(4Q34.1) WILD-TYPE
  R0                          52                            79
  R1                           5                             6
  R2                           1                             0
  RX                           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"
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  7(4Q34.1) MUTATED                                  0    24
  DEL PEAK  7(4Q34.1) WILD-TYPE                                1    12
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  7(4Q34.1) MUTATED                           5    36
  DEL PEAK  7(4Q34.1) WILD-TYPE                         3    73
D35V10, multiclass
                                  clus
vv                                 DEL PEAK  7(4Q34.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                     24
  BLACK OR AFRICAN AMERICAN                                  5
  WHITE                                                     36
                                  clus
vv                                 DEL PEAK  7(4Q34.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                       12
  BLACK OR AFRICAN AMERICAN                                    3
  WHITE                                                       73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V11, binary
                               cls
clus                             0  1
  DEL PEAK  7(4Q34.1) MUTATED    1 60
  DEL PEAK  7(4Q34.1) WILD-TYPE  2 83
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(4Q34.1) MUTATED      1   60
  DEL PEAK  7(4Q34.1) WILD-TYPE    2   83
                        clus
vv                       DEL PEAK  7(4Q34.1) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          60
                        clus
vv                       DEL PEAK  7(4Q34.1) WILD-TYPE
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                            83
[1] 2 2
[1] FALSE

Clustering(36) Variable = DEL PEAK  8(4Q34.3) MUTATION ANALYSIS
D36V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  8(4Q34.3) MUTATED   34 28
  DEL PEAK  8(4Q34.3) WILD-TYPE 57 38
  DEL PEAK  8(4Q34.3) MUTATED DEL PEAK  8(4Q34.3) WILD-TYPE 
                           62                            95 
  DEL PEAK  8(4Q34.3) MUTATED DEL PEAK  8(4Q34.3) WILD-TYPE 
                           28                            38 
$`DEL PEAK  8(4Q34.3) MUTATED`
TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10W TCGA-BC-A112 TCGA-BC-A217 TCGA-BC-A3KF 
       10.13        27.52         2.99         5.03        13.84         0.26 
TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-CC-5258 TCGA-CC-5261 TCGA-CC-A1HT 
       22.36         9.50        14.60         0.07         0.39         3.32 
TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 
        0.10         0.07         0.10         0.13        79.73        37.78 
TCGA-DD-A116 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A1EF TCGA-DD-A1EG 
       53.33         7.33         2.60         0.46        12.95        45.11 
TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39X TCGA-DD-A39Y 
       49.15         6.02        29.16        13.64        55.69         5.62 
TCGA-DD-A3A0 TCGA-DD-A3A2 TCGA-DD-A3A9 TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ 
       25.81        70.06        30.61        14.24        18.44        15.06 
TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A73B TCGA-ED-A66X TCGA-ED-A7PY TCGA-ED-A7PZ 
       29.56        73.81         9.30        13.35         0.20         0.20 
TCGA-ED-A7XP TCGA-ED-A8O5 TCGA-EP-A2KB TCGA-EP-A2KC TCGA-FV-A3I1 TCGA-FV-A496 
        0.20         0.20        10.98         0.62         8.12         0.33 
TCGA-FV-A4ZP TCGA-G3-A25S TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A5SI 
       60.36         1.22        58.49        14.86        21.53        14.70 
TCGA-G3-A5SM TCGA-G3-A7M9 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-MI-A75G TCGA-MI-A75I 
        4.37         1.84        11.84        13.38        14.24         8.71 
TCGA-NI-A4U2 TCGA-NI-A8LF 
       58.88        16.37 

$`DEL PEAK  8(4Q34.3) WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10S TCGA-BC-A10U TCGA-BC-A10X 
       48.99        27.91        37.32        46.78        27.52        25.32 
TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A216 TCGA-BC-A69I TCGA-CC-5260 
       23.34         1.12        69.57        44.42        12.72         2.86 
TCGA-CC-5262 TCGA-CC-5263 TCGA-DD-A115 TCGA-DD-A118 TCGA-DD-A11C TCGA-DD-A11D 
        3.39         4.24        83.57       113.00        21.76        51.29 
TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE 
       90.71        79.40        66.31        19.79        75.65         6.71 
TCGA-DD-A1EK TCGA-DD-A39V TCGA-DD-A39Z TCGA-DD-A3A1 TCGA-DD-A3A3 TCGA-DD-A3A4 
       18.35        21.14        19.76         7.66        17.59        20.12 
TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A4NA TCGA-DD-A4NB 
      102.74       107.11        13.78         0.36        33.14        32.52 
TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NP TCGA-DD-A4NQ 
       73.38        14.07        39.78        56.25        93.67        12.26 
TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73C TCGA-DD-A73D 
        0.30        80.75        66.35        10.98         7.56        10.98 
TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG 
        1.45        27.72       100.96        13.41        12.69        15.85 
TCGA-ED-A627 TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A82E TCGA-EP-A12J TCGA-EP-A26S 
       13.91         0.23         0.20         0.20        18.74        19.99 
TCGA-EP-A2KA TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B 
       11.74         9.96        11.93        22.85        14.40        32.45 
TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A4ZQ 
       19.10        27.88         6.38         0.13         0.03         0.39 
TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A3CH 
       51.06        53.79        28.27        30.74        22.13        25.64 
TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A6UC 
        5.92        19.53        19.23        11.97         7.99         7.76 
TCGA-G3-A7M7 TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-LG-A6GG 
        5.98         1.02         2.66         4.01         2.14         0.49 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75H TCGA-MR-A8JO TCGA-O8-A75V 
        9.57         5.10        12.85         1.71         4.44 

  DEL PEAK  8(4Q34.3) MUTATED DEL PEAK  8(4Q34.3) WILD-TYPE 
                         0.07                          0.03 
  DEL PEAK  8(4Q34.3) MUTATED DEL PEAK  8(4Q34.3) WILD-TYPE 
                        79.73                        113.00 
  DEL PEAK  8(4Q34.3) MUTATED DEL PEAK  8(4Q34.3) WILD-TYPE 
                       12.395                        18.350 
[1] "0.1 - 79.7 (12.4)"  "0.0 - 113.0 (18.4)"
[1] "hr=" "1.7"
D36V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IIIA
  DEL PEAK  8(4Q34.3) MUTATED        22       19         1         12
  DEL PEAK  8(4Q34.3) WILD-TYPE      43       18         1         19
                               vv
clus                            STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK  8(4Q34.3) MUTATED            2          1        1         1
  DEL PEAK  8(4Q34.3) WILD-TYPE          3          4        0         0
                               vv
clus                            STAGE IVB
  DEL PEAK  8(4Q34.3) MUTATED           1
  DEL PEAK  8(4Q34.3) WILD-TYPE         1
D36V3, multiclass
            clus
vv           DEL PEAK  8(4Q34.3) MUTATED DEL PEAK  8(4Q34.3) WILD-TYPE
  STAGE I                             22                            43
  STAGE II                            19                            18
  STAGE III                            1                             1
  STAGE IIIA                          12                            19
  STAGE IIIB                           2                             3
  STAGE IIIC                           1                             4
  STAGE IV                             1                             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  8(4Q34.3) MUTATED   24 20 18  3
  DEL PEAK  8(4Q34.3) WILD-TYPE 44 21 24  5
D36V4, multiclass
    clus
vv   DEL PEAK  8(4Q34.3) MUTATED DEL PEAK  8(4Q34.3) WILD-TYPE
  T1                          24                            44
  T2                          20                            21
  T3                          18                            24
  T4                           3                             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"
D36V5, binary
                               cls
clus                             0  1
  DEL PEAK  8(4Q34.3) MUTATED   38  2
  DEL PEAK  8(4Q34.3) WILD-TYPE 64  1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(4Q34.3) MUTATED     38    2
  DEL PEAK  8(4Q34.3) WILD-TYPE   64    1
   clus
vv  DEL PEAK  8(4Q34.3) MUTATED DEL PEAK  8(4Q34.3) WILD-TYPE
  0                          38                            64
  1                           2                             1
[1] 2 2
[1] FALSE
                               vv
clus                            M0 M1 MX
  DEL PEAK  8(4Q34.3) MUTATED   50  2 13
  DEL PEAK  8(4Q34.3) WILD-TYPE 70  1 24
D36V6, multiclass
    clus
vv   DEL PEAK  8(4Q34.3) MUTATED DEL PEAK  8(4Q34.3) WILD-TYPE
  M0                          50                            70
  M1                           2                             1
  MX                          13                            24
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V7, binary
                               cls
clus                             0  1
  DEL PEAK  8(4Q34.3) MUTATED   22 43
  DEL PEAK  8(4Q34.3) WILD-TYPE 38 57
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(4Q34.3) MUTATED     22   43
  DEL PEAK  8(4Q34.3) WILD-TYPE   38   57
        clus
vv       DEL PEAK  8(4Q34.3) MUTATED DEL PEAK  8(4Q34.3) WILD-TYPE
  FEMALE                          22                            38
  MALE                            43                            57
[1] 2 2
[1] FALSE
                               vv
clus                            FIBROLAMELLAR CARCINOMA
  DEL PEAK  8(4Q34.3) MUTATED                         0
  DEL PEAK  8(4Q34.3) WILD-TYPE                       2
                               vv
clus                            HEPATOCELLULAR CARCINOMA
  DEL PEAK  8(4Q34.3) MUTATED                         64
  DEL PEAK  8(4Q34.3) WILD-TYPE                       92
                               vv
clus                            HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK  8(4Q34.3) MUTATED                                  1
  DEL PEAK  8(4Q34.3) WILD-TYPE                                1
D36V8, multiclass
                                  clus
vv                                 DEL PEAK  8(4Q34.3) MUTATED
  FIBROLAMELLAR CARCINOMA                                    0
  HEPATOCELLULAR CARCINOMA                                  64
  HEPATOCHOLANGIOCARCINOMA (MIXED)                           1
                                  clus
vv                                 DEL PEAK  8(4Q34.3) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                      2
  HEPATOCELLULAR CARCINOMA                                    92
  HEPATOCHOLANGIOCARCINOMA (MIXED)                             1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            R0 R1 R2 RX
  DEL PEAK  8(4Q34.3) MUTATED   53  5  1  5
  DEL PEAK  8(4Q34.3) WILD-TYPE 78  6  0  7
D36V9, multiclass
    clus
vv   DEL PEAK  8(4Q34.3) MUTATED DEL PEAK  8(4Q34.3) WILD-TYPE
  R0                          53                            78
  R1                           5                             6
  R2                           1                             0
  RX                           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"
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  8(4Q34.3) MUTATED                                  0    22
  DEL PEAK  8(4Q34.3) WILD-TYPE                                1    14
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  8(4Q34.3) MUTATED                           5    38
  DEL PEAK  8(4Q34.3) WILD-TYPE                         3    71
D36V10, multiclass
                                  clus
vv                                 DEL PEAK  8(4Q34.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                     22
  BLACK OR AFRICAN AMERICAN                                  5
  WHITE                                                     38
                                  clus
vv                                 DEL PEAK  8(4Q34.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                       14
  BLACK OR AFRICAN AMERICAN                                    3
  WHITE                                                       71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V11, binary
                               cls
clus                             0  1
  DEL PEAK  8(4Q34.3) MUTATED    1 60
  DEL PEAK  8(4Q34.3) WILD-TYPE  2 83
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(4Q34.3) MUTATED      1   60
  DEL PEAK  8(4Q34.3) WILD-TYPE    2   83
                        clus
vv                       DEL PEAK  8(4Q34.3) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          60
                        clus
vv                       DEL PEAK  8(4Q34.3) WILD-TYPE
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                            83
[1] 2 2
[1] FALSE

Clustering(37) Variable = DEL PEAK  9(6Q27) MUTATION ANALYSIS
D37V1, survival
                             sevent
clus2                          0  1
  DEL PEAK  9(6Q27) MUTATED   37 25
  DEL PEAK  9(6Q27) WILD-TYPE 54 41
  DEL PEAK  9(6Q27) MUTATED DEL PEAK  9(6Q27) WILD-TYPE 
                         62                          95 
  DEL PEAK  9(6Q27) MUTATED DEL PEAK  9(6Q27) WILD-TYPE 
                         25                          41 
$`DEL PEAK  9(6Q27) MUTATED`
TCGA-BC-A10Q TCGA-BC-A3KF TCGA-BC-A5W4 TCGA-BC-A69I TCGA-CC-5260 TCGA-CC-A1HT 
       37.32         0.26         9.50        12.72         2.86         3.32 
TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MC TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A118 
        0.10         0.07         0.13        37.78        83.57       113.00 
TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11C TCGA-DD-A1E9 TCGA-DD-A1EE TCGA-DD-A1EG 
        7.33         2.60        21.76        90.71         6.71        45.11 
TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A39X TCGA-DD-A39Z 
       49.15         6.02        29.16        18.35        55.69        19.76 
TCGA-DD-A3A0 TCGA-DD-A3A8 TCGA-DD-A4NA TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK 
       25.81         0.36        33.14        14.24        15.06        39.78 
TCGA-DD-A4NN TCGA-DD-A4NS TCGA-DD-A73E TCGA-ED-A459 TCGA-ED-A66Y TCGA-ED-A7PX 
       29.56        80.75         1.45        13.41         0.23         0.20 
TCGA-ED-A7PZ TCGA-ED-A82E TCGA-ED-A8O5 TCGA-EP-A12J TCGA-EP-A3RK TCGA-ES-A2HS 
        0.20         0.20         0.20        18.74        11.93        22.85 
TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R2 TCGA-FV-A496 TCGA-FV-A4ZP 
       32.45        19.10        27.88         6.38         0.33        60.36 
TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A3CG TCGA-G3-A5SL 
        1.22        51.06        58.49        14.86        22.13         7.99 
TCGA-G3-A6UC TCGA-G3-A7M9 TCGA-LG-A6GG TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H 
        7.76         1.84         0.49         5.10        14.24        12.85 
TCGA-MI-A75I TCGA-NI-A8LF 
        8.71        16.37 

$`DEL PEAK  9(6Q27) WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
       48.99        27.91        10.13        46.78        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 
        2.99        25.32        23.34         1.12        69.57         5.03 
TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KG TCGA-BC-A69H TCGA-CC-5258 TCGA-CC-5261 
       44.42        13.84        22.36        14.60         0.07         0.39 
TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A3MB TCGA-DD-A113 TCGA-DD-A116 TCGA-DD-A11B 
        3.39         4.24         0.10        79.73        53.33         0.46 
TCGA-DD-A11D TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EF 
       51.29        79.40        66.31        19.79        75.65        12.95 
TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39Y TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 
       13.64        21.14         5.62         7.66        70.06        17.59 
TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NB 
       20.12       102.74       107.11        13.78        30.61        32.52 
TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NI TCGA-DD-A4NL TCGA-DD-A4NO TCGA-DD-A4NP 
       73.38        14.07        18.44        56.25        73.81        93.67 
TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C 
       12.26         0.30        66.35        10.98         9.30         7.56 
TCGA-DD-A73D TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 
       10.98        27.72       100.96        12.69        15.85        13.91 
TCGA-ED-A66X TCGA-ED-A7PY TCGA-ED-A7XP TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB 
       13.35         0.20         0.20        19.99        11.74        10.98 
TCGA-EP-A2KC TCGA-EP-A3JL TCGA-ES-A2HT TCGA-FV-A3I1 TCGA-FV-A3R3 TCGA-FV-A495 
        0.62         9.96        14.40         8.12         0.13         0.03 
TCGA-FV-A4ZQ TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Z TCGA-G3-A3CH 
        0.39        53.79        28.27        30.74        21.53        25.64 
TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SM 
        5.92        19.53        19.23        14.70        11.97         4.37 
TCGA-G3-A7M7 TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 
        5.98         1.02         2.66         4.01         2.14        11.84 
TCGA-KR-A7K7 TCGA-MI-A75C TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-O8-A75V 
       13.38         9.57         1.71        58.88         4.44 

  DEL PEAK  9(6Q27) MUTATED DEL PEAK  9(6Q27) WILD-TYPE 
                       0.07                        0.03 
  DEL PEAK  9(6Q27) MUTATED DEL PEAK  9(6Q27) WILD-TYPE 
                     113.00                      107.11 
  DEL PEAK  9(6Q27) MUTATED DEL PEAK  9(6Q27) WILD-TYPE 
                     13.825                      13.910 
[1] "0.1 - 113.0 (13.8)" "0.0 - 107.1 (13.9)"
[1] "hr=" "1"  
D37V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  9(6Q27) MUTATED        21       13         1         15          3
  DEL PEAK  9(6Q27) WILD-TYPE      44       24         1         16          2
                             vv
clus                          STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK  9(6Q27) MUTATED            4        1         0         1
  DEL PEAK  9(6Q27) WILD-TYPE          1        0         1         1
D37V3, multiclass
            clus
vv           DEL PEAK  9(6Q27) MUTATED DEL PEAK  9(6Q27) WILD-TYPE
  STAGE I                           21                          44
  STAGE II                          13                          24
  STAGE III                          1                           1
  STAGE IIIA                        15                          16
  STAGE IIIB                         3                           2
  STAGE IIIC                         4                           1
  STAGE IV                           1                           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(6Q27) MUTATED   22 16 20  3
  DEL PEAK  9(6Q27) WILD-TYPE 46 25 22  5
D37V4, multiclass
    clus
vv   DEL PEAK  9(6Q27) MUTATED DEL PEAK  9(6Q27) WILD-TYPE
  T1                        22                          46
  T2                        16                          25
  T3                        20                          22
  T4                         3                           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"
D37V5, binary
                             cls
clus                           0  1
  DEL PEAK  9(6Q27) MUTATED   38  2
  DEL PEAK  9(6Q27) WILD-TYPE 64  1
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  9(6Q27) MUTATED     38    2
  DEL PEAK  9(6Q27) WILD-TYPE   64    1
   clus
vv  DEL PEAK  9(6Q27) MUTATED DEL PEAK  9(6Q27) WILD-TYPE
  0                        38                          64
  1                         2                           1
[1] 2 2
[1] FALSE
                             vv
clus                          M0 M1 MX
  DEL PEAK  9(6Q27) MUTATED   51  2  9
  DEL PEAK  9(6Q27) WILD-TYPE 69  1 28
D37V6, multiclass
    clus
vv   DEL PEAK  9(6Q27) MUTATED DEL PEAK  9(6Q27) WILD-TYPE
  M0                        51                          69
  M1                         2                           1
  MX                         9                          28
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V7, binary
                             cls
clus                           0  1
  DEL PEAK  9(6Q27) MUTATED   24 38
  DEL PEAK  9(6Q27) WILD-TYPE 36 62
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  9(6Q27) MUTATED     24   38
  DEL PEAK  9(6Q27) WILD-TYPE   36   62
        clus
vv       DEL PEAK  9(6Q27) MUTATED DEL PEAK  9(6Q27) WILD-TYPE
  FEMALE                        24                          36
  MALE                          38                          62
[1] 2 2
[1] FALSE
                             vv
clus                          FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  DEL PEAK  9(6Q27) MUTATED                         0                       61
  DEL PEAK  9(6Q27) WILD-TYPE                       2                       95
                             vv
clus                          HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK  9(6Q27) MUTATED                                  1
  DEL PEAK  9(6Q27) WILD-TYPE                                1
D37V8, multiclass
                                  clus
vv                                 DEL PEAK  9(6Q27) MUTATED
  FIBROLAMELLAR CARCINOMA                                  0
  HEPATOCELLULAR CARCINOMA                                61
  HEPATOCHOLANGIOCARCINOMA (MIXED)                         1
                                  clus
vv                                 DEL PEAK  9(6Q27) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                    2
  HEPATOCELLULAR CARCINOMA                                  95
  HEPATOCHOLANGIOCARCINOMA (MIXED)                           1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          R0 R1 R2 RX
  DEL PEAK  9(6Q27) MUTATED   51  5  1  3
  DEL PEAK  9(6Q27) WILD-TYPE 80  6  0  9
D37V9, multiclass
    clus
vv   DEL PEAK  9(6Q27) MUTATED DEL PEAK  9(6Q27) WILD-TYPE
  R0                        51                          80
  R1                         5                           6
  R2                         1                           0
  RX                         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"
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  9(6Q27) MUTATED                                  0    15
  DEL PEAK  9(6Q27) WILD-TYPE                                1    21
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  9(6Q27) MUTATED                           4    42
  DEL PEAK  9(6Q27) WILD-TYPE                         4    67
D37V10, multiclass
                                  clus
vv                                 DEL PEAK  9(6Q27) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         0
  ASIAN                                                   15
  BLACK OR AFRICAN AMERICAN                                4
  WHITE                                                   42
                                  clus
vv                                 DEL PEAK  9(6Q27) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                     21
  BLACK OR AFRICAN AMERICAN                                  4
  WHITE                                                     67
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V11, binary
                             cls
clus                           0  1
  DEL PEAK  9(6Q27) MUTATED    0 58
  DEL PEAK  9(6Q27) WILD-TYPE  3 85
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  9(6Q27) MUTATED      0   58
  DEL PEAK  9(6Q27) WILD-TYPE    3   85
                        clus
vv                       DEL PEAK  9(6Q27) MUTATED DEL PEAK  9(6Q27) WILD-TYPE
  HISPANIC OR LATINO                             0                           3
  NOT HISPANIC OR LATINO                        58                          85
[1] 2 2
[1] FALSE

Clustering(38) Variable = DEL PEAK 10(8P23.2) MUTATION ANALYSIS
D38V1, survival
                               sevent
clus2                            0  1
  DEL PEAK 10(8P23.2) MUTATED   58 45
  DEL PEAK 10(8P23.2) WILD-TYPE 33 21
  DEL PEAK 10(8P23.2) MUTATED DEL PEAK 10(8P23.2) WILD-TYPE 
                          103                            54 
  DEL PEAK 10(8P23.2) MUTATED DEL PEAK 10(8P23.2) WILD-TYPE 
                           45                            21 
$`DEL PEAK 10(8P23.2) MUTATED`
TCGA-BC-4072 TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A112 
       48.99        10.13        46.78        27.52        27.52         5.03 
TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A69I 
       44.42        13.84         0.26        22.36        14.60        12.72 
TCGA-CC-5258 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 
        0.07         0.39         3.39         4.24         3.32         0.10 
TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 
        0.13        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         6.71        12.95        45.11         6.02 
TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y 
       29.16        18.35        13.64        21.14        55.69         5.62 
TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A3 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 
       19.76        25.81        17.59        13.78         0.36        30.61 
TCGA-DD-A4NA TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ 
       33.14        73.38        14.07        14.24        18.44        15.06 
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        66.35 
TCGA-DD-A73A TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G 
       10.98         7.56        10.98         1.45        27.72       100.96 
TCGA-ED-A459 TCGA-ED-A66X TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-EP-A12J TCGA-EP-A26S 
       13.41        13.35         0.20         0.20        18.74        19.99 
TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT 
       11.74         0.62         9.96        11.93        22.85        14.40 
TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A495 TCGA-FV-A4ZP 
       19.10        27.88         8.12         6.38         0.03        60.36 
TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y 
        0.39         1.22        28.27        30.74        58.49        14.86 
TCGA-G3-A3CG TCGA-G3-A3CJ TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A6UC TCGA-G3-A7M7 
       22.13        19.53        11.97         7.99         7.76         5.98 
TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-MI-A75C 
        1.02         2.66         4.01        11.84        13.38         9.57 
TCGA-MI-A75E TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF 
        5.10        12.85         8.71         1.71        58.88        16.37 
TCGA-O8-A75V 
        4.44 

$`DEL PEAK 10(8P23.2) WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z 
       27.91        37.32         2.99        25.32        23.34         1.12 
TCGA-BC-A110 TCGA-BC-A5W4 TCGA-CC-5260 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-DD-A114 
       69.57         9.50         2.86         0.07         0.10        37.78 
TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11D TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC 
        2.60         0.46        51.29        79.40        66.31        19.79 
TCGA-DD-A1ED TCGA-DD-A1EH TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A4 TCGA-DD-A3A5 
       75.65        49.15         7.66        70.06        20.12       102.74 
TCGA-DD-A3A6 TCGA-DD-A4NB TCGA-DD-A4NL TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A73B 
      107.11        32.52        56.25        93.67        12.26         9.30 
TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7XP 
       12.69        15.85        13.91         0.23         0.20         0.20 
TCGA-ED-A82E TCGA-ED-A8O5 TCGA-EP-A2KB TCGA-FV-A23B TCGA-FV-A3R3 TCGA-FV-A496 
        0.20         0.20        10.98        32.45         0.13         0.33 
TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CK 
       51.06        53.79        21.53        25.64         5.92        19.23 
TCGA-G3-A5SI TCGA-G3-A5SM TCGA-G3-A7M9 TCGA-KR-A7K0 TCGA-LG-A6GG TCGA-MI-A75G 
       14.70         4.37         1.84         2.14         0.49        14.24 

  DEL PEAK 10(8P23.2) MUTATED DEL PEAK 10(8P23.2) WILD-TYPE 
                         0.03                          0.07 
  DEL PEAK 10(8P23.2) MUTATED DEL PEAK 10(8P23.2) WILD-TYPE 
                       113.00                        107.11 
  DEL PEAK 10(8P23.2) MUTATED DEL PEAK 10(8P23.2) WILD-TYPE 
                        13.78                         14.47 
[1] "0.0 - 113.0 (13.8)" "0.1 - 107.1 (14.5)"
[1] "hr=" "1.3"
D38V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IIIA
  DEL PEAK 10(8P23.2) MUTATED        43       24         0         18
  DEL PEAK 10(8P23.2) WILD-TYPE      22       13         2         13
                               vv
clus                            STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 10(8P23.2) MUTATED            4          4        1         1
  DEL PEAK 10(8P23.2) WILD-TYPE          1          1        0         0
                               vv
clus                            STAGE IVB
  DEL PEAK 10(8P23.2) MUTATED           2
  DEL PEAK 10(8P23.2) WILD-TYPE         0
D38V3, multiclass
            clus
vv           DEL PEAK 10(8P23.2) MUTATED DEL PEAK 10(8P23.2) WILD-TYPE
  STAGE I                             43                            22
  STAGE II                            24                            13
  STAGE III                            0                             2
  STAGE IIIA                          18                            13
  STAGE IIIB                           4                             1
  STAGE IIIC                           4                             1
  STAGE IV                             1                             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 10(8P23.2) MUTATED   45 27 26  5
  DEL PEAK 10(8P23.2) WILD-TYPE 23 14 16  3
D38V4, multiclass
    clus
vv   DEL PEAK 10(8P23.2) MUTATED DEL PEAK 10(8P23.2) WILD-TYPE
  T1                          45                            23
  T2                          27                            14
  T3                          26                            16
  T4                           5                             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"
D38V5, binary
                               cls
clus                             0  1
  DEL PEAK 10(8P23.2) MUTATED   61  3
  DEL PEAK 10(8P23.2) WILD-TYPE 41  0
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(8P23.2) MUTATED     61    3
  DEL PEAK 10(8P23.2) WILD-TYPE   41    0
   clus
vv  DEL PEAK 10(8P23.2) MUTATED DEL PEAK 10(8P23.2) WILD-TYPE
  0                          61                            41
  1                           3                             0
[1] 2 2
[1] FALSE
                               vv
clus                            M0 M1 MX
  DEL PEAK 10(8P23.2) MUTATED   75  3 26
  DEL PEAK 10(8P23.2) WILD-TYPE 45  0 11
D38V6, multiclass
    clus
vv   DEL PEAK 10(8P23.2) MUTATED DEL PEAK 10(8P23.2) WILD-TYPE
  M0                          75                            45
  M1                           3                             0
  MX                          26                            11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V7, binary
                               cls
clus                             0  1
  DEL PEAK 10(8P23.2) MUTATED   35 69
  DEL PEAK 10(8P23.2) WILD-TYPE 25 31
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(8P23.2) MUTATED     35   69
  DEL PEAK 10(8P23.2) WILD-TYPE   25   31
        clus
vv       DEL PEAK 10(8P23.2) MUTATED DEL PEAK 10(8P23.2) WILD-TYPE
  FEMALE                          35                            25
  MALE                            69                            31
[1] 2 2
[1] FALSE
                               vv
clus                            FIBROLAMELLAR CARCINOMA
  DEL PEAK 10(8P23.2) MUTATED                         1
  DEL PEAK 10(8P23.2) WILD-TYPE                       1
                               vv
clus                            HEPATOCELLULAR CARCINOMA
  DEL PEAK 10(8P23.2) MUTATED                        101
  DEL PEAK 10(8P23.2) WILD-TYPE                       55
                               vv
clus                            HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK 10(8P23.2) MUTATED                                  2
  DEL PEAK 10(8P23.2) WILD-TYPE                                0
D38V8, multiclass
                                  clus
vv                                 DEL PEAK 10(8P23.2) MUTATED
  FIBROLAMELLAR CARCINOMA                                    1
  HEPATOCELLULAR CARCINOMA                                 101
  HEPATOCHOLANGIOCARCINOMA (MIXED)                           2
                                  clus
vv                                 DEL PEAK 10(8P23.2) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                      1
  HEPATOCELLULAR CARCINOMA                                    55
  HEPATOCHOLANGIOCARCINOMA (MIXED)                             0
[1] 3 2
[1] 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(8P23.2) MUTATED   83  7  1  8
  DEL PEAK 10(8P23.2) WILD-TYPE 48  4  0  4
D38V9, multiclass
    clus
vv   DEL PEAK 10(8P23.2) MUTATED DEL PEAK 10(8P23.2) WILD-TYPE
  R0                          83                            48
  R1                           7                             4
  R2                           1                             0
  RX                           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"
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 10(8P23.2) MUTATED                                  1    18
  DEL PEAK 10(8P23.2) WILD-TYPE                                0    18
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 10(8P23.2) MUTATED                           5    76
  DEL PEAK 10(8P23.2) WILD-TYPE                         3    33
D38V10, multiclass
                                  clus
vv                                 DEL PEAK 10(8P23.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                     18
  BLACK OR AFRICAN AMERICAN                                  5
  WHITE                                                     76
                                  clus
vv                                 DEL PEAK 10(8P23.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                       18
  BLACK OR AFRICAN AMERICAN                                    3
  WHITE                                                       33
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V11, binary
                               cls
clus                             0  1
  DEL PEAK 10(8P23.2) MUTATED    1 92
  DEL PEAK 10(8P23.2) WILD-TYPE  2 51
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(8P23.2) MUTATED      1   92
  DEL PEAK 10(8P23.2) WILD-TYPE    2   51
                        clus
vv                       DEL PEAK 10(8P23.2) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          92
                        clus
vv                       DEL PEAK 10(8P23.2) WILD-TYPE
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                            51
[1] 2 2
[1] FALSE

Clustering(39) Variable = DEL PEAK 11(9P21.3) MUTATION ANALYSIS
D39V1, survival
                               sevent
clus2                            0  1
  DEL PEAK 11(9P21.3) MUTATED   32 27
  DEL PEAK 11(9P21.3) WILD-TYPE 59 39
  DEL PEAK 11(9P21.3) MUTATED DEL PEAK 11(9P21.3) WILD-TYPE 
                           59                            98 
  DEL PEAK 11(9P21.3) MUTATED DEL PEAK 11(9P21.3) WILD-TYPE 
                           27                            39 
$`DEL PEAK 11(9P21.3) MUTATED`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10U 
       48.99        27.91        37.32        10.13        46.78        27.52 
TCGA-BC-A112 TCGA-BC-A3KF TCGA-BC-A5W4 TCGA-BC-A69H TCGA-CC-5258 TCGA-CC-5263 
        5.03         0.26         9.50        14.60         0.07         4.24 
TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A115 
        3.32         0.10         0.10         0.13        79.73        83.57 
TCGA-DD-A116 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A1EF 
       53.33         7.33         2.60         0.46        21.76        12.95 
TCGA-DD-A1EG TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39X TCGA-DD-A39Y 
       45.11         6.02        29.16        13.64        55.69         5.62 
TCGA-DD-A3A0 TCGA-DD-A3A9 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-A4NO TCGA-DD-A73F 
       25.81        30.61        73.38        18.44        73.81        27.72 
TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A66X TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-ED-A82E 
       13.41        12.69        13.35         0.20         0.20         0.20 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK TCGA-FV-A23B TCGA-FV-A3I0 
       11.74        10.98         0.62        11.93        32.45        27.88 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A3CJ 
        8.12         6.38        60.36         1.22        51.06        19.53 
TCGA-G3-A7M7 TCGA-KR-A7K7 TCGA-MI-A75G TCGA-MI-A75I TCGA-NI-A8LF 
        5.98        13.38        14.24         8.71        16.37 

$`DEL PEAK 11(9P21.3) WILD-TYPE`
TCGA-BC-A10T TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 
       27.52         2.99        25.32        23.34         1.12        69.57 
TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KG TCGA-BC-A69I TCGA-CC-5260 TCGA-CC-5261 
       44.42        13.84        22.36        12.72         2.86         0.39 
TCGA-CC-5262 TCGA-CC-A3MA TCGA-DD-A114 TCGA-DD-A118 TCGA-DD-A11D TCGA-DD-A1E9 
        3.39         0.07        37.78       113.00        51.29        90.71 
TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EH 
       79.40        66.31        19.79        75.65         6.71        49.15 
TCGA-DD-A1EK TCGA-DD-A39V TCGA-DD-A39Z TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 
       18.35        21.14        19.76         7.66        70.06        17.59 
TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A4NA 
       20.12       102.74       107.11        13.78         0.36        33.14 
TCGA-DD-A4NB TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL 
       32.52        14.07        14.24        15.06        39.78        56.25 
TCGA-DD-A4NN TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV 
       29.56        93.67        12.26         0.30        80.75        66.35 
TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73G 
       10.98         9.30         7.56        10.98         1.45       100.96 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A8O5 
       15.85        13.91         0.23         0.20         0.20         0.20 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A3JL TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A2QR 
       18.74        19.99         9.96        22.85        14.40        19.10 
TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25U TCGA-G3-A25V 
        0.13         0.03         0.33         0.39        53.79        28.27 
TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH 
       30.74        58.49        14.86        21.53        22.13        25.64 
TCGA-G3-A3CI TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM 
        5.92        19.23        14.70        11.97         7.99         4.37 
TCGA-G3-A6UC TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 
        7.76         1.84         1.02         2.66         4.01         2.14 
TCGA-KR-A7K2 TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75H TCGA-MR-A8JO 
       11.84         0.49         9.57         5.10        12.85         1.71 
TCGA-NI-A4U2 TCGA-O8-A75V 
       58.88         4.44 

  DEL PEAK 11(9P21.3) MUTATED DEL PEAK 11(9P21.3) WILD-TYPE 
                         0.07                          0.03 
  DEL PEAK 11(9P21.3) MUTATED DEL PEAK 11(9P21.3) WILD-TYPE 
                        83.57                        113.00 
  DEL PEAK 11(9P21.3) MUTATED DEL PEAK 11(9P21.3) WILD-TYPE 
                        13.35                         14.55 
[1] "0.1 - 83.6 (13.3)"  "0.0 - 113.0 (14.6)"
[1] "hr=" "1.4"
D39V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IIIA
  DEL PEAK 11(9P21.3) MUTATED        20       15         0         16
  DEL PEAK 11(9P21.3) WILD-TYPE      45       22         2         15
                               vv
clus                            STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 11(9P21.3) MUTATED            0          1        1         1
  DEL PEAK 11(9P21.3) WILD-TYPE          5          4        0         0
                               vv
clus                            STAGE IVB
  DEL PEAK 11(9P21.3) MUTATED           1
  DEL PEAK 11(9P21.3) WILD-TYPE         1
D39V3, multiclass
            clus
vv           DEL PEAK 11(9P21.3) MUTATED DEL PEAK 11(9P21.3) WILD-TYPE
  STAGE I                             20                            45
  STAGE II                            15                            22
  STAGE III                            0                             2
  STAGE IIIA                          16                            15
  STAGE IIIB                           0                             5
  STAGE IIIC                           1                             4
  STAGE IV                             1                             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 11(9P21.3) MUTATED   22 18 20  1
  DEL PEAK 11(9P21.3) WILD-TYPE 46 23 22  7
D39V4, multiclass
    clus
vv   DEL PEAK 11(9P21.3) MUTATED DEL PEAK 11(9P21.3) WILD-TYPE
  T1                          22                            46
  T2                          18                            23
  T3                          20                            22
  T4                           1                             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"
D39V5, binary
                               cls
clus                             0  1
  DEL PEAK 11(9P21.3) MUTATED   35  2
  DEL PEAK 11(9P21.3) WILD-TYPE 67  1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(9P21.3) MUTATED     35    2
  DEL PEAK 11(9P21.3) WILD-TYPE   67    1
   clus
vv  DEL PEAK 11(9P21.3) MUTATED DEL PEAK 11(9P21.3) WILD-TYPE
  0                          35                            67
  1                           2                             1
[1] 2 2
[1] FALSE
                               vv
clus                            M0 M1 MX
  DEL PEAK 11(9P21.3) MUTATED   42  2 17
  DEL PEAK 11(9P21.3) WILD-TYPE 78  1 20
D39V6, multiclass
    clus
vv   DEL PEAK 11(9P21.3) MUTATED DEL PEAK 11(9P21.3) WILD-TYPE
  M0                          42                            78
  M1                           2                             1
  MX                          17                            20
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V7, binary
                               cls
clus                             0  1
  DEL PEAK 11(9P21.3) MUTATED   20 41
  DEL PEAK 11(9P21.3) WILD-TYPE 40 59
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(9P21.3) MUTATED     20   41
  DEL PEAK 11(9P21.3) WILD-TYPE   40   59
        clus
vv       DEL PEAK 11(9P21.3) MUTATED DEL PEAK 11(9P21.3) WILD-TYPE
  FEMALE                          20                            40
  MALE                            41                            59
[1] 2 2
[1] FALSE
                               vv
clus                            FIBROLAMELLAR CARCINOMA
  DEL PEAK 11(9P21.3) MUTATED                         0
  DEL PEAK 11(9P21.3) WILD-TYPE                       2
                               vv
clus                            HEPATOCELLULAR CARCINOMA
  DEL PEAK 11(9P21.3) MUTATED                         60
  DEL PEAK 11(9P21.3) WILD-TYPE                       96
                               vv
clus                            HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK 11(9P21.3) MUTATED                                  1
  DEL PEAK 11(9P21.3) WILD-TYPE                                1
D39V8, multiclass
                                  clus
vv                                 DEL PEAK 11(9P21.3) MUTATED
  FIBROLAMELLAR CARCINOMA                                    0
  HEPATOCELLULAR CARCINOMA                                  60
  HEPATOCHOLANGIOCARCINOMA (MIXED)                           1
                                  clus
vv                                 DEL PEAK 11(9P21.3) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                      2
  HEPATOCELLULAR CARCINOMA                                    96
  HEPATOCHOLANGIOCARCINOMA (MIXED)                             1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            R0 R1 R2 RX
  DEL PEAK 11(9P21.3) MUTATED   46  7  1  5
  DEL PEAK 11(9P21.3) WILD-TYPE 85  4  0  7
D39V9, multiclass
    clus
vv   DEL PEAK 11(9P21.3) MUTATED DEL PEAK 11(9P21.3) WILD-TYPE
  R0                          46                            85
  R1                           7                             4
  R2                           1                             0
  RX                           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"
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 11(9P21.3) MUTATED                                  1    16
  DEL PEAK 11(9P21.3) WILD-TYPE                                0    20
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 11(9P21.3) MUTATED                           4    40
  DEL PEAK 11(9P21.3) WILD-TYPE                         4    69
D39V10, multiclass
                                  clus
vv                                 DEL PEAK 11(9P21.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                     16
  BLACK OR AFRICAN AMERICAN                                  4
  WHITE                                                     40
                                  clus
vv                                 DEL PEAK 11(9P21.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                       20
  BLACK OR AFRICAN AMERICAN                                    4
  WHITE                                                       69
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V11, binary
                               cls
clus                             0  1
  DEL PEAK 11(9P21.3) MUTATED    0 58
  DEL PEAK 11(9P21.3) WILD-TYPE  3 85
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(9P21.3) MUTATED      0   58
  DEL PEAK 11(9P21.3) WILD-TYPE    3   85
                        clus
vv                       DEL PEAK 11(9P21.3) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                          58
                        clus
vv                       DEL PEAK 11(9P21.3) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                            85
[1] 2 2
[1] FALSE

Clustering(40) Variable = DEL PEAK 12(10Q23.31) MUTATION ANALYSIS
D40V1, survival
                                 sevent
clus2                              0  1
  DEL PEAK 12(10Q23.31) MUTATED   25 16
  DEL PEAK 12(10Q23.31) WILD-TYPE 66 50
  DEL PEAK 12(10Q23.31) MUTATED DEL PEAK 12(10Q23.31) WILD-TYPE 
                             41                             116 
  DEL PEAK 12(10Q23.31) MUTATED DEL PEAK 12(10Q23.31) WILD-TYPE 
                             16                              50 
$`DEL PEAK 12(10Q23.31) MUTATED`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10W TCGA-BC-A10Y TCGA-BC-A216 
       27.91        37.32        10.13         2.99        23.34        44.42 
TCGA-BC-A217 TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-CC-5260 TCGA-CC-5263 TCGA-CC-A1HT 
       13.84        22.36         9.50         2.86         4.24         3.32 
TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A118 
        0.07         0.10         0.13        37.78        83.57       113.00 
TCGA-DD-A11A TCGA-DD-A11C TCGA-DD-A1EG TCGA-DD-A1EL TCGA-DD-A39Y TCGA-DD-A3A0 
        2.60        21.76        45.11        13.64         5.62        25.81 
TCGA-DD-A4NA TCGA-DD-A4NI TCGA-DD-A4NQ TCGA-ED-A459 TCGA-ED-A66Y TCGA-ED-A7PX 
       33.14        18.44        12.26        13.41         0.23         0.20 
TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A496 TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25X 
       19.10        27.88         0.33        51.06        53.79        58.49 
TCGA-G3-A5SJ TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-MR-A8JO TCGA-NI-A4U2 
       11.97        11.84        13.38         1.71        58.88 

$`DEL PEAK 12(10Q23.31) WILD-TYPE`
TCGA-BC-4072 TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10X TCGA-BC-A10Z 
       48.99        46.78        27.52        27.52        25.32         1.12 
TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A3KF TCGA-BC-A69H TCGA-BC-A69I TCGA-CC-5258 
       69.57         5.03         0.26        14.60        12.72         0.07 
TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-A3M9 TCGA-DD-A113 TCGA-DD-A116 TCGA-DD-A119 
        0.39         3.39         0.10        79.73        53.33         7.33 
TCGA-DD-A11B TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC 
        0.46        51.29        90.71        79.40        66.31        19.79 
TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ 
       75.65         6.71        12.95        49.15         6.02        29.16 
TCGA-DD-A1EK TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Z TCGA-DD-A3A1 TCGA-DD-A3A2 
       18.35        21.14        55.69        19.76         7.66        70.06 
TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 
       17.59        20.12       102.74       107.11        13.78         0.36 
TCGA-DD-A3A9 TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NJ 
       30.61        32.52        73.38        14.07        14.24        15.06 
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        93.67         0.30 
TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D 
       80.75        66.35        10.98         9.30         7.56        10.98 
TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 
        1.45        27.72       100.96        12.69        15.85        13.91 
TCGA-ED-A66X TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 
       13.35         0.20         0.20         0.20         0.20         0.20 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL 
       18.74        19.99        11.74        10.98         0.62         9.96 
TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A3I1 TCGA-FV-A3R2 
       11.93        22.85        14.40        32.45         8.12         6.38 
TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25V 
        0.13         0.03        60.36         0.39         1.22        28.27 
TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI 
       30.74        14.86        21.53        22.13        25.64         5.92 
TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC 
       19.53        19.23        14.70         7.99         4.37         7.76 
TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 
        5.98         1.84         1.02         2.66         4.01         2.14 
TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I 
        0.49         9.57         5.10        14.24        12.85         8.71 
TCGA-NI-A8LF TCGA-O8-A75V 
       16.37         4.44 

  DEL PEAK 12(10Q23.31) MUTATED DEL PEAK 12(10Q23.31) WILD-TYPE 
                           0.07                            0.03 
  DEL PEAK 12(10Q23.31) MUTATED DEL PEAK 12(10Q23.31) WILD-TYPE 
                         113.00                          107.11 
  DEL PEAK 12(10Q23.31) MUTATED DEL PEAK 12(10Q23.31) WILD-TYPE 
                         13.640                          14.155 
[1] "0.1 - 113.0 (13.6)" "0.0 - 107.1 (14.2)"
[1] "hr=" "1.1"
D40V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE III STAGE IIIA
  DEL PEAK 12(10Q23.31) MUTATED        12       12         0         13
  DEL PEAK 12(10Q23.31) WILD-TYPE      53       25         2         18
                                 vv
clus                              STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 12(10Q23.31) MUTATED            0          2        0         1
  DEL PEAK 12(10Q23.31) WILD-TYPE          5          3        1         0
                                 vv
clus                              STAGE IVB
  DEL PEAK 12(10Q23.31) MUTATED           0
  DEL PEAK 12(10Q23.31) WILD-TYPE         2
D40V3, multiclass
            clus
vv           DEL PEAK 12(10Q23.31) MUTATED DEL PEAK 12(10Q23.31) WILD-TYPE
  STAGE I                               12                              53
  STAGE II                              12                              25
  STAGE III                              0                               2
  STAGE IIIA                            13                              18
  STAGE IIIB                             0                               5
  STAGE IIIC                             2                               3
  STAGE IV                               0                               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 12(10Q23.31) MUTATED   13 14 14  3
  DEL PEAK 12(10Q23.31) WILD-TYPE 55 27 28  5
D40V4, multiclass
    clus
vv   DEL PEAK 12(10Q23.31) MUTATED DEL PEAK 12(10Q23.31) WILD-TYPE
  T1                            13                              55
  T2                            14                              27
  T3                            14                              28
  T4                             3                               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"
D40V5, binary
                                 cls
clus                               0  1
  DEL PEAK 12(10Q23.31) MUTATED   25  2
  DEL PEAK 12(10Q23.31) WILD-TYPE 77  1
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 12(10Q23.31) MUTATED     25    2
  DEL PEAK 12(10Q23.31) WILD-TYPE   77    1
   clus
vv  DEL PEAK 12(10Q23.31) MUTATED DEL PEAK 12(10Q23.31) WILD-TYPE
  0                            25                              77
  1                             2                               1
[1] 2 2
[1] FALSE
                                 vv
clus                              M0 M1 MX
  DEL PEAK 12(10Q23.31) MUTATED   35  0  9
  DEL PEAK 12(10Q23.31) WILD-TYPE 85  3 28
D40V6, multiclass
    clus
vv   DEL PEAK 12(10Q23.31) MUTATED DEL PEAK 12(10Q23.31) WILD-TYPE
  M0                            35                              85
  M1                             0                               3
  MX                             9                              28
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V7, binary
                                 cls
clus                               0  1
  DEL PEAK 12(10Q23.31) MUTATED   15 29
  DEL PEAK 12(10Q23.31) WILD-TYPE 45 71
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 12(10Q23.31) MUTATED     15   29
  DEL PEAK 12(10Q23.31) WILD-TYPE   45   71
        clus
vv       DEL PEAK 12(10Q23.31) MUTATED DEL PEAK 12(10Q23.31) WILD-TYPE
  FEMALE                            15                              45
  MALE                              29                              71
[1] 2 2
[1] FALSE
                                 vv
clus                              FIBROLAMELLAR CARCINOMA
  DEL PEAK 12(10Q23.31) MUTATED                         1
  DEL PEAK 12(10Q23.31) WILD-TYPE                       1
                                 vv
clus                              HEPATOCELLULAR CARCINOMA
  DEL PEAK 12(10Q23.31) MUTATED                         41
  DEL PEAK 12(10Q23.31) WILD-TYPE                      115
                                 vv
clus                              HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK 12(10Q23.31) MUTATED                                  2
  DEL PEAK 12(10Q23.31) WILD-TYPE                                0
D40V8, multiclass
                                  clus
vv                                 DEL PEAK 12(10Q23.31) MUTATED
  FIBROLAMELLAR CARCINOMA                                      1
  HEPATOCELLULAR CARCINOMA                                    41
  HEPATOCHOLANGIOCARCINOMA (MIXED)                             2
                                  clus
vv                                 DEL PEAK 12(10Q23.31) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                        1
  HEPATOCELLULAR CARCINOMA                                     115
  HEPATOCHOLANGIOCARCINOMA (MIXED)                               0
[1] 3 2
[1] 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(10Q23.31) MUTATED   32  4  0  7
  DEL PEAK 12(10Q23.31) WILD-TYPE 99  7  1  5
D40V9, multiclass
    clus
vv   DEL PEAK 12(10Q23.31) MUTATED DEL PEAK 12(10Q23.31) WILD-TYPE
  R0                            32                              99
  R1                             4                               7
  R2                             0                               1
  RX                             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"
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 12(10Q23.31) MUTATED                                  0    14
  DEL PEAK 12(10Q23.31) WILD-TYPE                                1    22
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 12(10Q23.31) MUTATED                           3    27
  DEL PEAK 12(10Q23.31) WILD-TYPE                         5    82
D40V10, multiclass
                                  clus
vv                                 DEL PEAK 12(10Q23.31) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                       14
  BLACK OR AFRICAN AMERICAN                                    3
  WHITE                                                       27
                                  clus
vv                                 DEL PEAK 12(10Q23.31) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               1
  ASIAN                                                         22
  BLACK OR AFRICAN AMERICAN                                      5
  WHITE                                                         82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V11, binary
                                 cls
clus                                0   1
  DEL PEAK 12(10Q23.31) MUTATED     1  37
  DEL PEAK 12(10Q23.31) WILD-TYPE   2 106
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 12(10Q23.31) MUTATED      1   37
  DEL PEAK 12(10Q23.31) WILD-TYPE    2  106
                        clus
vv                       DEL PEAK 12(10Q23.31) MUTATED
  HISPANIC OR LATINO                                 1
  NOT HISPANIC OR LATINO                            37
                        clus
vv                       DEL PEAK 12(10Q23.31) WILD-TYPE
  HISPANIC OR LATINO                                   2
  NOT HISPANIC OR LATINO                             106
[1] 2 2
[1] FALSE

Clustering(41) Variable = DEL PEAK 13(10Q25.2) MUTATION ANALYSIS
D41V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 13(10Q25.2) MUTATED   25 15
  DEL PEAK 13(10Q25.2) WILD-TYPE 66 51
  DEL PEAK 13(10Q25.2) MUTATED DEL PEAK 13(10Q25.2) WILD-TYPE 
                            40                            117 
  DEL PEAK 13(10Q25.2) MUTATED DEL PEAK 13(10Q25.2) WILD-TYPE 
                            15                             51 
$`DEL PEAK 13(10Q25.2) MUTATED`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10W TCGA-BC-A112 TCGA-BC-A216 
       27.91        37.32        10.13         2.99         5.03        44.42 
TCGA-BC-A217 TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-CC-5260 TCGA-CC-A1HT TCGA-CC-A3M9 
       13.84        22.36         9.50         2.86         3.32         0.10 
TCGA-CC-A3MA TCGA-CC-A3MC TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A11A TCGA-DD-A11C 
        0.07         0.13        37.78        83.57         2.60        21.76 
TCGA-DD-A1EG TCGA-DD-A1EL TCGA-DD-A39Y TCGA-DD-A4NA TCGA-DD-A4NI TCGA-DD-A4NQ 
       45.11        13.64         5.62        33.14        18.44        12.26 
TCGA-ED-A459 TCGA-ED-A66Y TCGA-ED-A7PX TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A496 
       13.41         0.23         0.20        19.10        27.88         0.33 
TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A5SJ TCGA-G3-A6UC 
       51.06        53.79        58.49        14.86        11.97         7.76 
TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-MR-A8JO TCGA-NI-A4U2 
       11.84        13.38         1.71        58.88 

$`DEL PEAK 13(10Q25.2) WILD-TYPE`
TCGA-BC-4072 TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10X TCGA-BC-A10Y 
       48.99        46.78        27.52        27.52        25.32        23.34 
TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A3KF TCGA-BC-A69H TCGA-BC-A69I TCGA-CC-5258 
        1.12        69.57         0.26        14.60        12.72         0.07 
TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A3MB TCGA-DD-A113 TCGA-DD-A116 
        0.39         3.39         4.24         0.10        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-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EH 
       66.31        19.79        75.65         6.71        12.95        49.15 
TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Z 
        6.02        29.16        18.35        21.14        55.69        19.76 
TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 
       25.81         7.66        70.06        17.59        20.12       102.74 
TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NB TCGA-DD-A4ND 
      107.11        13.78         0.36        30.61        32.52        73.38 
TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN 
       14.07        14.24        15.06        39.78        56.25        29.56 
TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A 
       73.81        93.67         0.30        80.75        66.35        10.98 
TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G 
        9.30         7.56        10.98         1.45        27.72       100.96 
TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A7PY TCGA-ED-A7PZ 
       12.69        15.85        13.91        13.35         0.20         0.20 
TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
        0.20         0.20         0.20        18.74        19.99        11.74 
TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT 
       10.98         0.62         9.96        11.93        22.85        14.40 
TCGA-FV-A23B TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A4ZP 
       32.45         8.12         6.38         0.13         0.03        60.36 
TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Z TCGA-G3-A3CG 
        0.39         1.22        28.27        30.74        21.53        22.13 
TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SL 
       25.64         5.92        19.53        19.23        14.70         7.99 
TCGA-G3-A5SM TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 
        4.37         5.98         1.84         1.02         2.66         4.01 
TCGA-KR-A7K0 TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H 
        2.14         0.49         9.57         5.10        14.24        12.85 
TCGA-MI-A75I TCGA-NI-A8LF TCGA-O8-A75V 
        8.71        16.37         4.44 

  DEL PEAK 13(10Q25.2) MUTATED DEL PEAK 13(10Q25.2) WILD-TYPE 
                          0.07                           0.03 
  DEL PEAK 13(10Q25.2) MUTATED DEL PEAK 13(10Q25.2) WILD-TYPE 
                         83.57                         113.00 
  DEL PEAK 13(10Q25.2) MUTATED DEL PEAK 13(10Q25.2) WILD-TYPE 
                        13.395                         14.240 
[1] "0.1 - 83.6 (13.4)"  "0.0 - 113.0 (14.2)"
[1] "hr=" "1.1"
D41V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IIIA
  DEL PEAK 13(10Q25.2) MUTATED        12       11         0         12
  DEL PEAK 13(10Q25.2) WILD-TYPE      53       26         2         19
                                vv
clus                             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 13(10Q25.2) MUTATED            1          2        0         1
  DEL PEAK 13(10Q25.2) WILD-TYPE          4          3        1         0
                                vv
clus                             STAGE IVB
  DEL PEAK 13(10Q25.2) MUTATED           0
  DEL PEAK 13(10Q25.2) WILD-TYPE         2
D41V3, multiclass
            clus
vv           DEL PEAK 13(10Q25.2) MUTATED DEL PEAK 13(10Q25.2) WILD-TYPE
  STAGE I                              12                             53
  STAGE II                             11                             26
  STAGE III                             0                              2
  STAGE IIIA                           12                             19
  STAGE IIIB                            1                              4
  STAGE IIIC                            2                              3
  STAGE IV                              0                              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 13(10Q25.2) MUTATED   13 13 15  2
  DEL PEAK 13(10Q25.2) WILD-TYPE 55 28 27  6
D41V4, multiclass
    clus
vv   DEL PEAK 13(10Q25.2) MUTATED DEL PEAK 13(10Q25.2) WILD-TYPE
  T1                           13                             55
  T2                           13                             28
  T3                           15                             27
  T4                            2                              6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V5, binary
                                cls
clus                              0  1
  DEL PEAK 13(10Q25.2) MUTATED   25  2
  DEL PEAK 13(10Q25.2) WILD-TYPE 77  1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 13(10Q25.2) MUTATED     25    2
  DEL PEAK 13(10Q25.2) WILD-TYPE   77    1
   clus
vv  DEL PEAK 13(10Q25.2) MUTATED DEL PEAK 13(10Q25.2) WILD-TYPE
  0                           25                             77
  1                            2                              1
[1] 2 2
[1] FALSE
                                vv
clus                             M0 M1 MX
  DEL PEAK 13(10Q25.2) MUTATED   34  0  9
  DEL PEAK 13(10Q25.2) WILD-TYPE 86  3 28
D41V6, multiclass
    clus
vv   DEL PEAK 13(10Q25.2) MUTATED DEL PEAK 13(10Q25.2) WILD-TYPE
  M0                           34                             86
  M1                            0                              3
  MX                            9                             28
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V7, binary
                                cls
clus                              0  1
  DEL PEAK 13(10Q25.2) MUTATED   15 28
  DEL PEAK 13(10Q25.2) WILD-TYPE 45 72
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 13(10Q25.2) MUTATED     15   28
  DEL PEAK 13(10Q25.2) WILD-TYPE   45   72
        clus
vv       DEL PEAK 13(10Q25.2) MUTATED DEL PEAK 13(10Q25.2) WILD-TYPE
  FEMALE                           15                             45
  MALE                             28                             72
[1] 2 2
[1] FALSE
                                vv
clus                             FIBROLAMELLAR CARCINOMA
  DEL PEAK 13(10Q25.2) MUTATED                         1
  DEL PEAK 13(10Q25.2) WILD-TYPE                       1
                                vv
clus                             HEPATOCELLULAR CARCINOMA
  DEL PEAK 13(10Q25.2) MUTATED                         40
  DEL PEAK 13(10Q25.2) WILD-TYPE                      116
                                vv
clus                             HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK 13(10Q25.2) MUTATED                                  2
  DEL PEAK 13(10Q25.2) WILD-TYPE                                0
D41V8, multiclass
                                  clus
vv                                 DEL PEAK 13(10Q25.2) MUTATED
  FIBROLAMELLAR CARCINOMA                                     1
  HEPATOCELLULAR CARCINOMA                                   40
  HEPATOCHOLANGIOCARCINOMA (MIXED)                            2
                                  clus
vv                                 DEL PEAK 13(10Q25.2) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                       1
  HEPATOCELLULAR CARCINOMA                                    116
  HEPATOCHOLANGIOCARCINOMA (MIXED)                              0
[1] 3 2
[1] 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(10Q25.2) MUTATED   32  4  0  6
  DEL PEAK 13(10Q25.2) WILD-TYPE 99  7  1  6
D41V9, multiclass
    clus
vv   DEL PEAK 13(10Q25.2) MUTATED DEL PEAK 13(10Q25.2) WILD-TYPE
  R0                           32                             99
  R1                            4                              7
  R2                            0                              1
  RX                            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"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 13(10Q25.2) MUTATED                                  0    14
  DEL PEAK 13(10Q25.2) WILD-TYPE                                1    22
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 13(10Q25.2) MUTATED                           3    26
  DEL PEAK 13(10Q25.2) WILD-TYPE                         5    83
D41V10, multiclass
                                  clus
vv                                 DEL PEAK 13(10Q25.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                      14
  BLACK OR AFRICAN AMERICAN                                   3
  WHITE                                                      26
                                  clus
vv                                 DEL PEAK 13(10Q25.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        22
  BLACK OR AFRICAN AMERICAN                                     5
  WHITE                                                        83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V11, binary
                                cls
clus                               0   1
  DEL PEAK 13(10Q25.2) MUTATED     1  36
  DEL PEAK 13(10Q25.2) WILD-TYPE   2 107
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 13(10Q25.2) MUTATED      1   36
  DEL PEAK 13(10Q25.2) WILD-TYPE    2  107
                        clus
vv                       DEL PEAK 13(10Q25.2) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           36
                        clus
vv                       DEL PEAK 13(10Q25.2) WILD-TYPE
  HISPANIC OR LATINO                                  2
  NOT HISPANIC OR LATINO                            107
[1] 2 2
[1] FALSE

Clustering(42) Variable = DEL PEAK 14(11Q14.1) MUTATION ANALYSIS
D42V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 14(11Q14.1) MUTATED   15 11
  DEL PEAK 14(11Q14.1) WILD-TYPE 76 55
  DEL PEAK 14(11Q14.1) MUTATED DEL PEAK 14(11Q14.1) WILD-TYPE 
                            26                            131 
  DEL PEAK 14(11Q14.1) MUTATED DEL PEAK 14(11Q14.1) WILD-TYPE 
                            11                             55 
$`DEL PEAK 14(11Q14.1) MUTATED`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10S TCGA-BC-A112 TCGA-BC-A217 TCGA-BC-A3KF 
       27.91        37.32        46.78         5.03        13.84         0.26 
TCGA-CC-5263 TCGA-CC-A3M9 TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A11A TCGA-DD-A1E9 
        4.24         0.10         0.13        79.73         2.60        90.71 
TCGA-DD-A1EF TCGA-DD-A1EJ TCGA-DD-A39X TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NI 
       12.95        29.16        55.69        32.52        73.38        18.44 
TCGA-DD-A73B TCGA-ED-A7PZ TCGA-EP-A2KC TCGA-FV-A4ZP TCGA-G3-A25S TCGA-G3-A5SJ 
        9.30         0.20         0.62        60.36         1.22        11.97 
TCGA-KR-A7K2 TCGA-KR-A7K7 
       11.84        13.38 

$`DEL PEAK 14(11Q14.1) WILD-TYPE`
TCGA-BC-4072 TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X 
       48.99        10.13        27.52        27.52         2.99        25.32 
TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A216 TCGA-BC-A3KG TCGA-BC-A5W4 
       23.34         1.12        69.57        44.42        22.36         9.50 
TCGA-BC-A69H TCGA-BC-A69I TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
       14.60        12.72         0.07         2.86         0.39         3.39 
TCGA-CC-A1HT TCGA-CC-A3MA TCGA-CC-A3MB TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 
        3.32         0.07         0.10        37.78        83.57        53.33 
TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1EA 
      113.00         7.33         0.46        21.76        51.29        79.40 
TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EG TCGA-DD-A1EH 
       66.31        19.79        75.65         6.71        45.11        49.15 
TCGA-DD-A1EI TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39Y TCGA-DD-A39Z 
        6.02        18.35        13.64        21.14         5.62        19.76 
TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 
       25.81         7.66        70.06        17.59        20.12       102.74 
TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NF 
      107.11        13.78         0.36        30.61        33.14        14.07 
TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO 
       14.24        15.06        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 
       93.67        12.26         0.30        80.75        66.35        10.98 
TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 
        7.56        10.98         1.45        27.72       100.96        13.41 
TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX 
       12.69        15.85        13.91        13.35         0.23         0.20 
TCGA-ED-A7PY TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-EP-A12J TCGA-EP-A26S 
        0.20         0.20         0.20         0.20        18.74        19.99 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT 
       11.74        10.98         9.96        11.93        22.85        14.40 
TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 
       32.45        19.10        27.88         8.12         6.38         0.13 
TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V 
        0.03         0.33         0.39        51.06        53.79        28.27 
TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH 
       30.74        58.49        14.86        21.53        22.13        25.64 
TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SL TCGA-G3-A5SM 
        5.92        19.53        19.23        14.70         7.99         4.37 
TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 
        7.76         5.98         1.84         1.02         2.66         4.01 
TCGA-KR-A7K0 TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H 
        2.14         0.49         9.57         5.10        14.24        12.85 
TCGA-MI-A75I TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V 
        8.71         1.71        58.88        16.37         4.44 

  DEL PEAK 14(11Q14.1) MUTATED DEL PEAK 14(11Q14.1) WILD-TYPE 
                          0.10                           0.03 
  DEL PEAK 14(11Q14.1) MUTATED DEL PEAK 14(11Q14.1) WILD-TYPE 
                         90.71                         113.00 
  DEL PEAK 14(11Q14.1) MUTATED DEL PEAK 14(11Q14.1) WILD-TYPE 
                        13.165                         14.240 
[1] "0.1 - 90.7 (13.2)"  "0.0 - 113.0 (14.2)"
[1] "hr=" "1"  
D42V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IIIA
  DEL PEAK 14(11Q14.1) MUTATED        12        5         0          6
  DEL PEAK 14(11Q14.1) WILD-TYPE      53       32         2         25
                                vv
clus                             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 14(11Q14.1) MUTATED            0          1        0         1
  DEL PEAK 14(11Q14.1) WILD-TYPE          5          4        1         0
                                vv
clus                             STAGE IVB
  DEL PEAK 14(11Q14.1) MUTATED           0
  DEL PEAK 14(11Q14.1) WILD-TYPE         2
D42V3, multiclass
            clus
vv           DEL PEAK 14(11Q14.1) MUTATED DEL PEAK 14(11Q14.1) WILD-TYPE
  STAGE I                              12                             53
  STAGE II                              5                             32
  STAGE III                             0                              2
  STAGE IIIA                            6                             25
  STAGE IIIB                            0                              5
  STAGE IIIC                            1                              4
  STAGE IV                              0                              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 14(11Q14.1) MUTATED   14  6  8  0
  DEL PEAK 14(11Q14.1) WILD-TYPE 54 35 34  8
D42V4, multiclass
    clus
vv   DEL PEAK 14(11Q14.1) MUTATED DEL PEAK 14(11Q14.1) WILD-TYPE
  T1                           14                             54
  T2                            6                             35
  T3                            8                             34
  T4                            0                              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"
D42V5, binary
                                cls
clus                              0  1
  DEL PEAK 14(11Q14.1) MUTATED   15  2
  DEL PEAK 14(11Q14.1) WILD-TYPE 87  1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 14(11Q14.1) MUTATED     15    2
  DEL PEAK 14(11Q14.1) WILD-TYPE   87    1
   clus
vv  DEL PEAK 14(11Q14.1) MUTATED DEL PEAK 14(11Q14.1) WILD-TYPE
  0                           15                             87
  1                            2                              1
[1] 2 2
[1] FALSE
                                vv
clus                             M0 M1 MX
  DEL PEAK 14(11Q14.1) MUTATED   22  0  6
  DEL PEAK 14(11Q14.1) WILD-TYPE 98  3 31
D42V6, multiclass
    clus
vv   DEL PEAK 14(11Q14.1) MUTATED DEL PEAK 14(11Q14.1) WILD-TYPE
  M0                           22                             98
  M1                            0                              3
  MX                            6                             31
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V7, binary
                                cls
clus                              0  1
  DEL PEAK 14(11Q14.1) MUTATED   10 18
  DEL PEAK 14(11Q14.1) WILD-TYPE 50 82
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 14(11Q14.1) MUTATED     10   18
  DEL PEAK 14(11Q14.1) WILD-TYPE   50   82
        clus
vv       DEL PEAK 14(11Q14.1) MUTATED DEL PEAK 14(11Q14.1) WILD-TYPE
  FEMALE                           10                             50
  MALE                             18                             82
[1] 2 2
[1] FALSE
                                vv
clus                             FIBROLAMELLAR CARCINOMA
  DEL PEAK 14(11Q14.1) MUTATED                         1
  DEL PEAK 14(11Q14.1) WILD-TYPE                       1
                                vv
clus                             HEPATOCELLULAR CARCINOMA
  DEL PEAK 14(11Q14.1) MUTATED                         26
  DEL PEAK 14(11Q14.1) WILD-TYPE                      130
                                vv
clus                             HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK 14(11Q14.1) MUTATED                                  1
  DEL PEAK 14(11Q14.1) WILD-TYPE                                1
D42V8, multiclass
                                  clus
vv                                 DEL PEAK 14(11Q14.1) MUTATED
  FIBROLAMELLAR CARCINOMA                                     1
  HEPATOCELLULAR CARCINOMA                                   26
  HEPATOCHOLANGIOCARCINOMA (MIXED)                            1
                                  clus
vv                                 DEL PEAK 14(11Q14.1) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                       1
  HEPATOCELLULAR CARCINOMA                                    130
  HEPATOCHOLANGIOCARCINOMA (MIXED)                              1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 14(11Q14.1) MUTATED    22   4   0   2
  DEL PEAK 14(11Q14.1) WILD-TYPE 109   7   1  10
D42V9, multiclass
    clus
vv   DEL PEAK 14(11Q14.1) MUTATED DEL PEAK 14(11Q14.1) WILD-TYPE
  R0                           22                            109
  R1                            4                              7
  R2                            0                              1
  RX                            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"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 14(11Q14.1) MUTATED                                  0     5
  DEL PEAK 14(11Q14.1) WILD-TYPE                                1    31
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 14(11Q14.1) MUTATED                           2    21
  DEL PEAK 14(11Q14.1) WILD-TYPE                         6    88
D42V10, multiclass
                                  clus
vv                                 DEL PEAK 14(11Q14.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       5
  BLACK OR AFRICAN AMERICAN                                   2
  WHITE                                                      21
                                  clus
vv                                 DEL PEAK 14(11Q14.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        31
  BLACK OR AFRICAN AMERICAN                                     6
  WHITE                                                        88
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V11, binary
                                cls
clus                               0   1
  DEL PEAK 14(11Q14.1) MUTATED     1  23
  DEL PEAK 14(11Q14.1) WILD-TYPE   2 120
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 14(11Q14.1) MUTATED      1   23
  DEL PEAK 14(11Q14.1) WILD-TYPE    2  120
                        clus
vv                       DEL PEAK 14(11Q14.1) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           23
                        clus
vv                       DEL PEAK 14(11Q14.1) WILD-TYPE
  HISPANIC OR LATINO                                  2
  NOT HISPANIC OR LATINO                            120
[1] 2 2
[1] FALSE

Clustering(43) Variable = DEL PEAK 15(11Q23.3) MUTATION ANALYSIS
D43V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 15(11Q23.3) MUTATED   17 13
  DEL PEAK 15(11Q23.3) WILD-TYPE 74 53
  DEL PEAK 15(11Q23.3) MUTATED DEL PEAK 15(11Q23.3) WILD-TYPE 
                            30                            127 
  DEL PEAK 15(11Q23.3) MUTATED DEL PEAK 15(11Q23.3) WILD-TYPE 
                            13                             53 
$`DEL PEAK 15(11Q23.3) MUTATED`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10S TCGA-BC-A112 TCGA-BC-A3KF TCGA-BC-A69H 
       27.91        37.32        46.78         5.03         0.26        14.60 
TCGA-CC-5263 TCGA-CC-A3MA TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A11A TCGA-DD-A1E9 
        4.24         0.07         0.13        79.73         2.60        90.71 
TCGA-DD-A1EF TCGA-DD-A1EJ TCGA-DD-A39X TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NI 
       12.95        29.16        55.69        32.52        73.38        18.44 
TCGA-DD-A4NN TCGA-DD-A73B TCGA-ED-A7PZ TCGA-EP-A2KC TCGA-FV-A4ZP TCGA-G3-A25S 
       29.56         9.30         0.20         0.62        60.36         1.22 
TCGA-G3-A25U TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-GJ-A6C0 TCGA-KR-A7K2 TCGA-KR-A7K7 
       53.79        14.70        11.97         1.02        11.84        13.38 

$`DEL PEAK 15(11Q23.3) WILD-TYPE`
TCGA-BC-4072 TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X 
       48.99        10.13        27.52        27.52         2.99        25.32 
TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KG 
       23.34         1.12        69.57        44.42        13.84        22.36 
TCGA-BC-A5W4 TCGA-BC-A69I TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
        9.50        12.72         0.07         2.86         0.39         3.39 
TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MB TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 
        3.32         0.10         0.10        37.78        83.57        53.33 
TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1EA 
      113.00         7.33         0.46        21.76        51.29        79.40 
TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EG TCGA-DD-A1EH 
       66.31        19.79        75.65         6.71        45.11        49.15 
TCGA-DD-A1EI TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39Y TCGA-DD-A39Z 
        6.02        18.35        13.64        21.14         5.62        19.76 
TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 
       25.81         7.66        70.06        17.59        20.12       102.74 
TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NF 
      107.11        13.78         0.36        30.61        33.14        14.07 
TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NO TCGA-DD-A4NP 
       14.24        15.06        39.78        56.25        73.81        93.67 
TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73C 
       12.26         0.30        80.75        66.35        10.98         7.56 
TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI 
       10.98         1.45        27.72       100.96        13.41        12.69 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY 
       15.85        13.91        13.35         0.23         0.20         0.20 
TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
        0.20         0.20         0.20        18.74        19.99        11.74 
TCGA-EP-A2KB TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B 
       10.98         9.96        11.93        22.85        14.40        32.45 
TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 
       19.10        27.88         8.12         6.38         0.13         0.03 
TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X 
        0.33         0.39        51.06        28.27        30.74        58.49 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ 
       14.86        21.53        22.13        25.64         5.92        19.53 
TCGA-G3-A3CK TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-A7M9 
       19.23         7.99         4.37         7.76         5.98         1.84 
TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E 
        2.66         4.01         2.14         0.49         9.57         5.10 
TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF 
       14.24        12.85         8.71         1.71        58.88        16.37 
TCGA-O8-A75V 
        4.44 

  DEL PEAK 15(11Q23.3) MUTATED DEL PEAK 15(11Q23.3) WILD-TYPE 
                          0.07                           0.03 
  DEL PEAK 15(11Q23.3) MUTATED DEL PEAK 15(11Q23.3) WILD-TYPE 
                         90.71                         113.00 
  DEL PEAK 15(11Q23.3) MUTATED DEL PEAK 15(11Q23.3) WILD-TYPE 
                         13.99                          13.91 
[1] "0.1 - 90.7 (14.0)"  "0.0 - 113.0 (13.9)"
[1] "hr=" "1"  
D43V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IIIA
  DEL PEAK 15(11Q23.3) MUTATED        14        7         0          6
  DEL PEAK 15(11Q23.3) WILD-TYPE      51       30         2         25
                                vv
clus                             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 15(11Q23.3) MUTATED            0          1        0         1
  DEL PEAK 15(11Q23.3) WILD-TYPE          5          4        1         0
                                vv
clus                             STAGE IVB
  DEL PEAK 15(11Q23.3) MUTATED           0
  DEL PEAK 15(11Q23.3) WILD-TYPE         2
D43V3, multiclass
            clus
vv           DEL PEAK 15(11Q23.3) MUTATED DEL PEAK 15(11Q23.3) WILD-TYPE
  STAGE I                              14                             51
  STAGE II                              7                             30
  STAGE III                             0                              2
  STAGE IIIA                            6                             25
  STAGE IIIB                            0                              5
  STAGE IIIC                            1                              4
  STAGE IV                              0                              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 15(11Q23.3) MUTATED   16  8  8  0
  DEL PEAK 15(11Q23.3) WILD-TYPE 52 33 34  8
D43V4, multiclass
    clus
vv   DEL PEAK 15(11Q23.3) MUTATED DEL PEAK 15(11Q23.3) WILD-TYPE
  T1                           16                             52
  T2                            8                             33
  T3                            8                             34
  T4                            0                              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"
D43V5, binary
                                cls
clus                              0  1
  DEL PEAK 15(11Q23.3) MUTATED   18  2
  DEL PEAK 15(11Q23.3) WILD-TYPE 84  1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 15(11Q23.3) MUTATED     18    2
  DEL PEAK 15(11Q23.3) WILD-TYPE   84    1
   clus
vv  DEL PEAK 15(11Q23.3) MUTATED DEL PEAK 15(11Q23.3) WILD-TYPE
  0                           18                             84
  1                            2                              1
[1] 2 2
[1] FALSE
                                vv
clus                             M0 M1 MX
  DEL PEAK 15(11Q23.3) MUTATED   25  0  7
  DEL PEAK 15(11Q23.3) WILD-TYPE 95  3 30
D43V6, multiclass
    clus
vv   DEL PEAK 15(11Q23.3) MUTATED DEL PEAK 15(11Q23.3) WILD-TYPE
  M0                           25                             95
  M1                            0                              3
  MX                            7                             30
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V7, binary
                                cls
clus                              0  1
  DEL PEAK 15(11Q23.3) MUTATED   12 20
  DEL PEAK 15(11Q23.3) WILD-TYPE 48 80
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 15(11Q23.3) MUTATED     12   20
  DEL PEAK 15(11Q23.3) WILD-TYPE   48   80
        clus
vv       DEL PEAK 15(11Q23.3) MUTATED DEL PEAK 15(11Q23.3) WILD-TYPE
  FEMALE                           12                             48
  MALE                             20                             80
[1] 2 2
[1] FALSE
                                vv
clus                             FIBROLAMELLAR CARCINOMA
  DEL PEAK 15(11Q23.3) MUTATED                         1
  DEL PEAK 15(11Q23.3) WILD-TYPE                       1
                                vv
clus                             HEPATOCELLULAR CARCINOMA
  DEL PEAK 15(11Q23.3) MUTATED                         30
  DEL PEAK 15(11Q23.3) WILD-TYPE                      126
                                vv
clus                             HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK 15(11Q23.3) MUTATED                                  1
  DEL PEAK 15(11Q23.3) WILD-TYPE                                1
D43V8, multiclass
                                  clus
vv                                 DEL PEAK 15(11Q23.3) MUTATED
  FIBROLAMELLAR CARCINOMA                                     1
  HEPATOCELLULAR CARCINOMA                                   30
  HEPATOCHOLANGIOCARCINOMA (MIXED)                            1
                                  clus
vv                                 DEL PEAK 15(11Q23.3) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                       1
  HEPATOCELLULAR CARCINOMA                                    126
  HEPATOCHOLANGIOCARCINOMA (MIXED)                              1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 15(11Q23.3) MUTATED    25   4   0   3
  DEL PEAK 15(11Q23.3) WILD-TYPE 106   7   1   9
D43V9, multiclass
    clus
vv   DEL PEAK 15(11Q23.3) MUTATED DEL PEAK 15(11Q23.3) WILD-TYPE
  R0                           25                            106
  R1                            4                              7
  R2                            0                              1
  RX                            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"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 15(11Q23.3) MUTATED                                  0     7
  DEL PEAK 15(11Q23.3) WILD-TYPE                                1    29
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 15(11Q23.3) MUTATED                           2    23
  DEL PEAK 15(11Q23.3) WILD-TYPE                         6    86
D43V10, multiclass
                                  clus
vv                                 DEL PEAK 15(11Q23.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       7
  BLACK OR AFRICAN AMERICAN                                   2
  WHITE                                                      23
                                  clus
vv                                 DEL PEAK 15(11Q23.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        29
  BLACK OR AFRICAN AMERICAN                                     6
  WHITE                                                        86
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V11, binary
                                cls
clus                               0   1
  DEL PEAK 15(11Q23.3) MUTATED     1  28
  DEL PEAK 15(11Q23.3) WILD-TYPE   2 115
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 15(11Q23.3) MUTATED      1   28
  DEL PEAK 15(11Q23.3) WILD-TYPE    2  115
                        clus
vv                       DEL PEAK 15(11Q23.3) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           28
                        clus
vv                       DEL PEAK 15(11Q23.3) WILD-TYPE
  HISPANIC OR LATINO                                  2
  NOT HISPANIC OR LATINO                            115
[1] 2 2
[1] FALSE

Clustering(44) Variable = DEL PEAK 16(12P12.1) MUTATION ANALYSIS
D44V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 16(12P12.1) MUTATED   19 15
  DEL PEAK 16(12P12.1) WILD-TYPE 72 51
  DEL PEAK 16(12P12.1) MUTATED DEL PEAK 16(12P12.1) WILD-TYPE 
                            34                            123 
  DEL PEAK 16(12P12.1) MUTATED DEL PEAK 16(12P12.1) WILD-TYPE 
                            15                             51 
$`DEL PEAK 16(12P12.1) MUTATED`
TCGA-BC-4073 TCGA-BC-A10Y TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A5W4 TCGA-CC-A1HT 
       27.91        23.34        13.84         0.26         9.50         3.32 
TCGA-CC-A3MA TCGA-CC-A3MC TCGA-DD-A119 TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EJ 
        0.07         0.13         7.33        45.11        49.15        29.16 
TCGA-DD-A1EL TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A3A1 TCGA-DD-A3A7 TCGA-DD-A4NA 
       13.64        55.69         5.62         7.66        13.78        33.14 
TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NO TCGA-DD-A73F TCGA-ED-A7XP 
       14.24        18.44        15.06        73.81        27.72         0.20 
TCGA-EP-A2KC TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A496 TCGA-G3-A25S TCGA-G3-A25Z 
        0.62         8.12         6.38         0.33         1.22        21.53 
TCGA-GJ-A6C0 TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A8JO 
        1.02        14.24         8.71         1.71 

$`DEL PEAK 16(12P12.1) WILD-TYPE`
TCGA-BC-4072 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
       48.99        37.32        10.13        46.78        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 
        2.99        25.32         1.12        69.57         5.03        44.42 
TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A69I TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 
       22.36        14.60        12.72         0.07         2.86         0.39 
TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A3M9 TCGA-CC-A3MB TCGA-DD-A113 TCGA-DD-A114 
        3.39         4.24         0.10         0.10        79.73        37.78 
TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-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-A1EI TCGA-DD-A1EK TCGA-DD-A39V TCGA-DD-A39Z 
        6.71        12.95         6.02        18.35        21.14        19.76 
TCGA-DD-A3A0 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 
       25.81        70.06        17.59        20.12       102.74       107.11 
TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NK 
        0.36        30.61        32.52        73.38        14.07        39.78 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS 
       56.25        29.56        93.67        12.26         0.30        80.75 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E 
       66.35        10.98         9.30         7.56        10.98         1.45 
TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X 
      100.96        13.41        12.69        15.85        13.91        13.35 
TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A82E TCGA-ED-A8O5 
        0.23         0.20         0.20         0.20         0.20         0.20 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A3JL TCGA-EP-A3RK 
       18.74        19.99        11.74        10.98         9.96        11.93 
TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R3 
       22.85        14.40        32.45        19.10        27.88         0.13 
TCGA-FV-A495 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V 
        0.03        60.36         0.39        51.06        53.79        28.27 
TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI 
       30.74        58.49        14.86        22.13        25.64         5.92 
TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM 
       19.53        19.23        14.70        11.97         7.99         4.37 
TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 
        7.76         5.98         1.84         2.66         4.01         2.14 
TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75H 
       11.84        13.38         0.49         9.57         5.10        12.85 
TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V 
       58.88        16.37         4.44 

  DEL PEAK 16(12P12.1) MUTATED DEL PEAK 16(12P12.1) WILD-TYPE 
                          0.07                           0.03 
  DEL PEAK 16(12P12.1) MUTATED DEL PEAK 16(12P12.1) WILD-TYPE 
                         73.81                         113.00 
  DEL PEAK 16(12P12.1) MUTATED DEL PEAK 16(12P12.1) WILD-TYPE 
                         11.57                          14.60 
[1] "0.1 - 73.8 (11.6)"  "0.0 - 113.0 (14.6)"
[1] "hr=" "1.6"
D44V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IIIA
  DEL PEAK 16(12P12.1) MUTATED        12        8         1          6
  DEL PEAK 16(12P12.1) WILD-TYPE      53       29         1         25
                                vv
clus                             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 16(12P12.1) MUTATED            2          2        1         0
  DEL PEAK 16(12P12.1) WILD-TYPE          3          3        0         1
                                vv
clus                             STAGE IVB
  DEL PEAK 16(12P12.1) MUTATED           0
  DEL PEAK 16(12P12.1) WILD-TYPE         2
D44V3, multiclass
            clus
vv           DEL PEAK 16(12P12.1) MUTATED DEL PEAK 16(12P12.1) WILD-TYPE
  STAGE I                              12                             53
  STAGE II                              8                             29
  STAGE III                             1                              1
  STAGE IIIA                            6                             25
  STAGE IIIB                            2                              3
  STAGE IIIC                            2                              3
  STAGE IV                              1                              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 16(12P12.1) MUTATED   13 10 10  1
  DEL PEAK 16(12P12.1) WILD-TYPE 55 31 32  7
D44V4, multiclass
    clus
vv   DEL PEAK 16(12P12.1) MUTATED DEL PEAK 16(12P12.1) WILD-TYPE
  T1                           13                             55
  T2                           10                             31
  T3                           10                             32
  T4                            1                              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"
D44V5, binary
                                cls
clus                              0  1
  DEL PEAK 16(12P12.1) MUTATED   20  2
  DEL PEAK 16(12P12.1) WILD-TYPE 82  1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 16(12P12.1) MUTATED     20    2
  DEL PEAK 16(12P12.1) WILD-TYPE   82    1
   clus
vv  DEL PEAK 16(12P12.1) MUTATED DEL PEAK 16(12P12.1) WILD-TYPE
  0                           20                             82
  1                            2                              1
[1] 2 2
[1] FALSE
                                vv
clus                             M0 M1 MX
  DEL PEAK 16(12P12.1) MUTATED   25  1  8
  DEL PEAK 16(12P12.1) WILD-TYPE 95  2 29
D44V6, multiclass
    clus
vv   DEL PEAK 16(12P12.1) MUTATED DEL PEAK 16(12P12.1) WILD-TYPE
  M0                           25                             95
  M1                            1                              2
  MX                            8                             29
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V7, binary
                                cls
clus                              0  1
  DEL PEAK 16(12P12.1) MUTATED   12 22
  DEL PEAK 16(12P12.1) WILD-TYPE 48 78
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 16(12P12.1) MUTATED     12   22
  DEL PEAK 16(12P12.1) WILD-TYPE   48   78
        clus
vv       DEL PEAK 16(12P12.1) MUTATED DEL PEAK 16(12P12.1) WILD-TYPE
  FEMALE                           12                             48
  MALE                             22                             78
[1] 2 2
[1] FALSE
                                vv
clus                             FIBROLAMELLAR CARCINOMA
  DEL PEAK 16(12P12.1) MUTATED                         1
  DEL PEAK 16(12P12.1) WILD-TYPE                       1
                                vv
clus                             HEPATOCELLULAR CARCINOMA
  DEL PEAK 16(12P12.1) MUTATED                         33
  DEL PEAK 16(12P12.1) WILD-TYPE                      123
                                vv
clus                             HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK 16(12P12.1) MUTATED                                  0
  DEL PEAK 16(12P12.1) WILD-TYPE                                2
D44V8, multiclass
                                  clus
vv                                 DEL PEAK 16(12P12.1) MUTATED
  FIBROLAMELLAR CARCINOMA                                     1
  HEPATOCELLULAR CARCINOMA                                   33
  HEPATOCHOLANGIOCARCINOMA (MIXED)                            0
                                  clus
vv                                 DEL PEAK 16(12P12.1) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                       1
  HEPATOCELLULAR CARCINOMA                                    123
  HEPATOCHOLANGIOCARCINOMA (MIXED)                              2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 16(12P12.1) MUTATED    27   3   1   2
  DEL PEAK 16(12P12.1) WILD-TYPE 104   8   0  10
D44V9, multiclass
    clus
vv   DEL PEAK 16(12P12.1) MUTATED DEL PEAK 16(12P12.1) WILD-TYPE
  R0                           27                            104
  R1                            3                              8
  R2                            1                              0
  RX                            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"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 16(12P12.1) MUTATED                                  0     7
  DEL PEAK 16(12P12.1) WILD-TYPE                                1    29
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 16(12P12.1) MUTATED                           3    22
  DEL PEAK 16(12P12.1) WILD-TYPE                         5    87
D44V10, multiclass
                                  clus
vv                                 DEL PEAK 16(12P12.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       7
  BLACK OR AFRICAN AMERICAN                                   3
  WHITE                                                      22
                                  clus
vv                                 DEL PEAK 16(12P12.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        29
  BLACK OR AFRICAN AMERICAN                                     5
  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"
D44V11, binary
                                cls
clus                               0   1
  DEL PEAK 16(12P12.1) MUTATED     0  29
  DEL PEAK 16(12P12.1) WILD-TYPE   3 114
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 16(12P12.1) MUTATED      0   29
  DEL PEAK 16(12P12.1) WILD-TYPE    3  114
                        clus
vv                       DEL PEAK 16(12P12.1) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           29
                        clus
vv                       DEL PEAK 16(12P12.1) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            114
[1] 2 2
[1] FALSE

Clustering(45) Variable = DEL PEAK 17(12Q24.33) MUTATION ANALYSIS
D45V1, survival
                                 sevent
clus2                              0  1
  DEL PEAK 17(12Q24.33) MUTATED   12 13
  DEL PEAK 17(12Q24.33) WILD-TYPE 79 53
  DEL PEAK 17(12Q24.33) MUTATED DEL PEAK 17(12Q24.33) WILD-TYPE 
                             25                             132 
  DEL PEAK 17(12Q24.33) MUTATED DEL PEAK 17(12Q24.33) WILD-TYPE 
                             13                              53 
$`DEL PEAK 17(12Q24.33) MUTATED`
TCGA-BC-A10Y TCGA-BC-A217 TCGA-BC-A5W4 TCGA-CC-5260 TCGA-CC-A1HT TCGA-CC-A3MA 
       23.34        13.84         9.50         2.86         3.32         0.07 
TCGA-CC-A3MC TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EL TCGA-DD-A39X TCGA-DD-A39Z 
        0.13        45.11        49.15        13.64        55.69        19.76 
TCGA-DD-A3A0 TCGA-DD-A3A5 TCGA-DD-A3A9 TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NO 
       25.81       102.74        30.61        18.44        15.06        73.81 
TCGA-ED-A459 TCGA-ED-A82E TCGA-EP-A2KC TCGA-FV-A3I1 TCGA-G3-A25Y TCGA-MI-A75G 
       13.41         0.20         0.62         8.12        14.86        14.24 
TCGA-NI-A8LF 
       16.37 

$`DEL PEAK 17(12Q24.33) WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T 
       48.99        27.91        37.32        10.13        46.78        27.52 
TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 
       27.52         2.99        25.32         1.12        69.57         5.03 
TCGA-BC-A216 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A69I TCGA-CC-5258 
       44.42         0.26        22.36        14.60        12.72         0.07 
TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A3M9 TCGA-CC-A3MB TCGA-DD-A113 
        0.39         3.39         4.24         0.10         0.10        79.73 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A 
       37.78        83.57        53.33       113.00         7.33         2.60 
TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB 
        0.46        21.76        51.29        90.71        79.40        66.31 
TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EI TCGA-DD-A1EJ 
       19.79        75.65         6.71        12.95         6.02        29.16 
TCGA-DD-A1EK TCGA-DD-A39V TCGA-DD-A39Y TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 
       18.35        21.14         5.62         7.66        70.06        17.59 
TCGA-DD-A3A4 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A4NA TCGA-DD-A4NB 
       20.12       107.11        13.78         0.36        33.14        32.52 
TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN 
       73.38        14.07        14.24        39.78        56.25        29.56 
TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A 
       93.67        12.26         0.30        80.75        66.35        10.98 
TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G 
        9.30         7.56        10.98         1.45        27.72       100.96 
TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX 
       12.69        15.85        13.91        13.35         0.23         0.20 
TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-ED-A8O5 TCGA-EP-A12J TCGA-EP-A26S 
        0.20         0.20         0.20         0.20        18.74        19.99 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT 
       11.74        10.98         9.96        11.93        22.85        14.40 
TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 
       32.45        19.10        27.88         6.38         0.13         0.03 
TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U 
        0.33        60.36         0.39         1.22        51.06        53.79 
TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH 
       28.27        30.74        58.49        21.53        22.13        25.64 
TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL 
        5.92        19.53        19.23        14.70        11.97         7.99 
TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ 
        4.37         7.76         5.98         1.84         1.02         2.66 
TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75C 
        4.01         2.14        11.84        13.38         0.49         9.57 
TCGA-MI-A75E TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-O8-A75V 
        5.10        12.85         8.71         1.71        58.88         4.44 

  DEL PEAK 17(12Q24.33) MUTATED DEL PEAK 17(12Q24.33) WILD-TYPE 
                           0.07                            0.03 
  DEL PEAK 17(12Q24.33) MUTATED DEL PEAK 17(12Q24.33) WILD-TYPE 
                         102.74                          113.00 
  DEL PEAK 17(12Q24.33) MUTATED DEL PEAK 17(12Q24.33) WILD-TYPE 
                          14.86                           13.58 
[1] "0.1 - 102.7 (14.9)" "0.0 - 113.0 (13.6)"
[1] "hr=" "1.3"
D45V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE III STAGE IIIA
  DEL PEAK 17(12Q24.33) MUTATED         7        8         2          5
  DEL PEAK 17(12Q24.33) WILD-TYPE      58       29         0         26
                                 vv
clus                              STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 17(12Q24.33) MUTATED            0          1        0         0
  DEL PEAK 17(12Q24.33) WILD-TYPE          5          4        1         1
                                 vv
clus                              STAGE IVB
  DEL PEAK 17(12Q24.33) MUTATED           1
  DEL PEAK 17(12Q24.33) WILD-TYPE         1
D45V3, multiclass
            clus
vv           DEL PEAK 17(12Q24.33) MUTATED DEL PEAK 17(12Q24.33) WILD-TYPE
  STAGE I                                7                              58
  STAGE II                               8                              29
  STAGE III                              2                               0
  STAGE IIIA                             5                              26
  STAGE IIIB                             0                               5
  STAGE IIIC                             1                               4
  STAGE IV                               0                               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 17(12Q24.33) MUTATED    7  8  7  3
  DEL PEAK 17(12Q24.33) WILD-TYPE 61 33 35  5
D45V4, multiclass
    clus
vv   DEL PEAK 17(12Q24.33) MUTATED DEL PEAK 17(12Q24.33) WILD-TYPE
  T1                             7                              61
  T2                             8                              33
  T3                             7                              35
  T4                             3                               5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V5, binary
                                 cls
clus                               0  1
  DEL PEAK 17(12Q24.33) MUTATED   16  0
  DEL PEAK 17(12Q24.33) WILD-TYPE 86  3
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 17(12Q24.33) MUTATED     16    0
  DEL PEAK 17(12Q24.33) WILD-TYPE   86    3
   clus
vv  DEL PEAK 17(12Q24.33) MUTATED DEL PEAK 17(12Q24.33) WILD-TYPE
  0                            16                              86
  1                             0                               3
[1] 2 2
[1] FALSE
                                 vv
clus                               M0  M1  MX
  DEL PEAK 17(12Q24.33) MUTATED    20   1   4
  DEL PEAK 17(12Q24.33) WILD-TYPE 100   2  33
D45V6, multiclass
    clus
vv   DEL PEAK 17(12Q24.33) MUTATED DEL PEAK 17(12Q24.33) WILD-TYPE
  M0                            20                             100
  M1                             1                               2
  MX                             4                              33
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V7, binary
                                 cls
clus                               0  1
  DEL PEAK 17(12Q24.33) MUTATED   10 15
  DEL PEAK 17(12Q24.33) WILD-TYPE 50 85
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 17(12Q24.33) MUTATED     10   15
  DEL PEAK 17(12Q24.33) WILD-TYPE   50   85
        clus
vv       DEL PEAK 17(12Q24.33) MUTATED DEL PEAK 17(12Q24.33) WILD-TYPE
  FEMALE                            10                              50
  MALE                              15                              85
[1] 2 2
[1] FALSE
                                 vv
clus                              FIBROLAMELLAR CARCINOMA
  DEL PEAK 17(12Q24.33) MUTATED                         0
  DEL PEAK 17(12Q24.33) WILD-TYPE                       2
                                 vv
clus                              HEPATOCELLULAR CARCINOMA
  DEL PEAK 17(12Q24.33) MUTATED                         25
  DEL PEAK 17(12Q24.33) WILD-TYPE                      131
                                 vv
clus                              HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK 17(12Q24.33) MUTATED                                  0
  DEL PEAK 17(12Q24.33) WILD-TYPE                                2
D45V8, multiclass
                                  clus
vv                                 DEL PEAK 17(12Q24.33) MUTATED
  FIBROLAMELLAR CARCINOMA                                      0
  HEPATOCELLULAR CARCINOMA                                    25
  HEPATOCHOLANGIOCARCINOMA (MIXED)                             0
                                  clus
vv                                 DEL PEAK 17(12Q24.33) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                        2
  HEPATOCELLULAR CARCINOMA                                     131
  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 17(12Q24.33) MUTATED    22   1   0   1
  DEL PEAK 17(12Q24.33) WILD-TYPE 109  10   1  11
D45V9, multiclass
    clus
vv   DEL PEAK 17(12Q24.33) MUTATED DEL PEAK 17(12Q24.33) WILD-TYPE
  R0                            22                             109
  R1                             1                              10
  R2                             0                               1
  RX                             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"
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 17(12Q24.33) MUTATED                                  0     7
  DEL PEAK 17(12Q24.33) WILD-TYPE                                1    29
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 17(12Q24.33) MUTATED                           2    15
  DEL PEAK 17(12Q24.33) WILD-TYPE                         6    94
D45V10, multiclass
                                  clus
vv                                 DEL PEAK 17(12Q24.33) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        7
  BLACK OR AFRICAN AMERICAN                                    2
  WHITE                                                       15
                                  clus
vv                                 DEL PEAK 17(12Q24.33) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               1
  ASIAN                                                         29
  BLACK OR AFRICAN AMERICAN                                      6
  WHITE                                                         94
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V11, binary
                                 cls
clus                                0   1
  DEL PEAK 17(12Q24.33) MUTATED     0  23
  DEL PEAK 17(12Q24.33) WILD-TYPE   3 120
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 17(12Q24.33) MUTATED      0   23
  DEL PEAK 17(12Q24.33) WILD-TYPE    3  120
                        clus
vv                       DEL PEAK 17(12Q24.33) MUTATED
  HISPANIC OR LATINO                                 0
  NOT HISPANIC OR LATINO                            23
                        clus
vv                       DEL PEAK 17(12Q24.33) WILD-TYPE
  HISPANIC OR LATINO                                   3
  NOT HISPANIC OR LATINO                             120
[1] 2 2
[1] FALSE

Clustering(46) Variable = DEL PEAK 18(13Q14.2) MUTATION ANALYSIS
D46V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 18(13Q14.2) MUTATED   40 30
  DEL PEAK 18(13Q14.2) WILD-TYPE 51 36
  DEL PEAK 18(13Q14.2) MUTATED DEL PEAK 18(13Q14.2) WILD-TYPE 
                            70                             87 
  DEL PEAK 18(13Q14.2) MUTATED DEL PEAK 18(13Q14.2) WILD-TYPE 
                            30                             36 
$`DEL PEAK 18(13Q14.2) MUTATED`
TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10W TCGA-BC-A10Y TCGA-BC-A10Z 
       37.32        10.13        27.52         2.99        23.34         1.12 
TCGA-BC-A112 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H 
        5.03        13.84         0.26        22.36         9.50        14.60 
TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT 
        0.07         2.86         0.39         3.39         4.24         3.32 
TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 
        0.10         0.07         0.13        79.73        37.78        83.57 
TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A11A TCGA-DD-A11C TCGA-DD-A1EF TCGA-DD-A1EI 
       53.33       113.00         2.60        21.76        12.95         6.02 
TCGA-DD-A1EK TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A3A0 TCGA-DD-A3A5 TCGA-DD-A3A9 
       18.35        55.69         5.62        25.81       102.74        30.61 
TCGA-DD-A4NA TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NQ 
       33.14        14.24        15.06        29.56        73.81        12.26 
TCGA-DD-A4NR TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI 
        0.30         1.45        27.72       100.96        13.41        12.69 
TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-EP-A3RK TCGA-FV-A3I0 
        0.23         0.20         0.20         0.20        11.93        27.88 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A495 TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25X 
        8.12         6.38         0.03         1.22        51.06        58.49 
TCGA-G3-A25Y TCGA-G3-A3CH TCGA-G3-A5SI TCGA-G3-A5SM TCGA-GJ-A6C0 TCGA-KR-A7K2 
       14.86        25.64        14.70         4.37         1.02        11.84 
TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A8JO TCGA-NI-A8LF 
       14.24         8.71         1.71        16.37 

$`DEL PEAK 18(13Q14.2) WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10S TCGA-BC-A10U TCGA-BC-A10X TCGA-BC-A110 
       48.99        27.91        46.78        27.52        25.32        69.57 
TCGA-BC-A216 TCGA-BC-A69I TCGA-CC-A3MB TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11D 
       44.42        12.72         0.10         7.33         0.46        51.29 
TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE 
       90.71        79.40        66.31        19.79        75.65         6.71 
TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39Z 
       45.11        49.15        29.16        13.64        21.14        19.76 
TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A6 TCGA-DD-A3A7 
        7.66        70.06        17.59        20.12       107.11        13.78 
TCGA-DD-A3A8 TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NI TCGA-DD-A4NK 
        0.36        32.52        73.38        14.07        18.44        39.78 
TCGA-DD-A4NL TCGA-DD-A4NP TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B 
       56.25        93.67        80.75        66.35        10.98         9.30 
TCGA-DD-A73C TCGA-DD-A73D TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A7PY 
        7.56        10.98        15.85        13.91        13.35         0.20 
TCGA-ED-A82E TCGA-ED-A8O5 TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB 
        0.20         0.20        18.74        19.99        11.74        10.98 
TCGA-EP-A2KC TCGA-EP-A3JL TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR 
        0.62         9.96        22.85        14.40        32.45        19.10 
TCGA-FV-A3R3 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25U TCGA-G3-A25V 
        0.13         0.33        60.36         0.39        53.79        28.27 
TCGA-G3-A25W TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
       30.74        21.53        22.13         5.92        19.53        19.23 
TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-HP-A5MZ 
       11.97         7.99         7.76         5.98         1.84         2.66 
TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E 
        4.01         2.14        13.38         0.49         9.57         5.10 
TCGA-MI-A75H TCGA-NI-A4U2 TCGA-O8-A75V 
       12.85        58.88         4.44 

  DEL PEAK 18(13Q14.2) MUTATED DEL PEAK 18(13Q14.2) WILD-TYPE 
                          0.03                           0.10 
  DEL PEAK 18(13Q14.2) MUTATED DEL PEAK 18(13Q14.2) WILD-TYPE 
                        113.00                         107.11 
  DEL PEAK 18(13Q14.2) MUTATED DEL PEAK 18(13Q14.2) WILD-TYPE 
                        12.475                         17.590 
[1] "0.0 - 113.0 (12.5)" "0.1 - 107.1 (17.6)"
[1] "hr=" "1.3"
D46V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IIIA
  DEL PEAK 18(13Q14.2) MUTATED        22       23         1         13
  DEL PEAK 18(13Q14.2) WILD-TYPE      43       14         1         18
                                vv
clus                             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 18(13Q14.2) MUTATED            1          3        0         0
  DEL PEAK 18(13Q14.2) WILD-TYPE          4          2        1         1
                                vv
clus                             STAGE IVB
  DEL PEAK 18(13Q14.2) MUTATED           2
  DEL PEAK 18(13Q14.2) WILD-TYPE         0
D46V3, multiclass
            clus
vv           DEL PEAK 18(13Q14.2) MUTATED DEL PEAK 18(13Q14.2) WILD-TYPE
  STAGE I                              22                             43
  STAGE II                             23                             14
  STAGE III                             1                              1
  STAGE IIIA                           13                             18
  STAGE IIIB                            1                              4
  STAGE IIIC                            3                              2
  STAGE IV                              0                              1
  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 18(13Q14.2) MUTATED   22 26 17  7
  DEL PEAK 18(13Q14.2) WILD-TYPE 46 15 25  1
D46V4, multiclass
    clus
vv   DEL PEAK 18(13Q14.2) MUTATED DEL PEAK 18(13Q14.2) WILD-TYPE
  T1                           22                             46
  T2                           26                             15
  T3                           17                             25
  T4                            7                              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"
D46V5, binary
                                cls
clus                              0  1
  DEL PEAK 18(13Q14.2) MUTATED   46  1
  DEL PEAK 18(13Q14.2) WILD-TYPE 56  2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(13Q14.2) MUTATED     46    1
  DEL PEAK 18(13Q14.2) WILD-TYPE   56    2
   clus
vv  DEL PEAK 18(13Q14.2) MUTATED DEL PEAK 18(13Q14.2) WILD-TYPE
  0                           46                             56
  1                            1                              2
[1] 2 2
[1] FALSE
                                vv
clus                             M0 M1 MX
  DEL PEAK 18(13Q14.2) MUTATED   55  2 15
  DEL PEAK 18(13Q14.2) WILD-TYPE 65  1 22
D46V6, multiclass
    clus
vv   DEL PEAK 18(13Q14.2) MUTATED DEL PEAK 18(13Q14.2) WILD-TYPE
  M0                           55                             65
  M1                            2                              1
  MX                           15                             22
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V7, binary
                                cls
clus                              0  1
  DEL PEAK 18(13Q14.2) MUTATED   30 42
  DEL PEAK 18(13Q14.2) WILD-TYPE 30 58
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(13Q14.2) MUTATED     30   42
  DEL PEAK 18(13Q14.2) WILD-TYPE   30   58
        clus
vv       DEL PEAK 18(13Q14.2) MUTATED DEL PEAK 18(13Q14.2) WILD-TYPE
  FEMALE                           30                             30
  MALE                             42                             58
[1] 2 2
[1] FALSE
                                vv
clus                             FIBROLAMELLAR CARCINOMA
  DEL PEAK 18(13Q14.2) MUTATED                         1
  DEL PEAK 18(13Q14.2) WILD-TYPE                       1
                                vv
clus                             HEPATOCELLULAR CARCINOMA
  DEL PEAK 18(13Q14.2) MUTATED                         69
  DEL PEAK 18(13Q14.2) WILD-TYPE                       87
                                vv
clus                             HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK 18(13Q14.2) MUTATED                                  2
  DEL PEAK 18(13Q14.2) WILD-TYPE                                0
D46V8, multiclass
                                  clus
vv                                 DEL PEAK 18(13Q14.2) MUTATED
  FIBROLAMELLAR CARCINOMA                                     1
  HEPATOCELLULAR CARCINOMA                                   69
  HEPATOCHOLANGIOCARCINOMA (MIXED)                            2
                                  clus
vv                                 DEL PEAK 18(13Q14.2) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                       1
  HEPATOCELLULAR CARCINOMA                                     87
  HEPATOCHOLANGIOCARCINOMA (MIXED)                              0
[1] 3 2
[1] 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(13Q14.2) MUTATED   55  5  0  9
  DEL PEAK 18(13Q14.2) WILD-TYPE 76  6  1  3
D46V9, multiclass
    clus
vv   DEL PEAK 18(13Q14.2) MUTATED DEL PEAK 18(13Q14.2) WILD-TYPE
  R0                           55                             76
  R1                            5                              6
  R2                            0                              1
  RX                            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"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 18(13Q14.2) MUTATED                                  0    24
  DEL PEAK 18(13Q14.2) WILD-TYPE                                1    12
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 18(13Q14.2) MUTATED                           3    45
  DEL PEAK 18(13Q14.2) WILD-TYPE                         5    64
D46V10, multiclass
                                  clus
vv                                 DEL PEAK 18(13Q14.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                      24
  BLACK OR AFRICAN AMERICAN                                   3
  WHITE                                                      45
                                  clus
vv                                 DEL PEAK 18(13Q14.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        12
  BLACK OR AFRICAN AMERICAN                                     5
  WHITE                                                        64
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V11, binary
                                cls
clus                              0  1
  DEL PEAK 18(13Q14.2) MUTATED    1 66
  DEL PEAK 18(13Q14.2) WILD-TYPE  2 77
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(13Q14.2) MUTATED      1   66
  DEL PEAK 18(13Q14.2) WILD-TYPE    2   77
                        clus
vv                       DEL PEAK 18(13Q14.2) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           66
                        clus
vv                       DEL PEAK 18(13Q14.2) WILD-TYPE
  HISPANIC OR LATINO                                  2
  NOT HISPANIC OR LATINO                             77
[1] 2 2
[1] FALSE

Clustering(47) Variable = DEL PEAK 19(13Q22.2) MUTATION ANALYSIS
D47V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 19(13Q22.2) MUTATED   32 23
  DEL PEAK 19(13Q22.2) WILD-TYPE 59 43
  DEL PEAK 19(13Q22.2) MUTATED DEL PEAK 19(13Q22.2) WILD-TYPE 
                            55                            102 
  DEL PEAK 19(13Q22.2) MUTATED DEL PEAK 19(13Q22.2) WILD-TYPE 
                            23                             43 
$`DEL PEAK 19(13Q22.2) MUTATED`
TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10W TCGA-BC-A10Y TCGA-BC-A112 
       37.32        10.13        27.52         2.99        23.34         5.03 
TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-CC-5260 
       13.84         0.26        22.36         9.50        14.60         2.86 
TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-DD-A113 TCGA-DD-A115 
        3.39         4.24         0.10         0.07        79.73        83.57 
TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A11C TCGA-DD-A1EF TCGA-DD-A1EI TCGA-DD-A1EK 
       53.33       113.00        21.76        12.95         6.02        18.35 
TCGA-DD-A39X TCGA-DD-A3A0 TCGA-DD-A3A5 TCGA-DD-A3A9 TCGA-DD-A4NH TCGA-DD-A4NJ 
       55.69        25.81       102.74        30.61        14.24        15.06 
TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A73F TCGA-DD-A73G 
       29.56        73.81        12.26         0.30        27.72       100.96 
TCGA-ED-A4XI TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-EP-A3RK 
       12.69         0.23         0.20         0.20         0.20        11.93 
TCGA-FV-A3I0 TCGA-FV-A3R2 TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25X TCGA-G3-A25Y 
       27.88         6.38         1.22        51.06        58.49        14.86 
TCGA-G3-A3CH TCGA-G3-A5SI TCGA-G3-A5SM TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A8JO 
       25.64        14.70         4.37        14.24         8.71         1.71 
TCGA-NI-A8LF 
       16.37 

$`DEL PEAK 19(13Q22.2) WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10S TCGA-BC-A10U TCGA-BC-A10X TCGA-BC-A10Z 
       48.99        27.91        46.78        27.52        25.32         1.12 
TCGA-BC-A110 TCGA-BC-A216 TCGA-BC-A69I TCGA-CC-5258 TCGA-CC-5261 TCGA-CC-A1HT 
       69.57        44.42        12.72         0.07         0.39         3.32 
TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A114 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B 
        0.10         0.13        37.78         7.33         2.60         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-A1EG TCGA-DD-A1EH TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39V 
        6.71        45.11        49.15        29.16        13.64        21.14 
TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 
        5.62        19.76         7.66        70.06        17.59        20.12 
TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND 
      107.11        13.78         0.36        33.14        32.52        73.38 
TCGA-DD-A4NF TCGA-DD-A4NI TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NP TCGA-DD-A4NS 
       14.07        18.44        39.78        56.25        93.67        80.75 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E 
       66.35        10.98         9.30         7.56        10.98         1.45 
TCGA-ED-A459 TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A7PY TCGA-ED-A82E 
       13.41        15.85        13.91        13.35         0.20         0.20 
TCGA-ED-A8O5 TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC 
        0.20        18.74        19.99        11.74        10.98         0.62 
TCGA-EP-A3JL TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I1 
        9.96        22.85        14.40        32.45        19.10         8.12 
TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25U 
        0.13         0.03         0.33        60.36         0.39        53.79 
TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CI TCGA-G3-A3CJ 
       28.27        30.74        21.53        22.13         5.92        19.53 
TCGA-G3-A3CK TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-A7M9 
       19.23        11.97         7.99         7.76         5.98         1.84 
TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 
        1.02         2.66         4.01         2.14        11.84        13.38 
TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75H TCGA-NI-A4U2 TCGA-O8-A75V 
        0.49         9.57         5.10        12.85        58.88         4.44 

  DEL PEAK 19(13Q22.2) MUTATED DEL PEAK 19(13Q22.2) WILD-TYPE 
                          0.07                           0.03 
  DEL PEAK 19(13Q22.2) MUTATED DEL PEAK 19(13Q22.2) WILD-TYPE 
                        113.00                         107.11 
  DEL PEAK 19(13Q22.2) MUTATED DEL PEAK 19(13Q22.2) WILD-TYPE 
                         14.24                          13.71 
[1] "0.1 - 113.0 (14.2)" "0.0 - 107.1 (13.7)"
[1] "hr=" "1.1"
D47V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IIIA
  DEL PEAK 19(13Q22.2) MUTATED        17       16         1         11
  DEL PEAK 19(13Q22.2) WILD-TYPE      48       21         1         20
                                vv
clus                             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 19(13Q22.2) MUTATED            1          2        0         0
  DEL PEAK 19(13Q22.2) WILD-TYPE          4          3        1         1
                                vv
clus                             STAGE IVB
  DEL PEAK 19(13Q22.2) MUTATED           2
  DEL PEAK 19(13Q22.2) WILD-TYPE         0
D47V3, multiclass
            clus
vv           DEL PEAK 19(13Q22.2) MUTATED DEL PEAK 19(13Q22.2) WILD-TYPE
  STAGE I                              17                             48
  STAGE II                             16                             21
  STAGE III                             1                              1
  STAGE IIIA                           11                             20
  STAGE IIIB                            1                              4
  STAGE IIIC                            2                              3
  STAGE IV                              0                              1
  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 19(13Q22.2) MUTATED   17 18 15  7
  DEL PEAK 19(13Q22.2) WILD-TYPE 51 23 27  1
D47V4, multiclass
    clus
vv   DEL PEAK 19(13Q22.2) MUTATED DEL PEAK 19(13Q22.2) WILD-TYPE
  T1                           17                             51
  T2                           18                             23
  T3                           15                             27
  T4                            7                              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"
D47V5, binary
                                cls
clus                              0  1
  DEL PEAK 19(13Q22.2) MUTATED   36  0
  DEL PEAK 19(13Q22.2) WILD-TYPE 66  3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(13Q22.2) MUTATED     36    0
  DEL PEAK 19(13Q22.2) WILD-TYPE   66    3
   clus
vv  DEL PEAK 19(13Q22.2) MUTATED DEL PEAK 19(13Q22.2) WILD-TYPE
  0                           36                             66
  1                            0                              3
[1] 2 2
[1] FALSE
                                vv
clus                             M0 M1 MX
  DEL PEAK 19(13Q22.2) MUTATED   43  2 12
  DEL PEAK 19(13Q22.2) WILD-TYPE 77  1 25
D47V6, multiclass
    clus
vv   DEL PEAK 19(13Q22.2) MUTATED DEL PEAK 19(13Q22.2) WILD-TYPE
  M0                           43                             77
  M1                            2                              1
  MX                           12                             25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V7, binary
                                cls
clus                              0  1
  DEL PEAK 19(13Q22.2) MUTATED   25 32
  DEL PEAK 19(13Q22.2) WILD-TYPE 35 68
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(13Q22.2) MUTATED     25   32
  DEL PEAK 19(13Q22.2) WILD-TYPE   35   68
        clus
vv       DEL PEAK 19(13Q22.2) MUTATED DEL PEAK 19(13Q22.2) WILD-TYPE
  FEMALE                           25                             35
  MALE                             32                             68
[1] 2 2
[1] FALSE
                                vv
clus                             FIBROLAMELLAR CARCINOMA
  DEL PEAK 19(13Q22.2) MUTATED                         1
  DEL PEAK 19(13Q22.2) WILD-TYPE                       1
                                vv
clus                             HEPATOCELLULAR CARCINOMA
  DEL PEAK 19(13Q22.2) MUTATED                         55
  DEL PEAK 19(13Q22.2) WILD-TYPE                      101
                                vv
clus                             HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK 19(13Q22.2) MUTATED                                  1
  DEL PEAK 19(13Q22.2) WILD-TYPE                                1
D47V8, multiclass
                                  clus
vv                                 DEL PEAK 19(13Q22.2) MUTATED
  FIBROLAMELLAR CARCINOMA                                     1
  HEPATOCELLULAR CARCINOMA                                   55
  HEPATOCHOLANGIOCARCINOMA (MIXED)                            1
                                  clus
vv                                 DEL PEAK 19(13Q22.2) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                       1
  HEPATOCELLULAR CARCINOMA                                    101
  HEPATOCHOLANGIOCARCINOMA (MIXED)                              1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             R0 R1 R2 RX
  DEL PEAK 19(13Q22.2) MUTATED   44  5  0  6
  DEL PEAK 19(13Q22.2) WILD-TYPE 87  6  1  6
D47V9, multiclass
    clus
vv   DEL PEAK 19(13Q22.2) MUTATED DEL PEAK 19(13Q22.2) WILD-TYPE
  R0                           44                             87
  R1                            5                              6
  R2                            0                              1
  RX                            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"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 19(13Q22.2) MUTATED                                  0    18
  DEL PEAK 19(13Q22.2) WILD-TYPE                                1    18
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 19(13Q22.2) MUTATED                           1    38
  DEL PEAK 19(13Q22.2) WILD-TYPE                         7    71
D47V10, multiclass
                                  clus
vv                                 DEL PEAK 19(13Q22.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                      18
  BLACK OR AFRICAN AMERICAN                                   1
  WHITE                                                      38
                                  clus
vv                                 DEL PEAK 19(13Q22.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        18
  BLACK OR AFRICAN AMERICAN                                     7
  WHITE                                                        71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V11, binary
                                cls
clus                              0  1
  DEL PEAK 19(13Q22.2) MUTATED    1 52
  DEL PEAK 19(13Q22.2) WILD-TYPE  2 91
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(13Q22.2) MUTATED      1   52
  DEL PEAK 19(13Q22.2) WILD-TYPE    2   91
                        clus
vv                       DEL PEAK 19(13Q22.2) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           52
                        clus
vv                       DEL PEAK 19(13Q22.2) WILD-TYPE
  HISPANIC OR LATINO                                  2
  NOT HISPANIC OR LATINO                             91
[1] 2 2
[1] FALSE

Clustering(48) Variable = DEL PEAK 20(14Q23.3) MUTATION ANALYSIS
D48V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 20(14Q23.3) MUTATED   32 21
  DEL PEAK 20(14Q23.3) WILD-TYPE 59 45
  DEL PEAK 20(14Q23.3) MUTATED DEL PEAK 20(14Q23.3) WILD-TYPE 
                            53                            104 
  DEL PEAK 20(14Q23.3) MUTATED DEL PEAK 20(14Q23.3) WILD-TYPE 
                            21                             45 
$`DEL PEAK 20(14Q23.3) MUTATED`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10Z TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A3KF 
       27.91        37.32         1.12         5.03        44.42         0.26 
TCGA-BC-A3KG TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-A1HT TCGA-CC-A3MA 
       22.36         0.07         2.86         0.39         3.32         0.07 
TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A115 TCGA-DD-A118 TCGA-DD-A11A 
        0.10         0.13        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        29.16        13.64 
TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A3A1 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NB 
       55.69         5.62         7.66        13.78        30.61        32.52 
TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NO TCGA-DD-A4NQ TCGA-DD-A73F TCGA-ED-A459 
       14.24        18.44        73.81        12.26        27.72        13.41 
TCGA-ED-A7PX TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-ED-A82E TCGA-EP-A12J TCGA-EP-A2KB 
        0.20         0.20         0.20         0.20        18.74        10.98 
TCGA-EP-A3RK TCGA-FV-A3I0 TCGA-FV-A4ZP TCGA-G3-A25S TCGA-G3-A25X TCGA-G3-A3CH 
       11.93        27.88        60.36         1.22        58.49        25.64 
TCGA-G3-A5SM TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-KR-A7K7 TCGA-NI-A8LF 
        4.37         1.84         1.02        13.38        16.37 

$`DEL PEAK 20(14Q23.3) WILD-TYPE`
TCGA-BC-4072 TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W 
       48.99        10.13        46.78        27.52        27.52         2.99 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A110 TCGA-BC-A217 TCGA-BC-A5W4 TCGA-BC-A69H 
       25.32        23.34        69.57        13.84         9.50        14.60 
TCGA-BC-A69I TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A3M9 TCGA-DD-A114 TCGA-DD-A116 
       12.72         3.39         4.24         0.10        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         6.71        12.95        49.15        18.35        21.14 
TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 
       19.76        25.81        70.06        17.59        20.12       102.74 
TCGA-DD-A3A6 TCGA-DD-A3A8 TCGA-DD-A4NA TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NJ 
      107.11         0.36        33.14        73.38        14.07        15.06 
TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NP TCGA-DD-A4NR TCGA-DD-A4NS 
       39.78        56.25        29.56        93.67         0.30        80.75 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E 
       66.35        10.98         9.30         7.56        10.98         1.45 
TCGA-DD-A73G TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y 
      100.96        12.69        15.85        13.91        13.35         0.23 
TCGA-ED-A7PY TCGA-ED-A8O5 TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3JL 
        0.20         0.20        19.99        11.74         0.62         9.96 
TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I1 TCGA-FV-A3R2 
       22.85        14.40        32.45        19.10         8.12         6.38 
TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25U 
        0.13         0.03         0.33         0.39        51.06        53.79 
TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CI 
       28.27        30.74        14.86        21.53        22.13         5.92 
TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A6UC 
       19.53        19.23        14.70        11.97         7.99         7.76 
TCGA-G3-A7M7 TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-LG-A6GG 
        5.98         2.66         4.01         2.14        11.84         0.49 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A8JO 
        9.57         5.10        14.24        12.85         8.71         1.71 
TCGA-NI-A4U2 TCGA-O8-A75V 
       58.88         4.44 

  DEL PEAK 20(14Q23.3) MUTATED DEL PEAK 20(14Q23.3) WILD-TYPE 
                          0.07                           0.03 
  DEL PEAK 20(14Q23.3) MUTATED DEL PEAK 20(14Q23.3) WILD-TYPE 
                        113.00                         107.11 
  DEL PEAK 20(14Q23.3) MUTATED DEL PEAK 20(14Q23.3) WILD-TYPE 
                         13.41                          14.32 
[1] "0.1 - 113.0 (13.4)" "0.0 - 107.1 (14.3)"
[1] "hr=" "1"  
D48V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IIIA
  DEL PEAK 20(14Q23.3) MUTATED        17       17         0         13
  DEL PEAK 20(14Q23.3) WILD-TYPE      48       20         2         18
                                vv
clus                             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 20(14Q23.3) MUTATED            3          2        0         0
  DEL PEAK 20(14Q23.3) WILD-TYPE          2          3        1         1
                                vv
clus                             STAGE IVB
  DEL PEAK 20(14Q23.3) MUTATED           1
  DEL PEAK 20(14Q23.3) WILD-TYPE         1
D48V3, multiclass
            clus
vv           DEL PEAK 20(14Q23.3) MUTATED DEL PEAK 20(14Q23.3) WILD-TYPE
  STAGE I                              17                             48
  STAGE II                             17                             20
  STAGE III                             0                              2
  STAGE IIIA                           13                             18
  STAGE IIIB                            3                              2
  STAGE IIIC                            2                              3
  STAGE IV                              0                              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 20(14Q23.3) MUTATED   18 18 17  2
  DEL PEAK 20(14Q23.3) WILD-TYPE 50 23 25  6
D48V4, multiclass
    clus
vv   DEL PEAK 20(14Q23.3) MUTATED DEL PEAK 20(14Q23.3) WILD-TYPE
  T1                           18                             50
  T2                           18                             23
  T3                           17                             25
  T4                            2                              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"
D48V5, binary
                                cls
clus                              0  1
  DEL PEAK 20(14Q23.3) MUTATED   35  1
  DEL PEAK 20(14Q23.3) WILD-TYPE 67  2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(14Q23.3) MUTATED     35    1
  DEL PEAK 20(14Q23.3) WILD-TYPE   67    2
   clus
vv  DEL PEAK 20(14Q23.3) MUTATED DEL PEAK 20(14Q23.3) WILD-TYPE
  0                           35                             67
  1                            1                              2
[1] 2 2
[1] FALSE
                                vv
clus                             M0 M1 MX
  DEL PEAK 20(14Q23.3) MUTATED   43  1 11
  DEL PEAK 20(14Q23.3) WILD-TYPE 77  2 26
D48V6, multiclass
    clus
vv   DEL PEAK 20(14Q23.3) MUTATED DEL PEAK 20(14Q23.3) WILD-TYPE
  M0                           43                             77
  M1                            1                              2
  MX                           11                             26
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V7, binary
                                cls
clus                              0  1
  DEL PEAK 20(14Q23.3) MUTATED   20 35
  DEL PEAK 20(14Q23.3) WILD-TYPE 40 65
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(14Q23.3) MUTATED     20   35
  DEL PEAK 20(14Q23.3) WILD-TYPE   40   65
        clus
vv       DEL PEAK 20(14Q23.3) MUTATED DEL PEAK 20(14Q23.3) WILD-TYPE
  FEMALE                           20                             40
  MALE                             35                             65
[1] 2 2
[1] FALSE
                                vv
clus                             FIBROLAMELLAR CARCINOMA
  DEL PEAK 20(14Q23.3) MUTATED                         1
  DEL PEAK 20(14Q23.3) WILD-TYPE                       1
                                vv
clus                             HEPATOCELLULAR CARCINOMA
  DEL PEAK 20(14Q23.3) MUTATED                         53
  DEL PEAK 20(14Q23.3) WILD-TYPE                      103
                                vv
clus                             HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK 20(14Q23.3) MUTATED                                  1
  DEL PEAK 20(14Q23.3) WILD-TYPE                                1
D48V8, multiclass
                                  clus
vv                                 DEL PEAK 20(14Q23.3) MUTATED
  FIBROLAMELLAR CARCINOMA                                     1
  HEPATOCELLULAR CARCINOMA                                   53
  HEPATOCHOLANGIOCARCINOMA (MIXED)                            1
                                  clus
vv                                 DEL PEAK 20(14Q23.3) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                       1
  HEPATOCELLULAR CARCINOMA                                    103
  HEPATOCHOLANGIOCARCINOMA (MIXED)                              1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             R0 R1 R2 RX
  DEL PEAK 20(14Q23.3) MUTATED   42  4  0  7
  DEL PEAK 20(14Q23.3) WILD-TYPE 89  7  1  5
D48V9, multiclass
    clus
vv   DEL PEAK 20(14Q23.3) MUTATED DEL PEAK 20(14Q23.3) WILD-TYPE
  R0                           42                             89
  R1                            4                              7
  R2                            0                              1
  RX                            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"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 20(14Q23.3) MUTATED                                  0    17
  DEL PEAK 20(14Q23.3) WILD-TYPE                                1    19
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 20(14Q23.3) MUTATED                           3    33
  DEL PEAK 20(14Q23.3) WILD-TYPE                         5    76
D48V10, multiclass
                                  clus
vv                                 DEL PEAK 20(14Q23.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                      17
  BLACK OR AFRICAN AMERICAN                                   3
  WHITE                                                      33
                                  clus
vv                                 DEL PEAK 20(14Q23.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        19
  BLACK OR AFRICAN AMERICAN                                     5
  WHITE                                                        76
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V11, binary
                                cls
clus                              0  1
  DEL PEAK 20(14Q23.3) MUTATED    1 48
  DEL PEAK 20(14Q23.3) WILD-TYPE  2 95
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(14Q23.3) MUTATED      1   48
  DEL PEAK 20(14Q23.3) WILD-TYPE    2   95
                        clus
vv                       DEL PEAK 20(14Q23.3) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           48
                        clus
vv                       DEL PEAK 20(14Q23.3) WILD-TYPE
  HISPANIC OR LATINO                                  2
  NOT HISPANIC OR LATINO                             95
[1] 2 2
[1] FALSE

Clustering(49) Variable = DEL PEAK 21(14Q32.33) MUTATION ANALYSIS
D49V1, survival
                                 sevent
clus2                              0  1
  DEL PEAK 21(14Q32.33) MUTATED   32 22
  DEL PEAK 21(14Q32.33) WILD-TYPE 59 44
  DEL PEAK 21(14Q32.33) MUTATED DEL PEAK 21(14Q32.33) WILD-TYPE 
                             54                             103 
  DEL PEAK 21(14Q32.33) MUTATED DEL PEAK 21(14Q32.33) WILD-TYPE 
                             22                              44 
$`DEL PEAK 21(14Q32.33) MUTATED`
TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10Z TCGA-BC-A112 TCGA-BC-A217 
       37.32        10.13        27.52         1.12         5.03        13.84 
TCGA-BC-A3KF TCGA-BC-A3KG TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-A1HT 
        0.26        22.36         0.07         2.86         0.39         3.32 
TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A115 TCGA-DD-A11A 
        0.07         0.10         0.13        79.73        83.57         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        29.16        13.64 
TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A3A1 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NB 
       55.69         5.62         7.66        13.78        30.61        32.52 
TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NO TCGA-DD-A4NQ TCGA-DD-A73G 
       14.24        18.44        15.06        73.81        12.26       100.96 
TCGA-ED-A459 TCGA-ED-A7PX TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-ED-A82E TCGA-EP-A12J 
       13.41         0.20         0.20         0.20         0.20        18.74 
TCGA-EP-A2KB TCGA-EP-A3RK TCGA-FV-A3I0 TCGA-FV-A495 TCGA-FV-A4ZP TCGA-G3-A25S 
       10.98        11.93        27.88         0.03        60.36         1.22 
TCGA-G3-A25X TCGA-G3-A3CH TCGA-G3-A5SM TCGA-G3-A7M9 TCGA-KR-A7K7 TCGA-NI-A8LF 
       58.49        25.64         4.37         1.84        13.38        16.37 

$`DEL PEAK 21(14Q32.33) WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10S TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X 
       48.99        27.91        46.78        27.52         2.99        25.32 
TCGA-BC-A10Y TCGA-BC-A110 TCGA-BC-A216 TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I 
       23.34        69.57        44.42         9.50        14.60        12.72 
TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A3M9 TCGA-DD-A114 TCGA-DD-A116 TCGA-DD-A118 
        3.39         4.24         0.10        37.78        53.33       113.00 
TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11D TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC 
        7.33         0.46        51.29        79.40        66.31        19.79 
TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EK TCGA-DD-A39V 
       75.65         6.71        12.95        49.15        18.35        21.14 
TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 
       19.76        25.81        70.06        17.59        20.12       102.74 
TCGA-DD-A3A6 TCGA-DD-A3A8 TCGA-DD-A4NA TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NK 
      107.11         0.36        33.14        73.38        14.07        39.78 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NP TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV 
       56.25        29.56        93.67         0.30        80.75        66.35 
TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F 
       10.98         9.30         7.56        10.98         1.45        27.72 
TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PY 
       12.69        15.85        13.91        13.35         0.23         0.20 
TCGA-ED-A8O5 TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3JL TCGA-ES-A2HS 
        0.20        19.99        11.74         0.62         9.96        22.85 
TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 
       14.40        32.45        19.10         8.12         6.38         0.13 
TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W 
        0.33         0.39        51.06        53.79        28.27        30.74 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
       14.86        21.53        22.13         5.92        19.53        19.23 
TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-GJ-A6C0 
       14.70        11.97         7.99         7.76         5.98         1.02 
TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-LG-A6GG TCGA-MI-A75C 
        2.66         4.01         2.14        11.84         0.49         9.57 
TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A8JO TCGA-NI-A4U2 
        5.10        14.24        12.85         8.71         1.71        58.88 
TCGA-O8-A75V 
        4.44 

  DEL PEAK 21(14Q32.33) MUTATED DEL PEAK 21(14Q32.33) WILD-TYPE 
                           0.03                            0.10 
  DEL PEAK 21(14Q32.33) MUTATED DEL PEAK 21(14Q32.33) WILD-TYPE 
                         100.96                          113.00 
  DEL PEAK 21(14Q32.33) MUTATED DEL PEAK 21(14Q32.33) WILD-TYPE 
                         13.395                          14.600 
[1] "0.0 - 101.0 (13.4)" "0.1 - 113.0 (14.6)"
[1] "hr=" "1.1"
D49V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE III STAGE IIIA
  DEL PEAK 21(14Q32.33) MUTATED        17       18         0         11
  DEL PEAK 21(14Q32.33) WILD-TYPE      48       19         2         20
                                 vv
clus                              STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 21(14Q32.33) MUTATED            3          2        0         0
  DEL PEAK 21(14Q32.33) WILD-TYPE          2          3        1         1
                                 vv
clus                              STAGE IVB
  DEL PEAK 21(14Q32.33) MUTATED           1
  DEL PEAK 21(14Q32.33) WILD-TYPE         1
D49V3, multiclass
            clus
vv           DEL PEAK 21(14Q32.33) MUTATED DEL PEAK 21(14Q32.33) WILD-TYPE
  STAGE I                               17                              48
  STAGE II                              18                              19
  STAGE III                              0                               2
  STAGE IIIA                            11                              20
  STAGE IIIB                             3                               2
  STAGE IIIC                             2                               3
  STAGE IV                               0                               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 21(14Q32.33) MUTATED   18 19 16  3
  DEL PEAK 21(14Q32.33) WILD-TYPE 50 22 26  5
D49V4, multiclass
    clus
vv   DEL PEAK 21(14Q32.33) MUTATED DEL PEAK 21(14Q32.33) WILD-TYPE
  T1                            18                              50
  T2                            19                              22
  T3                            16                              26
  T4                             3                               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"
D49V5, binary
                                 cls
clus                               0  1
  DEL PEAK 21(14Q32.33) MUTATED   34  1
  DEL PEAK 21(14Q32.33) WILD-TYPE 68  2
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 21(14Q32.33) MUTATED     34    1
  DEL PEAK 21(14Q32.33) WILD-TYPE   68    2
   clus
vv  DEL PEAK 21(14Q32.33) MUTATED DEL PEAK 21(14Q32.33) WILD-TYPE
  0                            34                              68
  1                             1                               2
[1] 2 2
[1] FALSE
                                 vv
clus                              M0 M1 MX
  DEL PEAK 21(14Q32.33) MUTATED   44  1 11
  DEL PEAK 21(14Q32.33) WILD-TYPE 76  2 26
D49V6, multiclass
    clus
vv   DEL PEAK 21(14Q32.33) MUTATED DEL PEAK 21(14Q32.33) WILD-TYPE
  M0                            44                              76
  M1                             1                               2
  MX                            11                              26
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V7, binary
                                 cls
clus                               0  1
  DEL PEAK 21(14Q32.33) MUTATED   21 35
  DEL PEAK 21(14Q32.33) WILD-TYPE 39 65
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 21(14Q32.33) MUTATED     21   35
  DEL PEAK 21(14Q32.33) WILD-TYPE   39   65
        clus
vv       DEL PEAK 21(14Q32.33) MUTATED DEL PEAK 21(14Q32.33) WILD-TYPE
  FEMALE                            21                              39
  MALE                              35                              65
[1] 2 2
[1] FALSE
                                 vv
clus                              FIBROLAMELLAR CARCINOMA
  DEL PEAK 21(14Q32.33) MUTATED                         1
  DEL PEAK 21(14Q32.33) WILD-TYPE                       1
                                 vv
clus                              HEPATOCELLULAR CARCINOMA
  DEL PEAK 21(14Q32.33) MUTATED                         54
  DEL PEAK 21(14Q32.33) WILD-TYPE                      102
                                 vv
clus                              HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK 21(14Q32.33) MUTATED                                  1
  DEL PEAK 21(14Q32.33) WILD-TYPE                                1
D49V8, multiclass
                                  clus
vv                                 DEL PEAK 21(14Q32.33) MUTATED
  FIBROLAMELLAR CARCINOMA                                      1
  HEPATOCELLULAR CARCINOMA                                    54
  HEPATOCHOLANGIOCARCINOMA (MIXED)                             1
                                  clus
vv                                 DEL PEAK 21(14Q32.33) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                        1
  HEPATOCELLULAR CARCINOMA                                     102
  HEPATOCHOLANGIOCARCINOMA (MIXED)                               1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              R0 R1 R2 RX
  DEL PEAK 21(14Q32.33) MUTATED   44  4  0  6
  DEL PEAK 21(14Q32.33) WILD-TYPE 87  7  1  6
D49V9, multiclass
    clus
vv   DEL PEAK 21(14Q32.33) MUTATED DEL PEAK 21(14Q32.33) WILD-TYPE
  R0                            44                              87
  R1                             4                               7
  R2                             0                               1
  RX                             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"
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 21(14Q32.33) MUTATED                                  0    17
  DEL PEAK 21(14Q32.33) WILD-TYPE                                1    19
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 21(14Q32.33) MUTATED                           3    34
  DEL PEAK 21(14Q32.33) WILD-TYPE                         5    75
D49V10, multiclass
                                  clus
vv                                 DEL PEAK 21(14Q32.33) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                       17
  BLACK OR AFRICAN AMERICAN                                    3
  WHITE                                                       34
                                  clus
vv                                 DEL PEAK 21(14Q32.33) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               1
  ASIAN                                                         19
  BLACK OR AFRICAN AMERICAN                                      5
  WHITE                                                         75
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V11, binary
                                 cls
clus                               0  1
  DEL PEAK 21(14Q32.33) MUTATED    1 49
  DEL PEAK 21(14Q32.33) WILD-TYPE  2 94
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 21(14Q32.33) MUTATED      1   49
  DEL PEAK 21(14Q32.33) WILD-TYPE    2   94
                        clus
vv                       DEL PEAK 21(14Q32.33) MUTATED
  HISPANIC OR LATINO                                 1
  NOT HISPANIC OR LATINO                            49
                        clus
vv                       DEL PEAK 21(14Q32.33) WILD-TYPE
  HISPANIC OR LATINO                                   2
  NOT HISPANIC OR LATINO                              94
[1] 2 2
[1] FALSE

Clustering(50) Variable = DEL PEAK 22(16Q23.2) MUTATION ANALYSIS
D50V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 22(16Q23.2) MUTATED   36 28
  DEL PEAK 22(16Q23.2) WILD-TYPE 55 38
  DEL PEAK 22(16Q23.2) MUTATED DEL PEAK 22(16Q23.2) WILD-TYPE 
                            64                             93 
  DEL PEAK 22(16Q23.2) MUTATED DEL PEAK 22(16Q23.2) WILD-TYPE 
                            28                             38 
$`DEL PEAK 22(16Q23.2) MUTATED`
TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10W TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A216 
       10.13        46.78         2.99        23.34         1.12        44.42 
TCGA-BC-A217 TCGA-BC-A3KG TCGA-BC-A69H TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 
       13.84        22.36        14.60         0.07         2.86         0.39 
TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A3M9 TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 
        3.39         4.24         0.10         0.10         0.13        79.73 
TCGA-DD-A114 TCGA-DD-A116 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A1EF TCGA-DD-A1EH 
       37.78        53.33         2.60         0.46        12.95        49.15 
TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A8 TCGA-DD-A3A9 
        6.02        29.16         5.62        19.76         0.36        30.61 
TCGA-DD-A4ND TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NN TCGA-DD-A4NO 
       73.38        14.24        18.44        15.06        29.56        73.81 
TCGA-DD-A4NQ TCGA-DD-A73B TCGA-DD-A73F TCGA-ED-A459 TCGA-ED-A5KG TCGA-ED-A66X 
       12.26         9.30        27.72        13.41        15.85        13.35 
TCGA-ED-A66Y TCGA-ED-A7PY TCGA-ED-A8O5 TCGA-EP-A2KB TCGA-ES-A2HS TCGA-FV-A23B 
        0.23         0.20         0.20        10.98        22.85        32.45 
TCGA-FV-A3I0 TCGA-FV-A3R2 TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25X TCGA-G3-A25Y 
       27.88         6.38         1.22        53.79        58.49        14.86 
TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A5SI TCGA-G3-A7M9 TCGA-KR-A7K7 TCGA-LG-A6GG 
       21.53        25.64        14.70         1.84        13.38         0.49 
TCGA-MI-A75G TCGA-MI-A75I TCGA-NI-A8LF TCGA-O8-A75V 
       14.24         8.71        16.37         4.44 

$`DEL PEAK 22(16Q23.2) WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10X 
       48.99        27.91        37.32        27.52        27.52        25.32 
TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A3KF TCGA-BC-A5W4 TCGA-BC-A69I TCGA-CC-A1HT 
       69.57         5.03         0.26         9.50        12.72         3.32 
TCGA-CC-A3MA TCGA-DD-A115 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11C TCGA-DD-A11D 
        0.07        83.57       113.00         7.33        21.76        51.29 
TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE 
       90.71        79.40        66.31        19.79        75.65         6.71 
TCGA-DD-A1EG TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A3A0 
       45.11        18.35        13.64        21.14        55.69        25.81 
TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 
        7.66        70.06        17.59        20.12       102.74       107.11 
TCGA-DD-A3A7 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NF TCGA-DD-A4NK TCGA-DD-A4NL 
       13.78        33.14        32.52        14.07        39.78        56.25 
TCGA-DD-A4NP TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73C 
       93.67         0.30        80.75        66.35        10.98         7.56 
TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73G TCGA-ED-A4XI TCGA-ED-A627 TCGA-ED-A7PX 
       10.98         1.45       100.96        12.69        13.91         0.20 
TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-ED-A82E TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
        0.20         0.20         0.20        18.74        19.99        11.74 
TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A2QR TCGA-FV-A3I1 
        0.62         9.96        11.93        14.40        19.10         8.12 
TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25T 
        0.13         0.03         0.33        60.36         0.39        51.06 
TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
       28.27        30.74        22.13         5.92        19.53        19.23 
TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-GJ-A6C0 
       11.97         7.99         4.37         7.76         5.98         1.02 
TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-MI-A75C TCGA-MI-A75E 
        2.66         4.01         2.14        11.84         9.57         5.10 
TCGA-MI-A75H TCGA-MR-A8JO TCGA-NI-A4U2 
       12.85         1.71        58.88 

  DEL PEAK 22(16Q23.2) MUTATED DEL PEAK 22(16Q23.2) WILD-TYPE 
                          0.07                           0.03 
  DEL PEAK 22(16Q23.2) MUTATED DEL PEAK 22(16Q23.2) WILD-TYPE 
                         79.73                         113.00 
  DEL PEAK 22(16Q23.2) MUTATED DEL PEAK 22(16Q23.2) WILD-TYPE 
                        13.625                         14.070 
[1] "0.1 - 79.7 (13.6)"  "0.0 - 113.0 (14.1)"
[1] "hr=" "1.6"
D50V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IIIA
  DEL PEAK 22(16Q23.2) MUTATED        21       22         1         11
  DEL PEAK 22(16Q23.2) WILD-TYPE      44       15         1         20
                                vv
clus                             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 22(16Q23.2) MUTATED            2          3        0         1
  DEL PEAK 22(16Q23.2) WILD-TYPE          3          2        1         0
                                vv
clus                             STAGE IVB
  DEL PEAK 22(16Q23.2) MUTATED           1
  DEL PEAK 22(16Q23.2) WILD-TYPE         1
D50V3, multiclass
            clus
vv           DEL PEAK 22(16Q23.2) MUTATED DEL PEAK 22(16Q23.2) WILD-TYPE
  STAGE I                              21                             44
  STAGE II                             22                             15
  STAGE III                             1                              1
  STAGE IIIA                           11                             20
  STAGE IIIB                            2                              3
  STAGE IIIC                            3                              2
  STAGE IV                              0                              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 22(16Q23.2) MUTATED   23 23 16  5
  DEL PEAK 22(16Q23.2) WILD-TYPE 45 18 26  3
D50V4, multiclass
    clus
vv   DEL PEAK 22(16Q23.2) MUTATED DEL PEAK 22(16Q23.2) WILD-TYPE
  T1                           23                             45
  T2                           23                             18
  T3                           16                             26
  T4                            5                              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"
D50V5, binary
                                cls
clus                              0  1
  DEL PEAK 22(16Q23.2) MUTATED   43  2
  DEL PEAK 22(16Q23.2) WILD-TYPE 59  1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 22(16Q23.2) MUTATED     43    2
  DEL PEAK 22(16Q23.2) WILD-TYPE   59    1
   clus
vv  DEL PEAK 22(16Q23.2) MUTATED DEL PEAK 22(16Q23.2) WILD-TYPE
  0                           43                             59
  1                            2                              1
[1] 2 2
[1] FALSE
                                vv
clus                             M0 M1 MX
  DEL PEAK 22(16Q23.2) MUTATED   52  1 14
  DEL PEAK 22(16Q23.2) WILD-TYPE 68  2 23
D50V6, multiclass
    clus
vv   DEL PEAK 22(16Q23.2) MUTATED DEL PEAK 22(16Q23.2) WILD-TYPE
  M0                           52                             68
  M1                            1                              2
  MX                           14                             23
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V7, binary
                                cls
clus                              0  1
  DEL PEAK 22(16Q23.2) MUTATED   28 39
  DEL PEAK 22(16Q23.2) WILD-TYPE 32 61
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 22(16Q23.2) MUTATED     28   39
  DEL PEAK 22(16Q23.2) WILD-TYPE   32   61
        clus
vv       DEL PEAK 22(16Q23.2) MUTATED DEL PEAK 22(16Q23.2) WILD-TYPE
  FEMALE                           28                             32
  MALE                             39                             61
[1] 2 2
[1] FALSE
                                vv
clus                             FIBROLAMELLAR CARCINOMA
  DEL PEAK 22(16Q23.2) MUTATED                         0
  DEL PEAK 22(16Q23.2) WILD-TYPE                       2
                                vv
clus                             HEPATOCELLULAR CARCINOMA
  DEL PEAK 22(16Q23.2) MUTATED                         66
  DEL PEAK 22(16Q23.2) WILD-TYPE                       90
                                vv
clus                             HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK 22(16Q23.2) MUTATED                                  1
  DEL PEAK 22(16Q23.2) WILD-TYPE                                1
D50V8, multiclass
                                  clus
vv                                 DEL PEAK 22(16Q23.2) MUTATED
  FIBROLAMELLAR CARCINOMA                                     0
  HEPATOCELLULAR CARCINOMA                                   66
  HEPATOCHOLANGIOCARCINOMA (MIXED)                            1
                                  clus
vv                                 DEL PEAK 22(16Q23.2) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                       2
  HEPATOCELLULAR CARCINOMA                                     90
  HEPATOCHOLANGIOCARCINOMA (MIXED)                              1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             R0 R1 R2 RX
  DEL PEAK 22(16Q23.2) MUTATED   56  3  0  7
  DEL PEAK 22(16Q23.2) WILD-TYPE 75  8  1  5
D50V9, multiclass
    clus
vv   DEL PEAK 22(16Q23.2) MUTATED DEL PEAK 22(16Q23.2) WILD-TYPE
  R0                           56                             75
  R1                            3                              8
  R2                            0                              1
  RX                            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"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 22(16Q23.2) MUTATED                                  0    25
  DEL PEAK 22(16Q23.2) WILD-TYPE                                1    11
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 22(16Q23.2) MUTATED                           3    37
  DEL PEAK 22(16Q23.2) WILD-TYPE                         5    72
D50V10, multiclass
                                  clus
vv                                 DEL PEAK 22(16Q23.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                      25
  BLACK OR AFRICAN AMERICAN                                   3
  WHITE                                                      37
                                  clus
vv                                 DEL PEAK 22(16Q23.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        11
  BLACK OR AFRICAN AMERICAN                                     5
  WHITE                                                        72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V11, binary
                                cls
clus                              0  1
  DEL PEAK 22(16Q23.2) MUTATED    3 60
  DEL PEAK 22(16Q23.2) WILD-TYPE  0 83
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 22(16Q23.2) MUTATED      3   60
  DEL PEAK 22(16Q23.2) WILD-TYPE    0   83
                        clus
vv                       DEL PEAK 22(16Q23.2) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           60
                        clus
vv                       DEL PEAK 22(16Q23.2) WILD-TYPE
  HISPANIC OR LATINO                                  0
  NOT HISPANIC OR LATINO                             83
[1] 2 2
[1] FALSE

Clustering(51) Variable = DEL PEAK 23(17P11.2) MUTATION ANALYSIS
D51V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 23(17P11.2) MUTATED   42 40
  DEL PEAK 23(17P11.2) WILD-TYPE 49 26
  DEL PEAK 23(17P11.2) MUTATED DEL PEAK 23(17P11.2) WILD-TYPE 
                            82                             75 
  DEL PEAK 23(17P11.2) MUTATED DEL PEAK 23(17P11.2) WILD-TYPE 
                            40                             26 
$`DEL PEAK 23(17P11.2) MUTATED`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10Y 
       48.99        27.91        10.13        27.52        27.52        23.34 
TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG 
        1.12        69.57         5.03        13.84         0.26        22.36 
TCGA-BC-A5W4 TCGA-BC-A69H TCGA-CC-5258 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 
        9.50        14.60         0.07         0.39         3.39         4.24 
TCGA-CC-A1HT TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A114 TCGA-DD-A115 
        3.32         0.07         0.10         0.13        37.78        83.57 
TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1EA 
       53.33       113.00         7.33        21.76        51.29        79.40 
TCGA-DD-A1EB TCGA-DD-A1EG TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL 
       66.31        45.11         6.02        29.16        18.35        13.64 
TCGA-DD-A39Y TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A7 TCGA-DD-A4NA 
        5.62        17.59        20.12       102.74        13.78        33.14 
TCGA-DD-A4NB TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NO TCGA-DD-A4NQ 
       32.52        14.24        18.44        15.06        73.81        12.26 
TCGA-DD-A73B TCGA-DD-A73E TCGA-ED-A459 TCGA-ED-A7PX TCGA-ED-A82E TCGA-EP-A2KC 
        9.30         1.45        13.41         0.20         0.20         0.62 
TCGA-ES-A2HS TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 
       22.85        32.45        19.10        27.88         8.12         6.38 
TCGA-FV-A495 TCGA-FV-A4ZP TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W 
        0.03        60.36         1.22        53.79        28.27        30.74 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A5SL TCGA-G3-A5SM 
       14.86        21.53        22.13        25.64         7.99         4.37 
TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-LG-A6GG TCGA-MI-A75E 
        1.84         1.02         2.14        11.84         0.49         5.10 
TCGA-MI-A75G TCGA-MI-A75I TCGA-NI-A4U2 TCGA-NI-A8LF 
       14.24         8.71        58.88        16.37 

$`DEL PEAK 23(17P11.2) WILD-TYPE`
TCGA-BC-A10Q TCGA-BC-A10S TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A216 TCGA-BC-A69I 
       37.32        46.78         2.99        25.32        44.42        12.72 
TCGA-CC-5260 TCGA-CC-A3M9 TCGA-DD-A113 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A1E9 
        2.86         0.10        79.73         2.60         0.46        90.71 
TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A39V 
       19.79        75.65         6.71        12.95        49.15        21.14 
TCGA-DD-A39X TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A6 
       55.69        19.76        25.81         7.66        70.06       107.11 
TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NK TCGA-DD-A4NL 
        0.36        30.61        73.38        14.07        39.78        56.25 
TCGA-DD-A4NN TCGA-DD-A4NP TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A 
       29.56        93.67         0.30        80.75        66.35        10.98 
TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A4XI TCGA-ED-A5KG 
        7.56        10.98        27.72       100.96        12.69        15.85 
TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XP 
       13.91        13.35         0.23         0.20         0.20         0.20 
TCGA-ED-A8O5 TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A3JL 
        0.20        18.74        19.99        11.74        10.98         9.96 
TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A3R3 TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25T 
       11.93        14.40         0.13         0.33         0.39        51.06 
TCGA-G3-A25X TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ 
       58.49         5.92        19.53        19.23        14.70        11.97 
TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K7 TCGA-MI-A75C 
        7.76         5.98         2.66         4.01        13.38         9.57 
TCGA-MI-A75H TCGA-MR-A8JO TCGA-O8-A75V 
       12.85         1.71         4.44 

  DEL PEAK 23(17P11.2) MUTATED DEL PEAK 23(17P11.2) WILD-TYPE 
                          0.03                           0.10 
  DEL PEAK 23(17P11.2) MUTATED DEL PEAK 23(17P11.2) WILD-TYPE 
                        113.00                         107.11 
  DEL PEAK 23(17P11.2) MUTATED DEL PEAK 23(17P11.2) WILD-TYPE 
                         14.42                          13.35 
[1] "0.0 - 113.0 (14.4)" "0.1 - 107.1 (13.3)"
[1] "hr=" "1.5"
D51V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IIIA
  DEL PEAK 23(17P11.2) MUTATED        27       22         1         16
  DEL PEAK 23(17P11.2) WILD-TYPE      38       15         1         15
                                vv
clus                             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 23(17P11.2) MUTATED            4          4        1         1
  DEL PEAK 23(17P11.2) WILD-TYPE          1          1        0         0
                                vv
clus                             STAGE IVB
  DEL PEAK 23(17P11.2) MUTATED           1
  DEL PEAK 23(17P11.2) WILD-TYPE         1
D51V3, multiclass
            clus
vv           DEL PEAK 23(17P11.2) MUTATED DEL PEAK 23(17P11.2) WILD-TYPE
  STAGE I                              27                             38
  STAGE II                             22                             15
  STAGE III                             1                              1
  STAGE IIIA                           16                             15
  STAGE IIIB                            4                              1
  STAGE IIIC                            4                              1
  STAGE IV                              1                              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 23(17P11.2) MUTATED   30 25 24  5
  DEL PEAK 23(17P11.2) WILD-TYPE 38 16 18  3
D51V4, multiclass
    clus
vv   DEL PEAK 23(17P11.2) MUTATED DEL PEAK 23(17P11.2) WILD-TYPE
  T1                           30                             38
  T2                           25                             16
  T3                           24                             18
  T4                            5                              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"
D51V5, binary
                                cls
clus                              0  1
  DEL PEAK 23(17P11.2) MUTATED   52  3
  DEL PEAK 23(17P11.2) WILD-TYPE 50  0
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(17P11.2) MUTATED     52    3
  DEL PEAK 23(17P11.2) WILD-TYPE   50    0
   clus
vv  DEL PEAK 23(17P11.2) MUTATED DEL PEAK 23(17P11.2) WILD-TYPE
  0                           52                             50
  1                            3                              0
[1] 2 2
[1] FALSE
                                vv
clus                             M0 M1 MX
  DEL PEAK 23(17P11.2) MUTATED   63  2 19
  DEL PEAK 23(17P11.2) WILD-TYPE 57  1 18
D51V6, multiclass
    clus
vv   DEL PEAK 23(17P11.2) MUTATED DEL PEAK 23(17P11.2) WILD-TYPE
  M0                           63                             57
  M1                            2                              1
  MX                           19                             18
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V7, binary
                                cls
clus                              0  1
  DEL PEAK 23(17P11.2) MUTATED   28 56
  DEL PEAK 23(17P11.2) WILD-TYPE 32 44
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(17P11.2) MUTATED     28   56
  DEL PEAK 23(17P11.2) WILD-TYPE   32   44
        clus
vv       DEL PEAK 23(17P11.2) MUTATED DEL PEAK 23(17P11.2) WILD-TYPE
  FEMALE                           28                             32
  MALE                             56                             44
[1] 2 2
[1] FALSE
                                vv
clus                             FIBROLAMELLAR CARCINOMA
  DEL PEAK 23(17P11.2) MUTATED                         1
  DEL PEAK 23(17P11.2) WILD-TYPE                       1
                                vv
clus                             HEPATOCELLULAR CARCINOMA
  DEL PEAK 23(17P11.2) MUTATED                         81
  DEL PEAK 23(17P11.2) WILD-TYPE                       75
                                vv
clus                             HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK 23(17P11.2) MUTATED                                  2
  DEL PEAK 23(17P11.2) WILD-TYPE                                0
D51V8, multiclass
                                  clus
vv                                 DEL PEAK 23(17P11.2) MUTATED
  FIBROLAMELLAR CARCINOMA                                     1
  HEPATOCELLULAR CARCINOMA                                   81
  HEPATOCHOLANGIOCARCINOMA (MIXED)                            2
                                  clus
vv                                 DEL PEAK 23(17P11.2) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                       1
  HEPATOCELLULAR CARCINOMA                                     75
  HEPATOCHOLANGIOCARCINOMA (MIXED)                              0
[1] 3 2
[1] 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(17P11.2) MUTATED   66  8  1  7
  DEL PEAK 23(17P11.2) WILD-TYPE 65  3  0  5
D51V9, multiclass
    clus
vv   DEL PEAK 23(17P11.2) MUTATED DEL PEAK 23(17P11.2) WILD-TYPE
  R0                           66                             65
  R1                            8                              3
  R2                            1                              0
  RX                            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"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 23(17P11.2) MUTATED                                  0    21
  DEL PEAK 23(17P11.2) WILD-TYPE                                1    15
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 23(17P11.2) MUTATED                           5    56
  DEL PEAK 23(17P11.2) WILD-TYPE                         3    53
D51V10, multiclass
                                  clus
vv                                 DEL PEAK 23(17P11.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                      21
  BLACK OR AFRICAN AMERICAN                                   5
  WHITE                                                      56
                                  clus
vv                                 DEL PEAK 23(17P11.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        15
  BLACK OR AFRICAN AMERICAN                                     3
  WHITE                                                        53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V11, binary
                                cls
clus                              0  1
  DEL PEAK 23(17P11.2) MUTATED    2 75
  DEL PEAK 23(17P11.2) WILD-TYPE  1 68
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(17P11.2) MUTATED      2   75
  DEL PEAK 23(17P11.2) WILD-TYPE    1   68
                        clus
vv                       DEL PEAK 23(17P11.2) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           75
                        clus
vv                       DEL PEAK 23(17P11.2) WILD-TYPE
  HISPANIC OR LATINO                                  1
  NOT HISPANIC OR LATINO                             68
[1] 2 2
[1] FALSE

Clustering(52) Variable = DEL PEAK 24(19P13.3) MUTATION ANALYSIS
D52V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 24(19P13.3) MUTATED   20 13
  DEL PEAK 24(19P13.3) WILD-TYPE 71 53
  DEL PEAK 24(19P13.3) MUTATED DEL PEAK 24(19P13.3) WILD-TYPE 
                            33                            124 
  DEL PEAK 24(19P13.3) MUTATED DEL PEAK 24(19P13.3) WILD-TYPE 
                            13                             53 
$`DEL PEAK 24(19P13.3) MUTATED`
TCGA-BC-A10W TCGA-BC-A112 TCGA-BC-A3KF TCGA-BC-A69H TCGA-CC-5258 TCGA-CC-5263 
        2.99         5.03         0.26        14.60         0.07         4.24 
TCGA-CC-A1HT TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A118 TCGA-DD-A11A TCGA-DD-A1EG 
        3.32         0.13        79.73       113.00         2.60        45.11 
TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A3A9 
        6.02        29.16        13.64        55.69         5.62        30.61 
TCGA-DD-A4NJ TCGA-DD-A4NQ TCGA-DD-A73D TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A7PZ 
       15.06        12.26        10.98        13.41        12.69         0.20 
TCGA-FV-A3I1 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-G3-A25S TCGA-G3-A25X TCGA-G3-A3CH 
        8.12         0.33        60.36         1.22        58.49        25.64 
TCGA-G3-A5SM TCGA-MI-A75C TCGA-NI-A8LF 
        4.37         9.57        16.37 

$`DEL PEAK 24(19P13.3) WILD-TYPE`
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-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A216 
       27.52        25.32        23.34         1.12        69.57        44.42 
TCGA-BC-A217 TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69I TCGA-CC-5260 TCGA-CC-5261 
       13.84        22.36         9.50        12.72         2.86         0.39 
TCGA-CC-5262 TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-DD-A114 TCGA-DD-A115 
        3.39         0.10         0.07         0.10        37.78        83.57 
TCGA-DD-A116 TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 
       53.33         7.33         0.46        21.76        51.29        90.71 
TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF 
       79.40        66.31        19.79        75.65         6.71        12.95 
TCGA-DD-A1EH TCGA-DD-A1EK TCGA-DD-A39V TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 
       49.15        18.35        21.14        19.76        25.81         7.66 
TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 
       70.06        17.59        20.12       102.74       107.11        13.78 
TCGA-DD-A3A8 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH 
        0.36        33.14        32.52        73.38        14.07        14.24 
TCGA-DD-A4NI TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP 
       18.44        39.78        56.25        29.56        73.81        93.67 
TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C 
        0.30        80.75        66.35        10.98         9.30         7.56 
TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X 
        1.45        27.72       100.96        15.85        13.91        13.35 
TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 
        0.23         0.20         0.20         0.20         0.20         0.20 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL 
       18.74        19.99        11.74        10.98         0.62         9.96 
TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 
       11.93        22.85        14.40        32.45        19.10        27.88 
TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25U 
        6.38         0.13         0.03         0.39        51.06        53.79 
TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CI 
       28.27        30.74        14.86        21.53        22.13         5.92 
TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A6UC 
       19.53        19.23        14.70        11.97         7.99         7.76 
TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 
        5.98         1.84         1.02         2.66         4.01         2.14 
TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H 
       11.84        13.38         0.49         5.10        14.24        12.85 
TCGA-MI-A75I TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-O8-A75V 
        8.71         1.71        58.88         4.44 

  DEL PEAK 24(19P13.3) MUTATED DEL PEAK 24(19P13.3) WILD-TYPE 
                          0.07                           0.03 
  DEL PEAK 24(19P13.3) MUTATED DEL PEAK 24(19P13.3) WILD-TYPE 
                        113.00                         107.11 
  DEL PEAK 24(19P13.3) MUTATED DEL PEAK 24(19P13.3) WILD-TYPE 
                         10.98                          14.55 
[1] "0.1 - 113.0 (11.0)" "0.0 - 107.1 (14.6)"
[1] "hr=" "1.1"
D52V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IIIA
  DEL PEAK 24(19P13.3) MUTATED        11       14         0          5
  DEL PEAK 24(19P13.3) WILD-TYPE      54       23         2         26
                                vv
clus                             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 24(19P13.3) MUTATED            0          1        0         0
  DEL PEAK 24(19P13.3) WILD-TYPE          5          4        1         1
                                vv
clus                             STAGE IVB
  DEL PEAK 24(19P13.3) MUTATED           1
  DEL PEAK 24(19P13.3) WILD-TYPE         1
D52V3, multiclass
            clus
vv           DEL PEAK 24(19P13.3) MUTATED DEL PEAK 24(19P13.3) WILD-TYPE
  STAGE I                              11                             54
  STAGE II                             14                             23
  STAGE III                             0                              2
  STAGE IIIA                            5                             26
  STAGE IIIB                            0                              5
  STAGE IIIC                            1                              4
  STAGE IV                              0                              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 24(19P13.3) MUTATED   12 14  6  2
  DEL PEAK 24(19P13.3) WILD-TYPE 56 27 36  6
D52V4, multiclass
    clus
vv   DEL PEAK 24(19P13.3) MUTATED DEL PEAK 24(19P13.3) WILD-TYPE
  T1                           12                             56
  T2                           14                             27
  T3                            6                             36
  T4                            2                              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"
D52V5, binary
                                cls
clus                              0  1
  DEL PEAK 24(19P13.3) MUTATED   20  1
  DEL PEAK 24(19P13.3) WILD-TYPE 82  2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(19P13.3) MUTATED     20    1
  DEL PEAK 24(19P13.3) WILD-TYPE   82    2
   clus
vv  DEL PEAK 24(19P13.3) MUTATED DEL PEAK 24(19P13.3) WILD-TYPE
  0                           20                             82
  1                            1                              2
[1] 2 2
[1] FALSE
                                vv
clus                             M0 M1 MX
  DEL PEAK 24(19P13.3) MUTATED   27  1  6
  DEL PEAK 24(19P13.3) WILD-TYPE 93  2 31
D52V6, multiclass
    clus
vv   DEL PEAK 24(19P13.3) MUTATED DEL PEAK 24(19P13.3) WILD-TYPE
  M0                           27                             93
  M1                            1                              2
  MX                            6                             31
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V7, binary
                                cls
clus                              0  1
  DEL PEAK 24(19P13.3) MUTATED   10 24
  DEL PEAK 24(19P13.3) WILD-TYPE 50 76
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(19P13.3) MUTATED     10   24
  DEL PEAK 24(19P13.3) WILD-TYPE   50   76
        clus
vv       DEL PEAK 24(19P13.3) MUTATED DEL PEAK 24(19P13.3) WILD-TYPE
  FEMALE                           10                             50
  MALE                             24                             76
[1] 2 2
[1] FALSE
                                vv
clus                             FIBROLAMELLAR CARCINOMA
  DEL PEAK 24(19P13.3) MUTATED                         0
  DEL PEAK 24(19P13.3) WILD-TYPE                       2
                                vv
clus                             HEPATOCELLULAR CARCINOMA
  DEL PEAK 24(19P13.3) MUTATED                         34
  DEL PEAK 24(19P13.3) WILD-TYPE                      122
                                vv
clus                             HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK 24(19P13.3) MUTATED                                  0
  DEL PEAK 24(19P13.3) WILD-TYPE                                2
D52V8, multiclass
                                  clus
vv                                 DEL PEAK 24(19P13.3) MUTATED
  FIBROLAMELLAR CARCINOMA                                     0
  HEPATOCELLULAR CARCINOMA                                   34
  HEPATOCHOLANGIOCARCINOMA (MIXED)                            0
                                  clus
vv                                 DEL PEAK 24(19P13.3) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                       2
  HEPATOCELLULAR CARCINOMA                                    122
  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(19P13.3) MUTATED    27   3   0   3
  DEL PEAK 24(19P13.3) WILD-TYPE 104   8   1   9
D52V9, multiclass
    clus
vv   DEL PEAK 24(19P13.3) MUTATED DEL PEAK 24(19P13.3) WILD-TYPE
  R0                           27                            104
  R1                            3                              8
  R2                            0                              1
  RX                            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"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 24(19P13.3) MUTATED                                  0    12
  DEL PEAK 24(19P13.3) WILD-TYPE                                1    24
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 24(19P13.3) MUTATED                           2    20
  DEL PEAK 24(19P13.3) WILD-TYPE                         6    89
D52V10, multiclass
                                  clus
vv                                 DEL PEAK 24(19P13.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                      12
  BLACK OR AFRICAN AMERICAN                                   2
  WHITE                                                      20
                                  clus
vv                                 DEL PEAK 24(19P13.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        24
  BLACK OR AFRICAN AMERICAN                                     6
  WHITE                                                        89
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V11, binary
                                cls
clus                               0   1
  DEL PEAK 24(19P13.3) MUTATED     1  32
  DEL PEAK 24(19P13.3) WILD-TYPE   2 111
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(19P13.3) MUTATED      1   32
  DEL PEAK 24(19P13.3) WILD-TYPE    2  111
                        clus
vv                       DEL PEAK 24(19P13.3) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           32
                        clus
vv                       DEL PEAK 24(19P13.3) WILD-TYPE
  HISPANIC OR LATINO                                  2
  NOT HISPANIC OR LATINO                            111
[1] 2 2
[1] FALSE

Clustering(53) Variable = DEL PEAK 25(22Q13.32) MUTATION ANALYSIS
D53V1, survival
                                 sevent
clus2                              0  1
  DEL PEAK 25(22Q13.32) MUTATED   26 18
  DEL PEAK 25(22Q13.32) WILD-TYPE 65 48
  DEL PEAK 25(22Q13.32) MUTATED DEL PEAK 25(22Q13.32) WILD-TYPE 
                             44                             113 
  DEL PEAK 25(22Q13.32) MUTATED DEL PEAK 25(22Q13.32) WILD-TYPE 
                             18                              48 
$`DEL PEAK 25(22Q13.32) MUTATED`
TCGA-BC-A10Q TCGA-BC-A10T TCGA-BC-A10Y TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG 
       37.32        27.52        23.34        13.84         0.26        22.36 
TCGA-BC-A5W4 TCGA-CC-5260 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-DD-A113 TCGA-DD-A114 
        9.50         2.86         3.32         0.10        79.73        37.78 
TCGA-DD-A115 TCGA-DD-A1EB TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A3A5 TCGA-DD-A3A6 
       83.57        66.31        55.69         5.62       102.74       107.11 
TCGA-DD-A3A7 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NO 
       13.78        33.14        32.52        18.44        15.06        73.81 
TCGA-DD-A4NP TCGA-DD-A73B TCGA-ED-A459 TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7XP 
       93.67         9.30        13.41         0.23         0.20         0.20 
TCGA-EP-A2KB TCGA-FV-A2QR TCGA-FV-A4ZP TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A3CJ 
       10.98        19.10        60.36         1.22        51.06        19.53 
TCGA-G3-A5SI TCGA-G3-A7M9 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-MI-A75G TCGA-MI-A75I 
       14.70         1.84        11.84        13.38        14.24         8.71 
TCGA-MR-A8JO TCGA-NI-A4U2 
        1.71        58.88 

$`DEL PEAK 25(22Q13.32) WILD-TYPE`
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-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A69H 
       25.32         1.12        69.57         5.03        44.42        14.60 
TCGA-BC-A69I TCGA-CC-5258 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A3MA 
       12.72         0.07         0.39         3.39         4.24         0.07 
TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A 
        0.10         0.13        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         6.71        12.95        45.11        49.15         6.02 
TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39Z TCGA-DD-A3A0 
       29.16        18.35        13.64        21.14        19.76        25.81 
TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A8 TCGA-DD-A3A9 
        7.66        70.06        17.59        20.12         0.36        30.61 
TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN 
       73.38        14.07        14.24        39.78        56.25        29.56 
TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73C 
       12.26         0.30        80.75        66.35        10.98         7.56 
TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A4XI TCGA-ED-A5KG 
       10.98         1.45        27.72       100.96        12.69        15.85 
TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A82E TCGA-ED-A8O5 
       13.91        13.35         0.20         0.20         0.20         0.20 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK 
       18.74        19.99        11.74         0.62         9.96        11.93 
TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 
       22.85        14.40        32.45        27.88         8.12         6.38 
TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25U TCGA-G3-A25V 
        0.13         0.03         0.33         0.39        53.79        28.27 
TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH 
       30.74        58.49        14.86        21.53        22.13        25.64 
TCGA-G3-A3CI TCGA-G3-A3CK TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC 
        5.92        19.23        11.97         7.99         4.37         7.76 
TCGA-G3-A7M7 TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-LG-A6GG 
        5.98         1.02         2.66         4.01         2.14         0.49 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75H TCGA-NI-A8LF TCGA-O8-A75V 
        9.57         5.10        12.85        16.37         4.44 

  DEL PEAK 25(22Q13.32) MUTATED DEL PEAK 25(22Q13.32) WILD-TYPE 
                           0.10                            0.03 
  DEL PEAK 25(22Q13.32) MUTATED DEL PEAK 25(22Q13.32) WILD-TYPE 
                         107.11                          113.00 
  DEL PEAK 25(22Q13.32) MUTATED DEL PEAK 25(22Q13.32) WILD-TYPE 
                          14.88                           13.35 
[1] "0.1 - 107.1 (14.9)" "0.0 - 113.0 (13.3)"
[1] "hr=" "1.4"
D53V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE III STAGE IIIA
  DEL PEAK 25(22Q13.32) MUTATED        14       14         1          9
  DEL PEAK 25(22Q13.32) WILD-TYPE      51       23         1         22
                                 vv
clus                              STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 25(22Q13.32) MUTATED            2          2        0         0
  DEL PEAK 25(22Q13.32) WILD-TYPE          3          3        1         1
                                 vv
clus                              STAGE IVB
  DEL PEAK 25(22Q13.32) MUTATED           0
  DEL PEAK 25(22Q13.32) WILD-TYPE         2
D53V3, multiclass
            clus
vv           DEL PEAK 25(22Q13.32) MUTATED DEL PEAK 25(22Q13.32) WILD-TYPE
  STAGE I                               14                              51
  STAGE II                              14                              23
  STAGE III                              1                               1
  STAGE IIIA                             9                              22
  STAGE IIIB                             2                               3
  STAGE IIIC                             2                               3
  STAGE IV                               0                               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
  DEL PEAK 25(22Q13.32) MUTATED   14 17 12  3
  DEL PEAK 25(22Q13.32) WILD-TYPE 54 24 30  5
D53V4, multiclass
    clus
vv   DEL PEAK 25(22Q13.32) MUTATED DEL PEAK 25(22Q13.32) WILD-TYPE
  T1                            14                              54
  T2                            17                              24
  T3                            12                              30
  T4                             3                               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"
D53V5, binary
                                 cls
clus                               0  1
  DEL PEAK 25(22Q13.32) MUTATED   28  1
  DEL PEAK 25(22Q13.32) WILD-TYPE 74  2
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 25(22Q13.32) MUTATED     28    1
  DEL PEAK 25(22Q13.32) WILD-TYPE   74    2
   clus
vv  DEL PEAK 25(22Q13.32) MUTATED DEL PEAK 25(22Q13.32) WILD-TYPE
  0                            28                              74
  1                             1                               2
[1] 2 2
[1] FALSE
                                 vv
clus                              M0 M1 MX
  DEL PEAK 25(22Q13.32) MUTATED   37  0  9
  DEL PEAK 25(22Q13.32) WILD-TYPE 83  3 28
D53V6, multiclass
    clus
vv   DEL PEAK 25(22Q13.32) MUTATED DEL PEAK 25(22Q13.32) WILD-TYPE
  M0                            37                              83
  M1                             0                               3
  MX                             9                              28
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V7, binary
                                 cls
clus                               0  1
  DEL PEAK 25(22Q13.32) MUTATED   19 27
  DEL PEAK 25(22Q13.32) WILD-TYPE 41 73
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 25(22Q13.32) MUTATED     19   27
  DEL PEAK 25(22Q13.32) WILD-TYPE   41   73
        clus
vv       DEL PEAK 25(22Q13.32) MUTATED DEL PEAK 25(22Q13.32) WILD-TYPE
  FEMALE                            19                              41
  MALE                              27                              73
[1] 2 2
[1] FALSE
                                 vv
clus                              FIBROLAMELLAR CARCINOMA
  DEL PEAK 25(22Q13.32) MUTATED                         2
  DEL PEAK 25(22Q13.32) WILD-TYPE                       0
                                 vv
clus                              HEPATOCELLULAR CARCINOMA
  DEL PEAK 25(22Q13.32) MUTATED                         43
  DEL PEAK 25(22Q13.32) WILD-TYPE                      113
                                 vv
clus                              HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK 25(22Q13.32) MUTATED                                  1
  DEL PEAK 25(22Q13.32) WILD-TYPE                                1
D53V8, multiclass
                                  clus
vv                                 DEL PEAK 25(22Q13.32) MUTATED
  FIBROLAMELLAR CARCINOMA                                      2
  HEPATOCELLULAR CARCINOMA                                    43
  HEPATOCHOLANGIOCARCINOMA (MIXED)                             1
                                  clus
vv                                 DEL PEAK 25(22Q13.32) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                        0
  HEPATOCELLULAR CARCINOMA                                     113
  HEPATOCHOLANGIOCARCINOMA (MIXED)                               1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              R0 R1 R2 RX
  DEL PEAK 25(22Q13.32) MUTATED   35  5  0  5
  DEL PEAK 25(22Q13.32) WILD-TYPE 96  6  1  7
D53V9, multiclass
    clus
vv   DEL PEAK 25(22Q13.32) MUTATED DEL PEAK 25(22Q13.32) WILD-TYPE
  R0                            35                              96
  R1                             5                               6
  R2                             0                               1
  RX                             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"
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 25(22Q13.32) MUTATED                                  1    10
  DEL PEAK 25(22Q13.32) WILD-TYPE                                0    26
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 25(22Q13.32) MUTATED                           2    31
  DEL PEAK 25(22Q13.32) WILD-TYPE                         6    78
D53V10, multiclass
                                  clus
vv                                 DEL PEAK 25(22Q13.32) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                       10
  BLACK OR AFRICAN AMERICAN                                    2
  WHITE                                                       31
                                  clus
vv                                 DEL PEAK 25(22Q13.32) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               0
  ASIAN                                                         26
  BLACK OR AFRICAN AMERICAN                                      6
  WHITE                                                         78
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V11, binary
                                 cls
clus                                0   1
  DEL PEAK 25(22Q13.32) MUTATED     1  37
  DEL PEAK 25(22Q13.32) WILD-TYPE   2 106
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 25(22Q13.32) MUTATED      1   37
  DEL PEAK 25(22Q13.32) WILD-TYPE    2  106
                        clus
vv                       DEL PEAK 25(22Q13.32) MUTATED
  HISPANIC OR LATINO                                 1
  NOT HISPANIC OR LATINO                            37
                        clus
vv                       DEL PEAK 25(22Q13.32) WILD-TYPE
  HISPANIC OR LATINO                                   2
  NOT HISPANIC OR LATINO                             106
[1] 2 2
[1] FALSE
