[1] "ofn"        "-oTCOAD-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/COAD-TP/22506513/COAD-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/COAD-TP/22508739/transformed.cor.cli.txt"

nPatients in clinical file=458, in cluster file=451, common to both=449
[1]  66 449
[1] "AMP PEAK  1(2Q33.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  1(2Q33.1) MUTATED AMP PEAK  1(2Q33.1) WILD-TYPE 
                           92                           357 
  AMP PEAK  1(2Q33.1) MUTATED AMP PEAK  1(2Q33.1) WILD-TYPE 
                           92                           357 
[1] "AMP PEAK  2(5P13.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  2(5P13.2) MUTATED AMP PEAK  2(5P13.2) WILD-TYPE 
                           86                           363 
  AMP PEAK  2(5P13.2) MUTATED AMP PEAK  2(5P13.2) WILD-TYPE 
                           86                           363 
[1] "AMP PEAK  3(6P21.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  3(6P21.1) MUTATED AMP PEAK  3(6P21.1) WILD-TYPE 
                           96                           353 
  AMP PEAK  3(6P21.1) MUTATED AMP PEAK  3(6P21.1) WILD-TYPE 
                           96                           353 
[1] "AMP PEAK  4(8P11.23) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  4(8P11.23) MUTATED AMP PEAK  4(8P11.23) WILD-TYPE 
                           157                            292 
  AMP PEAK  4(8P11.23) MUTATED AMP PEAK  4(8P11.23) WILD-TYPE 
                           157                            292 
[1] "AMP PEAK  5(8P11.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  5(8P11.21) MUTATED AMP PEAK  5(8P11.21) WILD-TYPE 
                           187                            262 
  AMP PEAK  5(8P11.21) MUTATED AMP PEAK  5(8P11.21) WILD-TYPE 
                           187                            262 
[1] "AMP PEAK  6(8Q24.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  6(8Q24.21) MUTATED AMP PEAK  6(8Q24.21) WILD-TYPE 
                           258                            191 
  AMP PEAK  6(8Q24.21) MUTATED AMP PEAK  6(8Q24.21) WILD-TYPE 
                           258                            191 
[1] "AMP PEAK  7(11P15.5) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  7(11P15.5) MUTATED AMP PEAK  7(11P15.5) WILD-TYPE 
                            91                            358 
  AMP PEAK  7(11P15.5) MUTATED AMP PEAK  7(11P15.5) WILD-TYPE 
                            91                            358 
[1] "AMP PEAK  8(12P13.33) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  8(12P13.33) MUTATED AMP PEAK  8(12P13.33) WILD-TYPE 
                            112                             337 
  AMP PEAK  8(12P13.33) MUTATED AMP PEAK  8(12P13.33) WILD-TYPE 
                            112                             337 
[1] "AMP PEAK  9(13Q12.13) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  9(13Q12.13) MUTATED AMP PEAK  9(13Q12.13) WILD-TYPE 
                            275                             174 
  AMP PEAK  9(13Q12.13) MUTATED AMP PEAK  9(13Q12.13) WILD-TYPE 
                            275                             174 
[1] "AMP PEAK 10(13Q22.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 10(13Q22.1) MUTATED AMP PEAK 10(13Q22.1) WILD-TYPE 
                           277                            172 
  AMP PEAK 10(13Q22.1) MUTATED AMP PEAK 10(13Q22.1) WILD-TYPE 
                           277                            172 
[1] "AMP PEAK 11(16P11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 11(16P11.2) MUTATED AMP PEAK 11(16P11.2) WILD-TYPE 
                           125                            324 
  AMP PEAK 11(16P11.2) MUTATED AMP PEAK 11(16P11.2) WILD-TYPE 
                           125                            324 
[1] "AMP PEAK 12(16Q12.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 12(16Q12.1) MUTATED AMP PEAK 12(16Q12.1) WILD-TYPE 
                           111                            338 
  AMP PEAK 12(16Q12.1) MUTATED AMP PEAK 12(16Q12.1) WILD-TYPE 
                           111                            338 
[1] "AMP PEAK 13(17P11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 13(17P11.2) MUTATED AMP PEAK 13(17P11.2) WILD-TYPE 
                            44                            405 
  AMP PEAK 13(17P11.2) MUTATED AMP PEAK 13(17P11.2) WILD-TYPE 
                            44                            405 
[1] "AMP PEAK 14(17Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 14(17Q12) MUTATED AMP PEAK 14(17Q12) WILD-TYPE 
                         114                          335 
  AMP PEAK 14(17Q12) MUTATED AMP PEAK 14(17Q12) WILD-TYPE 
                         114                          335 
[1] "AMP PEAK 15(17Q24.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 15(17Q24.1) MUTATED AMP PEAK 15(17Q24.1) WILD-TYPE 
                           106                            343 
  AMP PEAK 15(17Q24.1) MUTATED AMP PEAK 15(17Q24.1) WILD-TYPE 
                           106                            343 
[1] "AMP PEAK 16(19Q13.11) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 16(19Q13.11) MUTATED AMP PEAK 16(19Q13.11) WILD-TYPE 
                             95                             354 
  AMP PEAK 16(19Q13.11) MUTATED AMP PEAK 16(19Q13.11) WILD-TYPE 
                             95                             354 
[1] "AMP PEAK 17(20P12.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 17(20P12.1) MUTATED AMP PEAK 17(20P12.1) WILD-TYPE 
                           195                            254 
  AMP PEAK 17(20P12.1) MUTATED AMP PEAK 17(20P12.1) WILD-TYPE 
                           195                            254 
[1] "AMP PEAK 18(20P11.23) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 18(20P11.23) MUTATED AMP PEAK 18(20P11.23) WILD-TYPE 
                            219                             230 
  AMP PEAK 18(20P11.23) MUTATED AMP PEAK 18(20P11.23) WILD-TYPE 
                            219                             230 
[1] "AMP PEAK 19(20P11.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 19(20P11.21) MUTATED AMP PEAK 19(20P11.21) WILD-TYPE 
                            251                             198 
  AMP PEAK 19(20P11.21) MUTATED AMP PEAK 19(20P11.21) WILD-TYPE 
                            251                             198 
[1] "AMP PEAK 20(20Q11.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 20(20Q11.21) MUTATED AMP PEAK 20(20Q11.21) WILD-TYPE 
                            321                             128 
  AMP PEAK 20(20Q11.21) MUTATED AMP PEAK 20(20Q11.21) WILD-TYPE 
                            321                             128 
[1] "AMP PEAK 21(20Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 21(20Q12) MUTATED AMP PEAK 21(20Q12) WILD-TYPE 
                         322                          127 
  AMP PEAK 21(20Q12) MUTATED AMP PEAK 21(20Q12) WILD-TYPE 
                         322                          127 
[1] "AMP PEAK 22(20Q13.12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 22(20Q13.12) MUTATED AMP PEAK 22(20Q13.12) WILD-TYPE 
                            324                             125 
  AMP PEAK 22(20Q13.12) MUTATED AMP PEAK 22(20Q13.12) WILD-TYPE 
                            324                             125 
[1] "DEL PEAK  1(1P36.11) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                           167                            282 
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                           167                            282 
[1] "DEL PEAK  2(1P33) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE 
                        123                         326 
  DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE 
                        123                         326 
[1] "DEL PEAK  3(1P13.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  3(1P13.1) MUTATED DEL PEAK  3(1P13.1) WILD-TYPE 
                          118                           331 
  DEL PEAK  3(1P13.1) MUTATED DEL PEAK  3(1P13.1) WILD-TYPE 
                          118                           331 
[1] "DEL PEAK  4(2P21) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  4(2P21) MUTATED DEL PEAK  4(2P21) WILD-TYPE 
                         17                         432 
  DEL PEAK  4(2P21) MUTATED DEL PEAK  4(2P21) WILD-TYPE 
                         17                         432 
[1] "DEL PEAK  5(2Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE 
                           24                           425 
  DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE 
                           24                           425 
[1] "DEL PEAK  6(3P26.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  6(3P26.1) MUTATED DEL PEAK  6(3P26.1) WILD-TYPE 
                           71                           378 
  DEL PEAK  6(3P26.1) MUTATED DEL PEAK  6(3P26.1) WILD-TYPE 
                           71                           378 
[1] "DEL PEAK  7(3P14.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  7(3P14.2) MUTATED DEL PEAK  7(3P14.2) WILD-TYPE 
                           87                           362 
  DEL PEAK  7(3P14.2) MUTATED DEL PEAK  7(3P14.2) WILD-TYPE 
                           87                           362 
[1] "DEL PEAK  8(3Q26.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  8(3Q26.31) MUTATED DEL PEAK  8(3Q26.31) WILD-TYPE 
                            46                            403 
  DEL PEAK  8(3Q26.31) MUTATED DEL PEAK  8(3Q26.31) WILD-TYPE 
                            46                            403 
[1] "DEL PEAK  9(4P16.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  9(4P16.2) MUTATED DEL PEAK  9(4P16.2) WILD-TYPE 
                          138                           311 
  DEL PEAK  9(4P16.2) MUTATED DEL PEAK  9(4P16.2) WILD-TYPE 
                          138                           311 
[1] "DEL PEAK 10(4Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 10(4Q22.1) MUTATED DEL PEAK 10(4Q22.1) WILD-TYPE 
                          150                           299 
  DEL PEAK 10(4Q22.1) MUTATED DEL PEAK 10(4Q22.1) WILD-TYPE 
                          150                           299 
[1] "DEL PEAK 11(4Q35.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 11(4Q35.1) MUTATED DEL PEAK 11(4Q35.1) WILD-TYPE 
                          157                           292 
  DEL PEAK 11(4Q35.1) MUTATED DEL PEAK 11(4Q35.1) WILD-TYPE 
                          157                           292 
[1] "DEL PEAK 12(5Q12.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 12(5Q12.1) MUTATED DEL PEAK 12(5Q12.1) WILD-TYPE 
                          105                           344 
  DEL PEAK 12(5Q12.1) MUTATED DEL PEAK 12(5Q12.1) WILD-TYPE 
                          105                           344 
[1] "DEL PEAK 13(5Q21.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 13(5Q21.1) MUTATED DEL PEAK 13(5Q21.1) WILD-TYPE 
                          126                           323 
  DEL PEAK 13(5Q21.1) MUTATED DEL PEAK 13(5Q21.1) WILD-TYPE 
                          126                           323 
[1] "DEL PEAK 14(5Q22.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 14(5Q22.2) MUTATED DEL PEAK 14(5Q22.2) WILD-TYPE 
                          129                           320 
  DEL PEAK 14(5Q22.2) MUTATED DEL PEAK 14(5Q22.2) WILD-TYPE 
                          129                           320 
[1] "DEL PEAK 15(6P25.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE 
                           55                           394 
  DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE 
                           55                           394 
[1] "DEL PEAK 16(6Q26) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 16(6Q26) MUTATED DEL PEAK 16(6Q26) WILD-TYPE 
                         61                         388 
  DEL PEAK 16(6Q26) MUTATED DEL PEAK 16(6Q26) WILD-TYPE 
                         61                         388 
[1] "DEL PEAK 17(7Q31.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 17(7Q31.1) MUTATED DEL PEAK 17(7Q31.1) WILD-TYPE 
                           13                           436 
  DEL PEAK 17(7Q31.1) MUTATED DEL PEAK 17(7Q31.1) WILD-TYPE 
                           13                           436 
[1] "DEL PEAK 18(8P23.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 18(8P23.2) MUTATED DEL PEAK 18(8P23.2) WILD-TYPE 
                          188                           261 
  DEL PEAK 18(8P23.2) MUTATED DEL PEAK 18(8P23.2) WILD-TYPE 
                          188                           261 
[1] "DEL PEAK 19(8P22) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 19(8P22) MUTATED DEL PEAK 19(8P22) WILD-TYPE 
                        201                         248 
  DEL PEAK 19(8P22) MUTATED DEL PEAK 19(8P22) WILD-TYPE 
                        201                         248 
[1] "DEL PEAK 20(8Q11.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 20(8Q11.1) MUTATED DEL PEAK 20(8Q11.1) WILD-TYPE 
                           30                           419 
  DEL PEAK 20(8Q11.1) MUTATED DEL PEAK 20(8Q11.1) WILD-TYPE 
                           30                           419 
[1] "DEL PEAK 21(9P21.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 21(9P21.3) MUTATED DEL PEAK 21(9P21.3) WILD-TYPE 
                           61                           388 
  DEL PEAK 21(9P21.3) MUTATED DEL PEAK 21(9P21.3) WILD-TYPE 
                           61                           388 
[1] "DEL PEAK 22(10P15.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 22(10P15.3) MUTATED DEL PEAK 22(10P15.3) WILD-TYPE 
                            78                            371 
  DEL PEAK 22(10P15.3) MUTATED DEL PEAK 22(10P15.3) WILD-TYPE 
                            78                            371 
[1] "DEL PEAK 23(10Q21.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 23(10Q21.1) MUTATED DEL PEAK 23(10Q21.1) WILD-TYPE 
                            97                            352 
  DEL PEAK 23(10Q21.1) MUTATED DEL PEAK 23(10Q21.1) WILD-TYPE 
                            97                            352 
[1] "DEL PEAK 24(10Q23.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 24(10Q23.31) MUTATED DEL PEAK 24(10Q23.31) WILD-TYPE 
                            108                             341 
  DEL PEAK 24(10Q23.31) MUTATED DEL PEAK 24(10Q23.31) WILD-TYPE 
                            108                             341 
[1] "DEL PEAK 25(10Q25.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 25(10Q25.2) MUTATED DEL PEAK 25(10Q25.2) WILD-TYPE 
                           108                            341 
  DEL PEAK 25(10Q25.2) MUTATED DEL PEAK 25(10Q25.2) WILD-TYPE 
                           108                            341 
[1] "DEL PEAK 26(12P13.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 26(12P13.2) MUTATED DEL PEAK 26(12P13.2) WILD-TYPE 
                            60                            389 
  DEL PEAK 26(12P13.2) MUTATED DEL PEAK 26(12P13.2) WILD-TYPE 
                            60                            389 
[1] "DEL PEAK 27(13Q14.13) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 27(13Q14.13) MUTATED DEL PEAK 27(13Q14.13) WILD-TYPE 
                             19                             430 
  DEL PEAK 27(13Q14.13) MUTATED DEL PEAK 27(13Q14.13) WILD-TYPE 
                             19                             430 
[1] "DEL PEAK 28(14Q31.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 28(14Q31.1) MUTATED DEL PEAK 28(14Q31.1) WILD-TYPE 
                           149                            300 
  DEL PEAK 28(14Q31.1) MUTATED DEL PEAK 28(14Q31.1) WILD-TYPE 
                           149                            300 
[1] "DEL PEAK 29(15Q11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 29(15Q11.2) MUTATED DEL PEAK 29(15Q11.2) WILD-TYPE 
                           176                            273 
  DEL PEAK 29(15Q11.2) MUTATED DEL PEAK 29(15Q11.2) WILD-TYPE 
                           176                            273 
[1] "DEL PEAK 30(15Q15.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 30(15Q15.2) MUTATED DEL PEAK 30(15Q15.2) WILD-TYPE 
                           171                            278 
  DEL PEAK 30(15Q15.2) MUTATED DEL PEAK 30(15Q15.2) WILD-TYPE 
                           171                            278 
[1] "DEL PEAK 31(15Q21.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 31(15Q21.1) MUTATED DEL PEAK 31(15Q21.1) WILD-TYPE 
                           168                            281 
  DEL PEAK 31(15Q21.1) MUTATED DEL PEAK 31(15Q21.1) WILD-TYPE 
                           168                            281 
[1] "DEL PEAK 32(15Q22.33) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 32(15Q22.33) MUTATED DEL PEAK 32(15Q22.33) WILD-TYPE 
                            160                             289 
  DEL PEAK 32(15Q22.33) MUTATED DEL PEAK 32(15Q22.33) WILD-TYPE 
                            160                             289 
[1] "DEL PEAK 33(16P13.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 33(16P13.3) MUTATED DEL PEAK 33(16P13.3) WILD-TYPE 
                            56                            393 
  DEL PEAK 33(16P13.3) MUTATED DEL PEAK 33(16P13.3) WILD-TYPE 
                            56                            393 
[1] "DEL PEAK 34(16Q23.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 34(16Q23.1) MUTATED DEL PEAK 34(16Q23.1) WILD-TYPE 
                            60                            389 
  DEL PEAK 34(16Q23.1) MUTATED DEL PEAK 34(16Q23.1) WILD-TYPE 
                            60                            389 
[1] "DEL PEAK 35(17P12) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 35(17P12) MUTATED DEL PEAK 35(17P12) WILD-TYPE 
                         252                          197 
  DEL PEAK 35(17P12) MUTATED DEL PEAK 35(17P12) WILD-TYPE 
                         252                          197 
[1] "DEL PEAK 36(17Q24.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 36(17Q24.3) MUTATED DEL PEAK 36(17Q24.3) WILD-TYPE 
                            69                            380 
  DEL PEAK 36(17Q24.3) MUTATED DEL PEAK 36(17Q24.3) WILD-TYPE 
                            69                            380 
[1] "DEL PEAK 37(18P11.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 37(18P11.31) MUTATED DEL PEAK 37(18P11.31) WILD-TYPE 
                            247                             202 
  DEL PEAK 37(18P11.31) MUTATED DEL PEAK 37(18P11.31) WILD-TYPE 
                            247                             202 
[1] "DEL PEAK 38(18Q12.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 38(18Q12.2) MUTATED DEL PEAK 38(18Q12.2) WILD-TYPE 
                           272                            177 
  DEL PEAK 38(18Q12.2) MUTATED DEL PEAK 38(18Q12.2) WILD-TYPE 
                           272                            177 
[1] "DEL PEAK 39(18Q21.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 39(18Q21.2) MUTATED DEL PEAK 39(18Q21.2) WILD-TYPE 
                           286                            163 
  DEL PEAK 39(18Q21.2) MUTATED DEL PEAK 39(18Q21.2) WILD-TYPE 
                           286                            163 
[1] "DEL PEAK 40(18Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 40(18Q22.1) MUTATED DEL PEAK 40(18Q22.1) WILD-TYPE 
                           285                            164 
  DEL PEAK 40(18Q22.1) MUTATED DEL PEAK 40(18Q22.1) WILD-TYPE 
                           285                            164 
[1] "DEL PEAK 41(19P13.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 41(19P13.3) MUTATED DEL PEAK 41(19P13.3) WILD-TYPE 
                            63                            386 
  DEL PEAK 41(19P13.3) MUTATED DEL PEAK 41(19P13.3) WILD-TYPE 
                            63                            386 
[1] "DEL PEAK 42(20P12.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 42(20P12.1) MUTATED DEL PEAK 42(20P12.1) WILD-TYPE 
                            86                            363 
  DEL PEAK 42(20P12.1) MUTATED DEL PEAK 42(20P12.1) WILD-TYPE 
                            86                            363 
[1] "DEL PEAK 43(21Q11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 43(21Q11.2) MUTATED DEL PEAK 43(21Q11.2) WILD-TYPE 
                           140                            309 
  DEL PEAK 43(21Q11.2) MUTATED DEL PEAK 43(21Q11.2) WILD-TYPE 
                           140                            309 
[1] "DEL PEAK 44(22Q13.32) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 44(22Q13.32) MUTATED DEL PEAK 44(22Q13.32) WILD-TYPE 
                            158                             291 
  DEL PEAK 44(22Q13.32) MUTATED DEL PEAK 44(22Q13.32) WILD-TYPE 
                            158                             291 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                      
 [2] "VITAL_STATUS"                        
 [3] "DAYS_TO_DEATH"                       
 [4] "DAYS_TO_LAST_FOLLOWUP"               
 [5] "TUMOR_TISSUE_SITE"                   
 [6] "PATHOLOGIC_STAGE"                    
 [7] "PATHOLOGY_T_STAGE"                   
 [8] "PATHOLOGY_N_STAGE"                   
 [9] "PATHOLOGY_M_STAGE"                   
[10] "GENDER"                              
[11] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"
[12] "DAYS_TO_LAST_KNOWN_ALIVE"            
[13] "RADIATION_THERAPY"                   
[14] "HISTOLOGICAL_TYPE"                   
[15] "RESIDUAL_TUMOR"                      
[16] "NUMBER_OF_LYMPH_NODES"               
[17] "RACE"                                
[18] "ETHNICITY"                           

Input Data has 18 rows and 449 columns.

[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=58,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=88,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 4:'DAYS_TO_LAST_FOLLOWUP':	nDistinctValues=249,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'TUMOR_TISSUE_SITE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "TUMOR_TISSUE_SITE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'PATHOLOGIC_STAGE':	nDistinctValues=13,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY_T_STAGE':	nDistinctValues=7,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY_N_STAGE':	nDistinctValues=8,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY_M_STAGE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=16,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 12:'DAYS_TO_LAST_KNOWN_ALIVE':	nDistinctValues=10,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 13:'RADIATION_THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'HISTOLOGICAL_TYPE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'RESIDUAL_TUMOR':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'NUMBER_OF_LYMPH_NODES':	nDistinctValues=21,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 17:'RACE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 18:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "PATHOLOGY_T_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_N_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_M_STAGE is converted to rank data using modified categoies"
[1] "****** SUMMARY ***** "
Output Data has 449 columns, 1 survival variables, and 12 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
 [1] "YEARS_TO_BIRTH"        "PATHOLOGIC_STAGE"      "PATHOLOGY_T_STAGE"    
 [4] "PATHOLOGY_N_STAGE"     "PATHOLOGY_M_STAGE"     "GENDER"               
 [7] "RADIATION_THERAPY"     "HISTOLOGICAL_TYPE"     "RESIDUAL_TUMOR"       
[10] "NUMBER_OF_LYMPH_NODES" "RACE"                  "ETHNICITY"            
YEARS_TO_BIRTH, nv=58, binary=FALSE, numeric=TRUE
PATHOLOGIC_STAGE, nv=13, binary=FALSE, numeric=FALSE
PATHOLOGY_T_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T1  T2  T3  T4 
 11  77 305  55 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
 11  77 305  55 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T1  T2  T3  T4 
 11  77 305  55 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
 11  77 305  55 
PATHOLOGY_N_STAGE, nv=3, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2 
262 105  82 
[1] "table(vv)"
vv
 N0  N1  N2 
262 105  82 
$ClinVariableName
[1] "PATHOLOGY_N_STAGE"

$Table
vv
 N0  N1  N2 
262 105  82 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


 N0  N1  N2 
262 105  82 
PATHOLOGY_M_STAGE, nv=2, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
RADIATION_THERAPY, nv=2, binary=FALSE, numeric=FALSE
HISTOLOGICAL_TYPE, nv=2, binary=FALSE, numeric=FALSE
RESIDUAL_TUMOR, nv=4, binary=FALSE, numeric=FALSE
NUMBER_OF_LYMPH_NODES, nv=21, binary=FALSE, numeric=TRUE
RACE, nv=4, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = AMP PEAK  1(2Q33.1) MUTATION ANALYSIS
D1V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  1(2Q33.1) MUTATED    63  24
  AMP PEAK  1(2Q33.1) WILD-TYPE 272  77
  AMP PEAK  1(2Q33.1) MUTATED AMP PEAK  1(2Q33.1) WILD-TYPE 
                           87                           349 
  AMP PEAK  1(2Q33.1) MUTATED AMP PEAK  1(2Q33.1) WILD-TYPE 
                           24                            77 
$`AMP PEAK  1(2Q33.1) MUTATED`
TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3531 TCGA-AA-3562 TCGA-AA-3867 
       14.53        24.16         1.02        34.03        19.99        24.03 
TCGA-AA-3979 TCGA-AD-6548 TCGA-AD-6888 TCGA-G4-6310 TCGA-G4-6628 TCGA-NH-A8F7 
       24.00        21.37        15.52        63.62        79.69        17.85 
TCGA-3L-AA1B TCGA-5M-AAT4 TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-3807 TCGA-A6-3810 
       15.62         1.61        39.45        43.76        34.65        36.53 
TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6652 TCGA-A6-6654 
       32.91        30.44        32.71        29.16        24.69        23.87 
TCGA-A6-A566 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3673 TCGA-AA-3679 TCGA-AA-3685 
       24.92        29.00        29.00        50.04        15.02        37.05 
TCGA-AA-3696 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3971 
        5.03        10.06        35.05        33.07         0.00        16.08 
TCGA-AA-A00W TCGA-AA-A01I TCGA-AA-A01S TCGA-AA-A01X TCGA-AA-A02E TCGA-AD-6899 
       14.99        31.00         1.02        26.01         2.96         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AY-4070 TCGA-AY-6196 
       22.42        27.42        26.47        16.44        16.31         0.20 
TCGA-AY-A8YK TCGA-AZ-4616 TCGA-AZ-6607 TCGA-CA-6715 TCGA-CA-6716 TCGA-CK-4950 
       18.84         5.13         3.19        12.59        12.20        85.45 
TCGA-CK-5914 TCGA-CM-4750 TCGA-CM-5341 TCGA-CM-5862 TCGA-CM-5868 TCGA-CM-6161 
       21.99         8.02        29.06         5.03        17.03        15.02 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6166 TCGA-CM-6167 TCGA-D5-5537 TCGA-D5-5541 
       14.04        29.03        21.99        14.99        45.40        55.92 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6898 TCGA-DM-A0XD TCGA-DM-A1DA TCGA-DM-A280 
        4.80        17.13         7.53        24.43         7.50         7.76 
TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28F TCGA-F4-6459 TCGA-F4-6704 TCGA-G4-6295 
       14.04        26.47        35.97         8.61         1.55         8.35 
TCGA-G4-6299 TCGA-G4-6311 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A6GC TCGA-QG-A5YW 
       74.56        39.42        74.79        18.18        12.79        29.46 
TCGA-QG-A5YX TCGA-RU-A8FL TCGA-SS-A7HO 
       32.98        38.70        60.13 

$`AMP PEAK  1(2Q33.1) WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-AA-3506 TCGA-AA-3516 TCGA-AA-3520 
       24.33        45.60        13.94        58.03        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3543 TCGA-AA-3552 
       37.05        36.03         8.05        19.07         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 
       17.95        23.01        19.99         6.05         0.92        19.00 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 
       36.00        85.05        19.04        19.04        14.93        31.07 
TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 
       29.98        12.99        24.00         2.01        50.99        26.01 
TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6895 TCGA-AD-6964 
       19.07        38.04        21.99        39.06        25.08        10.88 
TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 
       75.95       106.75       100.01         1.94        49.08         5.88 
TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6314 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       28.21        23.51        35.93        22.09        35.80        26.17 
TCGA-G4-6625 TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT6 TCGA-A6-2672 TCGA-A6-2674 
       91.79         4.80        12.66         9.53        46.65        43.76 
TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 
       43.43        42.90        42.28        44.91        35.11        16.57 
TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3809 TCGA-A6-4107 TCGA-A6-5657 
       37.05        37.25        37.02        32.75        32.45        31.63 
TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 
       29.19        33.53        23.61        22.09        22.06        27.09 
TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 
       22.52        24.13         8.38        25.08        25.18        20.61 
TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 
       21.76        24.39        20.12        19.66        20.28        16.24 
TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 
       61.84        56.25         9.63         5.03         7.04         3.02 
TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
        1.02        37.05        35.01        63.98         6.97         1.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3538 
       38.99         1.02         9.07        19.07         0.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3680 TCGA-AA-3681 
        2.01        14.01        47.05        47.01        11.01         5.98 
TCGA-AA-3710 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       26.99         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        36.95        37.02         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 
        0.00        36.03        32.05         0.99        31.07        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       13.05        34.06        25.02        27.02         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       34.98        15.02        15.02        10.98        32.02        12.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01T TCGA-AA-A01V 
       31.00        38.07         1.02        35.01        33.04         1.02 
TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O 
       37.02        51.98        39.98         2.01         5.03         0.92 
TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
       22.03        41.00        39.98        18.05        40.96        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 
       83.24        24.53         0.46         0.92        14.50        27.09 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D 
        0.95        33.01        21.44        17.82        17.26        17.85 
TCGA-AY-A71X TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 
       19.33       109.28        58.39         1.41         5.65        32.94 
TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       22.36        65.00        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-CA-5254 TCGA-CA-5255 
       12.10        29.56         5.23        11.74        12.69        12.36 
TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.46        12.39        12.59        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5916 
       17.56       148.01        70.16        15.62        51.32        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5348 
       25.02        26.04        27.02        13.02        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6162 
       30.08        32.02        15.02        15.02        15.02        12.00 
TCGA-CM-6165 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       16.04        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-6529 TCGA-D5-6530 
       12.03        54.61        19.59        56.09        20.19        20.42 
TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       17.75        18.25        25.48        43.27        15.12        17.85 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       12.49        16.14        15.58        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XF TCGA-DM-A1D0 
       12.00        11.38        10.26       119.70        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB 
       92.75        49.91        13.32        12.59       140.38        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G 
      131.51       135.65       139.17        81.37       119.93        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 
      117.07        98.24        95.18        31.96        11.11        35.74 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       35.74         6.18        47.87        34.42        41.42        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6297 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
       82.39        67.30        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 
       85.48        61.91        36.00        26.43        26.04        13.78 
TCGA-G4-6626 TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB 
       46.75        10.98        19.33        19.33         9.93        15.65 
TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-T9-A92H 
       16.80        42.77         8.42        31.30        21.90        11.90 
TCGA-WS-AB45 
       70.03 

  AMP PEAK  1(2Q33.1) MUTATED AMP PEAK  1(2Q33.1) WILD-TYPE 
                            0                             0 
  AMP PEAK  1(2Q33.1) MUTATED AMP PEAK  1(2Q33.1) WILD-TYPE 
                        85.45                        148.01 
  AMP PEAK  1(2Q33.1) MUTATED AMP PEAK  1(2Q33.1) WILD-TYPE 
                        21.99                         22.06 
[1] "0.0 - 85.5 (22.0)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.5"
D1V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK  1(2Q33.1) MUTATED        13        0        5        20         1
  AMP PEAK  1(2Q33.1) WILD-TYPE      61        1       24       112         9
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  1(2Q33.1) MUTATED           1         5          2         15
  AMP PEAK  1(2Q33.1) WILD-TYPE         0        15          6         44
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK  1(2Q33.1) MUTATED           13       10         4         1
  AMP PEAK  1(2Q33.1) WILD-TYPE         28       35        13         1
D1V3, multiclass
            clus
vv           AMP PEAK  1(2Q33.1) MUTATED AMP PEAK  1(2Q33.1) WILD-TYPE
  STAGE I                             13                            61
  STAGE IA                             0                             1
  STAGE II                             5                            24
  STAGE IIA                           20                           112
  STAGE IIB                            1                             9
  STAGE IIC                            1                             0
  STAGE III                            5                            15
  STAGE IIIA                           2                             6
  STAGE IIIB                          15                            44
  STAGE IIIC                          13                            28
  STAGE IV                            10                            35
  STAGE IVA                            4                            13
  STAGE IVB                            1                             1
[1] 13  2
[1] 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(2Q33.1) MUTATED     3  13  66  10
  AMP PEAK  1(2Q33.1) WILD-TYPE   8  64 239  45
D1V4, multiclass
    clus
vv   AMP PEAK  1(2Q33.1) MUTATED AMP PEAK  1(2Q33.1) WILD-TYPE
  T1                           3                             8
  T2                          13                            64
  T3                          66                           239
  T4                          10                            45
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2
  AMP PEAK  1(2Q33.1) MUTATED    43  23  26
  AMP PEAK  1(2Q33.1) WILD-TYPE 219  82  56
D1V5, multiclass
    clus
vv   AMP PEAK  1(2Q33.1) MUTATED AMP PEAK  1(2Q33.1) WILD-TYPE
  N0                          43                           219
  N1                          23                            82
  N2                          26                            56
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V6, binary
                               cls
clus                              0   1
  AMP PEAK  1(2Q33.1) MUTATED    60  15
  AMP PEAK  1(2Q33.1) WILD-TYPE 268  49
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(2Q33.1) MUTATED     60   15
  AMP PEAK  1(2Q33.1) WILD-TYPE  268   49
   clus
vv  AMP PEAK  1(2Q33.1) MUTATED AMP PEAK  1(2Q33.1) WILD-TYPE
  0                          60                           268
  1                          15                            49
[1] 2 2
[1] FALSE
D1V7, binary
                               cls
clus                              0   1
  AMP PEAK  1(2Q33.1) MUTATED    40  52
  AMP PEAK  1(2Q33.1) WILD-TYPE 173 184
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(2Q33.1) MUTATED     40   52
  AMP PEAK  1(2Q33.1) WILD-TYPE  173  184
        clus
vv       AMP PEAK  1(2Q33.1) MUTATED AMP PEAK  1(2Q33.1) WILD-TYPE
  FEMALE                          40                           173
  MALE                            52                           184
[1] 2 2
[1] FALSE
D1V8, binary
                               cls
clus                              0   1
  AMP PEAK  1(2Q33.1) MUTATED    72   2
  AMP PEAK  1(2Q33.1) WILD-TYPE 298   7
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(2Q33.1) MUTATED     72    2
  AMP PEAK  1(2Q33.1) WILD-TYPE  298    7
     clus
vv    AMP PEAK  1(2Q33.1) MUTATED AMP PEAK  1(2Q33.1) WILD-TYPE
  NO                           72                           298
  YES                           2                             7
[1] 2 2
[1] FALSE
D1V9, binary
                               cls
clus                              0   1
  AMP PEAK  1(2Q33.1) MUTATED    81  11
  AMP PEAK  1(2Q33.1) WILD-TYPE 301  51
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(2Q33.1) MUTATED     81   11
  AMP PEAK  1(2Q33.1) WILD-TYPE  301   51
                               clus
vv                              AMP PEAK  1(2Q33.1) MUTATED
  COLON ADENOCARCINOMA                                   81
  COLON MUCINOUS ADENOCARCINOMA                          11
                               clus
vv                              AMP PEAK  1(2Q33.1) WILD-TYPE
  COLON ADENOCARCINOMA                                    301
  COLON MUCINOUS ADENOCARCINOMA                            51
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  1(2Q33.1) MUTATED    59   3   6   6
  AMP PEAK  1(2Q33.1) WILD-TYPE 264   1  19  19
D1V10, multiclass
    clus
vv   AMP PEAK  1(2Q33.1) MUTATED AMP PEAK  1(2Q33.1) WILD-TYPE
  R0                          59                           264
  R1                           3                             1
  R2                           6                            19
  RX                           6                            19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V11, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  1(2Q33.1) MUTATED                                  1     2
  AMP PEAK  1(2Q33.1) WILD-TYPE                                0     9
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  1(2Q33.1) MUTATED                          17    47
  AMP PEAK  1(2Q33.1) WILD-TYPE                        42   165
D1V12, multiclass
                                  clus
vv                                 AMP PEAK  1(2Q33.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      2
  BLACK OR AFRICAN AMERICAN                                 17
  WHITE                                                     47
                                  clus
vv                                 AMP PEAK  1(2Q33.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        9
  BLACK OR AFRICAN AMERICAN                                   42
  WHITE                                                      165
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V13, binary
                               cls
clus                              0   1
  AMP PEAK  1(2Q33.1) MUTATED     2  62
  AMP PEAK  1(2Q33.1) WILD-TYPE   2 207
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(2Q33.1) MUTATED      2   62
  AMP PEAK  1(2Q33.1) WILD-TYPE    2  207
                        clus
vv                       AMP PEAK  1(2Q33.1) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          62
                        clus
vv                       AMP PEAK  1(2Q33.1) WILD-TYPE
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                           207
[1] 2 2
[1] FALSE

Clustering(2) Variable = AMP PEAK  2(5P13.2) MUTATION ANALYSIS
D2V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  2(5P13.2) MUTATED    64  20
  AMP PEAK  2(5P13.2) WILD-TYPE 271  81
  AMP PEAK  2(5P13.2) MUTATED AMP PEAK  2(5P13.2) WILD-TYPE 
                           84                           352 
  AMP PEAK  2(5P13.2) MUTATED AMP PEAK  2(5P13.2) WILD-TYPE 
                           20                            81 
$`AMP PEAK  2(5P13.2) MUTATED`
TCGA-A6-2681 TCGA-AA-3552 TCGA-AA-3560 TCGA-AA-3688 TCGA-AA-3715 TCGA-AA-3844 
       45.60        13.02        19.99        19.00        19.04        14.93 
TCGA-AA-3867 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-A00Z TCGA-AZ-6608 TCGA-CK-5912 
       24.03        50.99        26.01        21.99         1.94        49.08 
TCGA-DM-A285 TCGA-G4-6625 TCGA-3L-AA1B TCGA-5M-AAT4 TCGA-A6-2674 TCGA-A6-2675 
        5.88        91.79        15.62         1.61        43.76        43.43 
TCGA-A6-2679 TCGA-A6-2685 TCGA-A6-3807 TCGA-A6-4107 TCGA-A6-6650 TCGA-A6-6651 
       44.91        37.25        34.65        32.45        20.61        21.76 
TCGA-AA-3488 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3553 TCGA-AA-3666 TCGA-AA-3678 
        5.03        26.01        12.99        24.00         2.01        47.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3842 TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3866 
        5.98        37.05        37.02        36.03         0.99        17.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-A00F TCGA-AA-A01D TCGA-AA-A029 TCGA-AA-A02E 
        2.01        21.99        34.03        10.98        51.98         2.96 
TCGA-AA-A02H TCGA-AA-A02W TCGA-AA-A03J TCGA-AD-6899 TCGA-AD-A5EK TCGA-AM-5821 
        2.01        41.00        40.96         5.79        16.44         0.92 
TCGA-AY-6196 TCGA-AY-A8YK TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6603 TCGA-CA-5254 
        0.20        18.84        62.79        49.41        29.56        12.69 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5860 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 
       25.02        13.02        32.02        15.02        14.04        29.03 
TCGA-CM-6167 TCGA-CM-6169 TCGA-CM-6678 TCGA-D5-5539 TCGA-D5-6531 TCGA-D5-6538 
       14.99        13.02        11.01        19.59        17.75        17.13 
TCGA-D5-6898 TCGA-D5-6924 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 TCGA-DM-A1D8 
        7.53        14.30        13.41        12.00        11.38        12.59 
TCGA-DM-A1DA TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6460 TCGA-F4-6704 TCGA-F4-6855 
        7.50        98.24        95.18        31.96         1.55        47.41 
TCGA-G4-6297 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A6GC TCGA-QG-A5Z1 TCGA-RU-A8FL 
       82.39        46.75        74.79        12.79         8.42        38.70 

$`AMP PEAK  2(5P13.2) WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3506 
       24.33        13.94        14.53        24.16         1.02        58.03 
TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 
       13.02        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3562 TCGA-AA-3662 
       34.03         0.99        17.95        23.01        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3860 TCGA-AA-3870 
        0.92        36.00        85.05        19.04        31.07        29.98 
TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
       12.99        24.00         2.01        24.00        19.07        38.04 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 
       39.06        21.37        15.52        25.08        10.88        75.95 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6314 
      106.75       100.01        28.21        23.51        63.62        35.93 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 TCGA-NH-A8F7 TCGA-4N-A93T 
       22.09        35.80        26.17        79.69        17.85         4.80 
TCGA-4T-AA8H TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2676 
       12.66         9.53        39.45        43.76        46.65        42.90 
TCGA-A6-2678 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2686 TCGA-A6-3809 
       42.28        35.11        16.57        37.05        37.02        32.75 
TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 
       36.53        32.91        31.63        30.44        29.19        33.53 
TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 
       23.61        22.09        22.06        32.71        29.16        27.09 
TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6652 
       22.52        24.13         8.38        25.08        25.18        24.69 
TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 
       24.39        23.87        20.12        19.66        20.28        16.24 
TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3489 TCGA-AA-3492 
       24.92        61.84        56.25         9.63         7.04         3.02 
TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
        1.02        37.05        35.01        63.98         6.97         1.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        29.00 
TCGA-AA-3534 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3555 TCGA-AA-3558 
       29.00        14.01        33.99        21.01        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 
       13.94        61.02        78.08         6.97        54.02        14.01 
TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3696 TCGA-AA-3710 
       50.04        47.05        15.02        11.01         5.03        26.99 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       10.06        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       15.95        38.99        36.95         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3855 TCGA-AA-3858 TCGA-AA-3864 
        0.00        33.07         0.00        32.05        31.07        53.00 
TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       26.01        20.98        34.03        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       25.02        27.02         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O 
       19.00        30.02        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       15.02        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04         1.02        26.01 
TCGA-AA-A01Z TCGA-AA-A02F TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y 
       37.02        39.98         5.03         0.92        22.03        39.98 
TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6901 TCGA-AD-6963 
       18.05        12.16        83.24        24.53        22.42        27.42 
TCGA-AD-6965 TCGA-AM-5820 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       26.47         0.46        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X 
       33.01        21.44        17.82        17.26        17.85        19.33 
TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 
      109.28        58.39         1.41         5.65        32.94         5.13 
TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6605 
       22.36        65.00        88.21         6.77        12.10         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 
       11.74         3.19        12.36        12.46        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        70.16        15.62        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-5341 TCGA-CM-5344 
       37.02        26.04         8.02        27.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       22.98        30.08        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6168 TCGA-CM-6170 
       17.03        12.00        16.04        21.99        12.99        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-5541 
       10.06        12.03        45.40        54.61        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       20.19        20.42        18.25        25.48        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 
       17.85         4.80        12.49        16.14        15.58        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 
       10.13        12.43         9.04         9.44        11.64        13.35 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       49.91        13.32       140.38        44.32       131.51       135.65 
TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E 
        7.76       139.17        14.04        26.47        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-F4-6459 TCGA-F4-6461 TCGA-F4-6463 
       35.97        60.79       117.07         8.61        11.11        35.74 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       35.74         6.18        47.87        34.42        41.42        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6295 
       33.67        13.25         0.53        35.31       133.18         8.35 
TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
       74.56        67.30        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6322 
       85.48        39.42        61.91        36.00        26.43        26.04 
TCGA-G4-6323 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA 
       13.78        18.18        10.98        19.33        19.33         9.93 
TCGA-NH-A6GB TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z2 
       15.65        16.80        42.77        29.46        32.98        31.30 
TCGA-QL-A97D TCGA-SS-A7HO TCGA-T9-A92H TCGA-WS-AB45 
       21.90        60.13        11.90        70.03 

  AMP PEAK  2(5P13.2) MUTATED AMP PEAK  2(5P13.2) WILD-TYPE 
                          0.2                           0.0 
  AMP PEAK  2(5P13.2) MUTATED AMP PEAK  2(5P13.2) WILD-TYPE 
                        98.24                        148.01 
  AMP PEAK  2(5P13.2) MUTATED AMP PEAK  2(5P13.2) WILD-TYPE 
                       19.315                        22.750 
[1] "0.2 - 98.2 (19.3)"  "0.0 - 148.0 (22.8)"
[1] "hr=" "1.1"
D2V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK  2(5P13.2) MUTATED        13        0        5        22         1
  AMP PEAK  2(5P13.2) WILD-TYPE      61        1       24       110         9
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  2(5P13.2) MUTATED           0         3          4          6
  AMP PEAK  2(5P13.2) WILD-TYPE         1        17          4         53
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK  2(5P13.2) MUTATED           13       13         3         1
  AMP PEAK  2(5P13.2) WILD-TYPE         28       32        14         1
D2V3, multiclass
            clus
vv           AMP PEAK  2(5P13.2) MUTATED AMP PEAK  2(5P13.2) WILD-TYPE
  STAGE I                             13                            61
  STAGE IA                             0                             1
  STAGE II                             5                            24
  STAGE IIA                           22                           110
  STAGE IIB                            1                             9
  STAGE IIC                            0                             1
  STAGE III                            3                            17
  STAGE IIIA                           4                             4
  STAGE IIIB                           6                            53
  STAGE IIIC                          13                            28
  STAGE IV                            13                            32
  STAGE IVA                            3                            14
  STAGE IVB                            1                             1
[1] 13  2
[1] 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(5P13.2) MUTATED     1  17  61   7
  AMP PEAK  2(5P13.2) WILD-TYPE  10  60 244  48
D2V4, multiclass
    clus
vv   AMP PEAK  2(5P13.2) MUTATED AMP PEAK  2(5P13.2) WILD-TYPE
  T1                           1                            10
  T2                          17                            60
  T3                          61                           244
  T4                           7                            48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2
  AMP PEAK  2(5P13.2) MUTATED    42  20  24
  AMP PEAK  2(5P13.2) WILD-TYPE 220  85  58
D2V5, multiclass
    clus
vv   AMP PEAK  2(5P13.2) MUTATED AMP PEAK  2(5P13.2) WILD-TYPE
  N0                          42                           220
  N1                          20                            85
  N2                          24                            58
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V6, binary
                               cls
clus                              0   1
  AMP PEAK  2(5P13.2) MUTATED    55  17
  AMP PEAK  2(5P13.2) WILD-TYPE 273  47
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(5P13.2) MUTATED     55   17
  AMP PEAK  2(5P13.2) WILD-TYPE  273   47
   clus
vv  AMP PEAK  2(5P13.2) MUTATED AMP PEAK  2(5P13.2) WILD-TYPE
  0                          55                           273
  1                          17                            47
[1] 2 2
[1] FALSE
D2V7, binary
                               cls
clus                              0   1
  AMP PEAK  2(5P13.2) MUTATED    44  42
  AMP PEAK  2(5P13.2) WILD-TYPE 169 194
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(5P13.2) MUTATED     44   42
  AMP PEAK  2(5P13.2) WILD-TYPE  169  194
        clus
vv       AMP PEAK  2(5P13.2) MUTATED AMP PEAK  2(5P13.2) WILD-TYPE
  FEMALE                          44                           169
  MALE                            42                           194
[1] 2 2
[1] FALSE
D2V8, binary
                               cls
clus                              0   1
  AMP PEAK  2(5P13.2) MUTATED    69   1
  AMP PEAK  2(5P13.2) WILD-TYPE 301   8
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(5P13.2) MUTATED     69    1
  AMP PEAK  2(5P13.2) WILD-TYPE  301    8
     clus
vv    AMP PEAK  2(5P13.2) MUTATED AMP PEAK  2(5P13.2) WILD-TYPE
  NO                           69                           301
  YES                           1                             8
[1] 2 2
[1] FALSE
D2V9, binary
                               cls
clus                              0   1
  AMP PEAK  2(5P13.2) MUTATED    74  12
  AMP PEAK  2(5P13.2) WILD-TYPE 308  50
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(5P13.2) MUTATED     74   12
  AMP PEAK  2(5P13.2) WILD-TYPE  308   50
                               clus
vv                              AMP PEAK  2(5P13.2) MUTATED
  COLON ADENOCARCINOMA                                   74
  COLON MUCINOUS ADENOCARCINOMA                          12
                               clus
vv                              AMP PEAK  2(5P13.2) WILD-TYPE
  COLON ADENOCARCINOMA                                    308
  COLON MUCINOUS ADENOCARCINOMA                            50
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  2(5P13.2) MUTATED    63   0   8   2
  AMP PEAK  2(5P13.2) WILD-TYPE 260   4  17  23
D2V10, multiclass
    clus
vv   AMP PEAK  2(5P13.2) MUTATED AMP PEAK  2(5P13.2) WILD-TYPE
  R0                          63                           260
  R1                           0                             4
  R2                           8                            17
  RX                           2                            23
[1] 4 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, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  2(5P13.2) MUTATED                                  1     1
  AMP PEAK  2(5P13.2) WILD-TYPE                                0    10
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  2(5P13.2) MUTATED                          12    40
  AMP PEAK  2(5P13.2) WILD-TYPE                        47   172
D2V12, multiclass
                                  clus
vv                                 AMP PEAK  2(5P13.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      1
  BLACK OR AFRICAN AMERICAN                                 12
  WHITE                                                     40
                                  clus
vv                                 AMP PEAK  2(5P13.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                       10
  BLACK OR AFRICAN AMERICAN                                   47
  WHITE                                                      172
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V13, binary
                               cls
clus                              0   1
  AMP PEAK  2(5P13.2) MUTATED     1  52
  AMP PEAK  2(5P13.2) WILD-TYPE   3 217
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(5P13.2) MUTATED      1   52
  AMP PEAK  2(5P13.2) WILD-TYPE    3  217
                        clus
vv                       AMP PEAK  2(5P13.2) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          52
                        clus
vv                       AMP PEAK  2(5P13.2) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           217
[1] 2 2
[1] FALSE

Clustering(3) Variable = AMP PEAK  3(6P21.1) MUTATION ANALYSIS
D3V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  3(6P21.1) MUTATED    72  20
  AMP PEAK  3(6P21.1) WILD-TYPE 263  81
  AMP PEAK  3(6P21.1) MUTATED AMP PEAK  3(6P21.1) WILD-TYPE 
                           92                           344 
  AMP PEAK  3(6P21.1) MUTATED AMP PEAK  3(6P21.1) WILD-TYPE 
                           20                            81 
$`AMP PEAK  3(6P21.1) MUTATED`
TCGA-AA-3552 TCGA-AA-3562 TCGA-AA-3697 TCGA-AA-3867 TCGA-G4-6294 TCGA-G4-6310 
       13.02        19.99        85.05        24.03        28.21        63.62 
TCGA-G4-6625 TCGA-A6-2675 TCGA-A6-2679 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5659 
       91.79        43.43        44.91        36.53        32.45        30.44 
TCGA-A6-5660 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6654 
       29.19        22.52        25.08        25.18        20.61        23.87 
TCGA-A6-A56B TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3542 TCGA-AA-3553 TCGA-AA-3561 
       56.25        29.00        29.00        12.99        24.00        13.94 
TCGA-AA-3679 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3869 
       15.02        10.06        35.05        17.03        10.06        27.02 
TCGA-AA-3930 TCGA-AA-3955 TCGA-AA-3968 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-A004 
        2.01        20.98        21.99        27.02         7.96        13.94 
TCGA-AA-A00F TCGA-AA-A00O TCGA-AA-A01I TCGA-AA-A02E TCGA-AA-A03J TCGA-AD-6901 
       34.03        27.02        31.00         2.96        40.96        22.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4071 TCGA-AY-6196 TCGA-AY-A54L TCGA-AZ-4682 
       26.47        14.50         0.95         0.20        17.26        22.36 
TCGA-AZ-4684 TCGA-CA-6719 TCGA-CK-4952 TCGA-CK-5914 TCGA-CM-4750 TCGA-CM-4752 
       65.00        14.30        15.62        21.99         8.02        13.02 
TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5864 
       29.06        22.98        30.08        32.02         5.03        15.02 
TCGA-CM-6169 TCGA-CM-6170 TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6533 TCGA-D5-6535 
       13.02        15.02        19.59        55.92        25.48        15.12 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6926 TCGA-D5-6929 
       17.13        12.49         7.53        10.13         9.04        13.41 
TCGA-D5-6932 TCGA-DM-A1D7 TCGA-DM-A1DA TCGA-DM-A288 TCGA-DM-A28H TCGA-DM-A28K 
       11.38        13.32         7.50        14.04       117.07        98.24 
TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6704 TCGA-F4-6854 
       95.18         8.61        31.96        35.74         1.55         0.53 
TCGA-G4-6297 TCGA-G4-6311 TCGA-G4-6626 TCGA-NH-A50U TCGA-NH-A6GC TCGA-QG-A5YW 
       82.39        39.42        46.75        10.98        12.79        29.46 
TCGA-QL-A97D TCGA-RU-A8FL 
       21.90        38.70 

$`AMP PEAK  3(6P21.1) WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 
       24.33        45.60        13.94        14.53        24.16         1.02 
TCGA-AA-3506 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
       58.03        13.02        24.03        37.05        36.03         8.05 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 
       19.07        34.03         0.99        17.95        23.01        19.99 
TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3713 TCGA-AA-3715 
        6.05         0.92        19.00        36.00        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       14.93        31.07        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 
       39.06        21.37        15.52        25.08        10.88        75.95 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6298 
      106.75       100.01         1.94        49.08         5.88        23.51 
TCGA-G4-6314 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 TCGA-NH-A8F7 
       35.93        22.09        35.80        26.17        79.69        17.85 
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-5M-AATE 
       15.62         4.80        12.66         1.61         9.53        39.45 
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2680 
       43.76        46.65        43.76        42.90        42.28        35.11 
TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3809 
       16.57        37.05        37.25        37.02        34.65        32.75 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       32.91        31.63        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6651 
       32.71        29.16        27.09        24.13         8.38        21.76 
TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 
       24.69        24.39        20.12        19.66        20.28        16.24 
TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 
       24.92        61.84         9.63         5.03         7.04         3.02 
TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
        1.02        37.05        35.01        63.98         6.97         1.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3538 
       38.99         1.02         9.07        19.07         0.00        26.01 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3655 
       14.01        33.99        21.01        29.95        20.98        61.02 
TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       78.08         6.97        54.02         2.01        14.01        50.04 
TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 
       47.05        47.01        11.01         5.98        37.05         5.03 
TCGA-AA-3710 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       26.99         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3850 TCGA-AA-3851 
       38.99        36.95        37.02         0.00         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 
        0.00        36.03        32.05         0.99        31.07        53.00 
TCGA-AA-3866 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       17.03        18.05        31.00        24.00        33.01        26.01 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
       34.03         2.01        16.08        13.05        34.06        25.02 
TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K 
       27.02        38.04        19.00        30.02        18.05        18.05 
TCGA-AA-A00N TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 
        4.01        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01K 
       15.02        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       26.01        37.02        51.98        39.98         2.01         5.03 
TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-5900 
        0.92        22.03        41.00        39.98        18.05        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-A5EK TCGA-AM-5820 
       83.24        24.53         5.79        27.42        16.44         0.46 
TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
        0.92        27.09        16.31        33.01        21.44        17.82 
TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 
       17.85        19.33        18.84       109.28        58.39         1.41 
TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.65        32.94         5.13        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77        12.10        29.56         5.23        11.74         3.19 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
       12.69        12.36        12.46        12.39        12.59        12.59 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.20        12.76        10.06        17.56       148.01        85.45 
TCGA-CK-4951 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       70.16        51.32        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 
       23.05        20.02        37.02        25.02        26.04        27.02 
TCGA-CM-5344 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
       22.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 
       11.01        10.06        12.03        45.40        54.61        56.09 
TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6536 
       20.19        20.42        17.75        18.25        43.27        17.85 
TCGA-D5-6537 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6923 TCGA-D5-6924 
        4.80        16.14        15.58        12.39        12.43        14.30 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 
        9.44        11.64        13.35        12.00        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D8 
       24.43        38.20       130.65        92.75        49.91        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 
      140.38        44.32       131.51       135.65         7.76       139.17 
TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-F4-6461 
       26.47        81.37       119.93        35.97        60.79        11.11 
TCGA-F4-6463 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       35.74         6.18        47.87        34.42        41.42        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6295 
       33.67        13.25        47.41        35.31       133.18         8.35 
TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
       74.56        67.30        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 
       85.48        61.91        36.00        26.43        26.04        13.78 
TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB 
       74.79        18.18        19.33        19.33         9.93        15.65 
TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-SS-A7HO 
       16.80        42.77        32.98         8.42        31.30        60.13 
TCGA-T9-A92H TCGA-WS-AB45 
       11.90        70.03 

  AMP PEAK  3(6P21.1) MUTATED AMP PEAK  3(6P21.1) WILD-TYPE 
                          0.2                           0.0 
  AMP PEAK  3(6P21.1) MUTATED AMP PEAK  3(6P21.1) WILD-TYPE 
                       117.07                        148.01 
  AMP PEAK  3(6P21.1) MUTATED AMP PEAK  3(6P21.1) WILD-TYPE 
                       22.175                        22.045 
[1] "0.2 - 117.1 (22.2)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1"  
D3V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK  3(6P21.1) MUTATED        13        0        2        24         1
  AMP PEAK  3(6P21.1) WILD-TYPE      61        1       27       108         9
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  3(6P21.1) MUTATED           0         2          4         15
  AMP PEAK  3(6P21.1) WILD-TYPE         1        18          4         44
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK  3(6P21.1) MUTATED           15       10         6         1
  AMP PEAK  3(6P21.1) WILD-TYPE         26       35        11         1
D3V3, multiclass
            clus
vv           AMP PEAK  3(6P21.1) MUTATED AMP PEAK  3(6P21.1) WILD-TYPE
  STAGE I                             13                            61
  STAGE IA                             0                             1
  STAGE II                             2                            27
  STAGE IIA                           24                           108
  STAGE IIB                            1                             9
  STAGE IIC                            0                             1
  STAGE III                            2                            18
  STAGE IIIA                           4                             4
  STAGE IIIB                          15                            44
  STAGE IIIC                          15                            26
  STAGE IV                            10                            35
  STAGE IVA                            6                            11
  STAGE IVB                            1                             1
[1] 13  2
[1] 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(6P21.1) MUTATED     2  14  71   9
  AMP PEAK  3(6P21.1) WILD-TYPE   9  63 234  46
D3V4, multiclass
    clus
vv   AMP PEAK  3(6P21.1) MUTATED AMP PEAK  3(6P21.1) WILD-TYPE
  T1                           2                             9
  T2                          14                            63
  T3                          71                           234
  T4                           9                            46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2
  AMP PEAK  3(6P21.1) MUTATED    46  22  28
  AMP PEAK  3(6P21.1) WILD-TYPE 216  83  54
D3V5, multiclass
    clus
vv   AMP PEAK  3(6P21.1) MUTATED AMP PEAK  3(6P21.1) WILD-TYPE
  N0                          46                           216
  N1                          22                            83
  N2                          28                            54
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V6, binary
                               cls
clus                              0   1
  AMP PEAK  3(6P21.1) MUTATED    67  17
  AMP PEAK  3(6P21.1) WILD-TYPE 261  47
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(6P21.1) MUTATED     67   17
  AMP PEAK  3(6P21.1) WILD-TYPE  261   47
   clus
vv  AMP PEAK  3(6P21.1) MUTATED AMP PEAK  3(6P21.1) WILD-TYPE
  0                          67                           261
  1                          17                            47
[1] 2 2
[1] FALSE
D3V7, binary
                               cls
clus                              0   1
  AMP PEAK  3(6P21.1) MUTATED    41  55
  AMP PEAK  3(6P21.1) WILD-TYPE 172 181
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(6P21.1) MUTATED     41   55
  AMP PEAK  3(6P21.1) WILD-TYPE  172  181
        clus
vv       AMP PEAK  3(6P21.1) MUTATED AMP PEAK  3(6P21.1) WILD-TYPE
  FEMALE                          41                           172
  MALE                            55                           181
[1] 2 2
[1] FALSE
D3V8, binary
                               cls
clus                              0   1
  AMP PEAK  3(6P21.1) MUTATED    79   2
  AMP PEAK  3(6P21.1) WILD-TYPE 291   7
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(6P21.1) MUTATED     79    2
  AMP PEAK  3(6P21.1) WILD-TYPE  291    7
     clus
vv    AMP PEAK  3(6P21.1) MUTATED AMP PEAK  3(6P21.1) WILD-TYPE
  NO                           79                           291
  YES                           2                             7
[1] 2 2
[1] FALSE
D3V9, binary
                               cls
clus                              0   1
  AMP PEAK  3(6P21.1) MUTATED    85   9
  AMP PEAK  3(6P21.1) WILD-TYPE 297  53
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(6P21.1) MUTATED     85    9
  AMP PEAK  3(6P21.1) WILD-TYPE  297   53
                               clus
vv                              AMP PEAK  3(6P21.1) MUTATED
  COLON ADENOCARCINOMA                                   85
  COLON MUCINOUS ADENOCARCINOMA                           9
                               clus
vv                              AMP PEAK  3(6P21.1) WILD-TYPE
  COLON ADENOCARCINOMA                                    297
  COLON MUCINOUS ADENOCARCINOMA                            53
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  3(6P21.1) MUTATED    68   1   7   4
  AMP PEAK  3(6P21.1) WILD-TYPE 255   3  18  21
D3V10, multiclass
    clus
vv   AMP PEAK  3(6P21.1) MUTATED AMP PEAK  3(6P21.1) WILD-TYPE
  R0                          68                           255
  R1                           1                             3
  R2                           7                            18
  RX                           4                            21
[1] 4 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, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  3(6P21.1) MUTATED                                  1     1
  AMP PEAK  3(6P21.1) WILD-TYPE                                0    10
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  3(6P21.1) MUTATED                          11    53
  AMP PEAK  3(6P21.1) WILD-TYPE                        48   159
D3V12, multiclass
                                  clus
vv                                 AMP PEAK  3(6P21.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      1
  BLACK OR AFRICAN AMERICAN                                 11
  WHITE                                                     53
                                  clus
vv                                 AMP PEAK  3(6P21.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                       10
  BLACK OR AFRICAN AMERICAN                                   48
  WHITE                                                      159
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V13, binary
                               cls
clus                              0   1
  AMP PEAK  3(6P21.1) MUTATED     0  63
  AMP PEAK  3(6P21.1) WILD-TYPE   4 206
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(6P21.1) MUTATED      0   63
  AMP PEAK  3(6P21.1) WILD-TYPE    4  206
                        clus
vv                       AMP PEAK  3(6P21.1) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                          63
                        clus
vv                       AMP PEAK  3(6P21.1) WILD-TYPE
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           206
[1] 2 2
[1] FALSE

Clustering(4) Variable = AMP PEAK  4(8P11.23) MUTATION ANALYSIS
D4V1, survival
                                sevent
clus2                              0   1
  AMP PEAK  4(8P11.23) MUTATED   120  29
  AMP PEAK  4(8P11.23) WILD-TYPE 215  72
  AMP PEAK  4(8P11.23) MUTATED AMP PEAK  4(8P11.23) WILD-TYPE 
                           149                            287 
  AMP PEAK  4(8P11.23) MUTATED AMP PEAK  4(8P11.23) WILD-TYPE 
                            29                             72 
$`AMP PEAK  4(8P11.23) MUTATED`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3524 
       24.33        45.60        13.94        24.16         1.02        36.03 
TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3688 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3860 
       19.99         6.05        19.00        19.04        19.04        31.07 
TCGA-AA-3867 TCGA-AA-3939 TCGA-AA-3979 TCGA-AA-A00Z TCGA-AZ-4681 TCGA-AZ-6608 
       24.03        12.99        24.00        21.99       106.75         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-3L-AA1B TCGA-4T-AA8H TCGA-5M-AATE 
       49.08         5.88        63.62        15.62        12.66        39.45 
TCGA-A6-2675 TCGA-A6-3807 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5666 TCGA-A6-5667 
       43.43        34.65        32.45        32.91        32.71        29.16 
TCGA-A6-6137 TCGA-A6-6648 TCGA-A6-6782 TCGA-A6-A5ZU TCGA-AA-3495 TCGA-AA-3502 
       27.09        25.18        20.28         9.63        37.05        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3534 TCGA-AA-3538 
        6.97         1.02        19.07         0.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3548 TCGA-AA-3558 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       12.99        33.99        20.98        78.08         6.97        54.02 
TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 
       14.01        50.04        47.01         5.98        37.05         5.03 
TCGA-AA-3811 TCGA-AA-3841 TCGA-AA-3846 TCGA-AA-3852 TCGA-AA-3858 TCGA-AA-3875 
       10.06        36.95        17.03         0.00        31.07        18.05 
TCGA-AA-3941 TCGA-AA-3975 TCGA-AA-A00K TCGA-AA-A00R TCGA-AA-A01D TCGA-AA-A01S 
       24.00        34.06        18.05         0.99        10.98         1.02 
TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02O TCGA-AD-5900 TCGA-AD-6899 TCGA-AD-6963 
       37.02        51.98         0.92        12.16         5.79        27.42 
TCGA-AD-A5EK TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-6197 TCGA-AY-A54L TCGA-AZ-4614 
       16.44        27.09        16.31        21.44        17.26         5.65 
TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
       32.94         5.13        22.36        62.79        88.21        49.41 
TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5797 TCGA-CA-6715 
        3.19        12.69        12.36        12.46        12.59        12.59 
TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-6748 TCGA-CM-4744 TCGA-CM-4746 
      148.01        15.62        51.32         2.01        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       25.02         8.02        22.98        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6164 TCGA-CM-6166 TCGA-CM-6167 
       15.02        15.02        15.02        29.03        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6172 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6679 
       12.99        13.02        11.01        11.08        11.08        10.06 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 
       55.92        20.19        25.48         4.80        17.13        16.14 
TCGA-D5-6898 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6932 TCGA-D5-7000 
        7.53        12.43        14.30         9.04        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XF TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A28H TCGA-DM-A28K 
      119.70        38.20         7.50        44.32       117.07        98.24 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6807 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 
       35.74         6.18        43.04        67.30        65.85        53.62 
TCGA-G4-6311 TCGA-G4-6320 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A6GB 
       39.42        26.43        46.75        74.79        18.18        15.65 
TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-RU-A8FL TCGA-WS-AB45 
       29.46        32.98         8.42        38.70        70.03 

$`AMP PEAK  4(8P11.23) WILD-TYPE`
TCGA-A6-4105 TCGA-AA-3506 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3525 
       14.53        58.03        13.02        24.03        37.05         8.05 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 
       19.07        34.03         0.99        13.02        17.95        23.01 
TCGA-AA-3560 TCGA-AA-3672 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3844 TCGA-AA-3870 
       19.99         0.92        36.00        85.05        14.93        29.98 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3986 TCGA-AA-A00L 
       24.00         2.01        50.99        26.01        19.07        38.04 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 
       39.06        21.37        15.52        25.08        10.88        75.95 
TCGA-AZ-6601 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6314 TCGA-G4-6321 TCGA-G4-6586 
      100.01        28.21        23.51        35.93        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-NH-A8F7 TCGA-4N-A93T TCGA-5M-AAT4 
       26.17        91.79        79.69        17.85         4.80         1.61 
TCGA-5M-AAT6 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 
        9.53        43.76        46.65        43.76        42.90        42.28 
TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 
       44.91        35.11        16.57        37.05        37.25        37.02 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 
       32.75        36.53        31.63        30.44        29.19        33.53 
TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 
       23.61        22.09        22.06        22.52        24.13         8.38 
TCGA-A6-6142 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.08        20.61        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B 
       20.12        19.66        16.24        24.92        61.84        56.25 
TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3510 TCGA-AA-3517 
        5.03         7.04         3.02         1.02        63.98        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3532 TCGA-AA-3544 TCGA-AA-3549 TCGA-AA-3553 
        1.02         9.07        29.00        14.01        21.01        24.00 
TCGA-AA-3555 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3666 TCGA-AA-3675 TCGA-AA-3679 
       29.95        13.94        61.02         2.01        47.05        15.02 
TCGA-AA-3680 TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       11.01        26.99        35.05         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3848 
       17.98        15.95        38.99        37.02         0.00        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3864 
        0.00        33.07        36.03        32.05         0.99        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 
       17.03        27.02        31.00         2.01        33.01        26.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 
       20.98        34.03         2.01        21.99        16.08        13.05 
TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       25.02        27.02         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00N TCGA-AA-A00O 
       19.00        30.02        34.03        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C 
       42.02        17.03        14.99        34.98        15.02        15.02 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A02E TCGA-AA-A02F 
       35.01        33.04         1.02        26.01         2.96        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        2.01         5.03        22.03        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6901 TCGA-AD-6965 TCGA-AM-5820 
       40.96        83.24        24.53        22.42        26.47         0.46 
TCGA-AM-5821 TCGA-AU-3779 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 
        0.92        14.50         0.95        33.01         0.20        17.82 
TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 
       17.85        19.33        18.84       109.28        58.39         1.41 
TCGA-AZ-4684 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       65.00         6.77        12.10        29.56         5.23        11.74 
TCGA-CA-5796 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.39        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 
       85.45        70.16        21.99        21.14        82.95       124.27 
TCGA-CM-4743 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       23.05        26.04        27.02        13.02        29.06        22.03 
TCGA-CM-5349 TCGA-CM-5868 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6165 TCGA-CM-6170 
       30.08        17.03        12.00        14.04        16.04        15.02 
TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-5537 
       14.04        12.95        13.05        11.01        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 
       54.61        19.59        56.09        20.42        17.75        18.25 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6920 
       43.27        15.12        17.85        12.49        15.58        12.39 
TCGA-D5-6922 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
       10.13         9.44        11.64        13.41        13.35        12.00 
TCGA-DM-A0XD TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       24.43       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 
      140.38       131.51       135.65         7.76       139.17        14.04 
TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28M 
       26.47        81.37       119.93        35.97        60.79        95.18 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        11.11        35.74        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       34.42        41.42        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6306 
       35.31       133.18         8.35        82.39        74.56        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6322 TCGA-G4-6323 
       55.04        85.48        61.91        36.00        26.04        13.78 
TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GC TCGA-NH-A8F8 
       10.98        19.33        19.33         9.93        12.79        16.80 
TCGA-QG-A5YV TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-SS-A7HO TCGA-T9-A92H 
       42.77        31.30        21.90        60.13        11.90 

  AMP PEAK  4(8P11.23) MUTATED AMP PEAK  4(8P11.23) WILD-TYPE 
                             0                              0 
  AMP PEAK  4(8P11.23) MUTATED AMP PEAK  4(8P11.23) WILD-TYPE 
                        148.01                         140.38 
  AMP PEAK  4(8P11.23) MUTATED AMP PEAK  4(8P11.23) WILD-TYPE 
                         20.19                          23.01 
[1] "0.0 - 148.0 (20.2)" "0.0 - 140.4 (23.0)"
[1] "hr=" "1.2"
D4V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK  4(8P11.23) MUTATED        31        0       15        40         3
  AMP PEAK  4(8P11.23) WILD-TYPE      43        1       14        92         7
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  4(8P11.23) MUTATED           1         8          2         18
  AMP PEAK  4(8P11.23) WILD-TYPE         0        12          6         41
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK  4(8P11.23) MUTATED           17       14         6         0
  AMP PEAK  4(8P11.23) WILD-TYPE         24       31        11         2
D4V3, multiclass
            clus
vv           AMP PEAK  4(8P11.23) MUTATED AMP PEAK  4(8P11.23) WILD-TYPE
  STAGE I                              31                             43
  STAGE IA                              0                              1
  STAGE II                             15                             14
  STAGE IIA                            40                             92
  STAGE IIB                             3                              7
  STAGE IIC                             1                              0
  STAGE III                             8                             12
  STAGE IIIA                            2                              6
  STAGE IIIB                           18                             41
  STAGE IIIC                           17                             24
  STAGE IV                             14                             31
  STAGE IVA                             6                             11
  STAGE IVB                             0                              2
[1] 13  2
[1] 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(8P11.23) MUTATED     3  31 106  17
  AMP PEAK  4(8P11.23) WILD-TYPE   8  46 199  38
D4V4, multiclass
    clus
vv   AMP PEAK  4(8P11.23) MUTATED AMP PEAK  4(8P11.23) WILD-TYPE
  T1                            3                              8
  T2                           31                             46
  T3                          106                            199
  T4                           17                             38
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2
  AMP PEAK  4(8P11.23) MUTATED    95  33  29
  AMP PEAK  4(8P11.23) WILD-TYPE 167  72  53
D4V5, multiclass
    clus
vv   AMP PEAK  4(8P11.23) MUTATED AMP PEAK  4(8P11.23) WILD-TYPE
  N0                           95                            167
  N1                           33                             72
  N2                           29                             53
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V6, binary
                                cls
clus                               0   1
  AMP PEAK  4(8P11.23) MUTATED   112  20
  AMP PEAK  4(8P11.23) WILD-TYPE 216  44
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  4(8P11.23) MUTATED    112   20
  AMP PEAK  4(8P11.23) WILD-TYPE  216   44
   clus
vv  AMP PEAK  4(8P11.23) MUTATED AMP PEAK  4(8P11.23) WILD-TYPE
  0                          112                            216
  1                           20                             44
[1] 2 2
[1] FALSE
D4V7, binary
                                cls
clus                               0   1
  AMP PEAK  4(8P11.23) MUTATED    76  81
  AMP PEAK  4(8P11.23) WILD-TYPE 137 155
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  4(8P11.23) MUTATED     76   81
  AMP PEAK  4(8P11.23) WILD-TYPE  137  155
        clus
vv       AMP PEAK  4(8P11.23) MUTATED AMP PEAK  4(8P11.23) WILD-TYPE
  FEMALE                           76                            137
  MALE                             81                            155
[1] 2 2
[1] FALSE
D4V8, binary
                                cls
clus                               0   1
  AMP PEAK  4(8P11.23) MUTATED   129   4
  AMP PEAK  4(8P11.23) WILD-TYPE 241   5
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  4(8P11.23) MUTATED    129    4
  AMP PEAK  4(8P11.23) WILD-TYPE  241    5
     clus
vv    AMP PEAK  4(8P11.23) MUTATED AMP PEAK  4(8P11.23) WILD-TYPE
  NO                           129                            241
  YES                            4                              5
[1] 2 2
[1] FALSE
D4V9, binary
                                cls
clus                               0   1
  AMP PEAK  4(8P11.23) MUTATED   140  16
  AMP PEAK  4(8P11.23) WILD-TYPE 242  46
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  4(8P11.23) MUTATED    140   16
  AMP PEAK  4(8P11.23) WILD-TYPE  242   46
                               clus
vv                              AMP PEAK  4(8P11.23) MUTATED
  COLON ADENOCARCINOMA                                   140
  COLON MUCINOUS ADENOCARCINOMA                           16
                               clus
vv                              AMP PEAK  4(8P11.23) WILD-TYPE
  COLON ADENOCARCINOMA                                     242
  COLON MUCINOUS ADENOCARCINOMA                             46
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK  4(8P11.23) MUTATED   114   1   9  12
  AMP PEAK  4(8P11.23) WILD-TYPE 209   3  16  13
D4V10, multiclass
    clus
vv   AMP PEAK  4(8P11.23) MUTATED AMP PEAK  4(8P11.23) WILD-TYPE
  R0                          114                            209
  R1                            1                              3
  R2                            9                             16
  RX                           12                             13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  4(8P11.23) MUTATED                                  0     5
  AMP PEAK  4(8P11.23) WILD-TYPE                                1     6
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  4(8P11.23) MUTATED                          18    81
  AMP PEAK  4(8P11.23) WILD-TYPE                        41   131
D4V12, multiclass
                                  clus
vv                                 AMP PEAK  4(8P11.23) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       5
  BLACK OR AFRICAN AMERICAN                                  18
  WHITE                                                      81
                                  clus
vv                                 AMP PEAK  4(8P11.23) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         6
  BLACK OR AFRICAN AMERICAN                                    41
  WHITE                                                       131
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V13, binary
                                cls
clus                               0   1
  AMP PEAK  4(8P11.23) MUTATED     1  99
  AMP PEAK  4(8P11.23) WILD-TYPE   3 170
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  4(8P11.23) MUTATED      1   99
  AMP PEAK  4(8P11.23) WILD-TYPE    3  170
                        clus
vv                       AMP PEAK  4(8P11.23) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           99
                        clus
vv                       AMP PEAK  4(8P11.23) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            170
[1] 2 2
[1] FALSE

Clustering(5) Variable = AMP PEAK  5(8P11.21) MUTATION ANALYSIS
D5V1, survival
                                sevent
clus2                              0   1
  AMP PEAK  5(8P11.21) MUTATED   143  36
  AMP PEAK  5(8P11.21) WILD-TYPE 192  65
  AMP PEAK  5(8P11.21) MUTATED AMP PEAK  5(8P11.21) WILD-TYPE 
                           179                            257 
  AMP PEAK  5(8P11.21) MUTATED AMP PEAK  5(8P11.21) WILD-TYPE 
                            36                             65 
$`AMP PEAK  5(8P11.21) MUTATED`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3524 
       24.33        45.60        13.94        24.16         1.02        36.03 
TCGA-AA-3552 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3713 
       13.02        19.99        19.99        19.00        36.00        19.04 
TCGA-AA-3715 TCGA-AA-3867 TCGA-AA-3939 TCGA-AA-3979 TCGA-AA-A00Z TCGA-AD-6888 
       19.04        24.03        12.99        24.00        21.99        15.52 
TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-3L-AA1B 
      106.75         1.94        49.08         5.88        63.62        15.62 
TCGA-4T-AA8H TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2680 
       12.66        39.45        43.76        43.76        43.43        35.11 
TCGA-A6-3807 TCGA-A6-4107 TCGA-A6-5657 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 
       34.65        32.45        31.63        32.71        29.16        27.09 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6782 TCGA-A6-A567 TCGA-A6-A5ZU TCGA-AA-3494 
       25.08        25.18        20.28        61.84         9.63         1.02 
TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3526 TCGA-AA-3532 
       37.05        35.01         6.97         1.02        19.07        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3553 
       29.00        26.01        12.99        14.01        33.99        24.00 
TCGA-AA-3558 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3673 
       20.98        78.08         6.97        54.02        14.01        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3811 
       47.01        15.02         5.98        37.05         5.03        10.06 
TCGA-AA-3841 TCGA-AA-3846 TCGA-AA-3852 TCGA-AA-3858 TCGA-AA-3869 TCGA-AA-3875 
       36.95        17.03         0.00        31.07        27.02        18.05 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3971 TCGA-AA-3975 TCGA-AA-A00D TCGA-AA-A00K 
        2.01        24.00        16.08        34.06        19.00        18.05 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A01G TCGA-AA-A01S TCGA-AA-A01Z TCGA-AA-A029 
        0.99        17.03        12.00         1.02        37.02        51.98 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AD-5900 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
        0.92        41.00        12.16         5.79        22.42        27.42 
TCGA-AD-A5EK TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-6197 TCGA-AY-A54L TCGA-AZ-4615 
       16.44         0.92        27.09        21.44        17.26        32.94 
TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6605 
        5.13        22.36        62.79        88.21        49.41         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5797 
       11.74         3.19        12.69        12.36        12.46        12.59 
TCGA-CA-6715 TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-6748 
       12.59        14.30       148.01        15.62        51.32         2.01 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-5348 
       20.02        37.02        25.02         8.02        27.02        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-6161 TCGA-CM-6164 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6172 
       15.02        29.03        14.99        12.99        13.02        11.01 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6679 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6533 
       11.08        11.08        10.06        55.92        20.19        25.48 
TCGA-D5-6534 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
       43.27         4.80        17.13        16.14        15.58         7.53 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6932 
       10.13        12.43        14.30         9.04        13.41        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1DA TCGA-DM-A1DB 
       10.26       119.70        38.20       130.65         7.50        44.32 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6805 
       98.24         8.61        35.74        35.74         6.18        34.42 
TCGA-F4-6807 TCGA-G4-6295 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6306 
       43.04         8.35        74.56        67.30        53.62        44.68 
TCGA-G4-6311 TCGA-G4-6320 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50U 
       39.42        26.43        46.75        74.79        18.18        10.98 
TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-RU-A8FL TCGA-WS-AB45 
       29.46        32.98         8.42        38.70        70.03 

$`AMP PEAK  5(8P11.21) WILD-TYPE`
TCGA-A6-4105 TCGA-AA-3506 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3525 
       14.53        58.03        13.02        24.03        37.05         8.05 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3662 
       19.07        34.03         0.99        17.95        23.01         6.05 
TCGA-AA-3672 TCGA-AA-3697 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3870 TCGA-AA-3950 
        0.92        85.05        14.93        31.07        29.98        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A024 
        2.01        50.99        26.01        19.07        38.04        39.06 
TCGA-AD-6548 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-6601 TCGA-G4-6294 
       21.37        25.08        10.88        75.95       100.01        28.21 
TCGA-G4-6298 TCGA-G4-6314 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       23.51        35.93        22.09        35.80        26.17        91.79 
TCGA-G4-6628 TCGA-NH-A8F7 TCGA-4N-A93T TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-A6-2672 
       79.69        17.85         4.80         1.61         9.53        46.65 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 
       42.90        42.28        44.91        16.57        37.05        37.25 
TCGA-A6-2686 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 
       37.02        32.75        36.53        32.91        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6138 TCGA-A6-6140 
       33.53        23.61        22.09        22.06        22.52        24.13 
TCGA-A6-6141 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
        8.38        20.61        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A56B TCGA-AA-3488 
       20.12        19.66        16.24        24.92        56.25         5.03 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        7.04         3.02        63.98        38.99         1.02         9.07 
TCGA-AA-3529 TCGA-AA-3549 TCGA-AA-3555 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3666 
        0.00        21.01        29.95        13.94        61.02         2.01 
TCGA-AA-3675 TCGA-AA-3680 TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
       47.05        11.01        26.99        35.05         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
       10.06         0.00        33.07        36.03        32.05         0.99 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3877 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       53.00        17.03        31.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3973 TCGA-AA-3977 TCGA-AA-3982 
       34.03         2.01        21.99        13.05        25.02        27.02 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00F 
        7.96        27.02        13.94        38.04        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00W TCGA-AA-A010 
       18.05         4.01        27.02        42.02        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01I TCGA-AA-A01K 
       15.02        15.02        10.98        32.02        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
       38.07         1.02        35.01        33.04         1.02        26.01 
TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02R TCGA-AA-A02Y 
        2.96        39.98         2.01         5.03        22.03        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6965 TCGA-AM-5820 
       18.05        40.96        83.24        24.53        26.47         0.46 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 
       14.50        16.31         0.95        33.01         0.20        17.82 
TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 
       17.85        19.33        18.84       109.28        58.39         1.41 
TCGA-AZ-4614 TCGA-AZ-4684 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-CA-5796 
        5.65        65.00         6.77        12.10        29.56        12.39 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 
       12.20        12.76        10.06        17.56        85.45        70.16 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4748 
       21.99        21.14        82.95       124.27        23.05        26.04 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5868 TCGA-CM-6162 TCGA-CM-6163 
       13.02        29.06        22.03        17.03        12.00        14.04 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 
       16.04        21.99        15.02        14.04        12.95        13.05 
TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       11.01        12.03        45.40        54.61        19.59        56.09 
TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6539 
       20.42        17.75        18.25        15.12        17.85        12.49 
TCGA-D5-6920 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-DM-A0XD 
       12.39         9.44        11.64        13.35        12.00        24.43 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1HA 
       92.75        49.91        13.32        12.59       140.38       131.51 
TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C 
      135.65         7.76       139.17        14.04        26.47        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28M TCGA-F4-6460 
      119.93        35.97        60.79       117.07        95.18        31.96 
TCGA-F4-6461 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6806 TCGA-F4-6808 TCGA-F4-6809 
       11.11        47.87         1.55        41.42        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6297 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        82.39        65.85 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6322 TCGA-G4-6323 
       55.04        85.48        61.91        36.00        26.04        13.78 
TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F8 
       19.33        19.33         9.93        15.65        12.79        16.80 
TCGA-QG-A5YV TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-SS-A7HO TCGA-T9-A92H 
       42.77        31.30        21.90        60.13        11.90 

  AMP PEAK  5(8P11.21) MUTATED AMP PEAK  5(8P11.21) WILD-TYPE 
                             0                              0 
  AMP PEAK  5(8P11.21) MUTATED AMP PEAK  5(8P11.21) WILD-TYPE 
                        148.01                         140.38 
  AMP PEAK  5(8P11.21) MUTATED AMP PEAK  5(8P11.21) WILD-TYPE 
                         20.19                          23.01 
[1] "0.0 - 148.0 (20.2)" "0.0 - 140.4 (23.0)"
[1] "hr=" "1.1"
D5V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK  5(8P11.21) MUTATED        33        0       17        50         3
  AMP PEAK  5(8P11.21) WILD-TYPE      41        1       12        82         7
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  5(8P11.21) MUTATED           1         9          3         23
  AMP PEAK  5(8P11.21) WILD-TYPE         0        11          5         36
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK  5(8P11.21) MUTATED           15       22         7         0
  AMP PEAK  5(8P11.21) WILD-TYPE         26       23        10         2
D5V3, multiclass
            clus
vv           AMP PEAK  5(8P11.21) MUTATED AMP PEAK  5(8P11.21) WILD-TYPE
  STAGE I                              33                             41
  STAGE IA                              0                              1
  STAGE II                             17                             12
  STAGE IIA                            50                             82
  STAGE IIB                             3                              7
  STAGE IIC                             1                              0
  STAGE III                             9                             11
  STAGE IIIA                            3                              5
  STAGE IIIB                           23                             36
  STAGE IIIC                           15                             26
  STAGE IV                             22                             23
  STAGE IVA                             7                             10
  STAGE IVB                             0                              2
[1] 13  2
[1] 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(8P11.21) MUTATED     3  34 131  19
  AMP PEAK  5(8P11.21) WILD-TYPE   8  43 174  36
D5V4, multiclass
    clus
vv   AMP PEAK  5(8P11.21) MUTATED AMP PEAK  5(8P11.21) WILD-TYPE
  T1                            3                              8
  T2                           34                             43
  T3                          131                            174
  T4                           19                             36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2
  AMP PEAK  5(8P11.21) MUTATED   113  40  34
  AMP PEAK  5(8P11.21) WILD-TYPE 149  65  48
D5V5, multiclass
    clus
vv   AMP PEAK  5(8P11.21) MUTATED AMP PEAK  5(8P11.21) WILD-TYPE
  N0                          113                            149
  N1                           40                             65
  N2                           34                             48
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V6, binary
                                cls
clus                               0   1
  AMP PEAK  5(8P11.21) MUTATED   133  29
  AMP PEAK  5(8P11.21) WILD-TYPE 195  35
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  5(8P11.21) MUTATED    133   29
  AMP PEAK  5(8P11.21) WILD-TYPE  195   35
   clus
vv  AMP PEAK  5(8P11.21) MUTATED AMP PEAK  5(8P11.21) WILD-TYPE
  0                          133                            195
  1                           29                             35
[1] 2 2
[1] FALSE
D5V7, binary
                                cls
clus                               0   1
  AMP PEAK  5(8P11.21) MUTATED    81 106
  AMP PEAK  5(8P11.21) WILD-TYPE 132 130
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  5(8P11.21) MUTATED     81  106
  AMP PEAK  5(8P11.21) WILD-TYPE  132  130
        clus
vv       AMP PEAK  5(8P11.21) MUTATED AMP PEAK  5(8P11.21) WILD-TYPE
  FEMALE                           81                            132
  MALE                            106                            130
[1] 2 2
[1] FALSE
D5V8, binary
                                cls
clus                               0   1
  AMP PEAK  5(8P11.21) MUTATED   157   5
  AMP PEAK  5(8P11.21) WILD-TYPE 213   4
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  5(8P11.21) MUTATED    157    5
  AMP PEAK  5(8P11.21) WILD-TYPE  213    4
     clus
vv    AMP PEAK  5(8P11.21) MUTATED AMP PEAK  5(8P11.21) WILD-TYPE
  NO                           157                            213
  YES                            5                              4
[1] 2 2
[1] FALSE
D5V9, binary
                                cls
clus                               0   1
  AMP PEAK  5(8P11.21) MUTATED   165  21
  AMP PEAK  5(8P11.21) WILD-TYPE 217  41
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  5(8P11.21) MUTATED    165   21
  AMP PEAK  5(8P11.21) WILD-TYPE  217   41
                               clus
vv                              AMP PEAK  5(8P11.21) MUTATED
  COLON ADENOCARCINOMA                                   165
  COLON MUCINOUS ADENOCARCINOMA                           21
                               clus
vv                              AMP PEAK  5(8P11.21) WILD-TYPE
  COLON ADENOCARCINOMA                                     217
  COLON MUCINOUS ADENOCARCINOMA                             41
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK  5(8P11.21) MUTATED   135   0  13  13
  AMP PEAK  5(8P11.21) WILD-TYPE 188   4  12  12
D5V10, multiclass
    clus
vv   AMP PEAK  5(8P11.21) MUTATED AMP PEAK  5(8P11.21) WILD-TYPE
  R0                          135                            188
  R1                            0                              4
  R2                           13                             12
  RX                           13                             12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  5(8P11.21) MUTATED                                  0     6
  AMP PEAK  5(8P11.21) WILD-TYPE                                1     5
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  5(8P11.21) MUTATED                          20    97
  AMP PEAK  5(8P11.21) WILD-TYPE                        39   115
D5V12, multiclass
                                  clus
vv                                 AMP PEAK  5(8P11.21) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       6
  BLACK OR AFRICAN AMERICAN                                  20
  WHITE                                                      97
                                  clus
vv                                 AMP PEAK  5(8P11.21) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         5
  BLACK OR AFRICAN AMERICAN                                    39
  WHITE                                                       115
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V13, binary
                                cls
clus                               0   1
  AMP PEAK  5(8P11.21) MUTATED     1 116
  AMP PEAK  5(8P11.21) WILD-TYPE   3 153
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  5(8P11.21) MUTATED      1  116
  AMP PEAK  5(8P11.21) WILD-TYPE    3  153
                        clus
vv                       AMP PEAK  5(8P11.21) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                          116
                        clus
vv                       AMP PEAK  5(8P11.21) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            153
[1] 2 2
[1] FALSE

Clustering(6) Variable = AMP PEAK  6(8Q24.21) MUTATION ANALYSIS
D6V1, survival
                                sevent
clus2                              0   1
  AMP PEAK  6(8Q24.21) MUTATED   189  60
  AMP PEAK  6(8Q24.21) WILD-TYPE 146  41
  AMP PEAK  6(8Q24.21) MUTATED AMP PEAK  6(8Q24.21) WILD-TYPE 
                           249                            187 
  AMP PEAK  6(8Q24.21) MUTATED AMP PEAK  6(8Q24.21) WILD-TYPE 
                            60                             41 
$`AMP PEAK  6(8Q24.21) MUTATED`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3520 
       24.33        45.60        13.94        24.16         1.02        24.03 
TCGA-AA-3524 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3556 TCGA-AA-3562 TCGA-AA-3662 
       36.03         0.99        13.02        23.01        19.99         6.05 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3867 TCGA-AA-3870 
       36.00        85.05        19.04        19.04        24.03        29.98 
TCGA-AA-3939 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-A00Z TCGA-AD-6548 TCGA-AD-6888 
       12.99        26.01        24.00        21.99        21.37        15.52 
TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6298 TCGA-G4-6310 
      106.75         1.94        49.08         5.88        23.51        63.62 
TCGA-G4-6314 TCGA-3L-AA1B TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-5M-AATE 
       35.93        15.62        12.66         1.61         9.53        39.45 
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2685 
       43.76        43.76        43.43        35.11        16.57        37.25 
TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 
       37.02        34.65        36.53        32.45        32.91        31.63 
TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6140 
       29.19        23.61        32.71        29.16        27.09        24.13 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6782 
       25.08        25.18        20.61        24.69        23.87        20.28 
TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 
       56.25         9.63         5.03         1.02        37.05        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        6.97         1.02        19.07         0.00        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3553 TCGA-AA-3558 
       26.01        12.99        14.01        33.99        24.00        20.98 
TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 
       78.08         6.97        54.02        14.01        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3811 TCGA-AA-3841 
       15.02         5.98        37.05         5.03        10.06        36.95 
TCGA-AA-3842 TCGA-AA-3846 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3856 
       37.02        17.03        33.07         0.00        36.03         0.99 
TCGA-AA-3858 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3941 
       31.07        17.03        27.02        18.05         2.01        24.00 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3975 TCGA-AA-3982 
       20.98        34.03         2.01        16.08        34.06        27.02 
TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00K TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A017 
       13.94        19.00        18.05         0.99        17.03        15.02 
TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01K TCGA-AA-A01S TCGA-AA-A01Z TCGA-AA-A029 
       10.98        12.00        31.00         1.02        37.02        51.98 
TCGA-AA-A02E TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02W TCGA-AD-5900 
        2.96         2.01         5.03         0.92        41.00        12.16 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5821 
        5.79        22.42        27.42        26.47        16.44         0.92 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-A54L TCGA-AY-A8YK 
       27.09        16.31         0.20        21.44        17.26        18.84 
TCGA-AZ-4308 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-4684 
      109.28         5.65        32.94         5.13        22.36        65.00 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 
       62.79        88.21        49.41        12.10        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5797 
       11.74         3.19        12.69        12.36        12.46        12.59 
TCGA-CA-6715 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5913 
       12.59        10.06        14.30       148.01        15.62        51.32 
TCGA-CK-5914 TCGA-CK-6748 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4750 
       21.99         2.01        20.02        37.02        25.02         8.02 
TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       27.02        13.02        29.06        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       14.04        29.03        21.99        14.99        12.99        13.02 
TCGA-CM-6676 TCGA-CM-6679 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       11.08        10.06        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 
       20.19        25.48        43.27        15.12         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6923 
       12.49        16.14        15.58         7.53        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       14.30         9.04        13.41        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1D9 TCGA-DM-A1DA 
       24.43        38.20       130.65        49.91       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
       44.32        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6805 TCGA-F4-6807 
       31.96        35.74        35.74         6.18        34.42        43.04 
TCGA-G4-6295 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
        8.35        74.56        67.30        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6311 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6626 TCGA-G4-6627 
       55.04        39.42        36.00        26.43        46.75        74.79 
TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A6GB TCGA-NH-A8F8 TCGA-QG-A5YW TCGA-QG-A5YX 
       18.18        10.98        15.65        16.80        29.46        32.98 
TCGA-QG-A5Z1 TCGA-RU-A8FL TCGA-WS-AB45 
        8.42        38.70        70.03 

$`AMP PEAK  6(8Q24.21) WILD-TYPE`
TCGA-A6-4105 TCGA-AA-3506 TCGA-AA-3516 TCGA-AA-3522 TCGA-AA-3525 TCGA-AA-3530 
       14.53        58.03        13.02        37.05         8.05        19.07 
TCGA-AA-3531 TCGA-AA-3554 TCGA-AA-3560 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3844 
       34.03        17.95        19.99         0.92        19.00        14.93 
TCGA-AA-3860 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3986 TCGA-AA-A00L 
       31.07        24.00         2.01        50.99        19.07        38.04 
TCGA-AA-A024 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-6601 TCGA-G4-6294 
       39.06        25.08        10.88        75.95       100.01        28.21 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-NH-A8F7 
       22.09        35.80        26.17        91.79        79.69        17.85 
TCGA-4N-A93T TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2684 
        4.80        46.65        42.90        42.28        44.91        37.05 
TCGA-A6-3809 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6138 
       32.75        30.44        33.53        22.09        22.06        22.52 
TCGA-A6-6141 TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 
        8.38        21.76        24.39        20.12        19.66        16.24 
TCGA-A6-A566 TCGA-A6-A567 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3517 
       24.92        61.84         7.04         3.02        63.98        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3549 TCGA-AA-3555 TCGA-AA-3561 TCGA-AA-3655 
        1.02         9.07        21.01        29.95        13.94        61.02 
TCGA-AA-3666 TCGA-AA-3675 TCGA-AA-3680 TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3818 
        2.01        47.05        11.01        26.99        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3845 
       25.02         1.02        17.98        15.95        38.99         0.00 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3855 TCGA-AA-3864 TCGA-AA-3877 TCGA-AA-3947 
       10.06         0.00        32.05        53.00        31.00        33.01 
TCGA-AA-3949 TCGA-AA-3968 TCGA-AA-3973 TCGA-AA-3977 TCGA-AA-3989 TCGA-AA-3994 
       26.01        21.99        13.05        25.02         7.96        27.02 
TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00N TCGA-AA-A00O 
       38.04        30.02        34.03        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01I 
       42.02        14.99        34.98        15.02        32.02        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
       38.07         1.02        35.01        33.04         1.02        26.01 
TCGA-AA-A02F TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6889 
       39.98        22.03        39.98        18.05        40.96        83.24 
TCGA-AD-6890 TCGA-AM-5820 TCGA-AU-3779 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 
       24.53         0.46        14.50         0.95        33.01        17.82 
TCGA-AY-A69D TCGA-AY-A71X TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-6599 TCGA-CA-5796 
       17.85        19.33        58.39         1.41         6.77        12.39 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-5916 
       12.20        12.76        17.56        85.45        70.16        21.14 
TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4748 TCGA-CM-5344 TCGA-CM-6162 
       82.95       124.27        23.05        26.04        22.03        12.00 
TCGA-CM-6165 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       16.04        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-6530 TCGA-D5-6531 
       11.08        11.01        12.03        45.40        20.42        17.75 
TCGA-D5-6532 TCGA-D5-6536 TCGA-D5-6920 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 
       18.25        17.85        12.39         9.44        11.64        13.35 
TCGA-D5-6931 TCGA-DM-A1D4 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1HA TCGA-DM-A1HB 
       12.00        92.75        13.32        12.59       131.51       135.65 
TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E 
        7.76       139.17        14.04        26.47        81.37       119.93 
TCGA-DM-A28M TCGA-F4-6461 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6806 TCGA-F4-6808 
       95.18        11.11        47.87         1.55        41.42        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6297 
       13.25         0.53        47.41        35.31       133.18        82.39 
TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6322 TCGA-G4-6323 TCGA-NH-A50V TCGA-NH-A5IV 
       85.48        61.91        26.04        13.78        19.33        19.33 
TCGA-NH-A6GA TCGA-NH-A6GC TCGA-QG-A5YV TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-SS-A7HO 
        9.93        12.79        42.77        31.30        21.90        60.13 
TCGA-T9-A92H 
       11.90 

  AMP PEAK  6(8Q24.21) MUTATED AMP PEAK  6(8Q24.21) WILD-TYPE 
                             0                              0 
  AMP PEAK  6(8Q24.21) MUTATED AMP PEAK  6(8Q24.21) WILD-TYPE 
                        148.01                         139.17 
  AMP PEAK  6(8Q24.21) MUTATED AMP PEAK  6(8Q24.21) WILD-TYPE 
                         21.99                          22.06 
[1] "0.0 - 148.0 (22.0)" "0.0 - 139.2 (22.1)"
[1] "hr=" "1.2"
D6V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK  6(8Q24.21) MUTATED        41        0       19        68         3
  AMP PEAK  6(8Q24.21) WILD-TYPE      33        1       10        64         7
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  6(8Q24.21) MUTATED           1         9          7         34
  AMP PEAK  6(8Q24.21) WILD-TYPE         0        11          1         25
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK  6(8Q24.21) MUTATED           24       33        13         0
  AMP PEAK  6(8Q24.21) WILD-TYPE         17       12         4         2
D6V3, multiclass
            clus
vv           AMP PEAK  6(8Q24.21) MUTATED AMP PEAK  6(8Q24.21) WILD-TYPE
  STAGE I                              41                             33
  STAGE IA                              0                              1
  STAGE II                             19                             10
  STAGE IIA                            68                             64
  STAGE IIB                             3                              7
  STAGE IIC                             1                              0
  STAGE III                             9                             11
  STAGE IIIA                            7                              1
  STAGE IIIB                           34                             25
  STAGE IIIC                           24                             17
  STAGE IV                             33                             12
  STAGE IVA                            13                              4
  STAGE IVB                             0                              2
[1] 13  2
[1] 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(8Q24.21) MUTATED     4  46 180  28
  AMP PEAK  6(8Q24.21) WILD-TYPE   7  31 125  27
D6V4, multiclass
    clus
vv   AMP PEAK  6(8Q24.21) MUTATED AMP PEAK  6(8Q24.21) WILD-TYPE
  T1                            4                              7
  T2                           46                             31
  T3                          180                            125
  T4                           28                             27
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2
  AMP PEAK  6(8Q24.21) MUTATED   146  58  54
  AMP PEAK  6(8Q24.21) WILD-TYPE 116  47  28
D6V5, multiclass
    clus
vv   AMP PEAK  6(8Q24.21) MUTATED AMP PEAK  6(8Q24.21) WILD-TYPE
  N0                          146                            116
  N1                           58                             47
  N2                           54                             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"
D6V6, binary
                                cls
clus                               0   1
  AMP PEAK  6(8Q24.21) MUTATED   180  46
  AMP PEAK  6(8Q24.21) WILD-TYPE 148  18
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  6(8Q24.21) MUTATED    180   46
  AMP PEAK  6(8Q24.21) WILD-TYPE  148   18
   clus
vv  AMP PEAK  6(8Q24.21) MUTATED AMP PEAK  6(8Q24.21) WILD-TYPE
  0                          180                            148
  1                           46                             18
[1] 2 2
[1] FALSE
D6V7, binary
                                cls
clus                               0   1
  AMP PEAK  6(8Q24.21) MUTATED   116 142
  AMP PEAK  6(8Q24.21) WILD-TYPE  97  94
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  6(8Q24.21) MUTATED    116  142
  AMP PEAK  6(8Q24.21) WILD-TYPE   97   94
        clus
vv       AMP PEAK  6(8Q24.21) MUTATED AMP PEAK  6(8Q24.21) WILD-TYPE
  FEMALE                          116                             97
  MALE                            142                             94
[1] 2 2
[1] FALSE
D6V8, binary
                                cls
clus                               0   1
  AMP PEAK  6(8Q24.21) MUTATED   211   5
  AMP PEAK  6(8Q24.21) WILD-TYPE 159   4
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  6(8Q24.21) MUTATED    211    5
  AMP PEAK  6(8Q24.21) WILD-TYPE  159    4
     clus
vv    AMP PEAK  6(8Q24.21) MUTATED AMP PEAK  6(8Q24.21) WILD-TYPE
  NO                           211                            159
  YES                            5                              4
[1] 2 2
[1] FALSE
D6V9, binary
                                cls
clus                               0   1
  AMP PEAK  6(8Q24.21) MUTATED   228  28
  AMP PEAK  6(8Q24.21) WILD-TYPE 154  34
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  6(8Q24.21) MUTATED    228   28
  AMP PEAK  6(8Q24.21) WILD-TYPE  154   34
                               clus
vv                              AMP PEAK  6(8Q24.21) MUTATED
  COLON ADENOCARCINOMA                                   228
  COLON MUCINOUS ADENOCARCINOMA                           28
                               clus
vv                              AMP PEAK  6(8Q24.21) WILD-TYPE
  COLON ADENOCARCINOMA                                     154
  COLON MUCINOUS ADENOCARCINOMA                             34
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK  6(8Q24.21) MUTATED   179   2  18  16
  AMP PEAK  6(8Q24.21) WILD-TYPE 144   2   7   9
D6V10, multiclass
    clus
vv   AMP PEAK  6(8Q24.21) MUTATED AMP PEAK  6(8Q24.21) WILD-TYPE
  R0                          179                            144
  R1                            2                              2
  R2                           18                              7
  RX                           16                              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"
D6V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  6(8Q24.21) MUTATED                                  0     7
  AMP PEAK  6(8Q24.21) WILD-TYPE                                1     4
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  6(8Q24.21) MUTATED                          33   130
  AMP PEAK  6(8Q24.21) WILD-TYPE                        26    82
D6V12, multiclass
                                  clus
vv                                 AMP PEAK  6(8Q24.21) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       7
  BLACK OR AFRICAN AMERICAN                                  33
  WHITE                                                     130
                                  clus
vv                                 AMP PEAK  6(8Q24.21) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         4
  BLACK OR AFRICAN AMERICAN                                    26
  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"
D6V13, binary
                                cls
clus                               0   1
  AMP PEAK  6(8Q24.21) MUTATED     3 162
  AMP PEAK  6(8Q24.21) WILD-TYPE   1 107
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  6(8Q24.21) MUTATED      3  162
  AMP PEAK  6(8Q24.21) WILD-TYPE    1  107
                        clus
vv                       AMP PEAK  6(8Q24.21) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                          162
                        clus
vv                       AMP PEAK  6(8Q24.21) WILD-TYPE
  HISPANIC OR LATINO                                  1
  NOT HISPANIC OR LATINO                            107
[1] 2 2
[1] FALSE

Clustering(7) Variable = AMP PEAK  7(11P15.5) MUTATION ANALYSIS
D7V1, survival
                                sevent
clus2                              0   1
  AMP PEAK  7(11P15.5) MUTATED    68  21
  AMP PEAK  7(11P15.5) WILD-TYPE 267  80
  AMP PEAK  7(11P15.5) MUTATED AMP PEAK  7(11P15.5) WILD-TYPE 
                            89                            347 
  AMP PEAK  7(11P15.5) MUTATED AMP PEAK  7(11P15.5) WILD-TYPE 
                            21                             80 
$`AMP PEAK  7(11P15.5) MUTATED`
TCGA-AA-3506 TCGA-AA-3520 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3552 TCGA-AA-3556 
       58.03        24.03        19.07        34.03        13.02        23.01 
TCGA-AA-3562 TCGA-AA-3867 TCGA-AA-3986 TCGA-AA-A00Z TCGA-AD-6888 TCGA-AZ-6608 
       19.99        24.03        19.07        21.99        15.52         1.94 
TCGA-G4-6310 TCGA-G4-6314 TCGA-A6-2671 TCGA-A6-2675 TCGA-A6-2679 TCGA-A6-5660 
       63.62        35.93        43.76        43.43        44.91        29.19 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6654 TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3494 
       25.08        25.18        23.87         9.63         5.03         1.02 
TCGA-AA-3519 TCGA-AA-3529 TCGA-AA-3534 TCGA-AA-3542 TCGA-AA-3553 TCGA-AA-3561 
        9.07         0.00        29.00        12.99        24.00        13.94 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3696 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3842 
       50.04        47.01         5.03        25.02        17.98        37.02 
TCGA-AA-3846 TCGA-AA-3851 TCGA-AA-3856 TCGA-AA-3875 TCGA-AA-3955 TCGA-AA-3982 
       17.03        33.07         0.99        18.05        20.98        27.02 
TCGA-AA-A00F TCGA-AA-A00U TCGA-AA-A01D TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01X 
       34.03        17.03        10.98         1.02         1.02        26.01 
TCGA-AA-A02F TCGA-AA-A02J TCGA-AD-6901 TCGA-AM-5820 TCGA-AY-4070 TCGA-AY-4071 
       39.98         5.03        22.42         0.46        16.31         0.95 
TCGA-AY-A8YK TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6603 TCGA-AZ-6607 TCGA-CA-5256 
       18.84        65.00        62.79        29.56         3.19        12.46 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4948 TCGA-CM-4750 TCGA-CM-5349 
       12.59        12.20        14.30       148.01         8.02        30.08 
TCGA-CM-5868 TCGA-CM-6164 TCGA-CM-6166 TCGA-CM-6677 TCGA-D5-5538 TCGA-D5-5540 
       17.03        29.03        21.99        11.08        54.61        56.09 
TCGA-D5-6533 TCGA-D5-6536 TCGA-D5-6898 TCGA-D5-6929 TCGA-DM-A1D6 TCGA-DM-A28F 
       25.48        17.85         7.53        13.41        49.91        35.97 
TCGA-DM-A28G TCGA-F4-6460 TCGA-F4-6463 TCGA-G4-6295 TCGA-G4-6299 TCGA-G4-6303 
       60.79        31.96        35.74         8.35        74.56        65.85 
TCGA-G4-6307 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-RU-A8FL TCGA-SS-A7HO 
       55.04        42.77        29.46        38.70        60.13 

$`AMP PEAK  7(11P15.5) WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 
       24.33        45.60        13.94        14.53        24.16         1.02 
TCGA-AA-3516 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3543 TCGA-AA-3554 
       13.02        37.05        36.03         8.05         0.99        17.95 
TCGA-AA-3560 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 
       19.99         6.05         0.92        19.00        36.00        85.05 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3870 TCGA-AA-3939 
       19.04        19.04        14.93        31.07        29.98        12.99 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-A00L 
       24.00         2.01        50.99        26.01        24.00        38.04 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 
       39.06        21.37        25.08        10.88        75.95       106.75 
TCGA-AZ-6601 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6321 
      100.01        49.08         5.88        28.21        23.51        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-NH-A8F7 TCGA-3L-AA1B 
       35.80        26.17        91.79        79.69        17.85        15.62 
TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2672 
        4.80        12.66         1.61         9.53        39.45        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2684 
       43.76        42.90        42.28        35.11        16.57        37.05 
TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4107 
       37.25        37.02        34.65        32.75        36.53        32.45 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 
       22.06        32.71        29.16        27.09        22.52        24.13 
TCGA-A6-6141 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 
        8.38        20.61        21.76        24.69        24.39        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B 
       19.66        20.28        16.24        24.92        61.84        56.25 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
        7.04         3.02        37.05        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3526 TCGA-AA-3532 TCGA-AA-3538 
        1.02        38.99         1.02        19.07        29.00        26.01 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3655 
       14.01        33.99        21.01        29.95        20.98        61.02 
TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3675 
       78.08         6.97        54.02         2.01        14.01        47.05 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3710 TCGA-AA-3811 
       15.02        11.01         5.98        37.05        26.99        10.06 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3821 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 
       35.05         0.99         1.02        15.95        38.99        36.95 
TCGA-AA-3845 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
        0.00        10.06         0.00         0.00        36.03        32.05 
TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3877 TCGA-AA-3930 
       31.07        53.00        17.03        27.02        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00        33.01        26.01        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3989 TCGA-AA-3994 
       16.08        13.05        34.06        25.02         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K 
       13.94        38.04        19.00        30.02        18.05        18.05 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00W TCGA-AA-A010 
        4.01        27.02        42.02         0.99        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        15.02        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01T TCGA-AA-A01Z TCGA-AA-A029 
       38.07         1.02        35.01        33.04        37.02        51.98 
TCGA-AA-A02E TCGA-AA-A02H TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y 
        2.96         2.01         0.92        22.03        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 
       27.42        26.47        16.44         0.92        14.50        27.09 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D 
       33.01         0.20        21.44        17.82        17.26        17.85 
TCGA-AY-A71X TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 
       19.33       109.28        58.39         1.41         5.65        32.94 
TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
        5.13        22.36        88.21        49.41         6.77        12.10 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        5.23        11.74        12.69        12.36        12.39        12.59 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 
       12.76        10.06        17.56        85.45        70.16        15.62 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 
       23.05        20.02        37.02        25.02        26.04        27.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5861 
       13.02        29.06        22.03        22.98        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
        5.03        15.02        15.02        15.02        12.00        14.04 
TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       16.04        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6678 TCGA-CM-6679 
       11.01        12.95        13.05        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 
       12.03        45.40        19.59        55.92        20.19        20.42 
TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 
       17.75        18.25        43.27        15.12         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       12.49        16.14        15.58        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 
       14.30         9.04         9.44        11.64        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       92.75        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A 
      131.51       135.65         7.76       139.17        14.04        26.47 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 
       81.37       119.93       117.07        98.24        95.18         8.61 
TCGA-F4-6461 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       11.11        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        43.04        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6297 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        82.39        67.30        53.62        44.68 
TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6322 
       85.48        39.42        61.91        36.00        26.43        26.04 
TCGA-G4-6323 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V 
       13.78        46.75        74.79        18.18        10.98        19.33 
TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F8 TCGA-QG-A5YX 
       19.33         9.93        15.65        12.79        16.80        32.98 
TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-T9-A92H TCGA-WS-AB45 
        8.42        31.30        21.90        11.90        70.03 

  AMP PEAK  7(11P15.5) MUTATED AMP PEAK  7(11P15.5) WILD-TYPE 
                             0                              0 
  AMP PEAK  7(11P15.5) MUTATED AMP PEAK  7(11P15.5) WILD-TYPE 
                        148.01                         140.38 
  AMP PEAK  7(11P15.5) MUTATED AMP PEAK  7(11P15.5) WILD-TYPE 
                         23.87                          21.99 
[1] "0.0 - 148.0 (23.9)" "0.0 - 140.4 (22.0)"
[1] "hr=" "1.1"
D7V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK  7(11P15.5) MUTATED        11        0        4        21         2
  AMP PEAK  7(11P15.5) WILD-TYPE      63        1       25       111         8
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  7(11P15.5) MUTATED           0         5          3         13
  AMP PEAK  7(11P15.5) WILD-TYPE         1        15          5         46
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK  7(11P15.5) MUTATED           11       12         6         0
  AMP PEAK  7(11P15.5) WILD-TYPE         30       33        11         2
D7V3, multiclass
            clus
vv           AMP PEAK  7(11P15.5) MUTATED AMP PEAK  7(11P15.5) WILD-TYPE
  STAGE I                              11                             63
  STAGE IA                              0                              1
  STAGE II                              4                             25
  STAGE IIA                            21                            111
  STAGE IIB                             2                              8
  STAGE IIC                             0                              1
  STAGE III                             5                             15
  STAGE IIIA                            3                              5
  STAGE IIIB                           13                             46
  STAGE IIIC                           11                             30
  STAGE IV                             12                             33
  STAGE IVA                             6                             11
  STAGE IVB                             0                              2
[1] 13  2
[1] 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(11P15.5) MUTATED     3  15  67   6
  AMP PEAK  7(11P15.5) WILD-TYPE   8  62 238  49
D7V4, multiclass
    clus
vv   AMP PEAK  7(11P15.5) MUTATED AMP PEAK  7(11P15.5) WILD-TYPE
  T1                            3                              8
  T2                           15                             62
  T3                           67                            238
  T4                            6                             49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2
  AMP PEAK  7(11P15.5) MUTATED    43  27  21
  AMP PEAK  7(11P15.5) WILD-TYPE 219  78  61
D7V5, multiclass
    clus
vv   AMP PEAK  7(11P15.5) MUTATED AMP PEAK  7(11P15.5) WILD-TYPE
  N0                           43                            219
  N1                           27                             78
  N2                           21                             61
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V6, binary
                                cls
clus                               0   1
  AMP PEAK  7(11P15.5) MUTATED    63  18
  AMP PEAK  7(11P15.5) WILD-TYPE 265  46
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  7(11P15.5) MUTATED     63   18
  AMP PEAK  7(11P15.5) WILD-TYPE  265   46
   clus
vv  AMP PEAK  7(11P15.5) MUTATED AMP PEAK  7(11P15.5) WILD-TYPE
  0                           63                            265
  1                           18                             46
[1] 2 2
[1] FALSE
D7V7, binary
                                cls
clus                               0   1
  AMP PEAK  7(11P15.5) MUTATED    45  46
  AMP PEAK  7(11P15.5) WILD-TYPE 168 190
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  7(11P15.5) MUTATED     45   46
  AMP PEAK  7(11P15.5) WILD-TYPE  168  190
        clus
vv       AMP PEAK  7(11P15.5) MUTATED AMP PEAK  7(11P15.5) WILD-TYPE
  FEMALE                           45                            168
  MALE                             46                            190
[1] 2 2
[1] FALSE
D7V8, binary
                                cls
clus                               0   1
  AMP PEAK  7(11P15.5) MUTATED    77   1
  AMP PEAK  7(11P15.5) WILD-TYPE 293   8
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  7(11P15.5) MUTATED     77    1
  AMP PEAK  7(11P15.5) WILD-TYPE  293    8
     clus
vv    AMP PEAK  7(11P15.5) MUTATED AMP PEAK  7(11P15.5) WILD-TYPE
  NO                            77                            293
  YES                            1                              8
[1] 2 2
[1] FALSE
D7V9, binary
                                cls
clus                               0   1
  AMP PEAK  7(11P15.5) MUTATED    85   4
  AMP PEAK  7(11P15.5) WILD-TYPE 297  58
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  7(11P15.5) MUTATED     85    4
  AMP PEAK  7(11P15.5) WILD-TYPE  297   58
                               clus
vv                              AMP PEAK  7(11P15.5) MUTATED
  COLON ADENOCARCINOMA                                    85
  COLON MUCINOUS ADENOCARCINOMA                            4
                               clus
vv                              AMP PEAK  7(11P15.5) WILD-TYPE
  COLON ADENOCARCINOMA                                     297
  COLON MUCINOUS ADENOCARCINOMA                             58
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK  7(11P15.5) MUTATED    62   1   7   6
  AMP PEAK  7(11P15.5) WILD-TYPE 261   3  18  19
D7V10, multiclass
    clus
vv   AMP PEAK  7(11P15.5) MUTATED AMP PEAK  7(11P15.5) WILD-TYPE
  R0                           62                            261
  R1                            1                              3
  R2                            7                             18
  RX                            6                             19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  7(11P15.5) MUTATED                                  0     4
  AMP PEAK  7(11P15.5) WILD-TYPE                                1     7
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  7(11P15.5) MUTATED                           8    40
  AMP PEAK  7(11P15.5) WILD-TYPE                        51   172
D7V12, multiclass
                                  clus
vv                                 AMP PEAK  7(11P15.5) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       4
  BLACK OR AFRICAN AMERICAN                                   8
  WHITE                                                      40
                                  clus
vv                                 AMP PEAK  7(11P15.5) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         7
  BLACK OR AFRICAN AMERICAN                                    51
  WHITE                                                       172
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V13, binary
                                cls
clus                               0   1
  AMP PEAK  7(11P15.5) MUTATED     0  50
  AMP PEAK  7(11P15.5) WILD-TYPE   4 219
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  7(11P15.5) MUTATED      0   50
  AMP PEAK  7(11P15.5) WILD-TYPE    4  219
                        clus
vv                       AMP PEAK  7(11P15.5) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           50
                        clus
vv                       AMP PEAK  7(11P15.5) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            219
[1] 2 2
[1] FALSE

Clustering(8) Variable = AMP PEAK  8(12P13.33) MUTATION ANALYSIS
D8V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK  8(12P13.33) MUTATED    80  26
  AMP PEAK  8(12P13.33) WILD-TYPE 255  75
  AMP PEAK  8(12P13.33) MUTATED AMP PEAK  8(12P13.33) WILD-TYPE 
                            106                             330 
  AMP PEAK  8(12P13.33) MUTATED AMP PEAK  8(12P13.33) WILD-TYPE 
                             26                              75 
$`AMP PEAK  8(12P13.33) MUTATED`
TCGA-A6-2682 TCGA-A6-4105 TCGA-AA-3506 TCGA-AA-3524 TCGA-AA-3560 TCGA-AA-3672 
       13.94        14.53        58.03        36.03        19.99         0.92 
TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AZ-6608 
       19.04        14.93        12.99        24.00         2.01         1.94 
TCGA-G4-6314 TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2679 TCGA-A6-2686 TCGA-A6-3807 
       35.93        15.62        12.66        44.91        37.02        34.65 
TCGA-A6-3809 TCGA-A6-5664 TCGA-A6-6142 TCGA-A6-6650 TCGA-A6-6780 TCGA-A6-6782 
       32.75        22.09        25.08        20.61        20.12        20.28 
TCGA-A6-A566 TCGA-AA-3494 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3542 
       24.92         1.02         0.00        29.00        29.00        12.99 
TCGA-AA-3660 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3710 
       78.08        11.01         5.98        37.05         5.03        26.99 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3851 TCGA-AA-3852 
       35.05         0.99        37.02         0.00        33.07         0.00 
TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A01G TCGA-AA-A01I 
       24.00        26.01        34.03        18.05        12.00        31.00 
TCGA-AA-A01T TCGA-AA-A029 TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03J 
       33.04        51.98         0.92        22.03        39.98        40.96 
TCGA-AD-5900 TCGA-AD-6963 TCGA-AD-6965 TCGA-AM-5821 TCGA-AY-A8YK TCGA-AZ-4323 
       12.16        27.42        26.47         0.92        18.84         1.41 
TCGA-AZ-4616 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5255 
        5.13        49.41         6.77        11.74         3.19        12.36 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-6748 TCGA-CM-4744 
      148.01        85.45        15.62        51.32         2.01        20.02 
TCGA-CM-4747 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6166 
       25.02        30.08        32.02        15.02        15.02        21.99 
TCGA-CM-6169 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6678 TCGA-D5-6529 TCGA-D5-6531 
       13.02        14.04        11.01        11.01        20.19        17.75 
TCGA-D5-6537 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6924 TCGA-D5-6928 TCGA-D5-6929 
        4.80        12.49        15.58        14.30        11.64        13.41 
TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A1D7 TCGA-DM-A1DB 
       12.00        10.26       119.70        24.43        13.32        44.32 
TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6703 TCGA-F4-6805 TCGA-G4-6306 TCGA-G4-6323 
       95.18         8.61        47.87        34.42        44.68        13.78 
TCGA-G4-6627 TCGA-NH-A50U TCGA-NH-A6GB TCGA-QL-A97D 
       74.79        10.98        15.65        21.90 

$`AMP PEAK  8(12P13.33) WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        45.60        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       37.05         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3688 TCGA-AA-3692 
       17.95        23.01        19.99         6.05        19.00        36.00 
TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3972 
       85.05        19.04        31.07        24.03        29.98        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 
       21.37        15.52        25.08        10.88        75.95       106.75 
TCGA-AZ-6601 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6310 
      100.01        49.08         5.88        28.21        23.51        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-NH-A8F7 
       22.09        35.80        26.17        91.79        79.69        17.85 
TCGA-4N-A93T TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2672 
        4.80         1.61         9.53        39.45        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2680 TCGA-A6-2683 
       43.76        43.43        42.90        42.28        35.11        16.57 
TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 
       37.05        37.25        36.53        32.45        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5665 TCGA-A6-5666 
       30.44        29.19        33.53        23.61        22.06        32.71 
TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6648 
       29.16        27.09        22.52        24.13         8.38        25.18 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-A565 
       21.76        24.69        24.39        23.87        19.66        16.24 
TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 
       61.84        56.25         9.63         5.03         7.04         3.02 
TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
       37.05        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3538 TCGA-AA-3544 TCGA-AA-3548 
        1.02         9.07        19.07        26.01        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        61.02 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3675 
        6.97        54.02         2.01        14.01        50.04        47.05 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3811 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       47.01        15.02        10.06        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       15.95        38.99        36.95        17.03        10.06         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3866 
       36.03        32.05         0.99        31.07        53.00        17.03 
TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3955 
       27.02        18.05        31.00         2.01        33.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       25.02        27.02         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       19.00        30.02        18.05         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C 
        0.99        17.03        14.99        34.98        15.02        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       10.98        32.02        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A02E TCGA-AA-A02F 
        1.02         1.02        26.01        37.02         2.96        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02W TCGA-AA-A03F TCGA-AD-6889 TCGA-AD-6890 
        2.01         5.03        41.00        18.05        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        16.44         0.46        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        21.44        17.82 
TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4614 
       17.26        17.85        19.33       109.28        58.39         5.65 
TCGA-AZ-4615 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6600 
       32.94        22.36        65.00        62.79        88.21        12.10 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-CA-5254 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 
       29.56         5.23        12.69        12.46        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4951 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 
       70.16        21.99        21.14        82.95       124.27        23.05 
TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 
       37.02        26.04         8.02        27.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5868 TCGA-CM-6161 
       22.03        22.98        15.02         5.03        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6168 
       12.00        14.04        29.03        16.04        14.99        12.99 
TCGA-CM-6170 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6679 
       15.02        12.95        13.05        11.08        11.08        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.42        18.25        25.48        43.27        15.12        17.85 
TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       17.13        16.14         7.53        12.39        10.13        12.43 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6930 TCGA-D5-6932 TCGA-DM-A0XF TCGA-DM-A1D0 
        9.04         9.44        13.35        11.38        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HA 
       92.75        49.91        12.59       140.38         7.50       131.51 
TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C 
      135.65         7.76       139.17        14.04        26.47        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6460 
      119.93        35.97        60.79       117.07        98.24        31.96 
TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6704 TCGA-F4-6806 
       11.11        35.74        35.74         6.18         1.55        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       43.04        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 
      133.18         8.35        82.39        74.56        67.30        65.85 
TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6317 
       53.62        55.04        85.48        39.42        61.91        36.00 
TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6626 TCGA-NH-A50T TCGA-NH-A50V TCGA-NH-A5IV 
       26.43        26.04        46.75        18.18        19.33        19.33 
TCGA-NH-A6GA TCGA-NH-A6GC TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX 
        9.93        12.79        16.80        42.77        29.46        32.98 
TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-RU-A8FL TCGA-SS-A7HO TCGA-T9-A92H TCGA-WS-AB45 
        8.42        31.30        38.70        60.13        11.90        70.03 

  AMP PEAK  8(12P13.33) MUTATED AMP PEAK  8(12P13.33) WILD-TYPE 
                              0                               0 
  AMP PEAK  8(12P13.33) MUTATED AMP PEAK  8(12P13.33) WILD-TYPE 
                         148.01                          140.38 
  AMP PEAK  8(12P13.33) MUTATED AMP PEAK  8(12P13.33) WILD-TYPE 
                         19.515                          23.560 
[1] "0.0 - 148.0 (19.5)" "0.0 - 140.4 (23.6)"
[1] "hr=" "1.3"
D8V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK  8(12P13.33) MUTATED        14        1        9        39         3
  AMP PEAK  8(12P13.33) WILD-TYPE      60        0       20        93         7
                                 vv
clus                              STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  8(12P13.33) MUTATED           0         5          2          7
  AMP PEAK  8(12P13.33) WILD-TYPE         1        15          6         52
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK  8(12P13.33) MUTATED           12       11         6         0
  AMP PEAK  8(12P13.33) WILD-TYPE         29       34        11         2
D8V3, multiclass
            clus
vv           AMP PEAK  8(12P13.33) MUTATED AMP PEAK  8(12P13.33) WILD-TYPE
  STAGE I                               14                              60
  STAGE IA                               1                               0
  STAGE II                               9                              20
  STAGE IIA                             39                              93
  STAGE IIB                              3                               7
  STAGE IIC                              0                               1
  STAGE III                              5                              15
  STAGE IIIA                             2                               6
  STAGE IIIB                             7                              52
  STAGE IIIC                            12                              29
  STAGE IV                              11                              34
  STAGE IVA                              6                              11
  STAGE IVB                              0                               2
[1] 13  2
[1] 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(12P13.33) MUTATED     0  17  77  17
  AMP PEAK  8(12P13.33) WILD-TYPE  11  60 228  38
D8V4, multiclass
    clus
vv   AMP PEAK  8(12P13.33) MUTATED AMP PEAK  8(12P13.33) WILD-TYPE
  T1                             0                              11
  T2                            17                              60
  T3                            77                             228
  T4                            17                              38
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               N0  N1  N2
  AMP PEAK  8(12P13.33) MUTATED    71  20  21
  AMP PEAK  8(12P13.33) WILD-TYPE 191  85  61
D8V5, multiclass
    clus
vv   AMP PEAK  8(12P13.33) MUTATED AMP PEAK  8(12P13.33) WILD-TYPE
  N0                            71                             191
  N1                            20                              85
  N2                            21                              61
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V6, binary
                                 cls
clus                                0   1
  AMP PEAK  8(12P13.33) MUTATED    80  17
  AMP PEAK  8(12P13.33) WILD-TYPE 248  47
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK  8(12P13.33) MUTATED     80   17
  AMP PEAK  8(12P13.33) WILD-TYPE  248   47
   clus
vv  AMP PEAK  8(12P13.33) MUTATED AMP PEAK  8(12P13.33) WILD-TYPE
  0                            80                             248
  1                            17                              47
[1] 2 2
[1] FALSE
D8V7, binary
                                 cls
clus                                0   1
  AMP PEAK  8(12P13.33) MUTATED    55  57
  AMP PEAK  8(12P13.33) WILD-TYPE 158 179
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK  8(12P13.33) MUTATED     55   57
  AMP PEAK  8(12P13.33) WILD-TYPE  158  179
        clus
vv       AMP PEAK  8(12P13.33) MUTATED AMP PEAK  8(12P13.33) WILD-TYPE
  FEMALE                            55                             158
  MALE                              57                             179
[1] 2 2
[1] FALSE
D8V8, binary
                                 cls
clus                                0   1
  AMP PEAK  8(12P13.33) MUTATED    88   2
  AMP PEAK  8(12P13.33) WILD-TYPE 282   7
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK  8(12P13.33) MUTATED     88    2
  AMP PEAK  8(12P13.33) WILD-TYPE  282    7
     clus
vv    AMP PEAK  8(12P13.33) MUTATED AMP PEAK  8(12P13.33) WILD-TYPE
  NO                             88                             282
  YES                             2                               7
[1] 2 2
[1] FALSE
D8V9, binary
                                 cls
clus                                0   1
  AMP PEAK  8(12P13.33) MUTATED    95  16
  AMP PEAK  8(12P13.33) WILD-TYPE 287  46
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK  8(12P13.33) MUTATED     95   16
  AMP PEAK  8(12P13.33) WILD-TYPE  287   46
                               clus
vv                              AMP PEAK  8(12P13.33) MUTATED
  COLON ADENOCARCINOMA                                     95
  COLON MUCINOUS ADENOCARCINOMA                            16
                               clus
vv                              AMP PEAK  8(12P13.33) WILD-TYPE
  COLON ADENOCARCINOMA                                      287
  COLON MUCINOUS ADENOCARCINOMA                              46
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  AMP PEAK  8(12P13.33) MUTATED    82   2   3   5
  AMP PEAK  8(12P13.33) WILD-TYPE 241   2  22  20
D8V10, multiclass
    clus
vv   AMP PEAK  8(12P13.33) MUTATED AMP PEAK  8(12P13.33) WILD-TYPE
  R0                            82                             241
  R1                             2                               2
  R2                             3                              22
  RX                             5                              20
[1] 4 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, continuous
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  8(12P13.33) MUTATED                                  0     1
  AMP PEAK  8(12P13.33) WILD-TYPE                                1    10
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  8(12P13.33) MUTATED                          12    56
  AMP PEAK  8(12P13.33) WILD-TYPE                        47   156
D8V12, multiclass
                                  clus
vv                                 AMP PEAK  8(12P13.33) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        1
  BLACK OR AFRICAN AMERICAN                                   12
  WHITE                                                       56
                                  clus
vv                                 AMP PEAK  8(12P13.33) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               1
  ASIAN                                                         10
  BLACK OR AFRICAN AMERICAN                                     47
  WHITE                                                        156
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V13, binary
                                 cls
clus                                0   1
  AMP PEAK  8(12P13.33) MUTATED     0  67
  AMP PEAK  8(12P13.33) WILD-TYPE   4 202
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK  8(12P13.33) MUTATED      0   67
  AMP PEAK  8(12P13.33) WILD-TYPE    4  202
                        clus
vv                       AMP PEAK  8(12P13.33) MUTATED
  HISPANIC OR LATINO                                 0
  NOT HISPANIC OR LATINO                            67
                        clus
vv                       AMP PEAK  8(12P13.33) WILD-TYPE
  HISPANIC OR LATINO                                   4
  NOT HISPANIC OR LATINO                             202
[1] 2 2
[1] FALSE

Clustering(9) Variable = AMP PEAK  9(13Q12.13) MUTATION ANALYSIS
D9V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK  9(13Q12.13) MUTATED   208  59
  AMP PEAK  9(13Q12.13) WILD-TYPE 127  42
  AMP PEAK  9(13Q12.13) MUTATED AMP PEAK  9(13Q12.13) WILD-TYPE 
                            267                             169 
  AMP PEAK  9(13Q12.13) MUTATED AMP PEAK  9(13Q12.13) WILD-TYPE 
                             59                              42 
$`AMP PEAK  9(13Q12.13) MUTATED`
TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3506 
       45.60        13.94        14.53        24.16         1.02        58.03 
TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3560 
       24.03        36.03        34.03         0.99        13.02        19.99 
TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3688 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 
       19.99         6.05        19.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3972 TCGA-AA-3976 
       31.07        24.03        29.98        12.99        50.99        26.01 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AD-6548 TCGA-AZ-4313 TCGA-AZ-4681 
       24.00        19.07        38.04        21.37        75.95       106.75 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6310 
        1.94        49.08         5.88        28.21        23.51        63.62 
TCGA-G4-6314 TCGA-G4-6586 TCGA-G4-6625 TCGA-NH-A8F7 TCGA-3L-AA1B TCGA-4N-A93T 
       35.93        35.80        91.79        17.85        15.62         4.80 
TCGA-4T-AA8H TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       12.66         9.53        39.45        43.76        46.65        43.76 
TCGA-A6-2675 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-3807 
       43.43        42.28        44.91        35.11        16.57        34.65 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.45        32.91        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 
       33.53        23.61        32.71        29.16        27.09        22.52 
TCGA-A6-6140 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 
       24.13        25.08        25.18        20.61        21.76        24.69 
TCGA-A6-6654 TCGA-A6-6782 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 
       23.87        20.28        61.84        56.25         9.63         5.03 
TCGA-AA-3489 TCGA-AA-3495 TCGA-AA-3511 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3532 
        7.04        37.05         6.97        38.99         9.07        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       29.00        26.01        12.99        14.01        33.99        21.01 
TCGA-AA-3553 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3660 TCGA-AA-3666 TCGA-AA-3667 
       24.00        20.98        13.94        78.08         2.01        14.01 
TCGA-AA-3673 TCGA-AA-3679 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3811 
       50.04        15.02         5.98        37.05         5.03        10.06 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3846 
       35.05         0.99        25.02        36.95        37.02        17.03 
TCGA-AA-3848 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3866 TCGA-AA-3869 
       10.06        32.05         0.99        31.07        17.03        27.02 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 
        2.01        24.00        26.01        20.98        34.03        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       16.08        13.05        34.06        27.02         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00Q TCGA-AA-A00W TCGA-AA-A017 
       13.94        19.00        34.03        42.02        14.99        15.02 
TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01T 
       15.02        10.98        32.02        12.00        31.00        33.04 
TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03J 
        2.96        39.98         2.01        41.00        39.98        40.96 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK 
       24.53         5.79        22.42        27.42        26.47        16.44 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-A54L 
       14.50        16.31         0.95        33.01        21.44        17.26 
TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-4684 
       18.84       109.28         1.41         5.13        22.36        65.00 
TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       62.79        49.41        12.10        29.56         5.23        11.74 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-6715 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.69        12.36        12.59        14.30        17.56       148.01 
TCGA-CK-5914 TCGA-CK-6748 TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-4752 
       21.99         2.01        20.02        25.02         8.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 
       29.06        22.03        22.98        30.08        32.02         5.03 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       15.02        17.03        15.02        14.04        29.03        16.04 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6676 
       14.99        12.99        13.02        15.02        11.01        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       11.08        11.01        10.06        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        17.75        18.25        25.48        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6898 TCGA-D5-6922 
       17.85         4.80        17.13        12.49         7.53        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 
       12.43        14.30         9.04        13.41        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       10.26       119.70       130.65        92.75        49.91        13.32 
TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A280 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28E 
        7.50       131.51         7.76        14.04        26.47       119.93 
TCGA-DM-A28F TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6570 TCGA-F4-6806 TCGA-F4-6807 
       35.97         8.61        31.96         6.18        41.42        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6295 
       33.67        13.25         0.53        47.41       133.18         8.35 
TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6311 TCGA-G4-6317 
       82.39        74.56        65.85        44.68        39.42        36.00 
TCGA-G4-6320 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50V TCGA-NH-A6GB 
       26.43        46.75        74.79        18.18        19.33        15.65 
TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QL-A97D 
       16.80        42.77        29.46        32.98         8.42        21.90 
TCGA-RU-A8FL TCGA-SS-A7HO TCGA-T9-A92H 
       38.70        60.13        11.90 

$`AMP PEAK  9(13Q12.13) WILD-TYPE`
TCGA-A6-2677 TCGA-AA-3516 TCGA-AA-3522 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3554 
       24.33        13.02        37.05         8.05        19.07        17.95 
TCGA-AA-3556 TCGA-AA-3672 TCGA-AA-3692 TCGA-AA-3713 TCGA-AA-3950 TCGA-AA-3952 
       23.01         0.92        36.00        19.04        24.00         2.01 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-6601 
       21.99        39.06        15.52        25.08        10.88       100.01 
TCGA-G4-6321 TCGA-G4-6588 TCGA-G4-6628 TCGA-5M-AAT4 TCGA-A6-2676 TCGA-A6-2684 
       22.09        26.17        79.69         1.61        42.90        37.05 
TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-5657 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6141 
       37.25        37.02        31.63        22.09        22.06         8.38 
TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 TCGA-AA-3492 
       24.39        20.12        19.66        16.24        24.92         3.02 
TCGA-AA-3494 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3518 TCGA-AA-3526 
        1.02        35.01        63.98         1.02         1.02        19.07 
TCGA-AA-3529 TCGA-AA-3555 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3675 
        0.00        29.95        61.02         6.97        54.02        47.05 
TCGA-AA-3678 TCGA-AA-3680 TCGA-AA-3710 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       47.01        11.01        26.99         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3845 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       38.99         0.00         0.00        33.07         0.00        36.03 
TCGA-AA-3864 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3947 TCGA-AA-3966 TCGA-AA-3977 
       53.00        18.05        31.00        33.01         2.01        25.02 
TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O 
       38.04        30.02        18.05        18.05         4.01        27.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A010 TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
        0.99        17.03        34.98        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 
       35.01         1.02         1.02        26.01        37.02        51.98 
TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6889 
        5.03         0.92        22.03        18.05        12.16        83.24 
TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-6196 TCGA-AY-6386 TCGA-AY-A69D 
        0.46         0.92        27.09         0.20        17.82        17.85 
TCGA-AY-A71X TCGA-AZ-4315 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-5407 TCGA-AZ-6599 
       19.33        58.39         5.65        32.94        88.21         6.77 
TCGA-AZ-6607 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6716 TCGA-CA-6717 
        3.19        12.46        12.39        12.59        12.20        12.76 
TCGA-CA-6718 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5916 
       10.06        85.45        70.16        15.62        51.32        21.14 
TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-4751 
       82.95       124.27        23.05        37.02        26.04        27.02 
TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-6162 TCGA-CM-6166 TCGA-CM-6171 TCGA-CM-6674 
       15.02        15.02        12.00        21.99        14.04        12.95 
TCGA-CM-6675 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6540 
       13.05        12.03        45.40        20.19        20.42        16.14 
TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-DM-A0XD 
       15.58        12.39         9.44        11.64        13.35        24.43 
TCGA-DM-A0XF TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A282 
       38.20        12.59       140.38        44.32       135.65       139.17 
TCGA-DM-A28C TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6461 
       81.37        60.79       117.07        98.24        95.18        11.11 
TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6856 
       35.74        35.74        47.87         1.55        34.42        35.31 
TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6322 
       67.30        53.62        55.04        85.48        61.91        26.04 
TCGA-G4-6323 TCGA-NH-A50U TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GC TCGA-QG-A5Z2 
       13.78        10.98        19.33         9.93        12.79        31.30 
TCGA-WS-AB45 
       70.03 

  AMP PEAK  9(13Q12.13) MUTATED AMP PEAK  9(13Q12.13) WILD-TYPE 
                           0.53                            0.00 
  AMP PEAK  9(13Q12.13) MUTATED AMP PEAK  9(13Q12.13) WILD-TYPE 
                         148.01                          140.38 
  AMP PEAK  9(13Q12.13) MUTATED AMP PEAK  9(13Q12.13) WILD-TYPE 
                          22.36                           22.03 
[1] "0.5 - 148.0 (22.4)" "0.0 - 140.4 (22.0)"
[1] "hr=" "1.1"
D9V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK  9(13Q12.13) MUTATED        43        0       15        69         4
  AMP PEAK  9(13Q12.13) WILD-TYPE      31        1       14        63         6
                                 vv
clus                              STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  9(13Q12.13) MUTATED           1        11          8         40
  AMP PEAK  9(13Q12.13) WILD-TYPE         0         9          0         19
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK  9(13Q12.13) MUTATED           26       37        14         0
  AMP PEAK  9(13Q12.13) WILD-TYPE         15        8         3         2
D9V3, multiclass
            clus
vv           AMP PEAK  9(13Q12.13) MUTATED AMP PEAK  9(13Q12.13) WILD-TYPE
  STAGE I                               43                              31
  STAGE IA                               0                               1
  STAGE II                              15                              14
  STAGE IIA                             69                              63
  STAGE IIB                              4                               6
  STAGE IIC                              1                               0
  STAGE III                             11                               9
  STAGE IIIA                             8                               0
  STAGE IIIB                            40                              19
  STAGE IIIC                            26                              15
  STAGE IV                              37                               8
  STAGE IVA                             14                               3
  STAGE IVB                              0                               2
[1] 13  2
[1] 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(13Q12.13) MUTATED     7  46 189  33
  AMP PEAK  9(13Q12.13) WILD-TYPE   4  31 116  22
D9V4, multiclass
    clus
vv   AMP PEAK  9(13Q12.13) MUTATED AMP PEAK  9(13Q12.13) WILD-TYPE
  T1                             7                               4
  T2                            46                              31
  T3                           189                             116
  T4                            33                              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               N0  N1  N2
  AMP PEAK  9(13Q12.13) MUTATED   142  76  57
  AMP PEAK  9(13Q12.13) WILD-TYPE 120  29  25
D9V5, multiclass
    clus
vv   AMP PEAK  9(13Q12.13) MUTATED AMP PEAK  9(13Q12.13) WILD-TYPE
  N0                           142                             120
  N1                            76                              29
  N2                            57                              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"
D9V6, binary
                                 cls
clus                                0   1
  AMP PEAK  9(13Q12.13) MUTATED   191  51
  AMP PEAK  9(13Q12.13) WILD-TYPE 137  13
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK  9(13Q12.13) MUTATED    191   51
  AMP PEAK  9(13Q12.13) WILD-TYPE  137   13
   clus
vv  AMP PEAK  9(13Q12.13) MUTATED AMP PEAK  9(13Q12.13) WILD-TYPE
  0                           191                             137
  1                            51                              13
[1] 2 2
[1] FALSE
D9V7, binary
                                 cls
clus                                0   1
  AMP PEAK  9(13Q12.13) MUTATED   129 146
  AMP PEAK  9(13Q12.13) WILD-TYPE  84  90
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK  9(13Q12.13) MUTATED    129  146
  AMP PEAK  9(13Q12.13) WILD-TYPE   84   90
        clus
vv       AMP PEAK  9(13Q12.13) MUTATED AMP PEAK  9(13Q12.13) WILD-TYPE
  FEMALE                           129                              84
  MALE                             146                              90
[1] 2 2
[1] FALSE
D9V8, binary
                                 cls
clus                                0   1
  AMP PEAK  9(13Q12.13) MUTATED   239   6
  AMP PEAK  9(13Q12.13) WILD-TYPE 131   3
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK  9(13Q12.13) MUTATED    239    6
  AMP PEAK  9(13Q12.13) WILD-TYPE  131    3
     clus
vv    AMP PEAK  9(13Q12.13) MUTATED AMP PEAK  9(13Q12.13) WILD-TYPE
  NO                            239                             131
  YES                             6                               3
[1] 2 2
[1] FALSE
D9V9, binary
                                 cls
clus                                0   1
  AMP PEAK  9(13Q12.13) MUTATED   254  19
  AMP PEAK  9(13Q12.13) WILD-TYPE 128  43
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK  9(13Q12.13) MUTATED    254   19
  AMP PEAK  9(13Q12.13) WILD-TYPE  128   43
                               clus
vv                              AMP PEAK  9(13Q12.13) MUTATED
  COLON ADENOCARCINOMA                                    254
  COLON MUCINOUS ADENOCARCINOMA                            19
                               clus
vv                              AMP PEAK  9(13Q12.13) WILD-TYPE
  COLON ADENOCARCINOMA                                      128
  COLON MUCINOUS ADENOCARCINOMA                              43
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  AMP PEAK  9(13Q12.13) MUTATED   195   2  20  10
  AMP PEAK  9(13Q12.13) WILD-TYPE 128   2   5  15
D9V10, multiclass
    clus
vv   AMP PEAK  9(13Q12.13) MUTATED AMP PEAK  9(13Q12.13) WILD-TYPE
  R0                           195                             128
  R1                             2                               2
  R2                            20                               5
  RX                            10                              15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V11, continuous
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  9(13Q12.13) MUTATED                                  0     4
  AMP PEAK  9(13Q12.13) WILD-TYPE                                1     7
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  9(13Q12.13) MUTATED                          37   136
  AMP PEAK  9(13Q12.13) WILD-TYPE                        22    76
D9V12, multiclass
                                  clus
vv                                 AMP PEAK  9(13Q12.13) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        4
  BLACK OR AFRICAN AMERICAN                                   37
  WHITE                                                      136
                                  clus
vv                                 AMP PEAK  9(13Q12.13) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               1
  ASIAN                                                          7
  BLACK OR AFRICAN AMERICAN                                     22
  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"
D9V13, binary
                                 cls
clus                                0   1
  AMP PEAK  9(13Q12.13) MUTATED     3 167
  AMP PEAK  9(13Q12.13) WILD-TYPE   1 102
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK  9(13Q12.13) MUTATED      3  167
  AMP PEAK  9(13Q12.13) WILD-TYPE    1  102
                        clus
vv                       AMP PEAK  9(13Q12.13) MUTATED
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           167
                        clus
vv                       AMP PEAK  9(13Q12.13) WILD-TYPE
  HISPANIC OR LATINO                                   1
  NOT HISPANIC OR LATINO                             102
[1] 2 2
[1] FALSE

Clustering(10) Variable = AMP PEAK 10(13Q22.1) MUTATION ANALYSIS
D10V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 10(13Q22.1) MUTATED   207  62
  AMP PEAK 10(13Q22.1) WILD-TYPE 128  39
  AMP PEAK 10(13Q22.1) MUTATED AMP PEAK 10(13Q22.1) WILD-TYPE 
                           269                            167 
  AMP PEAK 10(13Q22.1) MUTATED AMP PEAK 10(13Q22.1) WILD-TYPE 
                            62                             39 
$`AMP PEAK 10(13Q22.1) MUTATED`
TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3506 
       45.60        13.94        14.53        24.16         1.02        58.03 
TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3560 
       24.03        36.03        34.03         0.99        13.02        19.99 
TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3688 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 
       19.99         6.05        19.00        85.05        19.04        14.93 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 
       24.03        29.98        12.99         2.01        50.99        26.01 
TCGA-AA-3986 TCGA-AA-A00L TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4313 
       19.07        38.04        21.37        15.52        25.08        75.95 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6310 
        1.94        49.08         5.88        28.21        23.51        63.62 
TCGA-G4-6314 TCGA-G4-6586 TCGA-G4-6625 TCGA-NH-A8F7 TCGA-3L-AA1B TCGA-4N-A93T 
       35.93        35.80        91.79        17.85        15.62         4.80 
TCGA-4T-AA8H TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       12.66         9.53        39.45        43.76        46.65        43.76 
TCGA-A6-2675 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-3807 
       43.43        42.28        44.91        35.11        16.57        34.65 
TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 
       36.53        32.45        32.91        30.44        29.19        33.53 
TCGA-A6-5662 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 
       23.61        32.71        29.16        27.09        22.52        24.13 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       25.08        25.18        20.61        21.76        24.69        23.87 
TCGA-A6-6782 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 
       20.28        61.84        56.25         9.63         5.03         7.04 
TCGA-AA-3495 TCGA-AA-3511 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3532 TCGA-AA-3534 
       37.05         6.97        38.99         9.07        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3558 
       26.01        12.99        14.01        21.01        24.00        20.98 
TCGA-AA-3561 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       13.94        78.08        54.02         2.01        14.01        50.04 
TCGA-AA-3679 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
       15.02         5.98        37.05        10.06        35.05         0.99 
TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3855 TCGA-AA-3856 
       36.95        37.02        17.03        10.06        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3941 
       31.07        17.03        27.02        18.05         2.01        24.00 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 
       26.01        20.98        34.03        21.99        16.08        13.05 
TCGA-AA-3975 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D 
       34.06        27.02         7.96        27.02        13.94        19.00 
TCGA-AA-A00F TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01C 
       34.03        42.02        17.03        14.99        15.02        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01S TCGA-AA-A01T 
       10.98        32.02        12.00        31.00         1.02        33.04 
TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03J 
        2.96        39.98         2.01        41.00        39.98        40.96 
TCGA-AD-5900 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       12.16        24.53         5.79        22.42        27.42        26.47 
TCGA-AD-A5EK TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       16.44        14.50        16.31         0.95        33.01        21.44 
TCGA-AY-A54L TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
       17.26        18.84       109.28         1.41         5.13        22.36 
TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 
       65.00        62.79        49.41        12.10        29.56         5.23 
TCGA-AZ-6606 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-6715 TCGA-CA-6719 TCGA-CK-4947 
       11.74        12.69        12.36        12.59        14.30        17.56 
TCGA-CK-4948 TCGA-CK-5914 TCGA-CK-6748 TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4750 
      148.01        21.99         2.01        20.02        25.02         8.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 
        5.03        15.02        17.03        15.02        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 
       16.04        14.99        12.99        13.02        15.02        11.01 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-D5-5538 TCGA-D5-5539 
       11.08        11.08        11.01        10.06        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        17.75        18.25        25.48        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6898 
       15.12        17.85         4.80        17.13        12.49         7.53 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6931 
       10.13        12.43        14.30         9.04        13.41        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A280 
       92.75        49.91        13.32         7.50       131.51         7.76 
TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28E TCGA-DM-A28F TCGA-F4-6460 TCGA-F4-6570 
       14.04        26.47       119.93        35.97        31.96         6.18 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        43.04        33.67        13.25         0.53        47.41 
TCGA-G4-6293 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 
      133.18         8.35        82.39        74.56        65.85        44.68 
TCGA-G4-6311 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T 
       39.42        36.00        26.43        46.75        74.79        18.18 
TCGA-NH-A50V TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW 
       19.33         9.93        15.65        16.80        42.77        29.46 
TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QL-A97D TCGA-RU-A8FL TCGA-SS-A7HO 
       32.98         8.42        21.90        38.70        60.13 

$`AMP PEAK 10(13Q22.1) WILD-TYPE`
TCGA-A6-2677 TCGA-AA-3516 TCGA-AA-3522 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3554 
       24.33        13.02        37.05         8.05        19.07        17.95 
TCGA-AA-3556 TCGA-AA-3672 TCGA-AA-3692 TCGA-AA-3713 TCGA-AA-3860 TCGA-AA-3950 
       23.01         0.92        36.00        19.04        31.07        24.00 
TCGA-AA-3979 TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       24.00        21.99        39.06        10.88       106.75       100.01 
TCGA-G4-6321 TCGA-G4-6588 TCGA-G4-6628 TCGA-5M-AAT4 TCGA-A6-2676 TCGA-A6-2684 
       22.09        26.17        79.69         1.61        42.90        37.05 
TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3809 TCGA-A6-5657 TCGA-A6-5664 TCGA-A6-5665 
       37.25        37.02        32.75        31.63        22.09        22.06 
TCGA-A6-6141 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 
        8.38        24.39        20.12        19.66        16.24        24.92 
TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3518 
        3.02         1.02        35.01        63.98         1.02         1.02 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3548 TCGA-AA-3555 TCGA-AA-3655 TCGA-AA-3663 
       19.07         0.00        33.99        29.95        61.02         6.97 
TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3680 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3819 
       47.05        47.01        11.01         5.03        26.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3845 TCGA-AA-3850 
        1.02        17.98        15.95        38.99         0.00         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3864 TCGA-AA-3877 TCGA-AA-3947 
       33.07         0.00        36.03        53.00        31.00        33.01 
TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K 
        2.01        25.02        38.04        30.02        18.05        18.05 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A010 TCGA-AA-A01K TCGA-AA-A01P 
        4.01        27.02         0.99        34.98        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 
        1.02        35.01         1.02        26.01        37.02        51.98 
TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A03F TCGA-AD-6889 TCGA-AM-5820 
        5.03         0.92        22.03        18.05        83.24         0.46 
TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-6196 TCGA-AY-6386 TCGA-AY-A69D TCGA-AY-A71X 
        0.92        27.09         0.20        17.82        17.85        19.33 
TCGA-AZ-4315 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6607 
       58.39         5.65        32.94        88.21         6.77         3.19 
TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.46        12.39        12.59        12.20        12.76        10.06 
TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 
       85.45        70.16        15.62        51.32        21.14        82.95 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-5861 
      124.27        23.05        37.02        26.04        27.02        15.02 
TCGA-CM-5863 TCGA-CM-6162 TCGA-CM-6166 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 
       15.02        12.00        21.99        14.04        12.95        13.05 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6540 TCGA-D5-6541 
       12.03        45.40        20.19        20.42        16.14        15.58 
TCGA-D5-6920 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-DM-A1D8 TCGA-DM-A1D9 
       12.39         9.44        11.64        13.35        12.59       140.38 
TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A28C TCGA-DM-A28G TCGA-DM-A28H 
       44.32       135.65       139.17        81.37        60.79       117.07 
TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 
       98.24        95.18         8.61        11.11        35.74        35.74 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6856 TCGA-G4-6302 TCGA-G4-6304 
       47.87         1.55        34.42        35.31        67.30        53.62 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6322 TCGA-G4-6323 TCGA-NH-A50U 
       55.04        85.48        61.91        26.04        13.78        10.98 
TCGA-NH-A5IV TCGA-NH-A6GC TCGA-QG-A5Z2 TCGA-T9-A92H TCGA-WS-AB45 
       19.33        12.79        31.30        11.90        70.03 

  AMP PEAK 10(13Q22.1) MUTATED AMP PEAK 10(13Q22.1) WILD-TYPE 
                          0.53                           0.00 
  AMP PEAK 10(13Q22.1) MUTATED AMP PEAK 10(13Q22.1) WILD-TYPE 
                        148.01                         140.38 
  AMP PEAK 10(13Q22.1) MUTATED AMP PEAK 10(13Q22.1) WILD-TYPE 
                         21.99                          22.09 
[1] "0.5 - 148.0 (22.0)" "0.0 - 140.4 (22.1)"
[1] "hr=" "1.1"
D10V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK 10(13Q22.1) MUTATED        45        0       16        66         3
  AMP PEAK 10(13Q22.1) WILD-TYPE      29        1       13        66         7
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 10(13Q22.1) MUTATED           1        12          8         41
  AMP PEAK 10(13Q22.1) WILD-TYPE         0         8          0         18
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 10(13Q22.1) MUTATED           28       36        14         0
  AMP PEAK 10(13Q22.1) WILD-TYPE         13        9         3         2
D10V3, multiclass
            clus
vv           AMP PEAK 10(13Q22.1) MUTATED AMP PEAK 10(13Q22.1) WILD-TYPE
  STAGE I                              45                             29
  STAGE IA                              0                              1
  STAGE II                             16                             13
  STAGE IIA                            66                             66
  STAGE IIB                             3                              7
  STAGE IIC                             1                              0
  STAGE III                            12                              8
  STAGE IIIA                            8                              0
  STAGE IIIB                           41                             18
  STAGE IIIC                           28                             13
  STAGE IV                             36                              9
  STAGE IVA                            14                              3
  STAGE IVB                             0                              2
[1] 13  2
[1] 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(13Q22.1) MUTATED     8  47 189  33
  AMP PEAK 10(13Q22.1) WILD-TYPE   3  30 116  22
D10V4, multiclass
    clus
vv   AMP PEAK 10(13Q22.1) MUTATED AMP PEAK 10(13Q22.1) WILD-TYPE
  T1                            8                              3
  T2                           47                             30
  T3                          189                            116
  T4                           33                             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2
  AMP PEAK 10(13Q22.1) MUTATED   141  78  58
  AMP PEAK 10(13Q22.1) WILD-TYPE 121  27  24
D10V5, multiclass
    clus
vv   AMP PEAK 10(13Q22.1) MUTATED AMP PEAK 10(13Q22.1) WILD-TYPE
  N0                          141                            121
  N1                           78                             27
  N2                           58                             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"
D10V6, binary
                                cls
clus                               0   1
  AMP PEAK 10(13Q22.1) MUTATED   192  50
  AMP PEAK 10(13Q22.1) WILD-TYPE 136  14
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 10(13Q22.1) MUTATED    192   50
  AMP PEAK 10(13Q22.1) WILD-TYPE  136   14
   clus
vv  AMP PEAK 10(13Q22.1) MUTATED AMP PEAK 10(13Q22.1) WILD-TYPE
  0                          192                            136
  1                           50                             14
[1] 2 2
[1] FALSE
D10V7, binary
                                cls
clus                               0   1
  AMP PEAK 10(13Q22.1) MUTATED   126 151
  AMP PEAK 10(13Q22.1) WILD-TYPE  87  85
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 10(13Q22.1) MUTATED    126  151
  AMP PEAK 10(13Q22.1) WILD-TYPE   87   85
        clus
vv       AMP PEAK 10(13Q22.1) MUTATED AMP PEAK 10(13Q22.1) WILD-TYPE
  FEMALE                          126                             87
  MALE                            151                             85
[1] 2 2
[1] FALSE
D10V8, binary
                                cls
clus                               0   1
  AMP PEAK 10(13Q22.1) MUTATED   237   6
  AMP PEAK 10(13Q22.1) WILD-TYPE 133   3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 10(13Q22.1) MUTATED    237    6
  AMP PEAK 10(13Q22.1) WILD-TYPE  133    3
     clus
vv    AMP PEAK 10(13Q22.1) MUTATED AMP PEAK 10(13Q22.1) WILD-TYPE
  NO                           237                            133
  YES                            6                              3
[1] 2 2
[1] FALSE
D10V9, binary
                                cls
clus                               0   1
  AMP PEAK 10(13Q22.1) MUTATED   255  19
  AMP PEAK 10(13Q22.1) WILD-TYPE 127  43
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 10(13Q22.1) MUTATED    255   19
  AMP PEAK 10(13Q22.1) WILD-TYPE  127   43
                               clus
vv                              AMP PEAK 10(13Q22.1) MUTATED
  COLON ADENOCARCINOMA                                   255
  COLON MUCINOUS ADENOCARCINOMA                           19
                               clus
vv                              AMP PEAK 10(13Q22.1) WILD-TYPE
  COLON ADENOCARCINOMA                                     127
  COLON MUCINOUS ADENOCARCINOMA                             43
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 10(13Q22.1) MUTATED   196   2  19  10
  AMP PEAK 10(13Q22.1) WILD-TYPE 127   2   6  15
D10V10, multiclass
    clus
vv   AMP PEAK 10(13Q22.1) MUTATED AMP PEAK 10(13Q22.1) WILD-TYPE
  R0                          196                            127
  R1                            2                              2
  R2                           19                              6
  RX                           10                             15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 10(13Q22.1) MUTATED                                  0     4
  AMP PEAK 10(13Q22.1) WILD-TYPE                                1     7
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 10(13Q22.1) MUTATED                          37   138
  AMP PEAK 10(13Q22.1) WILD-TYPE                        22    74
D10V12, multiclass
                                  clus
vv                                 AMP PEAK 10(13Q22.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       4
  BLACK OR AFRICAN AMERICAN                                  37
  WHITE                                                     138
                                  clus
vv                                 AMP PEAK 10(13Q22.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         7
  BLACK OR AFRICAN AMERICAN                                    22
  WHITE                                                        74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V13, binary
                                cls
clus                               0   1
  AMP PEAK 10(13Q22.1) MUTATED     3 169
  AMP PEAK 10(13Q22.1) WILD-TYPE   1 100
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 10(13Q22.1) MUTATED      3  169
  AMP PEAK 10(13Q22.1) WILD-TYPE    1  100
                        clus
vv                       AMP PEAK 10(13Q22.1) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                          169
                        clus
vv                       AMP PEAK 10(13Q22.1) WILD-TYPE
  HISPANIC OR LATINO                                  1
  NOT HISPANIC OR LATINO                            100
[1] 2 2
[1] FALSE

Clustering(11) Variable = AMP PEAK 11(16P11.2) MUTATION ANALYSIS
D11V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 11(16P11.2) MUTATED    97  23
  AMP PEAK 11(16P11.2) WILD-TYPE 238  78
  AMP PEAK 11(16P11.2) MUTATED AMP PEAK 11(16P11.2) WILD-TYPE 
                           120                            316 
  AMP PEAK 11(16P11.2) MUTATED AMP PEAK 11(16P11.2) WILD-TYPE 
                            23                             78 
$`AMP PEAK 11(16P11.2) MUTATED`
TCGA-A6-2677 TCGA-A6-2681 TCGA-AA-3552 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3688 
       24.33        45.60        13.02        19.99        19.99        19.00 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 
       14.93        31.07        24.03        29.98        12.99         2.01 
TCGA-AA-3976 TCGA-AZ-6608 TCGA-CK-5912 TCGA-G4-6310 TCGA-G4-6314 TCGA-5M-AATE 
       26.01         1.94        49.08        63.62        35.93        39.45 
TCGA-A6-2671 TCGA-A6-2675 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2685 
       43.76        43.43        44.91        35.11        16.57        37.25 
TCGA-A6-4107 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5667 TCGA-A6-6140 TCGA-A6-6142 
       32.45        30.44        29.19        29.16        24.13        25.08 
TCGA-A6-6650 TCGA-A6-6654 TCGA-AA-3532 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3548 
       20.61        23.87        29.00        26.01        12.99        33.99 
TCGA-AA-3553 TCGA-AA-3673 TCGA-AA-3679 TCGA-AA-3812 TCGA-AA-3841 TCGA-AA-3842 
       24.00        50.04        15.02        35.05        36.95        37.02 
TCGA-AA-3846 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3856 TCGA-AA-3866 TCGA-AA-3869 
       17.03        33.07         0.00         0.99        17.03        27.02 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3982 
        2.01        24.00        20.98        34.03        16.08        27.02 
TCGA-AA-A00F TCGA-AA-A00Q TCGA-AA-A01C TCGA-AA-A01G TCGA-AA-A01T TCGA-AA-A02W 
       34.03        42.02        15.02        12.00        33.04        41.00 
TCGA-AA-A03J TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AY-4071 TCGA-AY-5543 
       40.96        22.42        27.42        26.47         0.95        33.01 
TCGA-AY-6196 TCGA-AY-A54L TCGA-AY-A8YK TCGA-AZ-4616 TCGA-AZ-5403 TCGA-AZ-6603 
        0.20        17.26        18.84         5.13        62.79        29.56 
TCGA-AZ-6605 TCGA-CA-5254 TCGA-CA-5797 TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-5914 
        5.23        12.69        12.59        14.30       148.01        21.99 
TCGA-CM-4744 TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5860 
       20.02         8.02        13.02        22.03        22.98        32.02 
TCGA-CM-5868 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6170 
       17.03        14.04        29.03        21.99        14.99        15.02 
TCGA-CM-6172 TCGA-CM-6679 TCGA-D5-5539 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6535 
       11.01        10.06        19.59        18.25        25.48        15.12 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6922 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A0XF 
       17.13        12.49        10.13        13.41        11.38        38.20 
TCGA-DM-A1D7 TCGA-DM-A28F TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6704 TCGA-G4-6297 
       13.32        35.97         8.61        31.96         1.55        82.39 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6311 TCGA-G4-6320 
       74.56        65.85        44.68        55.04        39.42        26.43 
TCGA-G4-6323 TCGA-G4-6626 TCGA-NH-A6GB TCGA-NH-A6GC TCGA-QL-A97D TCGA-T9-A92H 
       13.78        46.75        15.65        12.79        21.90        11.90 

$`AMP PEAK 11(16P11.2) WILD-TYPE`
TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3506 TCGA-AA-3516 
       13.94        14.53        24.16         1.02        58.03        13.02 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 
       24.03        37.05        36.03         8.05        19.07        34.03 
TCGA-AA-3543 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3692 
        0.99        17.95        23.01         6.05         0.92        36.00 
TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3950 TCGA-AA-3972 TCGA-AA-3979 
       85.05        19.04        19.04        24.00        50.99        24.00 
TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 
       19.07        38.04        21.99        39.06        21.37        15.52 
TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-DM-A285 
       25.08        10.88        75.95       106.75       100.01         5.88 
TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       28.21        23.51        22.09        35.80        26.17        91.79 
TCGA-G4-6628 TCGA-NH-A8F7 TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 
       79.69        17.85        15.62         4.80        12.66         1.61 
TCGA-5M-AAT6 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2684 
        9.53        46.65        43.76        42.90        42.28        37.05 
TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 
       37.02        34.65        32.75        36.53        32.91        31.63 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 
       33.53        23.61        22.09        22.06        32.71        27.09 
TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       22.52         8.38        25.18        21.76        24.69        24.39 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 
       20.12        19.66        20.28        16.24        24.92        61.84 
TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 
       56.25         9.63         5.03         7.04         3.02         1.02 
TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
       37.05        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3534 TCGA-AA-3544 
        1.02         9.07        19.07         0.00        29.00        14.01 
TCGA-AA-3549 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       21.01        29.95        20.98        13.94        61.02        78.08 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3675 TCGA-AA-3678 
        6.97        54.02         2.01        14.01        47.05        47.01 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        26.99        10.06 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3845 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3858 
        0.00        10.06         0.00        36.03        32.05        31.07 
TCGA-AA-3864 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3966 
       53.00        18.05        31.00        33.01        26.01         2.01 
TCGA-AA-3968 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3989 TCGA-AA-3994 
       21.99        13.05        34.06        25.02         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K 
       13.94        38.04        19.00        30.02        18.05        18.05 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 
        4.01        27.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       15.02        10.98        32.02        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
        1.02        35.01         1.02         1.02        26.01        37.02 
TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O 
       51.98         2.96        39.98         2.01         5.03         0.92 
TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 
       22.03        39.98        18.05        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 
        5.79        16.44         0.46         0.92        14.50        27.09 
TCGA-AY-4070 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A69D TCGA-AY-A71X TCGA-AZ-4308 
       16.31        21.44        17.82        17.85        19.33       109.28 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4682 TCGA-AZ-4684 
       58.39         1.41         5.65        32.94        22.36        65.00 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6606 TCGA-AZ-6607 
       88.21        49.41         6.77        12.10        11.74         3.19 
TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
       12.36        12.46        12.39        12.59        12.20        12.76 
TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 
       10.06        17.56        85.45        70.16        15.62        51.32 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4746 
       21.14        82.95         2.01       124.27        23.05        37.02 
TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-5341 TCGA-CM-5349 TCGA-CM-5861 
       25.02        26.04        27.02        29.06        30.08        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6165 
        5.03        15.02        15.02        15.02        12.00        16.04 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       12.99        13.02        14.04        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 
       11.08        11.01        12.03        45.40        54.61        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6534 TCGA-D5-6536 
       55.92        20.19        20.42        17.75        43.27        17.85 
TCGA-D5-6537 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6923 
        4.80        16.14        15.58         7.53        12.39        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 
       14.30         9.04         9.44        11.64        13.35        12.00 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
       10.26       119.70        24.43       130.65        92.75        49.91 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E 
        7.76       139.17        14.04        26.47        81.37       119.93 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6461 TCGA-F4-6463 
       60.79       117.07        98.24        95.18        11.11        35.74 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       35.74         6.18        47.87        34.42        41.42        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6295 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6317 
        8.35        67.30        53.62        85.48        61.91        36.00 
TCGA-G4-6322 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV 
       26.04        74.79        18.18        10.98        19.33        19.33 
TCGA-NH-A6GA TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 
        9.93        16.80        42.77        29.46        32.98         8.42 
TCGA-QG-A5Z2 TCGA-RU-A8FL TCGA-SS-A7HO TCGA-WS-AB45 
       31.30        38.70        60.13        70.03 

  AMP PEAK 11(16P11.2) MUTATED AMP PEAK 11(16P11.2) WILD-TYPE 
                             0                              0 
  AMP PEAK 11(16P11.2) MUTATED AMP PEAK 11(16P11.2) WILD-TYPE 
                        148.01                         140.38 
  AMP PEAK 11(16P11.2) MUTATED AMP PEAK 11(16P11.2) WILD-TYPE 
                        23.425                         21.990 
[1] "0.0 - 148.0 (23.4)" "0.0 - 140.4 (22.0)"
[1] "hr=" "1.1"
D11V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK 11(16P11.2) MUTATED        14        1        3        30         1
  AMP PEAK 11(16P11.2) WILD-TYPE      60        0       26       102         9
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 11(16P11.2) MUTATED           0         6          7         19
  AMP PEAK 11(16P11.2) WILD-TYPE         1        14          1         40
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 11(16P11.2) MUTATED           17       15         5         1
  AMP PEAK 11(16P11.2) WILD-TYPE         24       30        12         1
D11V3, multiclass
            clus
vv           AMP PEAK 11(16P11.2) MUTATED AMP PEAK 11(16P11.2) WILD-TYPE
  STAGE I                              14                             60
  STAGE IA                              1                              0
  STAGE II                              3                             26
  STAGE IIA                            30                            102
  STAGE IIB                             1                              9
  STAGE IIC                             0                              1
  STAGE III                             6                             14
  STAGE IIIA                            7                              1
  STAGE IIIB                           19                             40
  STAGE IIIC                           17                             24
  STAGE IV                             15                             30
  STAGE IVA                             5                             12
  STAGE IVB                             1                              1
[1] 13  2
[1] 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(16P11.2) MUTATED     3  19  91  11
  AMP PEAK 11(16P11.2) WILD-TYPE   8  58 214  44
D11V4, multiclass
    clus
vv   AMP PEAK 11(16P11.2) MUTATED AMP PEAK 11(16P11.2) WILD-TYPE
  T1                            3                              8
  T2                           19                             58
  T3                           91                            214
  T4                           11                             44
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2
  AMP PEAK 11(16P11.2) MUTATED    55  37  33
  AMP PEAK 11(16P11.2) WILD-TYPE 207  68  49
D11V5, multiclass
    clus
vv   AMP PEAK 11(16P11.2) MUTATED AMP PEAK 11(16P11.2) WILD-TYPE
  N0                           55                            207
  N1                           37                             68
  N2                           33                             49
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V6, binary
                                cls
clus                               0   1
  AMP PEAK 11(16P11.2) MUTATED    86  21
  AMP PEAK 11(16P11.2) WILD-TYPE 242  43
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 11(16P11.2) MUTATED     86   21
  AMP PEAK 11(16P11.2) WILD-TYPE  242   43
   clus
vv  AMP PEAK 11(16P11.2) MUTATED AMP PEAK 11(16P11.2) WILD-TYPE
  0                           86                            242
  1                           21                             43
[1] 2 2
[1] FALSE
D11V7, binary
                                cls
clus                               0   1
  AMP PEAK 11(16P11.2) MUTATED    61  64
  AMP PEAK 11(16P11.2) WILD-TYPE 152 172
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 11(16P11.2) MUTATED     61   64
  AMP PEAK 11(16P11.2) WILD-TYPE  152  172
        clus
vv       AMP PEAK 11(16P11.2) MUTATED AMP PEAK 11(16P11.2) WILD-TYPE
  FEMALE                           61                            152
  MALE                             64                            172
[1] 2 2
[1] FALSE
D11V8, binary
                                cls
clus                               0   1
  AMP PEAK 11(16P11.2) MUTATED   108   2
  AMP PEAK 11(16P11.2) WILD-TYPE 262   7
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 11(16P11.2) MUTATED    108    2
  AMP PEAK 11(16P11.2) WILD-TYPE  262    7
     clus
vv    AMP PEAK 11(16P11.2) MUTATED AMP PEAK 11(16P11.2) WILD-TYPE
  NO                           108                            262
  YES                            2                              7
[1] 2 2
[1] FALSE
D11V9, binary
                                cls
clus                               0   1
  AMP PEAK 11(16P11.2) MUTATED   115   7
  AMP PEAK 11(16P11.2) WILD-TYPE 267  55
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 11(16P11.2) MUTATED    115    7
  AMP PEAK 11(16P11.2) WILD-TYPE  267   55
                               clus
vv                              AMP PEAK 11(16P11.2) MUTATED
  COLON ADENOCARCINOMA                                   115
  COLON MUCINOUS ADENOCARCINOMA                            7
                               clus
vv                              AMP PEAK 11(16P11.2) WILD-TYPE
  COLON ADENOCARCINOMA                                     267
  COLON MUCINOUS ADENOCARCINOMA                             55
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 11(16P11.2) MUTATED    95   1   7   5
  AMP PEAK 11(16P11.2) WILD-TYPE 228   3  18  20
D11V10, multiclass
    clus
vv   AMP PEAK 11(16P11.2) MUTATED AMP PEAK 11(16P11.2) WILD-TYPE
  R0                           95                            228
  R1                            1                              3
  R2                            7                             18
  RX                            5                             20
[1] 4 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, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 11(16P11.2) MUTATED                                  1     3
  AMP PEAK 11(16P11.2) WILD-TYPE                                0     8
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 11(16P11.2) MUTATED                          15    61
  AMP PEAK 11(16P11.2) WILD-TYPE                        44   151
D11V12, multiclass
                                  clus
vv                                 AMP PEAK 11(16P11.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       3
  BLACK OR AFRICAN AMERICAN                                  15
  WHITE                                                      61
                                  clus
vv                                 AMP PEAK 11(16P11.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         8
  BLACK OR AFRICAN AMERICAN                                    44
  WHITE                                                       151
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V13, binary
                                cls
clus                               0   1
  AMP PEAK 11(16P11.2) MUTATED     2  74
  AMP PEAK 11(16P11.2) WILD-TYPE   2 195
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 11(16P11.2) MUTATED      2   74
  AMP PEAK 11(16P11.2) WILD-TYPE    2  195
                        clus
vv                       AMP PEAK 11(16P11.2) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           74
                        clus
vv                       AMP PEAK 11(16P11.2) WILD-TYPE
  HISPANIC OR LATINO                                  2
  NOT HISPANIC OR LATINO                            195
[1] 2 2
[1] FALSE

Clustering(12) Variable = AMP PEAK 12(16Q12.1) MUTATION ANALYSIS
D12V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 12(16Q12.1) MUTATED    90  16
  AMP PEAK 12(16Q12.1) WILD-TYPE 245  85
  AMP PEAK 12(16Q12.1) MUTATED AMP PEAK 12(16Q12.1) WILD-TYPE 
                           106                            330 
  AMP PEAK 12(16Q12.1) MUTATED AMP PEAK 12(16Q12.1) WILD-TYPE 
                            16                             85 
$`AMP PEAK 12(16Q12.1) MUTATED`
TCGA-A6-2677 TCGA-A6-2681 TCGA-AA-3552 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3688 
       24.33        45.60        13.02        19.99        19.99        19.00 
TCGA-AA-3844 TCGA-AA-3867 TCGA-AA-3939 TCGA-AA-3976 TCGA-AZ-6608 TCGA-CK-5912 
       14.93        24.03        12.99        26.01         1.94        49.08 
TCGA-G4-6310 TCGA-G4-6314 TCGA-5M-AATE TCGA-A6-2675 TCGA-A6-2678 TCGA-A6-2679 
       63.62        35.93        39.45        43.43        42.28        44.91 
TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2685 TCGA-A6-4107 TCGA-A6-5659 TCGA-A6-5660 
       35.11        16.57        37.25        32.45        30.44        29.19 
TCGA-A6-5667 TCGA-A6-6140 TCGA-A6-6142 TCGA-A6-6654 TCGA-AA-3532 TCGA-AA-3538 
       29.16        24.13        25.08        23.87        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3548 TCGA-AA-3553 TCGA-AA-3673 TCGA-AA-3679 TCGA-AA-3841 
       12.99        33.99        24.00        50.04        15.02        36.95 
TCGA-AA-3842 TCGA-AA-3846 TCGA-AA-3851 TCGA-AA-3856 TCGA-AA-3866 TCGA-AA-3869 
       37.02        17.03        33.07         0.99        17.03        27.02 
TCGA-AA-3941 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3982 TCGA-AA-A00F 
       24.00        20.98        34.03        16.08        27.02        34.03 
TCGA-AA-A00Q TCGA-AA-A01C TCGA-AA-A01G TCGA-AA-A01T TCGA-AA-A02W TCGA-AA-A03J 
       42.02        15.02        12.00        33.04        41.00        40.96 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AY-4071 TCGA-AY-6196 TCGA-AY-A54L 
       22.42        27.42        26.47         0.95         0.20        17.26 
TCGA-AY-A8YK TCGA-AZ-4616 TCGA-AZ-5403 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-CA-5797 
       18.84         5.13        62.79        29.56         5.23        12.59 
TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-5914 TCGA-CM-4744 TCGA-CM-4750 TCGA-CM-5344 
       14.30       148.01        21.99        20.02         8.02        22.03 
TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5868 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6166 
       22.98        32.02        17.03        14.04        29.03        21.99 
TCGA-CM-6167 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6679 TCGA-D5-5539 TCGA-D5-6532 
       14.99        15.02        11.01        10.06        19.59        18.25 
TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6922 TCGA-D5-6929 
       25.48        15.12        17.13        12.49        10.13        13.41 
TCGA-D5-6932 TCGA-DM-A0XF TCGA-DM-A28F TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6704 
       11.38        38.20        35.97         8.61        31.96         1.55 
TCGA-G4-6297 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6311 TCGA-G4-6320 TCGA-G4-6323 
       82.39        44.68        55.04        39.42        26.43        13.78 
TCGA-NH-A6GB TCGA-NH-A6GC TCGA-QL-A97D TCGA-T9-A92H 
       15.65        12.79        21.90        11.90 

$`AMP PEAK 12(16Q12.1) WILD-TYPE`
TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3506 TCGA-AA-3516 
       13.94        14.53        24.16         1.02        58.03        13.02 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 
       24.03        37.05        36.03         8.05        19.07        34.03 
TCGA-AA-3543 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3692 
        0.99        17.95        23.01         6.05         0.92        36.00 
TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3860 TCGA-AA-3870 TCGA-AA-3950 
       85.05        19.04        19.04        31.07        29.98        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
        2.01        50.99        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 
       39.06        21.37        15.52        25.08        10.88        75.95 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6321 
      106.75       100.01         5.88        28.21        23.51        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-NH-A8F7 TCGA-3L-AA1B 
       35.80        26.17        91.79        79.69        17.85        15.62 
TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-A6-2671 TCGA-A6-2672 
        4.80        12.66         1.61         9.53        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2684 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3809 
       43.76        42.90        37.05        37.02        34.65        32.75 
TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       36.53        32.91        31.63        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6648 
       22.06        32.71        27.09        22.52         8.38        25.18 
TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 
       20.61        21.76        24.69        24.39        20.12        19.66 
TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU 
       20.28        16.24        24.92        61.84        56.25         9.63 
TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 
        5.03         7.04         3.02         1.02        37.05        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
       63.98         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3534 TCGA-AA-3544 TCGA-AA-3549 TCGA-AA-3555 
       19.07         0.00        29.00        14.01        21.01        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3680 TCGA-AA-3681 
        2.01        14.01        47.05        47.01        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
       37.05         5.03        26.99        10.06        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3845 
       25.02         1.02        17.98        15.95        38.99         0.00 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3858 
       10.06         0.00         0.00        36.03        32.05        31.07 
TCGA-AA-3864 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 
       53.00        18.05        31.00         2.01        33.01        26.01 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3989 
        2.01        21.99        13.05        34.06        25.02         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J 
       27.02        13.94        38.04        19.00        30.02        18.05 
TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       18.05         4.01        27.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01I TCGA-AA-A01K 
       34.98        15.02        10.98        32.02        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01X 
       38.07         1.02        35.01         1.02         1.02        26.01 
TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        51.98         2.96        39.98         2.01         5.03 
TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6889 
        0.92        22.03        39.98        18.05        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 
       24.53         5.79        16.44         0.46         0.92        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A69D 
       27.09        16.31        33.01        21.44        17.82        17.85 
TCGA-AY-A71X TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 
       19.33       109.28        58.39         1.41         5.65        32.94 
TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        65.00        88.21        49.41         6.77        12.10 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 
       11.74         3.19        12.69        12.36        12.46        12.39 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4950 
       12.59        12.20        12.76        10.06        17.56        85.45 
TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       70.16        15.62        51.32        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 
      124.27        23.05        37.02        25.02        26.04        27.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       13.02        29.06        30.08        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6168 TCGA-CM-6169 
       15.02        15.02        12.00        16.04        12.99        13.02 
TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       14.04        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       12.03        45.40        54.61        56.09        55.92        20.19 
TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6540 
       20.42        17.75        43.27        17.85         4.80        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
       15.58         7.53        12.39        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 
        9.44        11.64        13.35        12.00        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       24.43       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 
      140.38         7.50        44.32       131.51       135.65         7.76 
TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G 
      139.17        14.04        26.47        81.37       119.93        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 
      117.07        98.24        95.18        11.11        35.74        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
        6.18        47.87        34.42        41.42        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6295 
       13.25         0.53        47.41        35.31       133.18         8.35 
TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6309 TCGA-G4-6315 
       74.56        67.30        65.85        53.62        85.48        61.91 
TCGA-G4-6317 TCGA-G4-6322 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50U 
       36.00        26.04        46.75        74.79        18.18        10.98 
TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW 
       19.33        19.33         9.93        16.80        42.77        29.46 
TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-RU-A8FL TCGA-SS-A7HO TCGA-WS-AB45 
       32.98         8.42        31.30        38.70        60.13        70.03 

  AMP PEAK 12(16Q12.1) MUTATED AMP PEAK 12(16Q12.1) WILD-TYPE 
                           0.2                            0.0 
  AMP PEAK 12(16Q12.1) MUTATED AMP PEAK 12(16Q12.1) WILD-TYPE 
                        148.01                         140.38 
  AMP PEAK 12(16Q12.1) MUTATED AMP PEAK 12(16Q12.1) WILD-TYPE 
                        23.425                         21.990 
[1] "0.2 - 148.0 (23.4)" "0.0 - 140.4 (22.0)"
[1] "hr=" "1.5"
D12V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK 12(16Q12.1) MUTATED        14        1        3        23         1
  AMP PEAK 12(16Q12.1) WILD-TYPE      60        0       26       109         9
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 12(16Q12.1) MUTATED           0         6          7         19
  AMP PEAK 12(16Q12.1) WILD-TYPE         1        14          1         40
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 12(16Q12.1) MUTATED           15       11         4         1
  AMP PEAK 12(16Q12.1) WILD-TYPE         26       34        13         1
D12V3, multiclass
            clus
vv           AMP PEAK 12(16Q12.1) MUTATED AMP PEAK 12(16Q12.1) WILD-TYPE
  STAGE I                              14                             60
  STAGE IA                              1                              0
  STAGE II                              3                             26
  STAGE IIA                            23                            109
  STAGE IIB                             1                              9
  STAGE IIC                             0                              1
  STAGE III                             6                             14
  STAGE IIIA                            7                              1
  STAGE IIIB                           19                             40
  STAGE IIIC                           15                             26
  STAGE IV                             11                             34
  STAGE IVA                             4                             13
  STAGE IVB                             1                              1
[1] 13  2
[1] 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(16Q12.1) MUTATED     3  19  77  11
  AMP PEAK 12(16Q12.1) WILD-TYPE   8  58 228  44
D12V4, multiclass
    clus
vv   AMP PEAK 12(16Q12.1) MUTATED AMP PEAK 12(16Q12.1) WILD-TYPE
  T1                            3                              8
  T2                           19                             58
  T3                           77                            228
  T4                           11                             44
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2
  AMP PEAK 12(16Q12.1) MUTATED    48  35  28
  AMP PEAK 12(16Q12.1) WILD-TYPE 214  70  54
D12V5, multiclass
    clus
vv   AMP PEAK 12(16Q12.1) MUTATED AMP PEAK 12(16Q12.1) WILD-TYPE
  N0                           48                            214
  N1                           35                             70
  N2                           28                             54
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V6, binary
                                cls
clus                               0   1
  AMP PEAK 12(16Q12.1) MUTATED    77  16
  AMP PEAK 12(16Q12.1) WILD-TYPE 251  48
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(16Q12.1) MUTATED     77   16
  AMP PEAK 12(16Q12.1) WILD-TYPE  251   48
   clus
vv  AMP PEAK 12(16Q12.1) MUTATED AMP PEAK 12(16Q12.1) WILD-TYPE
  0                           77                            251
  1                           16                             48
[1] 2 2
[1] FALSE
D12V7, binary
                                cls
clus                               0   1
  AMP PEAK 12(16Q12.1) MUTATED    55  56
  AMP PEAK 12(16Q12.1) WILD-TYPE 158 180
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(16Q12.1) MUTATED     55   56
  AMP PEAK 12(16Q12.1) WILD-TYPE  158  180
        clus
vv       AMP PEAK 12(16Q12.1) MUTATED AMP PEAK 12(16Q12.1) WILD-TYPE
  FEMALE                           55                            158
  MALE                             56                            180
[1] 2 2
[1] FALSE
D12V8, binary
                                cls
clus                               0   1
  AMP PEAK 12(16Q12.1) MUTATED    98   2
  AMP PEAK 12(16Q12.1) WILD-TYPE 272   7
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(16Q12.1) MUTATED     98    2
  AMP PEAK 12(16Q12.1) WILD-TYPE  272    7
     clus
vv    AMP PEAK 12(16Q12.1) MUTATED AMP PEAK 12(16Q12.1) WILD-TYPE
  NO                            98                            272
  YES                            2                              7
[1] 2 2
[1] FALSE
D12V9, binary
                                cls
clus                               0   1
  AMP PEAK 12(16Q12.1) MUTATED   103   6
  AMP PEAK 12(16Q12.1) WILD-TYPE 279  56
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(16Q12.1) MUTATED    103    6
  AMP PEAK 12(16Q12.1) WILD-TYPE  279   56
                               clus
vv                              AMP PEAK 12(16Q12.1) MUTATED
  COLON ADENOCARCINOMA                                   103
  COLON MUCINOUS ADENOCARCINOMA                            6
                               clus
vv                              AMP PEAK 12(16Q12.1) WILD-TYPE
  COLON ADENOCARCINOMA                                     279
  COLON MUCINOUS ADENOCARCINOMA                             56
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 12(16Q12.1) MUTATED    85   1   6   4
  AMP PEAK 12(16Q12.1) WILD-TYPE 238   3  19  21
D12V10, multiclass
    clus
vv   AMP PEAK 12(16Q12.1) MUTATED AMP PEAK 12(16Q12.1) WILD-TYPE
  R0                           85                            238
  R1                            1                              3
  R2                            6                             19
  RX                            4                             21
[1] 4 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, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 12(16Q12.1) MUTATED                                  1     2
  AMP PEAK 12(16Q12.1) WILD-TYPE                                0     9
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 12(16Q12.1) MUTATED                          12    57
  AMP PEAK 12(16Q12.1) WILD-TYPE                        47   155
D12V12, multiclass
                                  clus
vv                                 AMP PEAK 12(16Q12.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                  12
  WHITE                                                      57
                                  clus
vv                                 AMP PEAK 12(16Q12.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         9
  BLACK OR AFRICAN AMERICAN                                    47
  WHITE                                                       155
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V13, binary
                                cls
clus                               0   1
  AMP PEAK 12(16Q12.1) MUTATED     2  66
  AMP PEAK 12(16Q12.1) WILD-TYPE   2 203
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(16Q12.1) MUTATED      2   66
  AMP PEAK 12(16Q12.1) WILD-TYPE    2  203
                        clus
vv                       AMP PEAK 12(16Q12.1) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           66
                        clus
vv                       AMP PEAK 12(16Q12.1) WILD-TYPE
  HISPANIC OR LATINO                                  2
  NOT HISPANIC OR LATINO                            203
[1] 2 2
[1] FALSE

Clustering(13) Variable = AMP PEAK 13(17P11.2) MUTATION ANALYSIS
D13V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 13(17P11.2) MUTATED    34   8
  AMP PEAK 13(17P11.2) WILD-TYPE 301  93
  AMP PEAK 13(17P11.2) MUTATED AMP PEAK 13(17P11.2) WILD-TYPE 
                            42                            394 
  AMP PEAK 13(17P11.2) MUTATED AMP PEAK 13(17P11.2) WILD-TYPE 
                             8                             93 
$`AMP PEAK 13(17P11.2) MUTATED`
TCGA-AA-3939 TCGA-AD-6888 TCGA-DM-A285 TCGA-G4-6298 TCGA-G4-6314 TCGA-3L-AA1B 
       12.99        15.52         5.88        23.51        35.93        15.62 
TCGA-4N-A93T TCGA-4T-AA8H TCGA-A6-2680 TCGA-A6-2686 TCGA-A6-3810 TCGA-A6-5657 
        4.80        12.66        35.11        37.02        36.53        31.63 
TCGA-A6-5659 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6142 TCGA-A6-A56B TCGA-AA-3679 
       30.44        32.71        29.16        25.08        56.25        15.02 
TCGA-AA-3812 TCGA-AA-3821 TCGA-AA-3841 TCGA-AA-3846 TCGA-AA-3856 TCGA-AA-3956 
       35.05         1.02        36.95        17.03         0.99        34.03 
TCGA-AA-3966 TCGA-AA-3973 TCGA-AA-3975 TCGA-AZ-5407 TCGA-AZ-6607 TCGA-CA-6719 
        2.01        13.05        34.06        88.21         3.19        14.30 
TCGA-CM-5341 TCGA-CM-6163 TCGA-CM-6678 TCGA-D5-6537 TCGA-D5-6924 TCGA-DM-A288 
       29.06        14.04        11.01         4.80        14.30        14.04 
TCGA-DM-A28E TCGA-DM-A28M TCGA-F4-6704 TCGA-G4-6299 TCGA-G4-6307 TCGA-G4-6317 
      119.93        95.18         1.55        74.56        55.04        36.00 

$`AMP PEAK 13(17P11.2) WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 
       24.33        45.60        13.94        14.53        24.16         1.02 
TCGA-AA-3506 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
       58.03        13.02        24.03        37.05        36.03         8.05 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 
       19.07        34.03         0.99        13.02        17.95        23.01 
TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 
       19.99        19.99         6.05         0.92        19.00        36.00 
TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 
       85.05        19.04        19.04        14.93        31.07        24.03 
TCGA-AA-3870 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 
       29.98        24.00         2.01        50.99        26.01        24.00 
TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6895 
       19.07        38.04        21.99        39.06        21.37        25.08 
TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 
       10.88        75.95       106.75       100.01         1.94        49.08 
TCGA-G4-6294 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       28.21        63.62        22.09        35.80        26.17        91.79 
TCGA-G4-6628 TCGA-NH-A8F7 TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2671 
       79.69        17.85         1.61         9.53        39.45        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 
       46.65        43.76        43.43        42.90        42.28        44.91 
TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-4107 
       16.57        37.05        37.25        34.65        32.75        32.45 
TCGA-A6-5656 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       32.91        29.19        33.53        23.61        22.09        22.06 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6650 
       27.09        22.52        24.13         8.38        25.18        20.61 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A5ZU TCGA-AA-3488 
       20.28        16.24        24.92        61.84         9.63         5.03 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 
        7.04         3.02         1.02        37.05        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       61.02        78.08         6.97        54.02         2.01        14.01 
TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.05        47.01        11.01         5.98        37.05 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 
        5.03        26.99        10.06         0.99        25.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3848 TCGA-AA-3850 
       15.95        38.99        37.02         0.00        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3858 TCGA-AA-3864 
       33.07         0.00        36.03        32.05        31.07        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3977 
       33.01        26.01        20.98        21.99        16.08        25.02 
TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       27.02         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        51.98         2.96        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03         0.92        22.03        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 
       27.42        26.47        16.44         0.46         0.92        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        21.44 
TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 
       17.82        17.26        17.85        19.33        18.84       109.28 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 
       58.39         1.41         5.65        32.94         5.13        22.36 
TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 
       65.00        62.79        49.41         6.77        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 
        5.23        11.74        12.69        12.36        12.46        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 
       12.59        12.59        12.20        12.76        10.06        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        70.16        15.62        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 
       37.02        25.02        26.04         8.02        27.02        13.02 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6164 
       15.02        15.02        17.03        15.02        12.00        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 
       55.92        20.19        20.42        17.75        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       43.27        15.12        17.85        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 
       15.58         7.53        12.39        10.13        12.43         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A28A TCGA-DM-A28C 
      131.51       135.65         7.76       139.17        26.47        81.37 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 
       11.11        35.74        35.74         6.18        47.87        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        43.04        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6302 TCGA-G4-6303 
       35.31       133.18         8.35        82.39        67.30        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6320 
       53.62        44.68        85.48        39.42        61.91        26.43 
TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50U 
       26.04        13.78        46.75        74.79        18.18        10.98 
TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F8 
       19.33        19.33         9.93        15.65        12.79        16.80 
TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D 
       42.77        29.46        32.98         8.42        31.30        21.90 
TCGA-RU-A8FL TCGA-SS-A7HO TCGA-T9-A92H TCGA-WS-AB45 
       38.70        60.13        11.90        70.03 

  AMP PEAK 13(17P11.2) MUTATED AMP PEAK 13(17P11.2) WILD-TYPE 
                          0.99                           0.00 
  AMP PEAK 13(17P11.2) MUTATED AMP PEAK 13(17P11.2) WILD-TYPE 
                        119.93                         148.01 
  AMP PEAK 13(17P11.2) MUTATED AMP PEAK 13(17P11.2) WILD-TYPE 
                        24.295                         22.030 
[1] "1.0 - 119.9 (24.3)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.2"
D13V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK 13(17P11.2) MUTATED         6        0        1        15         0
  AMP PEAK 13(17P11.2) WILD-TYPE      68        1       28       117        10
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 13(17P11.2) MUTATED           1         1          1          8
  AMP PEAK 13(17P11.2) WILD-TYPE         0        19          7         51
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 13(17P11.2) MUTATED            4        5         2         0
  AMP PEAK 13(17P11.2) WILD-TYPE         37       40        15         2
D13V3, multiclass
            clus
vv           AMP PEAK 13(17P11.2) MUTATED AMP PEAK 13(17P11.2) WILD-TYPE
  STAGE I                               6                             68
  STAGE IA                              0                              1
  STAGE II                              1                             28
  STAGE IIA                            15                            117
  STAGE IIB                             0                             10
  STAGE IIC                             1                              0
  STAGE III                             1                             19
  STAGE IIIA                            1                              7
  STAGE IIIB                            8                             51
  STAGE IIIC                            4                             37
  STAGE IV                              5                             40
  STAGE IVA                             2                             15
  STAGE IVB                             0                              2
[1] 13  2
[1] 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(17P11.2) MUTATED     2   5  31   6
  AMP PEAK 13(17P11.2) WILD-TYPE   9  72 274  49
D13V4, multiclass
    clus
vv   AMP PEAK 13(17P11.2) MUTATED AMP PEAK 13(17P11.2) WILD-TYPE
  T1                            2                              9
  T2                            5                             72
  T3                           31                            274
  T4                            6                             49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2
  AMP PEAK 13(17P11.2) MUTATED    23  12   9
  AMP PEAK 13(17P11.2) WILD-TYPE 239  93  73
D13V5, multiclass
    clus
vv   AMP PEAK 13(17P11.2) MUTATED AMP PEAK 13(17P11.2) WILD-TYPE
  N0                           23                            239
  N1                           12                             93
  N2                            9                             73
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V6, binary
                                cls
clus                               0   1
  AMP PEAK 13(17P11.2) MUTATED    31   7
  AMP PEAK 13(17P11.2) WILD-TYPE 297  57
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 13(17P11.2) MUTATED     31    7
  AMP PEAK 13(17P11.2) WILD-TYPE  297   57
   clus
vv  AMP PEAK 13(17P11.2) MUTATED AMP PEAK 13(17P11.2) WILD-TYPE
  0                           31                            297
  1                            7                             57
[1] 2 2
[1] FALSE
D13V7, binary
                                cls
clus                               0   1
  AMP PEAK 13(17P11.2) MUTATED    19  25
  AMP PEAK 13(17P11.2) WILD-TYPE 194 211
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 13(17P11.2) MUTATED     19   25
  AMP PEAK 13(17P11.2) WILD-TYPE  194  211
        clus
vv       AMP PEAK 13(17P11.2) MUTATED AMP PEAK 13(17P11.2) WILD-TYPE
  FEMALE                           19                            194
  MALE                             25                            211
[1] 2 2
[1] FALSE
D13V8, binary
                                cls
clus                               0   1
  AMP PEAK 13(17P11.2) MUTATED    35   0
  AMP PEAK 13(17P11.2) WILD-TYPE 335   9
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 13(17P11.2) MUTATED     35    0
  AMP PEAK 13(17P11.2) WILD-TYPE  335    9
     clus
vv    AMP PEAK 13(17P11.2) MUTATED AMP PEAK 13(17P11.2) WILD-TYPE
  NO                            35                            335
  YES                            0                              9
[1] 2 2
[1] FALSE
D13V9, binary
                                cls
clus                               0   1
  AMP PEAK 13(17P11.2) MUTATED    38   6
  AMP PEAK 13(17P11.2) WILD-TYPE 344  56
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 13(17P11.2) MUTATED     38    6
  AMP PEAK 13(17P11.2) WILD-TYPE  344   56
                               clus
vv                              AMP PEAK 13(17P11.2) MUTATED
  COLON ADENOCARCINOMA                                    38
  COLON MUCINOUS ADENOCARCINOMA                            6
                               clus
vv                              AMP PEAK 13(17P11.2) WILD-TYPE
  COLON ADENOCARCINOMA                                     344
  COLON MUCINOUS ADENOCARCINOMA                             56
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 13(17P11.2) MUTATED    32   0   2   1
  AMP PEAK 13(17P11.2) WILD-TYPE 291   4  23  24
D13V10, multiclass
    clus
vv   AMP PEAK 13(17P11.2) MUTATED AMP PEAK 13(17P11.2) WILD-TYPE
  R0                           32                            291
  R1                            0                              4
  R2                            2                             23
  RX                            1                             24
[1] 4 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, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 13(17P11.2) MUTATED                                  1     1
  AMP PEAK 13(17P11.2) WILD-TYPE                                0    10
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 13(17P11.2) MUTATED                           7    22
  AMP PEAK 13(17P11.2) WILD-TYPE                        52   190
D13V12, multiclass
                                  clus
vv                                 AMP PEAK 13(17P11.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       1
  BLACK OR AFRICAN AMERICAN                                   7
  WHITE                                                      22
                                  clus
vv                                 AMP PEAK 13(17P11.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                        10
  BLACK OR AFRICAN AMERICAN                                    52
  WHITE                                                       190
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V13, binary
                                cls
clus                               0   1
  AMP PEAK 13(17P11.2) MUTATED     0  31
  AMP PEAK 13(17P11.2) WILD-TYPE   4 238
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 13(17P11.2) MUTATED      0   31
  AMP PEAK 13(17P11.2) WILD-TYPE    4  238
                        clus
vv                       AMP PEAK 13(17P11.2) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           31
                        clus
vv                       AMP PEAK 13(17P11.2) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            238
[1] 2 2
[1] FALSE

Clustering(14) Variable = AMP PEAK 14(17Q12) MUTATION ANALYSIS
D14V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 14(17Q12) MUTATED    91  18
  AMP PEAK 14(17Q12) WILD-TYPE 244  83
  AMP PEAK 14(17Q12) MUTATED AMP PEAK 14(17Q12) WILD-TYPE 
                         109                          327 
  AMP PEAK 14(17Q12) MUTATED AMP PEAK 14(17Q12) WILD-TYPE 
                          18                           83 
$`AMP PEAK 14(17Q12) MUTATED`
TCGA-A6-2677 TCGA-A6-4105 TCGA-AA-3496 TCGA-AA-3506 TCGA-AA-3524 TCGA-AA-3556 
       24.33        14.53         1.02        58.03        36.03        23.01 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3867 TCGA-AA-3939 TCGA-AA-3972 TCGA-AA-A00L 
       36.00        85.05        24.03        12.99        50.99        38.04 
TCGA-AA-A00Z TCGA-AD-6888 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6314 TCGA-NH-A8F7 
       21.99        15.52         5.88        63.62        35.93        17.85 
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AATE TCGA-A6-2674 TCGA-A6-2675 
       15.62        12.66         1.61        39.45        43.76        43.43 
TCGA-A6-2686 TCGA-A6-3810 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5666 TCGA-A6-5667 
       37.02        36.53        30.44        29.19        32.71        29.16 
TCGA-A6-6137 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6652 TCGA-A6-6782 TCGA-AA-3494 
       27.09        25.08        25.18        24.69        20.28         1.02 
TCGA-AA-3495 TCGA-AA-3517 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3542 TCGA-AA-3553 
       37.05        38.99         0.00        29.00        12.99        24.00 
TCGA-AA-3679 TCGA-AA-3812 TCGA-AA-3821 TCGA-AA-3846 TCGA-AA-3856 TCGA-AA-3869 
       15.02        35.05         1.02        17.03         0.99        27.02 
TCGA-AA-3875 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3973 TCGA-AA-3982 TCGA-AA-3994 
       18.05        34.03         2.01        13.05        27.02        27.02 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01S TCGA-AA-A02O TCGA-AA-A02W TCGA-AD-6890 
       32.02        12.00         1.02         0.92        41.00        24.53 
TCGA-AD-6963 TCGA-AD-A5EK TCGA-AY-4070 TCGA-AY-A8YK TCGA-AZ-5407 TCGA-AZ-6600 
       27.42        16.44        16.31        18.84        88.21        12.10 
TCGA-AZ-6603 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-6715 TCGA-CA-6719 TCGA-CK-4948 
       29.56         3.19        12.69        12.59        14.30       148.01 
TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5868 TCGA-CM-6163 
        8.02        13.02        29.06        22.03        17.03        14.04 
TCGA-CM-6164 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6678 
       29.03        21.99        14.99        13.05        11.08        11.01 
TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6537 
       19.59        55.92        18.25        25.48        15.12         4.80 
TCGA-D5-6538 TCGA-D5-6924 TCGA-D5-6929 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       17.13        14.30        13.41        24.43        38.20       130.65 
TCGA-DM-A28M TCGA-F4-6704 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6307 TCGA-G4-6311 
       95.18         1.55        74.56        65.85        55.04        39.42 
TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6626 TCGA-NH-A6GB TCGA-QG-A5YW TCGA-QG-A5YX 
       36.00        26.43        46.75        15.65        29.46        32.98 
TCGA-RU-A8FL 
       38.70 

$`AMP PEAK 14(17Q12) WILD-TYPE`
TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-6649 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       45.60        13.94        24.16        13.02        24.03        37.05 
TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 
        8.05        19.07        34.03         0.99        13.02        17.95 
TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3713 
       19.99        19.99         6.05         0.92        19.00        19.04 
TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3870 TCGA-AA-3950 TCGA-AA-3952 
       19.04        14.93        31.07        29.98        24.00         2.01 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6895 
       26.01        24.00        19.07        39.06        21.37        25.08 
TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 
       10.88        75.95       106.75       100.01         1.94        49.08 
TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       28.21        23.51        22.09        35.80        26.17        91.79 
TCGA-G4-6628 TCGA-4N-A93T TCGA-5M-AAT6 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2676 
       79.69         4.80         9.53        43.76        46.65        42.90 
TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 
       42.28        44.91        35.11        16.57        37.05        37.25 
TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5661 
       34.65        32.75        32.45        32.91        31.63        33.53 
TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 
       23.61        22.09        22.06        22.52        24.13         8.38 
TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       20.61        21.76        24.39        23.87        20.12        19.66 
TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 
       16.24        24.92        61.84        56.25         9.63         5.03 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
        7.04         3.02        35.01        63.98         6.97         1.02 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3544 
        1.02         9.07        19.07        29.00        26.01        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       33.99        21.01        29.95        20.98        13.94        61.02 
TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       78.08         6.97        54.02         2.01        14.01        50.04 
TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 
       47.05        47.01        11.01         5.98        37.05         5.03 
TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 
       26.99        10.06         0.99        25.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3848 TCGA-AA-3850 
       38.99        36.95        37.02         0.00        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3858 TCGA-AA-3864 
       33.07         0.00        36.03        32.05        31.07        53.00 
TCGA-AA-3866 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       17.03        31.00         2.01        24.00        33.01        26.01 
TCGA-AA-3955 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3989 
       20.98        21.99        16.08        34.06        25.02         7.96 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01I 
       14.99        34.98        15.02        15.02        10.98        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01T TCGA-AA-A01V 
       31.00        38.07         1.02        35.01        33.04         1.02 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        51.98         2.96        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        5.03        22.03        39.98        18.05        40.96        12.16 
TCGA-AD-6889 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6965 TCGA-AM-5820 TCGA-AM-5821 
       83.24         5.79        22.42        26.47         0.46         0.92 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       14.50        27.09         0.95        33.01         0.20        21.44 
TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X TCGA-AZ-4308 TCGA-AZ-4315 
       17.82        17.26        17.85        19.33       109.28        58.39 
TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-4684 
        1.41         5.65        32.94         5.13        22.36        65.00 
TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-CA-5255 
       62.79        49.41         6.77         5.23        11.74        12.36 
TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.46        12.39        12.59        12.20        12.76        10.06 
TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 
       17.56        85.45        70.16        15.62        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-5348 TCGA-CM-5349 
       37.02        25.02        26.04        27.02        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6161 
       32.02        15.02         5.03        15.02        15.02        15.02 
TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       12.00        16.04        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6677 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.01        12.95        11.08        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6534 
       54.61        56.09        20.19        20.42        17.75        43.27 
TCGA-D5-6536 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.85        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 
       10.13        12.43         9.04         9.44        11.64        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A1D4 TCGA-DM-A1D6 
       12.00        11.38        10.26       119.70        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C 
      135.65         7.76       139.17        14.04        26.47        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       31.96        11.11        35.74        35.74         6.18        47.87 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6302 
       47.41        35.31       133.18         8.35        82.39        67.30 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6322 TCGA-G4-6323 
       53.62        44.68        85.48        61.91        26.04        13.78 
TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA 
       74.79        18.18        10.98        19.33        19.33         9.93 
TCGA-NH-A6GC TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D 
       12.79        16.80        42.77         8.42        31.30        21.90 
TCGA-SS-A7HO TCGA-T9-A92H TCGA-WS-AB45 
       60.13        11.90        70.03 

  AMP PEAK 14(17Q12) MUTATED AMP PEAK 14(17Q12) WILD-TYPE 
                           0                            0 
  AMP PEAK 14(17Q12) MUTATED AMP PEAK 14(17Q12) WILD-TYPE 
                      148.01                       140.38 
  AMP PEAK 14(17Q12) MUTATED AMP PEAK 14(17Q12) WILD-TYPE 
                       24.33                        21.90 
[1] "0.0 - 148.0 (24.3)" "0.0 - 140.4 (21.9)"
[1] "hr=" "1.5"
D14V2, continuous
                              vv
clus                           STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK 14(17Q12) MUTATED        14        0        5        30         1
  AMP PEAK 14(17Q12) WILD-TYPE      60        1       24       102         9
                              vv
clus                           STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 14(17Q12) MUTATED           1         4          3         15
  AMP PEAK 14(17Q12) WILD-TYPE         0        16          5         44
                              vv
clus                           STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 14(17Q12) MUTATED           12       18         6         1
  AMP PEAK 14(17Q12) WILD-TYPE         29       27        11         1
D14V3, multiclass
            clus
vv           AMP PEAK 14(17Q12) MUTATED AMP PEAK 14(17Q12) WILD-TYPE
  STAGE I                            14                           60
  STAGE IA                            0                            1
  STAGE II                            5                           24
  STAGE IIA                          30                          102
  STAGE IIB                           1                            9
  STAGE IIC                           1                            0
  STAGE III                           4                           16
  STAGE IIIA                          3                            5
  STAGE IIIB                         15                           44
  STAGE IIIC                         12                           29
  STAGE IV                           18                           27
  STAGE IVA                           6                           11
  STAGE IVB                           1                            1
[1] 13  2
[1] 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(17Q12) MUTATED     5  13  85  11
  AMP PEAK 14(17Q12) WILD-TYPE   6  64 220  44
D14V4, multiclass
    clus
vv   AMP PEAK 14(17Q12) MUTATED AMP PEAK 14(17Q12) WILD-TYPE
  T1                          5                            6
  T2                         13                           64
  T3                         85                          220
  T4                         11                           44
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            N0  N1  N2
  AMP PEAK 14(17Q12) MUTATED    58  30  26
  AMP PEAK 14(17Q12) WILD-TYPE 204  75  56
D14V5, multiclass
    clus
vv   AMP PEAK 14(17Q12) MUTATED AMP PEAK 14(17Q12) WILD-TYPE
  N0                         58                          204
  N1                         30                           75
  N2                         26                           56
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V6, binary
                              cls
clus                             0   1
  AMP PEAK 14(17Q12) MUTATED    70  25
  AMP PEAK 14(17Q12) WILD-TYPE 258  39
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 14(17Q12) MUTATED     70   25
  AMP PEAK 14(17Q12) WILD-TYPE  258   39
   clus
vv  AMP PEAK 14(17Q12) MUTATED AMP PEAK 14(17Q12) WILD-TYPE
  0                         70                          258
  1                         25                           39
[1] 2 2
[1] FALSE
D14V7, binary
                              cls
clus                             0   1
  AMP PEAK 14(17Q12) MUTATED    48  66
  AMP PEAK 14(17Q12) WILD-TYPE 165 170
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 14(17Q12) MUTATED     48   66
  AMP PEAK 14(17Q12) WILD-TYPE  165  170
        clus
vv       AMP PEAK 14(17Q12) MUTATED AMP PEAK 14(17Q12) WILD-TYPE
  FEMALE                         48                          165
  MALE                           66                          170
[1] 2 2
[1] FALSE
D14V8, binary
                              cls
clus                             0   1
  AMP PEAK 14(17Q12) MUTATED    93   3
  AMP PEAK 14(17Q12) WILD-TYPE 277   6
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 14(17Q12) MUTATED     93    3
  AMP PEAK 14(17Q12) WILD-TYPE  277    6
     clus
vv    AMP PEAK 14(17Q12) MUTATED AMP PEAK 14(17Q12) WILD-TYPE
  NO                          93                          277
  YES                          3                            6
[1] 2 2
[1] FALSE
D14V9, binary
                              cls
clus                             0   1
  AMP PEAK 14(17Q12) MUTATED   101  11
  AMP PEAK 14(17Q12) WILD-TYPE 281  51
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 14(17Q12) MUTATED    101   11
  AMP PEAK 14(17Q12) WILD-TYPE  281   51
                               clus
vv                              AMP PEAK 14(17Q12) MUTATED
  COLON ADENOCARCINOMA                                 101
  COLON MUCINOUS ADENOCARCINOMA                         11
                               clus
vv                              AMP PEAK 14(17Q12) WILD-TYPE
  COLON ADENOCARCINOMA                                   281
  COLON MUCINOUS ADENOCARCINOMA                           51
[1] 2 2
[1] FALSE
                              vv
clus                            R0  R1  R2  RX
  AMP PEAK 14(17Q12) MUTATED    78   1  10   4
  AMP PEAK 14(17Q12) WILD-TYPE 245   3  15  21
D14V10, multiclass
    clus
vv   AMP PEAK 14(17Q12) MUTATED AMP PEAK 14(17Q12) WILD-TYPE
  R0                         78                          245
  R1                          1                            3
  R2                         10                           15
  RX                          4                           21
[1] 4 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, continuous
                              vv
clus                           AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 14(17Q12) MUTATED                                  1     3
  AMP PEAK 14(17Q12) WILD-TYPE                                0     8
                              vv
clus                           BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 14(17Q12) MUTATED                          18    52
  AMP PEAK 14(17Q12) WILD-TYPE                        41   160
D14V12, multiclass
                                  clus
vv                                 AMP PEAK 14(17Q12) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          1
  ASIAN                                                     3
  BLACK OR AFRICAN AMERICAN                                18
  WHITE                                                    52
                                  clus
vv                                 AMP PEAK 14(17Q12) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       8
  BLACK OR AFRICAN AMERICAN                                  41
  WHITE                                                     160
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V13, binary
                              cls
clus                             0   1
  AMP PEAK 14(17Q12) MUTATED     3  69
  AMP PEAK 14(17Q12) WILD-TYPE   1 200
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 14(17Q12) MUTATED      3   69
  AMP PEAK 14(17Q12) WILD-TYPE    1  200
                        clus
vv                       AMP PEAK 14(17Q12) MUTATED
  HISPANIC OR LATINO                              3
  NOT HISPANIC OR LATINO                         69
                        clus
vv                       AMP PEAK 14(17Q12) WILD-TYPE
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                          200
[1] 2 2
[1] FALSE

Clustering(15) Variable = AMP PEAK 15(17Q24.1) MUTATION ANALYSIS
D15V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 15(17Q24.1) MUTATED    88  15
  AMP PEAK 15(17Q24.1) WILD-TYPE 247  86
  AMP PEAK 15(17Q24.1) MUTATED AMP PEAK 15(17Q24.1) WILD-TYPE 
                           103                            333 
  AMP PEAK 15(17Q24.1) MUTATED AMP PEAK 15(17Q24.1) WILD-TYPE 
                            15                             86 
$`AMP PEAK 15(17Q24.1) MUTATED`
TCGA-A6-2677 TCGA-A6-4105 TCGA-AA-3496 TCGA-AA-3506 TCGA-AA-3556 TCGA-AA-3692 
       24.33        14.53         1.02        58.03        23.01        36.00 
TCGA-AA-3697 TCGA-AA-3867 TCGA-AA-3939 TCGA-AA-3972 TCGA-AA-A00L TCGA-AA-A00Z 
       85.05        24.03        12.99        50.99        38.04        21.99 
TCGA-AD-6888 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6625 TCGA-NH-A8F7 
       15.52         5.88        63.62        35.93        91.79        17.85 
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AATE TCGA-A6-2675 
       15.62         4.80        12.66         1.61        39.45        43.43 
TCGA-A6-2678 TCGA-A6-2686 TCGA-A6-3810 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5666 
       42.28        37.02        36.53        30.44        29.19        32.71 
TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6652 TCGA-A6-6782 
       29.16        27.09        25.08        25.18        24.69        20.28 
TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3553 TCGA-AA-3679 TCGA-AA-3812 TCGA-AA-3821 
        1.02        37.05        24.00        15.02        35.05         1.02 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3956 TCGA-AA-3966 
       17.03        10.06        36.03         0.99        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3982 TCGA-AA-A004 TCGA-AA-A01G 
       21.99        13.05        34.06        27.02        13.94        12.00 
TCGA-AA-A01S TCGA-AA-A01Z TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02W TCGA-AD-6890 
        1.02        37.02         5.03         0.92        41.00        24.53 
TCGA-AD-6963 TCGA-AD-A5EK TCGA-AU-3779 TCGA-AY-4070 TCGA-AZ-5407 TCGA-AZ-6603 
       27.42        16.44        14.50        16.31        88.21        29.56 
TCGA-CA-5254 TCGA-CA-6715 TCGA-CK-4948 TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5341 
       12.69        12.59       148.01         8.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5868 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6166 TCGA-CM-6167 
       22.03        17.03        14.04        29.03        21.99        14.99 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6678 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5541 
       13.05        11.08        11.01        54.61        19.59        55.92 
TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6924 TCGA-D5-6929 
       25.48        15.12         4.80        17.13        14.30        13.41 
TCGA-DM-A1D0 TCGA-DM-A28M TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6307 TCGA-G4-6311 
      130.65        95.18        74.56        65.85        55.04        39.42 
TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6626 TCGA-NH-A6GB TCGA-QG-A5YW TCGA-QG-A5YX 
       36.00        26.43        46.75        15.65        29.46        32.98 
TCGA-RU-A8FL 
       38.70 

$`AMP PEAK 15(17Q24.1) WILD-TYPE`
TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-6649 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       45.60        13.94        24.16        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 
       17.95        19.99        19.99         6.05         0.92        19.00 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3870 TCGA-AA-3950 
       19.04        19.04        14.93        31.07        29.98        24.00 
TCGA-AA-3952 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A024 TCGA-AD-6548 
        2.01        26.01        24.00        19.07        39.06        21.37 
TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 
       25.08        10.88        75.95       106.75       100.01         1.94 
TCGA-CK-5912 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       49.08        28.21        23.51        22.09        35.80        26.17 
TCGA-G4-6628 TCGA-5M-AAT6 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       79.69         9.53        43.76        46.65        43.76        42.90 
TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-3807 
       44.91        35.11        16.57        37.05        37.25        34.65 
TCGA-A6-3809 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5661 TCGA-A6-5662 
       32.75        32.45        32.91        31.63        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6650 
       22.09        22.06        22.52        24.13         8.38        20.61 
TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 
       21.76        24.39        23.87        20.12        19.66        16.24 
TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 
       24.92        61.84        56.25         9.63         5.03         7.04 
TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3555 
       26.01        12.99        14.01        33.99        21.01        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3680 
        2.01        14.01        50.04        47.05        47.01        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3818 
        5.98        37.05         5.03        26.99        10.06         0.99 
TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 
       25.02        17.98        15.95        38.99        36.95        37.02 
TCGA-AA-3845 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3855 TCGA-AA-3858 
        0.00         0.00        33.07         0.00        32.05        31.07 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3971 TCGA-AA-3977 
       24.00        33.01        26.01        20.98        16.08        25.02 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
        7.96        27.02        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D 
       17.03        14.99        34.98        15.02        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       32.02        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F 
       33.04         1.02        26.01        51.98         2.96        39.98 
TCGA-AA-A02H TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        2.01        22.03        39.98        18.05        40.96        12.16 
TCGA-AD-6889 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6965 TCGA-AM-5820 TCGA-AM-5821 
       83.24         5.79        22.42        26.47         0.46         0.92 
TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       27.09         0.95        33.01         0.20        21.44        17.82 
TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4315 
       17.26        17.85        19.33        18.84       109.28        58.39 
TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-4684 
        1.41         5.65        32.94         5.13        22.36        65.00 
TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6605 TCGA-AZ-6606 
       62.79        49.41         6.77        12.10         5.23        11.74 
TCGA-AZ-6607 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6716 
        3.19        12.36        12.46        12.39        12.59        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 
       12.76        10.06        14.30        17.56        85.45        70.16 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 
      124.27        23.05        20.02        37.02        25.02        26.04 
TCGA-CM-4751 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       27.02        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6168 
       15.02        15.02        15.02        12.00        16.04        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6677 
       13.02        15.02        14.04        11.01        12.95        11.08 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5540 TCGA-D5-6529 TCGA-D5-6530 
       10.06        12.03        45.40        56.09        20.19        20.42 
TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6539 TCGA-D5-6540 
       17.75        18.25        43.27        17.85        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 
       15.58         7.53        12.39        10.13        12.43         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
        9.44        11.64        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
      119.70        24.43        38.20        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E 
        7.76       139.17        14.04        26.47        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
       11.11        35.74        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6302 
       47.41        35.31       133.18         8.35        82.39        67.30 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6322 TCGA-G4-6323 
       53.62        44.68        85.48        61.91        26.04        13.78 
TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA 
       74.79        18.18        10.98        19.33        19.33         9.93 
TCGA-NH-A6GC TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D 
       12.79        16.80        42.77         8.42        31.30        21.90 
TCGA-SS-A7HO TCGA-T9-A92H TCGA-WS-AB45 
       60.13        11.90        70.03 

  AMP PEAK 15(17Q24.1) MUTATED AMP PEAK 15(17Q24.1) WILD-TYPE 
                          0.92                           0.00 
  AMP PEAK 15(17Q24.1) MUTATED AMP PEAK 15(17Q24.1) WILD-TYPE 
                        148.01                         140.38 
  AMP PEAK 15(17Q24.1) MUTATED AMP PEAK 15(17Q24.1) WILD-TYPE 
                         24.33                          21.76 
[1] "0.9 - 148.0 (24.3)" "0.0 - 140.4 (21.8)"
[1] "hr=" "1.8"
D15V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK 15(17Q24.1) MUTATED        16        0        5        28         1
  AMP PEAK 15(17Q24.1) WILD-TYPE      58        1       24       104         9
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 15(17Q24.1) MUTATED           1         4          3         16
  AMP PEAK 15(17Q24.1) WILD-TYPE         0        16          5         43
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 15(17Q24.1) MUTATED            9       13         5         1
  AMP PEAK 15(17Q24.1) WILD-TYPE         32       32        12         1
D15V3, multiclass
            clus
vv           AMP PEAK 15(17Q24.1) MUTATED AMP PEAK 15(17Q24.1) WILD-TYPE
  STAGE I                              16                             58
  STAGE IA                              0                              1
  STAGE II                              5                             24
  STAGE IIA                            28                            104
  STAGE IIB                             1                              9
  STAGE IIC                             1                              0
  STAGE III                             4                             16
  STAGE IIIA                            3                              5
  STAGE IIIB                           16                             43
  STAGE IIIC                            9                             32
  STAGE IV                             13                             32
  STAGE IVA                             5                             12
  STAGE IVB                             1                              1
[1] 13  2
[1] 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(17Q24.1) MUTATED     4  16  78   8
  AMP PEAK 15(17Q24.1) WILD-TYPE   7  61 227  47
D15V4, multiclass
    clus
vv   AMP PEAK 15(17Q24.1) MUTATED AMP PEAK 15(17Q24.1) WILD-TYPE
  T1                            4                              7
  T2                           16                             61
  T3                           78                            227
  T4                            8                             47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2
  AMP PEAK 15(17Q24.1) MUTATED    59  30  17
  AMP PEAK 15(17Q24.1) WILD-TYPE 203  75  65
D15V5, multiclass
    clus
vv   AMP PEAK 15(17Q24.1) MUTATED AMP PEAK 15(17Q24.1) WILD-TYPE
  N0                           59                            203
  N1                           30                             75
  N2                           17                             65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V6, binary
                                cls
clus                               0   1
  AMP PEAK 15(17Q24.1) MUTATED    69  19
  AMP PEAK 15(17Q24.1) WILD-TYPE 259  45
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(17Q24.1) MUTATED     69   19
  AMP PEAK 15(17Q24.1) WILD-TYPE  259   45
   clus
vv  AMP PEAK 15(17Q24.1) MUTATED AMP PEAK 15(17Q24.1) WILD-TYPE
  0                           69                            259
  1                           19                             45
[1] 2 2
[1] FALSE
D15V7, binary
                                cls
clus                               0   1
  AMP PEAK 15(17Q24.1) MUTATED    52  54
  AMP PEAK 15(17Q24.1) WILD-TYPE 161 182
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(17Q24.1) MUTATED     52   54
  AMP PEAK 15(17Q24.1) WILD-TYPE  161  182
        clus
vv       AMP PEAK 15(17Q24.1) MUTATED AMP PEAK 15(17Q24.1) WILD-TYPE
  FEMALE                           52                            161
  MALE                             54                            182
[1] 2 2
[1] FALSE
D15V8, binary
                                cls
clus                               0   1
  AMP PEAK 15(17Q24.1) MUTATED    90   3
  AMP PEAK 15(17Q24.1) WILD-TYPE 280   6
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(17Q24.1) MUTATED     90    3
  AMP PEAK 15(17Q24.1) WILD-TYPE  280    6
     clus
vv    AMP PEAK 15(17Q24.1) MUTATED AMP PEAK 15(17Q24.1) WILD-TYPE
  NO                            90                            280
  YES                            3                              6
[1] 2 2
[1] FALSE
D15V9, binary
                                cls
clus                               0   1
  AMP PEAK 15(17Q24.1) MUTATED    96   9
  AMP PEAK 15(17Q24.1) WILD-TYPE 286  53
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(17Q24.1) MUTATED     96    9
  AMP PEAK 15(17Q24.1) WILD-TYPE  286   53
                               clus
vv                              AMP PEAK 15(17Q24.1) MUTATED
  COLON ADENOCARCINOMA                                    96
  COLON MUCINOUS ADENOCARCINOMA                            9
                               clus
vv                              AMP PEAK 15(17Q24.1) WILD-TYPE
  COLON ADENOCARCINOMA                                     286
  COLON MUCINOUS ADENOCARCINOMA                             53
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 15(17Q24.1) MUTATED    77   1   8   3
  AMP PEAK 15(17Q24.1) WILD-TYPE 246   3  17  22
D15V10, multiclass
    clus
vv   AMP PEAK 15(17Q24.1) MUTATED AMP PEAK 15(17Q24.1) WILD-TYPE
  R0                           77                            246
  R1                            1                              3
  R2                            8                             17
  RX                            3                             22
[1] 4 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, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 15(17Q24.1) MUTATED                                  0     2
  AMP PEAK 15(17Q24.1) WILD-TYPE                                1     9
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 15(17Q24.1) MUTATED                          17    51
  AMP PEAK 15(17Q24.1) WILD-TYPE                        42   161
D15V12, multiclass
                                  clus
vv                                 AMP PEAK 15(17Q24.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                  17
  WHITE                                                      51
                                  clus
vv                                 AMP PEAK 15(17Q24.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         9
  BLACK OR AFRICAN AMERICAN                                    42
  WHITE                                                       161
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V13, binary
                                cls
clus                               0   1
  AMP PEAK 15(17Q24.1) MUTATED     3  65
  AMP PEAK 15(17Q24.1) WILD-TYPE   1 204
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(17Q24.1) MUTATED      3   65
  AMP PEAK 15(17Q24.1) WILD-TYPE    1  204
                        clus
vv                       AMP PEAK 15(17Q24.1) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           65
                        clus
vv                       AMP PEAK 15(17Q24.1) WILD-TYPE
  HISPANIC OR LATINO                                  1
  NOT HISPANIC OR LATINO                            204
[1] 2 2
[1] FALSE

Clustering(16) Variable = AMP PEAK 16(19Q13.11) MUTATION ANALYSIS
D16V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 16(19Q13.11) MUTATED    73  17
  AMP PEAK 16(19Q13.11) WILD-TYPE 262  84
  AMP PEAK 16(19Q13.11) MUTATED AMP PEAK 16(19Q13.11) WILD-TYPE 
                             90                             346 
  AMP PEAK 16(19Q13.11) MUTATED AMP PEAK 16(19Q13.11) WILD-TYPE 
                             17                              84 
$`AMP PEAK 16(19Q13.11) MUTATED`
TCGA-A6-2681 TCGA-A6-4105 TCGA-AA-3506 TCGA-AA-3522 TCGA-AA-3552 TCGA-AA-3939 
       45.60        14.53        58.03        37.05        13.02        12.99 
TCGA-AA-3972 TCGA-AA-A00Z TCGA-AD-6888 TCGA-G4-6310 TCGA-NH-A8F7 TCGA-3L-AA1B 
       50.99        21.99        15.52        63.62        17.85        15.62 
TCGA-4T-AA8H TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2675 TCGA-A6-2683 TCGA-A6-2686 
       12.66        39.45        43.76        43.43        16.57        37.02 
TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-5657 TCGA-A6-5667 TCGA-A6-6142 TCGA-A6-6648 
       34.65        36.53        31.63        29.16        25.08        25.18 
TCGA-A6-6651 TCGA-A6-6654 TCGA-A6-A567 TCGA-A6-A56B TCGA-AA-3502 TCGA-AA-3542 
       21.76        23.87        61.84        56.25        35.01        12.99 
TCGA-AA-3685 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3842 TCGA-AA-3851 TCGA-AA-3854 
       37.05        35.05         0.99        37.02        33.07        36.03 
TCGA-AA-3973 TCGA-AA-A00K TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A01G TCGA-AA-A029 
       13.05        18.05        27.02        42.02        12.00        51.98 
TCGA-AA-A02F TCGA-AA-A02O TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-A5EK TCGA-AU-3779 
       39.98         0.92         5.79        22.42        16.44        14.50 
TCGA-AY-6196 TCGA-AY-A69D TCGA-AY-A8YK TCGA-AZ-5407 TCGA-AZ-6603 TCGA-AZ-6606 
        0.20        17.85        18.84        88.21        29.56        11.74 
TCGA-CA-5255 TCGA-CA-6719 TCGA-CK-4950 TCGA-CK-5914 TCGA-CK-6748 TCGA-CM-4746 
       12.36        14.30        85.45        21.99         2.01        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 
       25.02        13.02        29.06        32.02         5.03        15.02 
TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6166 TCGA-CM-6676 TCGA-D5-5539 
       15.02        14.04        29.03        21.99        11.08        19.59 
TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 
       15.12         4.80        11.64        13.41        12.00        11.38 
TCGA-DM-A0X9 TCGA-DM-A28F TCGA-F4-6459 TCGA-F4-6463 TCGA-F4-6855 TCGA-G4-6297 
      119.70        35.97         8.61        35.74        47.41        82.39 
TCGA-G4-6299 TCGA-G4-6311 TCGA-G4-6320 TCGA-G4-6627 TCGA-QG-A5YW TCGA-QL-A97D 
       74.56        39.42        26.43        74.79        29.46        21.90 

$`AMP PEAK 16(19Q13.11) WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2682 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        13.94        24.16         1.02        13.02        24.03 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3554 
       36.03         8.05        19.07        34.03         0.99        17.95 
TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 
       23.01        19.99        19.99         6.05         0.92        19.00 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 
       36.00        85.05        19.04        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3976 TCGA-AA-3979 
       24.03        29.98        24.00         2.01        26.01        24.00 
TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6895 TCGA-AD-6964 
       19.07        38.04        39.06        21.37        25.08        10.88 
TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 
       75.95       106.75       100.01         1.94        49.08         5.88 
TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6314 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       28.21        23.51        35.93        22.09        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-4N-A93T TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-A6-2672 
       91.79        79.69         4.80         1.61         9.53        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2684 
       43.76        42.90        42.28        44.91        35.11        37.05 
TCGA-A6-2685 TCGA-A6-3809 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 
       37.25        32.75        32.45        32.91        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 
       33.53        23.61        22.09        22.06        32.71        27.09 
TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6653 
       22.52        24.13         8.38        20.61        24.69        24.39 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A5ZU 
       20.12        19.66        20.28        16.24        24.92         9.63 
TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3510 
        5.03         7.04         3.02         1.02        37.05        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3544 TCGA-AA-3548 
        0.00        29.00        29.00        26.01        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        61.02 
TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       78.08         6.97        54.02         2.01        14.01        50.04 
TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3696 
       47.05        47.01        15.02        11.01         5.98         5.03 
TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       26.99        10.06        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       38.99        36.95         0.00        17.03        10.06         0.00 
TCGA-AA-3852 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3866 
        0.00        32.05         0.99        31.07        53.00        17.03 
TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       34.06        25.02        27.02         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00N 
       38.04        19.00        30.02        34.03        18.05         4.01 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C 
        0.99        17.03        14.99        34.98        15.02        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       10.98        32.02        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04         1.02        26.01        37.02 
TCGA-AA-A02E TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y 
        2.96         2.01         5.03        22.03        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6963 
       18.05        40.96        12.16        83.24        24.53        27.42 
TCGA-AD-6965 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       26.47         0.46         0.92        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A71X TCGA-AZ-4308 
       33.01        21.44        17.82        17.26        19.33       109.28 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 
       58.39         1.41         5.65        32.94         5.13        22.36 
TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6605 
       65.00        62.79        49.41         6.77        12.10         5.23 
TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        3.19        12.69        12.46        12.39        12.59        12.59 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4951 
       12.20        12.76        10.06        17.56       148.01        70.16 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 
       15.62        51.32        21.14        82.95       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-5344 TCGA-CM-5348 
       20.02        26.04         8.02        27.02        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6162 TCGA-CM-6165 
       30.08        15.02        15.02        17.03        12.00        16.04 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       12.95        13.05        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 
       45.40        54.61        56.09        55.92        20.19        20.42 
TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6538 
       17.75        18.25        25.48        43.27        17.85        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6930 TCGA-D5-7000 
       12.43        14.30         9.04         9.44        13.35        10.26 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E 
        7.76       139.17        14.04        26.47        81.37       119.93 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6460 TCGA-F4-6461 
       60.79       117.07        98.24        95.18        31.96        11.11 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6856 TCGA-G4-6293 
       43.04        33.67        13.25         0.53        35.31       133.18 
TCGA-G4-6295 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
        8.35        67.30        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        26.04        13.78        46.75 
TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB 
       18.18        10.98        19.33        19.33         9.93        15.65 
TCGA-NH-A6GC TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 
       12.79        16.80        42.77        32.98         8.42        31.30 
TCGA-RU-A8FL TCGA-SS-A7HO TCGA-T9-A92H TCGA-WS-AB45 
       38.70        60.13        11.90        70.03 

  AMP PEAK 16(19Q13.11) MUTATED AMP PEAK 16(19Q13.11) WILD-TYPE 
                            0.2                             0.0 
  AMP PEAK 16(19Q13.11) MUTATED AMP PEAK 16(19Q13.11) WILD-TYPE 
                         119.70                          148.01 
  AMP PEAK 16(19Q13.11) MUTATED AMP PEAK 16(19Q13.11) WILD-TYPE 
                         24.445                          22.010 
[1] "0.2 - 119.7 (24.4)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.3"
D16V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK 16(19Q13.11) MUTATED        13        0        4        30         0
  AMP PEAK 16(19Q13.11) WILD-TYPE      61        1       25       102        10
                                 vv
clus                              STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 16(19Q13.11) MUTATED           0         3          3         15
  AMP PEAK 16(19Q13.11) WILD-TYPE         1        17          5         44
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 16(19Q13.11) MUTATED            9       11         5         0
  AMP PEAK 16(19Q13.11) WILD-TYPE         32       34        12         2
D16V3, multiclass
            clus
vv           AMP PEAK 16(19Q13.11) MUTATED AMP PEAK 16(19Q13.11) WILD-TYPE
  STAGE I                               13                              61
  STAGE IA                               0                               1
  STAGE II                               4                              25
  STAGE IIA                             30                             102
  STAGE IIB                              0                              10
  STAGE IIC                              0                               1
  STAGE III                              3                              17
  STAGE IIIA                             3                               5
  STAGE IIIB                            15                              44
  STAGE IIIC                             9                              32
  STAGE IV                              11                              34
  STAGE IVA                              5                              12
  STAGE IVB                              0                               2
[1] 13  2
[1] 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(19Q13.11) MUTATED     2  14  71   8
  AMP PEAK 16(19Q13.11) WILD-TYPE   9  63 234  47
D16V4, multiclass
    clus
vv   AMP PEAK 16(19Q13.11) MUTATED AMP PEAK 16(19Q13.11) WILD-TYPE
  T1                             2                               9
  T2                            14                              63
  T3                            71                             234
  T4                             8                              47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               N0  N1  N2
  AMP PEAK 16(19Q13.11) MUTATED    50  30  15
  AMP PEAK 16(19Q13.11) WILD-TYPE 212  75  67
D16V5, multiclass
    clus
vv   AMP PEAK 16(19Q13.11) MUTATED AMP PEAK 16(19Q13.11) WILD-TYPE
  N0                            50                             212
  N1                            30                              75
  N2                            15                              67
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V6, binary
                                 cls
clus                                0   1
  AMP PEAK 16(19Q13.11) MUTATED    61  16
  AMP PEAK 16(19Q13.11) WILD-TYPE 267  48
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 16(19Q13.11) MUTATED     61   16
  AMP PEAK 16(19Q13.11) WILD-TYPE  267   48
   clus
vv  AMP PEAK 16(19Q13.11) MUTATED AMP PEAK 16(19Q13.11) WILD-TYPE
  0                            61                             267
  1                            16                              48
[1] 2 2
[1] FALSE
D16V7, binary
                                 cls
clus                                0   1
  AMP PEAK 16(19Q13.11) MUTATED    38  57
  AMP PEAK 16(19Q13.11) WILD-TYPE 175 179
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 16(19Q13.11) MUTATED     38   57
  AMP PEAK 16(19Q13.11) WILD-TYPE  175  179
        clus
vv       AMP PEAK 16(19Q13.11) MUTATED AMP PEAK 16(19Q13.11) WILD-TYPE
  FEMALE                            38                             175
  MALE                              57                             179
[1] 2 2
[1] FALSE
D16V8, binary
                                 cls
clus                                0   1
  AMP PEAK 16(19Q13.11) MUTATED    80   3
  AMP PEAK 16(19Q13.11) WILD-TYPE 290   6
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 16(19Q13.11) MUTATED     80    3
  AMP PEAK 16(19Q13.11) WILD-TYPE  290    6
     clus
vv    AMP PEAK 16(19Q13.11) MUTATED AMP PEAK 16(19Q13.11) WILD-TYPE
  NO                             80                             290
  YES                             3                               6
[1] 2 2
[1] FALSE
D16V9, binary
                                 cls
clus                                0   1
  AMP PEAK 16(19Q13.11) MUTATED    83  12
  AMP PEAK 16(19Q13.11) WILD-TYPE 299  50
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 16(19Q13.11) MUTATED     83   12
  AMP PEAK 16(19Q13.11) WILD-TYPE  299   50
                               clus
vv                              AMP PEAK 16(19Q13.11) MUTATED
  COLON ADENOCARCINOMA                                     83
  COLON MUCINOUS ADENOCARCINOMA                            12
                               clus
vv                              AMP PEAK 16(19Q13.11) WILD-TYPE
  COLON ADENOCARCINOMA                                      299
  COLON MUCINOUS ADENOCARCINOMA                              50
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  AMP PEAK 16(19Q13.11) MUTATED    70   1   4   6
  AMP PEAK 16(19Q13.11) WILD-TYPE 253   3  21  19
D16V10, multiclass
    clus
vv   AMP PEAK 16(19Q13.11) MUTATED AMP PEAK 16(19Q13.11) WILD-TYPE
  R0                            70                             253
  R1                             1                               3
  R2                             4                              21
  RX                             6                              19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V11, continuous
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 16(19Q13.11) MUTATED                                  0     2
  AMP PEAK 16(19Q13.11) WILD-TYPE                                1     9
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 16(19Q13.11) MUTATED                          15    52
  AMP PEAK 16(19Q13.11) WILD-TYPE                        44   160
D16V12, multiclass
                                  clus
vv                                 AMP PEAK 16(19Q13.11) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        2
  BLACK OR AFRICAN AMERICAN                                   15
  WHITE                                                       52
                                  clus
vv                                 AMP PEAK 16(19Q13.11) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               1
  ASIAN                                                          9
  BLACK OR AFRICAN AMERICAN                                     44
  WHITE                                                        160
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V13, binary
                                 cls
clus                                0   1
  AMP PEAK 16(19Q13.11) MUTATED     1  64
  AMP PEAK 16(19Q13.11) WILD-TYPE   3 205
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 16(19Q13.11) MUTATED      1   64
  AMP PEAK 16(19Q13.11) WILD-TYPE    3  205
                        clus
vv                       AMP PEAK 16(19Q13.11) MUTATED
  HISPANIC OR LATINO                                 1
  NOT HISPANIC OR LATINO                            64
                        clus
vv                       AMP PEAK 16(19Q13.11) WILD-TYPE
  HISPANIC OR LATINO                                   3
  NOT HISPANIC OR LATINO                             205
[1] 2 2
[1] FALSE

Clustering(17) Variable = AMP PEAK 17(20P12.1) MUTATION ANALYSIS
D17V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 17(20P12.1) MUTATED   143  46
  AMP PEAK 17(20P12.1) WILD-TYPE 192  55
  AMP PEAK 17(20P12.1) MUTATED AMP PEAK 17(20P12.1) WILD-TYPE 
                           189                            247 
  AMP PEAK 17(20P12.1) MUTATED AMP PEAK 17(20P12.1) WILD-TYPE 
                            46                             55 
$`AMP PEAK 17(20P12.1) MUTATED`
TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-6649 TCGA-AA-3506 TCGA-AA-3520 TCGA-AA-3530 
       45.60        13.94        24.16        58.03        24.03        19.07 
TCGA-AA-3552 TCGA-AA-3556 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3688 TCGA-AA-3692 
       13.02        23.01        19.99         6.05        19.00        36.00 
TCGA-AA-3844 TCGA-AA-3939 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 
       14.93        12.99        50.99        26.01        24.00        19.07 
TCGA-AA-A00L TCGA-AA-A00Z TCGA-AD-6895 TCGA-AZ-4681 TCGA-CK-5912 TCGA-DM-A285 
       38.04        21.99        25.08       106.75        49.08         5.88 
TCGA-G4-6294 TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6625 TCGA-NH-A8F7 TCGA-3L-AA1B 
       28.21        63.62        35.93        91.79        17.85        15.62 
TCGA-4N-A93T TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2679 
        4.80        39.45        43.76        43.76        43.43        44.91 
TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4107 
       35.11        16.57        37.02        34.65        36.53        32.45 
TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-6137 TCGA-A6-6142 TCGA-A6-6652 TCGA-A6-6782 
       32.91        30.44        27.09        25.08        24.69        20.28 
TCGA-A6-A567 TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3494 TCGA-AA-3511 
       61.84         9.63         5.03         7.04         1.02         6.97 
TCGA-AA-3514 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3544 TCGA-AA-3549 
        1.02         0.00        29.00        29.00        14.01        21.01 
TCGA-AA-3558 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3679 
       20.98         2.01        14.01        50.04        47.05        15.02 
TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3811 TCGA-AA-3818 TCGA-AA-3842 TCGA-AA-3845 
       37.05         5.03        10.06         0.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3866 
       17.03        10.06        33.07         0.99        31.07        17.03 
TCGA-AA-3875 TCGA-AA-3941 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3973 TCGA-AA-3975 
       18.05        24.00        34.03        21.99        13.05        34.06 
TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00U 
       27.02         7.96        13.94        18.05         4.01        17.03 
TCGA-AA-A00W TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01T 
       14.99        15.02        10.98        12.00        31.00        33.04 
TCGA-AA-A01X TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O 
       26.01        51.98         2.96         2.01         5.03         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AD-5900 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       41.00        39.98        12.16        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-A5EK TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-A54L TCGA-AY-A69D 
       27.42        16.44        16.31         0.95        17.26        17.85 
TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4684 TCGA-AZ-6598 
       19.33        18.84         1.41         5.13        65.00        49.41 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 
       12.10        29.56         3.19        12.69        12.36        12.46 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 TCGA-CM-4744 
       12.59        12.59        14.30        17.56        85.45        20.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5862 TCGA-CM-5863 
       25.02        13.02        29.06        22.98         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6165 TCGA-CM-6166 
       15.02        17.03        15.02        14.04        16.04        21.99 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6677 TCGA-CM-6678 TCGA-D5-5537 TCGA-D5-5538 
       14.04        11.01        11.08        11.01        45.40        54.61 
TCGA-D5-5539 TCGA-D5-6529 TCGA-D5-6531 TCGA-D5-6539 TCGA-D5-6920 TCGA-D5-6922 
       19.59        20.19        17.75        12.49        12.39        10.13 
TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A1D8 
        9.04        11.64        13.41        10.26       119.70        12.59 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28F TCGA-DM-A28H 
        7.50        44.32       139.17        14.04        35.97       117.07 
TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6704 TCGA-F4-6855 
       95.18         8.61        35.74         6.18         1.55        47.41 
TCGA-G4-6293 TCGA-G4-6297 TCGA-G4-6307 TCGA-G4-6311 TCGA-G4-6317 TCGA-G4-6322 
      133.18        82.39        55.04        39.42        36.00        26.04 
TCGA-G4-6323 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A6GB TCGA-NH-A6GC 
       13.78        46.75        74.79        18.18        15.65        12.79 
TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX 
       42.77        29.46        32.98 

$`AMP PEAK 17(20P12.1) WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3522 TCGA-AA-3524 
       24.33        14.53         1.02        13.02        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3554 TCGA-AA-3560 TCGA-AA-3672 
        8.05        34.03         0.99        17.95        19.99         0.92 
TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 
       85.05        19.04        19.04        31.07        24.03        29.98 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 
       24.00         2.01        39.06        21.37        15.52        10.88 
TCGA-AZ-4313 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-G4-6298 TCGA-G4-6321 TCGA-G4-6586 
       75.95       100.01         1.94        23.51        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6628 TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-A6-2672 
       26.17        79.69        12.66         1.61         9.53        46.65 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-3809 TCGA-A6-5657 
       42.90        42.28        37.05        37.25        32.75        31.63 
TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 
       29.19        33.53        23.61        22.09        22.06        32.71 
TCGA-A6-5667 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6650 
       29.16        22.52        24.13         8.38        25.18        20.61 
TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 
       21.76        24.39        23.87        20.12        19.66        16.24 
TCGA-A6-A566 TCGA-A6-A56B TCGA-AA-3492 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 
       24.92        56.25         3.02        37.05        35.01        63.98 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3538 TCGA-AA-3542 
       38.99         1.02         9.07        19.07        26.01        12.99 
TCGA-AA-3548 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       33.99        24.00        29.95        13.94        61.02        78.08 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3678 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3710 
        6.97        54.02        47.01        11.01         5.98        26.99 
TCGA-AA-3812 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
       35.05        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3841 TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3864 
       36.95         0.00         0.00        36.03        32.05        53.00 
TCGA-AA-3869 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       27.02        31.00         2.01        33.01        26.01        20.98 
TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3977 TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00D 
        2.01        16.08        25.02        27.02        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       30.02        34.03        18.05        27.02        42.02         0.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01F TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       34.98        15.02        32.02        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A02F TCGA-AA-A02R 
       35.01         1.02         1.02        37.02        39.98        22.03 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6889 TCGA-AD-6965 TCGA-AM-5820 TCGA-AM-5821 
       18.05        40.96        83.24        26.47         0.46         0.92 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       14.50        27.09        33.01         0.20        21.44        17.82 
TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4682 TCGA-AZ-5403 
      109.28        58.39         5.65        32.94        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-CA-5796 TCGA-CA-6716 
       88.21         6.77         5.23        11.74        12.39        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4948 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 
       12.76        10.06       148.01        70.16        15.62        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14        82.95         2.01       124.27        23.05 
TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-5344 TCGA-CM-5349 
       37.02        26.04         8.02        27.02        22.03        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-6162 TCGA-CM-6164 TCGA-CM-6167 TCGA-CM-6168 
       32.02        15.02        12.00        29.03        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6679 
       13.02        15.02        12.95        13.05        11.08        10.06 
TCGA-CM-6680 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6533 
       12.03        56.09        55.92        20.42        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 
       43.27        15.12        17.85         4.80        17.13        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6930 
       15.58         7.53        12.43        14.30         9.44        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       12.00        11.38        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 
       49.91        13.32       140.38       131.51       135.65         7.76 
TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6460 
       26.47        81.37       119.93        60.79        98.24        31.96 
TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       11.11        35.74        47.87        34.42        41.42        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6856 TCGA-G4-6295 TCGA-G4-6299 
       33.67        13.25         0.53        35.31         8.35        74.56 
TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6315 
       67.30        65.85        53.62        44.68        85.48        61.91 
TCGA-G4-6320 TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A8F8 
       26.43        10.98        19.33        19.33         9.93        16.80 
TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-RU-A8FL TCGA-SS-A7HO TCGA-T9-A92H 
        8.42        31.30        21.90        38.70        60.13        11.90 
TCGA-WS-AB45 
       70.03 

  AMP PEAK 17(20P12.1) MUTATED AMP PEAK 17(20P12.1) WILD-TYPE 
                             0                              0 
  AMP PEAK 17(20P12.1) MUTATED AMP PEAK 17(20P12.1) WILD-TYPE 
                        139.17                         148.01 
  AMP PEAK 17(20P12.1) MUTATED AMP PEAK 17(20P12.1) WILD-TYPE 
                         19.07                          24.13 
[1] "0.0 - 139.2 (19.1)" "0.0 - 148.0 (24.1)"
[1] "hr=" "1.3"
D17V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK 17(20P12.1) MUTATED        36        1       10        48         3
  AMP PEAK 17(20P12.1) WILD-TYPE      38        0       19        84         7
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 17(20P12.1) MUTATED           0         7          6         21
  AMP PEAK 17(20P12.1) WILD-TYPE         1        13          2         38
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 17(20P12.1) MUTATED           17       30         9         1
  AMP PEAK 17(20P12.1) WILD-TYPE         24       15         8         1
D17V3, multiclass
            clus
vv           AMP PEAK 17(20P12.1) MUTATED AMP PEAK 17(20P12.1) WILD-TYPE
  STAGE I                              36                             38
  STAGE IA                              1                              0
  STAGE II                             10                             19
  STAGE IIA                            48                             84
  STAGE IIB                             3                              7
  STAGE IIC                             0                              1
  STAGE III                             7                             13
  STAGE IIIA                            6                              2
  STAGE IIIB                           21                             38
  STAGE IIIC                           17                             24
  STAGE IV                             30                             15
  STAGE IVA                             9                              8
  STAGE IVB                             1                              1
[1] 13  2
[1] 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(20P12.1) MUTATED     5  38 129  22
  AMP PEAK 17(20P12.1) WILD-TYPE   6  39 176  33
D17V4, multiclass
    clus
vv   AMP PEAK 17(20P12.1) MUTATED AMP PEAK 17(20P12.1) WILD-TYPE
  T1                            5                              6
  T2                           38                             39
  T3                          129                            176
  T4                           22                             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"
                                vv
clus                              N0  N1  N2
  AMP PEAK 17(20P12.1) MUTATED   105  51  39
  AMP PEAK 17(20P12.1) WILD-TYPE 157  54  43
D17V5, multiclass
    clus
vv   AMP PEAK 17(20P12.1) MUTATED AMP PEAK 17(20P12.1) WILD-TYPE
  N0                          105                            157
  N1                           51                             54
  N2                           39                             43
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V6, binary
                                cls
clus                               0   1
  AMP PEAK 17(20P12.1) MUTATED   128  40
  AMP PEAK 17(20P12.1) WILD-TYPE 200  24
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(20P12.1) MUTATED    128   40
  AMP PEAK 17(20P12.1) WILD-TYPE  200   24
   clus
vv  AMP PEAK 17(20P12.1) MUTATED AMP PEAK 17(20P12.1) WILD-TYPE
  0                          128                            200
  1                           40                             24
[1] 2 2
[1] FALSE
D17V7, binary
                                cls
clus                               0   1
  AMP PEAK 17(20P12.1) MUTATED    86 109
  AMP PEAK 17(20P12.1) WILD-TYPE 127 127
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(20P12.1) MUTATED     86  109
  AMP PEAK 17(20P12.1) WILD-TYPE  127  127
        clus
vv       AMP PEAK 17(20P12.1) MUTATED AMP PEAK 17(20P12.1) WILD-TYPE
  FEMALE                           86                            127
  MALE                            109                            127
[1] 2 2
[1] FALSE
D17V8, binary
                                cls
clus                               0   1
  AMP PEAK 17(20P12.1) MUTATED   158   7
  AMP PEAK 17(20P12.1) WILD-TYPE 212   2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(20P12.1) MUTATED    158    7
  AMP PEAK 17(20P12.1) WILD-TYPE  212    2
     clus
vv    AMP PEAK 17(20P12.1) MUTATED AMP PEAK 17(20P12.1) WILD-TYPE
  NO                           158                            212
  YES                            7                              2
[1] 2 2
[1] FALSE
D17V9, binary
                                cls
clus                               0   1
  AMP PEAK 17(20P12.1) MUTATED   174  19
  AMP PEAK 17(20P12.1) WILD-TYPE 208  43
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(20P12.1) MUTATED    174   19
  AMP PEAK 17(20P12.1) WILD-TYPE  208   43
                               clus
vv                              AMP PEAK 17(20P12.1) MUTATED
  COLON ADENOCARCINOMA                                   174
  COLON MUCINOUS ADENOCARCINOMA                           19
                               clus
vv                              AMP PEAK 17(20P12.1) WILD-TYPE
  COLON ADENOCARCINOMA                                     208
  COLON MUCINOUS ADENOCARCINOMA                             43
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 17(20P12.1) MUTATED   137   2  17  10
  AMP PEAK 17(20P12.1) WILD-TYPE 186   2   8  15
D17V10, multiclass
    clus
vv   AMP PEAK 17(20P12.1) MUTATED AMP PEAK 17(20P12.1) WILD-TYPE
  R0                          137                            186
  R1                            2                              2
  R2                           17                              8
  RX                           10                             15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 17(20P12.1) MUTATED                                  1     6
  AMP PEAK 17(20P12.1) WILD-TYPE                                0     5
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 17(20P12.1) MUTATED                          24    88
  AMP PEAK 17(20P12.1) WILD-TYPE                        35   124
D17V12, multiclass
                                  clus
vv                                 AMP PEAK 17(20P12.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       6
  BLACK OR AFRICAN AMERICAN                                  24
  WHITE                                                      88
                                  clus
vv                                 AMP PEAK 17(20P12.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         5
  BLACK OR AFRICAN AMERICAN                                    35
  WHITE                                                       124
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V13, binary
                                cls
clus                               0   1
  AMP PEAK 17(20P12.1) MUTATED     1 111
  AMP PEAK 17(20P12.1) WILD-TYPE   3 158
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(20P12.1) MUTATED      1  111
  AMP PEAK 17(20P12.1) WILD-TYPE    3  158
                        clus
vv                       AMP PEAK 17(20P12.1) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                          111
                        clus
vv                       AMP PEAK 17(20P12.1) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            158
[1] 2 2
[1] FALSE

Clustering(18) Variable = AMP PEAK 18(20P11.23) MUTATION ANALYSIS
D18V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 18(20P11.23) MUTATED   161  52
  AMP PEAK 18(20P11.23) WILD-TYPE 174  49
  AMP PEAK 18(20P11.23) MUTATED AMP PEAK 18(20P11.23) WILD-TYPE 
                            213                             223 
  AMP PEAK 18(20P11.23) MUTATED AMP PEAK 18(20P11.23) WILD-TYPE 
                             52                              49 
$`AMP PEAK 18(20P11.23) MUTATED`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 
       24.33        45.60        13.94        14.53        24.16         1.02 
TCGA-AA-3506 TCGA-AA-3530 TCGA-AA-3552 TCGA-AA-3556 TCGA-AA-3562 TCGA-AA-3662 
       58.03        19.07        13.02        23.01        19.99         6.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3844 TCGA-AA-3939 TCGA-AA-3972 TCGA-AA-3976 
       19.00        36.00        14.93        12.99        50.99        26.01 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AD-6548 TCGA-AD-6895 
       24.00        19.07        38.04        21.99        21.37        25.08 
TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6310 
      106.75         1.94        49.08         5.88        28.21        63.62 
TCGA-G4-6314 TCGA-G4-6625 TCGA-3L-AA1B TCGA-4N-A93T TCGA-5M-AAT4 TCGA-5M-AATE 
       35.93        91.79        15.62         4.80         1.61        39.45 
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 
       43.76        43.76        43.43        44.91        35.11        16.57 
TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5659 TCGA-A6-5667 
       37.02        34.65        36.53        32.45        30.44        29.16 
TCGA-A6-6137 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6782 
       27.09        25.08        25.18        24.69        23.87        20.28 
TCGA-A6-A567 TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3494 TCGA-AA-3511 
       61.84         9.63         5.03         7.04         1.02         6.97 
TCGA-AA-3514 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3544 TCGA-AA-3549 
        1.02         0.00        29.00        29.00        14.01        21.01 
TCGA-AA-3558 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3679 
       20.98         2.01        14.01        50.04        47.05        15.02 
TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3811 TCGA-AA-3818 TCGA-AA-3837 TCGA-AA-3842 
       37.05         5.03        10.06         0.99        38.99        37.02 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3856 TCGA-AA-3858 
        0.00        17.03        10.06        33.07         0.99        31.07 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3941 TCGA-AA-3956 TCGA-AA-3966 
       17.03        27.02        18.05        24.00        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-A004 
       21.99        16.08        13.05        27.02         7.96        13.94 
TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A01C TCGA-AA-A01D 
       18.05         4.01        17.03        14.99        15.02        10.98 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A029 
       12.00        31.00         1.02        33.04        26.01        51.98 
TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02W 
        2.96        39.98         2.01         5.03         0.92        41.00 
TCGA-AA-A02Y TCGA-AD-5900 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       39.98        12.16        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AD-A5EK TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-A54L TCGA-AY-A69D 
       26.47        16.44        14.50        16.31        17.26        17.85 
TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4684 TCGA-AZ-5403 
       19.33        18.84         1.41         5.13        65.00        62.79 
TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 
       49.41        12.10        29.56         3.19        12.69        12.36 
TCGA-CA-5256 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 
       12.46        12.59        12.59        12.20        14.30        17.56 
TCGA-CK-4950 TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5341 
       85.45        20.02        25.02         8.02        13.02        29.06 
TCGA-CM-5348 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       22.98         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6171 TCGA-CM-6172 
       14.04        29.03        16.04        21.99        14.04        11.01 
TCGA-CM-6677 TCGA-CM-6678 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5541 
       11.08        11.01        45.40        54.61        19.59        55.92 
TCGA-D5-6529 TCGA-D5-6531 TCGA-D5-6536 TCGA-D5-6539 TCGA-D5-6898 TCGA-D5-6920 
       20.19        17.75        17.85        12.49         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-7000 TCGA-DM-A0X9 
       10.13         9.04        11.64        13.41        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A1D0 TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A282 
       24.43       130.65        12.59         7.50       131.51       139.17 
TCGA-DM-A288 TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28H TCGA-DM-A28M TCGA-F4-6459 
       14.04       119.93        35.97       117.07        95.18         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6704 TCGA-F4-6855 TCGA-G4-6293 
       31.96        35.74         6.18         1.55        47.41       133.18 
TCGA-G4-6297 TCGA-G4-6307 TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6322 TCGA-G4-6323 
       82.39        55.04        39.42        61.91        26.04        13.78 
TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A6GB TCGA-NH-A6GC TCGA-QG-A5YV 
       46.75        74.79        18.18        15.65        12.79        42.77 
TCGA-QG-A5YW TCGA-QG-A5YX TCGA-T9-A92H 
       29.46        32.98        11.90 

$`AMP PEAK 18(20P11.23) WILD-TYPE`
TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3531 
       13.02        24.03        37.05        36.03         8.05        34.03 
TCGA-AA-3543 TCGA-AA-3554 TCGA-AA-3560 TCGA-AA-3672 TCGA-AA-3697 TCGA-AA-3713 
        0.99        17.95        19.99         0.92        85.05        19.04 
TCGA-AA-3715 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3950 TCGA-AA-3952 
       19.04        31.07        24.03        29.98        24.00         2.01 
TCGA-AA-A024 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-6601 TCGA-G4-6298 
       39.06        15.52        10.88        75.95       100.01        23.51 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 TCGA-NH-A8F7 TCGA-4T-AA8H 
       22.09        35.80        26.17        79.69        17.85        12.66 
TCGA-5M-AAT6 TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2684 TCGA-A6-2685 
        9.53        46.65        42.90        42.28        37.05        37.25 
TCGA-A6-3809 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.75        32.91        31.63        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 
       22.09        22.06        32.71        22.52        24.13         8.38 
TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 
       20.61        21.76        24.39        20.12        19.66        16.24 
TCGA-A6-A566 TCGA-A6-A56B TCGA-AA-3492 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 
       24.92        56.25         3.02        37.05        35.01        63.98 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3538 TCGA-AA-3542 
       38.99         1.02         9.07        19.07        26.01        12.99 
TCGA-AA-3548 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       33.99        24.00        29.95        13.94        61.02        78.08 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3678 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3710 
        6.97        54.02        47.01        11.01         5.98        26.99 
TCGA-AA-3812 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3841 
       35.05        25.02         1.02        17.98        15.95        36.95 
TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3864 TCGA-AA-3877 
        0.00         0.00        36.03        32.05        53.00        31.00 
TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3975 TCGA-AA-3977 
        2.01        33.01        26.01        20.98        34.06        25.02 
TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       27.02        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01F 
       27.02        42.02         0.99        34.98        15.02        32.02 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01V TCGA-AA-A01Z 
       31.00        38.07         1.02        35.01         1.02        37.02 
TCGA-AA-A02R TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6889 TCGA-AM-5820 TCGA-AM-5821 
       22.03        18.05        40.96        83.24         0.46         0.92 
TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       27.09         0.95        33.01         0.20        21.44        17.82 
TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4682 TCGA-AZ-5407 
      109.28        58.39         5.65        32.94        22.36        88.21 
TCGA-AZ-6599 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-CA-5796 TCGA-CA-6717 TCGA-CA-6718 
        6.77         5.23        11.74        12.39        12.76        10.06 
TCGA-CK-4948 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
      148.01        70.16        15.62        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-4748 
       82.95         2.01       124.27        23.05        37.02        26.04 
TCGA-CM-4751 TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-6162 
       27.02        22.03        30.08        32.02        15.02        12.00 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6674 TCGA-CM-6675 
       14.99        12.99        13.02        15.02        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5540 TCGA-D5-6530 TCGA-D5-6532 
       11.08        10.06        12.03        56.09        20.42        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 
       25.48        43.27        15.12         4.80        17.13        16.14 
TCGA-D5-6541 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6930 TCGA-D5-6931 
       15.58        12.43        14.30         9.44        13.35        12.00 
TCGA-D5-6932 TCGA-DM-A0XF TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D9 
       11.38        38.20        92.75        49.91        13.32       140.38 
TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28G 
       44.32       135.65         7.76        26.47        81.37        60.79 
TCGA-DM-A28K TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 
       98.24        11.11        35.74        47.87        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6856 TCGA-G4-6295 
       43.04        33.67        13.25         0.53        35.31         8.35 
TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 
       74.56        67.30        65.85        53.62        44.68        85.48 
TCGA-G4-6317 TCGA-G4-6320 TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA 
       36.00        26.43        10.98        19.33        19.33         9.93 
TCGA-NH-A8F8 TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-RU-A8FL TCGA-SS-A7HO 
       16.80         8.42        31.30        21.90        38.70        60.13 
TCGA-WS-AB45 
       70.03 

  AMP PEAK 18(20P11.23) MUTATED AMP PEAK 18(20P11.23) WILD-TYPE 
                              0                               0 
  AMP PEAK 18(20P11.23) MUTATED AMP PEAK 18(20P11.23) WILD-TYPE 
                         139.17                          148.01 
  AMP PEAK 18(20P11.23) MUTATED AMP PEAK 18(20P11.23) WILD-TYPE 
                          19.07                           24.13 
[1] "0.0 - 139.2 (19.1)" "0.0 - 148.0 (24.1)"
[1] "hr=" "1.2"
D18V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK 18(20P11.23) MUTATED        35        1       11        57         3
  AMP PEAK 18(20P11.23) WILD-TYPE      39        0       18        75         7
                                 vv
clus                              STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 18(20P11.23) MUTATED           0         9          8         25
  AMP PEAK 18(20P11.23) WILD-TYPE         1        11          0         34
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 18(20P11.23) MUTATED           19       34        10         1
  AMP PEAK 18(20P11.23) WILD-TYPE         22       11         7         1
D18V3, multiclass
            clus
vv           AMP PEAK 18(20P11.23) MUTATED AMP PEAK 18(20P11.23) WILD-TYPE
  STAGE I                               35                              39
  STAGE IA                               1                               0
  STAGE II                              11                              18
  STAGE IIA                             57                              75
  STAGE IIB                              3                               7
  STAGE IIC                              0                               1
  STAGE III                              9                              11
  STAGE IIIA                             8                               0
  STAGE IIIB                            25                              34
  STAGE IIIC                            19                              22
  STAGE IV                              34                              11
  STAGE IVA                             10                               7
  STAGE IVB                              1                               1
[1] 13  2
[1] 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(20P11.23) MUTATED     5  39 150  24
  AMP PEAK 18(20P11.23) WILD-TYPE   6  38 155  31
D18V4, multiclass
    clus
vv   AMP PEAK 18(20P11.23) MUTATED AMP PEAK 18(20P11.23) WILD-TYPE
  T1                             5                               6
  T2                            39                              38
  T3                           150                             155
  T4                            24                              31
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               N0  N1  N2
  AMP PEAK 18(20P11.23) MUTATED   116  61  42
  AMP PEAK 18(20P11.23) WILD-TYPE 146  44  40
D18V5, multiclass
    clus
vv   AMP PEAK 18(20P11.23) MUTATED AMP PEAK 18(20P11.23) WILD-TYPE
  N0                           116                             146
  N1                            61                              44
  N2                            42                              40
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V6, binary
                                 cls
clus                                0   1
  AMP PEAK 18(20P11.23) MUTATED   148  45
  AMP PEAK 18(20P11.23) WILD-TYPE 180  19
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 18(20P11.23) MUTATED    148   45
  AMP PEAK 18(20P11.23) WILD-TYPE  180   19
   clus
vv  AMP PEAK 18(20P11.23) MUTATED AMP PEAK 18(20P11.23) WILD-TYPE
  0                           148                             180
  1                            45                              19
[1] 2 2
[1] FALSE
D18V7, binary
                                 cls
clus                                0   1
  AMP PEAK 18(20P11.23) MUTATED    98 121
  AMP PEAK 18(20P11.23) WILD-TYPE 115 115
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 18(20P11.23) MUTATED     98  121
  AMP PEAK 18(20P11.23) WILD-TYPE  115  115
        clus
vv       AMP PEAK 18(20P11.23) MUTATED AMP PEAK 18(20P11.23) WILD-TYPE
  FEMALE                            98                             115
  MALE                             121                             115
[1] 2 2
[1] FALSE
D18V8, binary
                                 cls
clus                                0   1
  AMP PEAK 18(20P11.23) MUTATED   177   6
  AMP PEAK 18(20P11.23) WILD-TYPE 193   3
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 18(20P11.23) MUTATED    177    6
  AMP PEAK 18(20P11.23) WILD-TYPE  193    3
     clus
vv    AMP PEAK 18(20P11.23) MUTATED AMP PEAK 18(20P11.23) WILD-TYPE
  NO                            177                             193
  YES                             6                               3
[1] 2 2
[1] FALSE
D18V9, binary
                                 cls
clus                                0   1
  AMP PEAK 18(20P11.23) MUTATED   197  21
  AMP PEAK 18(20P11.23) WILD-TYPE 185  41
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 18(20P11.23) MUTATED    197   21
  AMP PEAK 18(20P11.23) WILD-TYPE  185   41
                               clus
vv                              AMP PEAK 18(20P11.23) MUTATED
  COLON ADENOCARCINOMA                                    197
  COLON MUCINOUS ADENOCARCINOMA                            21
                               clus
vv                              AMP PEAK 18(20P11.23) WILD-TYPE
  COLON ADENOCARCINOMA                                      185
  COLON MUCINOUS ADENOCARCINOMA                              41
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  AMP PEAK 18(20P11.23) MUTATED   149   3  19  11
  AMP PEAK 18(20P11.23) WILD-TYPE 174   1   6  14
D18V10, multiclass
    clus
vv   AMP PEAK 18(20P11.23) MUTATED AMP PEAK 18(20P11.23) WILD-TYPE
  R0                           149                             174
  R1                             3                               1
  R2                            19                               6
  RX                            11                              14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V11, continuous
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 18(20P11.23) MUTATED                                  1     7
  AMP PEAK 18(20P11.23) WILD-TYPE                                0     4
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 18(20P11.23) MUTATED                          25   105
  AMP PEAK 18(20P11.23) WILD-TYPE                        34   107
D18V12, multiclass
                                  clus
vv                                 AMP PEAK 18(20P11.23) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        7
  BLACK OR AFRICAN AMERICAN                                   25
  WHITE                                                      105
                                  clus
vv                                 AMP PEAK 18(20P11.23) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               0
  ASIAN                                                          4
  BLACK OR AFRICAN AMERICAN                                     34
  WHITE                                                        107
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V13, binary
                                 cls
clus                                0   1
  AMP PEAK 18(20P11.23) MUTATED     2 129
  AMP PEAK 18(20P11.23) WILD-TYPE   2 140
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 18(20P11.23) MUTATED      2  129
  AMP PEAK 18(20P11.23) WILD-TYPE    2  140
                        clus
vv                       AMP PEAK 18(20P11.23) MUTATED
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                           129
                        clus
vv                       AMP PEAK 18(20P11.23) WILD-TYPE
  HISPANIC OR LATINO                                   2
  NOT HISPANIC OR LATINO                             140
[1] 2 2
[1] FALSE

Clustering(19) Variable = AMP PEAK 19(20P11.21) MUTATION ANALYSIS
D19V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 19(20P11.21) MUTATED   186  57
  AMP PEAK 19(20P11.21) WILD-TYPE 149  44
  AMP PEAK 19(20P11.21) MUTATED AMP PEAK 19(20P11.21) WILD-TYPE 
                            243                             193 
  AMP PEAK 19(20P11.21) MUTATED AMP PEAK 19(20P11.21) WILD-TYPE 
                             57                              44 
$`AMP PEAK 19(20P11.21) MUTATED`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 
       24.33        45.60        13.94        14.53        24.16         1.02 
TCGA-AA-3506 TCGA-AA-3530 TCGA-AA-3552 TCGA-AA-3556 TCGA-AA-3562 TCGA-AA-3662 
       58.03        19.07        13.02        23.01        19.99         6.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3844 TCGA-AA-3939 TCGA-AA-3972 
       19.00        36.00        85.05        14.93        12.99        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AD-6548 
       26.01        24.00        19.07        38.04        21.99        21.37 
TCGA-AD-6895 TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6294 
       25.08       106.75         1.94        49.08         5.88        28.21 
TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6625 TCGA-NH-A8F7 TCGA-3L-AA1B 
       23.51        63.62        35.93        91.79        17.85        15.62 
TCGA-4N-A93T TCGA-5M-AAT4 TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 
        4.80         1.61        39.45        43.76        43.76        43.43 
TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 
       44.91        35.11        16.57        37.02        34.65        36.53 
TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5667 TCGA-A6-6137 
       32.45        32.91        30.44        29.19        29.16        27.09 
TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6652 TCGA-A6-6782 
       22.52        24.13        25.08        25.18        24.69        20.28 
TCGA-A6-A567 TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3494 TCGA-AA-3511 
       61.84         9.63         5.03         7.04         1.02         6.97 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3542 
        1.02        38.99         0.00        29.00        29.00        12.99 
TCGA-AA-3544 TCGA-AA-3549 TCGA-AA-3558 TCGA-AA-3660 TCGA-AA-3666 TCGA-AA-3667 
       14.01        21.01        20.98        78.08         2.01        14.01 
TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3679 TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3811 
       50.04        47.05        15.02        37.05         5.03        10.06 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3846 
        0.99        25.02        38.99        37.02         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3866 TCGA-AA-3869 
       10.06        33.07         0.99        31.07        17.03        27.02 
TCGA-AA-3875 TCGA-AA-3941 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       18.05        24.00        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-A004 
       16.08        13.05        34.06        27.02         7.96        13.94 
TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01C 
       18.05         4.01        17.03        14.99        15.02        15.02 
TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A029 
       10.98        12.00        31.00        33.04        26.01        51.98 
TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02W 
        2.96        39.98         2.01         5.03         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       39.98        40.96        12.16        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        16.44        14.50        16.31         0.95 
TCGA-AY-6196 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4323 
        0.20        17.26        17.85        19.33        18.84         1.41 
TCGA-AZ-4616 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6603 
        5.13        65.00        62.79        49.41        12.10        29.56 
TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5797 TCGA-CA-6715 
        3.19        12.69        12.36        12.46        12.59        12.59 
TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-5914 TCGA-CM-4744 
       12.20        14.30        17.56        85.45        21.99        20.02 
TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       25.02         8.02        13.02        29.06        22.03        22.98 
TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       32.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6169 TCGA-CM-6170 
       14.04        29.03        16.04        21.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-D5-5537 
       14.04        11.01        11.08        11.01        10.06        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6531 TCGA-D5-6532 
       54.61        19.59        55.92        20.19        17.75        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6539 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       25.48        43.27        12.49         7.53        12.39        10.13 
TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        9.04        11.64        13.41        10.26       119.70        24.43 
TCGA-DM-A1D0 TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A288 
      130.65        12.59         7.50       131.51       139.17        14.04 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28H TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 
      119.93        35.97       117.07        95.18         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6704 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6855 
       35.74         6.18         1.55        33.67        13.25        47.41 
TCGA-G4-6293 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 
      133.18         8.35        82.39        65.85        44.68        55.04 
TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6626 TCGA-G4-6627 
       39.42        61.91        26.04        13.78        46.75        74.79 
TCGA-NH-A50T TCGA-NH-A6GB TCGA-NH-A6GC TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX 
       18.18        15.65        12.79        42.77        29.46        32.98 
TCGA-QG-A5Z1 TCGA-QL-A97D TCGA-T9-A92H 
        8.42        21.90        11.90 

$`AMP PEAK 19(20P11.21) WILD-TYPE`
TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3531 
       13.02        24.03        37.05        36.03         8.05        34.03 
TCGA-AA-3543 TCGA-AA-3554 TCGA-AA-3560 TCGA-AA-3672 TCGA-AA-3713 TCGA-AA-3715 
        0.99        17.95        19.99         0.92        19.04        19.04 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-A024 
       31.07        24.03        29.98        24.00         2.01        39.06 
TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-6601 TCGA-G4-6321 TCGA-G4-6586 
       15.52        10.88        75.95       100.01        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6628 TCGA-4T-AA8H TCGA-5M-AAT6 TCGA-A6-2672 TCGA-A6-2676 
       26.17        79.69        12.66         9.53        46.65        42.90 
TCGA-A6-2678 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-3809 TCGA-A6-5657 TCGA-A6-5661 
       42.28        37.05        37.25        32.75        31.63        33.53 
TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6141 TCGA-A6-6650 
       23.61        22.09        22.06        32.71         8.38        20.61 
TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 
       21.76        24.39        23.87        20.12        19.66        16.24 
TCGA-A6-A566 TCGA-A6-A56B TCGA-AA-3492 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 
       24.92        56.25         3.02        37.05        35.01        63.98 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3538 TCGA-AA-3548 TCGA-AA-3553 
        1.02         9.07        19.07        26.01        33.99        24.00 
TCGA-AA-3555 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3678 
       29.95        13.94        61.02         6.97        54.02        47.01 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3821 TCGA-AA-3831 
       11.01         5.98        26.99        35.05         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3841 TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       15.95        36.95         0.00         0.00        36.03        32.05 
TCGA-AA-3864 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3977 
       53.00        31.00         2.01        33.01        26.01        25.02 
TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       27.02        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A010 TCGA-AA-A01F TCGA-AA-A01K 
       27.02        42.02         0.99        34.98        32.02        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01Z 
       38.07         1.02        35.01         1.02         1.02        37.02 
TCGA-AA-A02R TCGA-AA-A03F TCGA-AD-6889 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 
       22.03        18.05        83.24         0.46         0.92        27.09 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4614 
       33.01        21.44        17.82       109.28        58.39         5.65 
TCGA-AZ-4615 TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6605 TCGA-AZ-6606 
       32.94        22.36        88.21         6.77         5.23        11.74 
TCGA-CA-5796 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4948 TCGA-CK-4951 TCGA-CK-4952 
       12.39        12.76        10.06       148.01        70.16        15.62 
TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       51.32        21.14        82.95         2.01       124.27        23.05 
TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-6162 
       37.02        26.04        27.02        30.08        15.02        12.00 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6680 
       14.99        12.99        12.95        13.05        11.08        12.03 
TCGA-D5-5540 TCGA-D5-6530 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       56.09        20.42        15.12        17.85         4.80        17.13 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6930 
       16.14        15.58        12.43        14.30         9.44        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-DM-A0XF TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       12.00        11.38        38.20        92.75        49.91        13.32 
TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A28A TCGA-DM-A28C 
      140.38        44.32       135.65         7.76        26.47        81.37 
TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6703 TCGA-F4-6805 
       60.79        98.24        11.11        35.74        47.87        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6854 TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6302 
       41.42        43.04         0.53        35.31        74.56        67.30 
TCGA-G4-6304 TCGA-G4-6309 TCGA-G4-6317 TCGA-G4-6320 TCGA-NH-A50U TCGA-NH-A50V 
       53.62        85.48        36.00        26.43        10.98        19.33 
TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A8F8 TCGA-QG-A5Z2 TCGA-RU-A8FL TCGA-SS-A7HO 
       19.33         9.93        16.80        31.30        38.70        60.13 
TCGA-WS-AB45 
       70.03 

  AMP PEAK 19(20P11.21) MUTATED AMP PEAK 19(20P11.21) WILD-TYPE 
                              0                               0 
  AMP PEAK 19(20P11.21) MUTATED AMP PEAK 19(20P11.21) WILD-TYPE 
                         139.17                          148.01 
  AMP PEAK 19(20P11.21) MUTATED AMP PEAK 19(20P11.21) WILD-TYPE 
                          20.19                           24.39 
[1] "0.0 - 139.2 (20.2)" "0.0 - 148.0 (24.4)"
[1] "hr=" "1.1"
D19V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK 19(20P11.21) MUTATED        43        1       15        66         3
  AMP PEAK 19(20P11.21) WILD-TYPE      31        0       14        66         7
                                 vv
clus                              STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 19(20P11.21) MUTATED           0         8          8         29
  AMP PEAK 19(20P11.21) WILD-TYPE         1        12          0         30
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 19(20P11.21) MUTATED           22       36        11         1
  AMP PEAK 19(20P11.21) WILD-TYPE         19        9         6         1
D19V3, multiclass
            clus
vv           AMP PEAK 19(20P11.21) MUTATED AMP PEAK 19(20P11.21) WILD-TYPE
  STAGE I                               43                              31
  STAGE IA                               1                               0
  STAGE II                              15                              14
  STAGE IIA                             66                              66
  STAGE IIB                              3                               7
  STAGE IIC                              0                               1
  STAGE III                              8                              12
  STAGE IIIA                             8                               0
  STAGE IIIB                            29                              30
  STAGE IIIC                            22                              19
  STAGE IV                              36                               9
  STAGE IVA                             11                               6
  STAGE IVB                              1                               1
[1] 13  2
[1] 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(20P11.21) MUTATED     7  47 169  27
  AMP PEAK 19(20P11.21) WILD-TYPE   4  30 136  28
D19V4, multiclass
    clus
vv   AMP PEAK 19(20P11.21) MUTATED AMP PEAK 19(20P11.21) WILD-TYPE
  T1                             7                               4
  T2                            47                              30
  T3                           169                             136
  T4                            27                              28
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               N0  N1  N2
  AMP PEAK 19(20P11.21) MUTATED   139  66  46
  AMP PEAK 19(20P11.21) WILD-TYPE 123  39  36
D19V5, multiclass
    clus
vv   AMP PEAK 19(20P11.21) MUTATED AMP PEAK 19(20P11.21) WILD-TYPE
  N0                           139                             123
  N1                            66                              39
  N2                            46                              36
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V6, binary
                                 cls
clus                                0   1
  AMP PEAK 19(20P11.21) MUTATED   170  48
  AMP PEAK 19(20P11.21) WILD-TYPE 158  16
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 19(20P11.21) MUTATED    170   48
  AMP PEAK 19(20P11.21) WILD-TYPE  158   16
   clus
vv  AMP PEAK 19(20P11.21) MUTATED AMP PEAK 19(20P11.21) WILD-TYPE
  0                           170                             158
  1                            48                              16
[1] 2 2
[1] FALSE
D19V7, binary
                                 cls
clus                                0   1
  AMP PEAK 19(20P11.21) MUTATED   112 139
  AMP PEAK 19(20P11.21) WILD-TYPE 101  97
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 19(20P11.21) MUTATED    112  139
  AMP PEAK 19(20P11.21) WILD-TYPE  101   97
        clus
vv       AMP PEAK 19(20P11.21) MUTATED AMP PEAK 19(20P11.21) WILD-TYPE
  FEMALE                           112                             101
  MALE                             139                              97
[1] 2 2
[1] FALSE
D19V8, binary
                                 cls
clus                                0   1
  AMP PEAK 19(20P11.21) MUTATED   205   7
  AMP PEAK 19(20P11.21) WILD-TYPE 165   2
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 19(20P11.21) MUTATED    205    7
  AMP PEAK 19(20P11.21) WILD-TYPE  165    2
     clus
vv    AMP PEAK 19(20P11.21) MUTATED AMP PEAK 19(20P11.21) WILD-TYPE
  NO                            205                             165
  YES                             7                               2
[1] 2 2
[1] FALSE
D19V9, binary
                                 cls
clus                                0   1
  AMP PEAK 19(20P11.21) MUTATED   226  23
  AMP PEAK 19(20P11.21) WILD-TYPE 156  39
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 19(20P11.21) MUTATED    226   23
  AMP PEAK 19(20P11.21) WILD-TYPE  156   39
                               clus
vv                              AMP PEAK 19(20P11.21) MUTATED
  COLON ADENOCARCINOMA                                    226
  COLON MUCINOUS ADENOCARCINOMA                            23
                               clus
vv                              AMP PEAK 19(20P11.21) WILD-TYPE
  COLON ADENOCARCINOMA                                      156
  COLON MUCINOUS ADENOCARCINOMA                              39
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  AMP PEAK 19(20P11.21) MUTATED   174   3  20  12
  AMP PEAK 19(20P11.21) WILD-TYPE 149   1   5  13
D19V10, multiclass
    clus
vv   AMP PEAK 19(20P11.21) MUTATED AMP PEAK 19(20P11.21) WILD-TYPE
  R0                           174                             149
  R1                             3                               1
  R2                            20                               5
  RX                            12                              13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V11, continuous
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 19(20P11.21) MUTATED                                  1     7
  AMP PEAK 19(20P11.21) WILD-TYPE                                0     4
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 19(20P11.21) MUTATED                          31   121
  AMP PEAK 19(20P11.21) WILD-TYPE                        28    91
D19V12, multiclass
                                  clus
vv                                 AMP PEAK 19(20P11.21) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        7
  BLACK OR AFRICAN AMERICAN                                   31
  WHITE                                                      121
                                  clus
vv                                 AMP PEAK 19(20P11.21) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               0
  ASIAN                                                          4
  BLACK OR AFRICAN AMERICAN                                     28
  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"
D19V13, binary
                                 cls
clus                                0   1
  AMP PEAK 19(20P11.21) MUTATED     3 149
  AMP PEAK 19(20P11.21) WILD-TYPE   1 120
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 19(20P11.21) MUTATED      3  149
  AMP PEAK 19(20P11.21) WILD-TYPE    1  120
                        clus
vv                       AMP PEAK 19(20P11.21) MUTATED
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           149
                        clus
vv                       AMP PEAK 19(20P11.21) WILD-TYPE
  HISPANIC OR LATINO                                   1
  NOT HISPANIC OR LATINO                             120
[1] 2 2
[1] FALSE

Clustering(20) Variable = AMP PEAK 20(20Q11.21) MUTATION ANALYSIS
D20V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 20(20Q11.21) MUTATED   243  69
  AMP PEAK 20(20Q11.21) WILD-TYPE  92  32
  AMP PEAK 20(20Q11.21) MUTATED AMP PEAK 20(20Q11.21) WILD-TYPE 
                            312                             124 
  AMP PEAK 20(20Q11.21) MUTATED AMP PEAK 20(20Q11.21) WILD-TYPE 
                             69                              32 
$`AMP PEAK 20(20Q11.21) MUTATED`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 
       24.33        45.60        13.94        14.53        24.16         1.02 
TCGA-AA-3506 TCGA-AA-3524 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3552 TCGA-AA-3556 
       58.03        36.03        19.07        34.03        13.02        23.01 
TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 
       19.99        19.99         6.05        19.00        36.00        85.05 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3939 TCGA-AA-3972 TCGA-AA-3976 
       14.93        31.07        24.03        12.99        50.99        26.01 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AD-6548 TCGA-AD-6888 
       24.00        19.07        38.04        21.99        21.37        15.52 
TCGA-AD-6895 TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6294 
       25.08       106.75         1.94        49.08         5.88        28.21 
TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6625 TCGA-NH-A8F7 TCGA-3L-AA1B 
       23.51        63.62        35.93        91.79        17.85        15.62 
TCGA-4N-A93T TCGA-5M-AAT4 TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 
        4.80         1.61        39.45        43.76        43.76        43.43 
TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 
       44.91        35.11        16.57        37.25        37.02        34.65 
TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 
       36.53        32.45        32.91        30.44        29.19        23.61 
TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6142 
       32.71        29.16        27.09        22.52        24.13        25.08 
TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6782 
       25.18        20.61        21.76        24.69        23.87        20.28 
TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3494 
       61.84        56.25         9.63         5.03         7.04         1.02 
TCGA-AA-3495 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3526 
       37.05         6.97         1.02        38.99         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3660 
       33.99        21.01        24.00        20.98        13.94        78.08 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01        50.04        47.05        47.01        15.02 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
        5.98        37.05         5.03        10.06        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3846 
       25.02        38.99        36.95        37.02         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3866 
       10.06        33.07        32.05         0.99        31.07        17.03 
TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3941 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       27.02        18.05        24.00        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3982 TCGA-AA-3989 
       21.99        16.08        13.05        34.06        27.02         7.96 
TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O 
       13.94        19.00        34.03        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D 
       42.02        17.03        14.99        15.02        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01S TCGA-AA-A01T 
       32.02        12.00        31.00        31.00         1.02        33.04 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        51.98         2.96        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03J TCGA-AD-5900 
        5.03         0.92        41.00        39.98        40.96        12.16 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK 
       24.53         5.79        22.42        27.42        26.47        16.44 
TCGA-AM-5820 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
        0.46        14.50        16.31         0.95        33.01         0.20 
TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4323 
       17.26        17.85        19.33        18.84       109.28         1.41 
TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6600 
        5.13        22.36        65.00        62.79        49.41        12.10 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 
       29.56         5.23         3.19        12.69        12.36        12.46 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        12.59        12.20        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-5914 TCGA-CK-6748 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
       85.45        21.99         2.01        20.02        37.02        25.02 
TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
        8.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       32.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6676 TCGA-CM-6677 
       13.02        15.02        14.04        11.01        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       11.01        10.06        45.40        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       55.92        20.19        17.75        18.25        25.48        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6898 
       15.12        17.85         4.80        17.13        12.49         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6928 
       12.39        10.13        12.43        14.30         9.04        11.64 
TCGA-D5-6929 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       13.41        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1DA 
      130.65        92.75        49.91        13.32        12.59         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28E 
       44.32       131.51       139.17        14.04        26.47       119.93 
TCGA-DM-A28F TCGA-DM-A28H TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6463 
       35.97       117.07        95.18         8.61        31.96        35.74 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6704 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.74         6.18         1.55        41.42        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6295 TCGA-G4-6297 
       13.25         0.53        47.41       133.18         8.35        82.39 
TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6317 
       65.85        44.68        55.04        39.42        61.91        36.00 
TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T 
       26.43        26.04        13.78        46.75        74.79        18.18 
TCGA-NH-A50V TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW 
       19.33        15.65        12.79        16.80        42.77        29.46 
TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QL-A97D TCGA-RU-A8FL TCGA-SS-A7HO TCGA-T9-A92H 
       32.98         8.42        21.90        38.70        60.13        11.90 

$`AMP PEAK 20(20Q11.21) WILD-TYPE`
TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3525 TCGA-AA-3543 TCGA-AA-3554 
       13.02        24.03        37.05         8.05         0.99        17.95 
TCGA-AA-3672 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3870 TCGA-AA-3950 TCGA-AA-3952 
        0.92        19.04        19.04        29.98        24.00         2.01 
TCGA-AA-A024 TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-6601 TCGA-G4-6321 TCGA-G4-6586 
       39.06        10.88        75.95       100.01        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6628 TCGA-4T-AA8H TCGA-5M-AAT6 TCGA-A6-2672 TCGA-A6-2676 
       26.17        79.69        12.66         9.53        46.65        42.90 
TCGA-A6-2678 TCGA-A6-2684 TCGA-A6-3809 TCGA-A6-5657 TCGA-A6-5661 TCGA-A6-5664 
       42.28        37.05        32.75        31.63        33.53        22.09 
TCGA-A6-5665 TCGA-A6-6141 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 
       22.06         8.38        24.39        20.12        19.66        16.24 
TCGA-A6-A566 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3518 TCGA-AA-3555 
       24.92         3.02        35.01        63.98         1.02        29.95 
TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3680 TCGA-AA-3710 TCGA-AA-3821 
       61.02         6.97        54.02        11.01        26.99         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3864 
       17.98        15.95         0.00         0.00        36.03        53.00 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3977 TCGA-AA-3994 
       31.00         2.01        33.01        26.01        25.02        27.02 
TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00R TCGA-AA-A010 TCGA-AA-A01P 
       38.04        30.02        18.05         0.99        34.98        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01V TCGA-AA-A02R TCGA-AA-A03F TCGA-AD-6889 
        1.02        35.01         1.02        22.03        18.05        83.24 
TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4614 
        0.92        27.09        21.44        17.82        58.39         5.65 
TCGA-AZ-4615 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6606 TCGA-CA-5796 TCGA-CA-6717 
       32.94        88.21         6.77        11.74        12.39        12.76 
TCGA-CA-6718 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 
       10.06        70.16        15.62        51.32        21.14        82.95 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-5861 TCGA-CM-6162 
      124.27        23.05        26.04        27.02        15.02        12.00 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6680 TCGA-D5-6530 TCGA-D5-6540 TCGA-D5-6541 
       12.95        13.05        12.03        20.42        16.14        15.58 
TCGA-D5-6927 TCGA-D5-6930 TCGA-D5-6931 TCGA-DM-A1D9 TCGA-DM-A1HB TCGA-DM-A280 
        9.44        13.35        12.00       140.38       135.65         7.76 
TCGA-DM-A28C TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6461 TCGA-F4-6703 TCGA-F4-6805 
       81.37        60.79        98.24        11.11        47.87        34.42 
TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6309 TCGA-NH-A50U 
       35.31        74.56        67.30        53.62        85.48        10.98 
TCGA-NH-A5IV TCGA-NH-A6GA TCGA-QG-A5Z2 TCGA-WS-AB45 
       19.33         9.93        31.30        70.03 

  AMP PEAK 20(20Q11.21) MUTATED AMP PEAK 20(20Q11.21) WILD-TYPE 
                              0                               0 
  AMP PEAK 20(20Q11.21) MUTATED AMP PEAK 20(20Q11.21) WILD-TYPE 
                         148.01                          140.38 
  AMP PEAK 20(20Q11.21) MUTATED AMP PEAK 20(20Q11.21) WILD-TYPE 
                         21.990                          23.525 
[1] "0.0 - 148.0 (22.0)" "0.0 - 140.4 (23.5)"
[1] "hr=" "1"  
D20V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK 20(20Q11.21) MUTATED        53        1       17        85         4
  AMP PEAK 20(20Q11.21) WILD-TYPE      21        0       12        47         6
                                 vv
clus                              STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 20(20Q11.21) MUTATED           1        14          8         43
  AMP PEAK 20(20Q11.21) WILD-TYPE         0         6          0         16
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 20(20Q11.21) MUTATED           32       39        15         1
  AMP PEAK 20(20Q11.21) WILD-TYPE          9        6         2         1
D20V3, multiclass
            clus
vv           AMP PEAK 20(20Q11.21) MUTATED AMP PEAK 20(20Q11.21) WILD-TYPE
  STAGE I                               53                              21
  STAGE IA                               1                               0
  STAGE II                              17                              12
  STAGE IIA                             85                              47
  STAGE IIB                              4                               6
  STAGE IIC                              1                               0
  STAGE III                             14                               6
  STAGE IIIA                             8                               0
  STAGE IIIB                            43                              16
  STAGE IIIC                            32                               9
  STAGE IV                              39                               6
  STAGE IVA                             15                               2
  STAGE IVB                              1                               1
[1] 13  2
[1] 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(20Q11.21) MUTATED     7  58 222  33
  AMP PEAK 20(20Q11.21) WILD-TYPE   4  19  83  22
D20V4, multiclass
    clus
vv   AMP PEAK 20(20Q11.21) MUTATED AMP PEAK 20(20Q11.21) WILD-TYPE
  T1                             7                               4
  T2                            58                              19
  T3                           222                              83
  T4                            33                              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               N0  N1  N2
  AMP PEAK 20(20Q11.21) MUTATED   173  85  63
  AMP PEAK 20(20Q11.21) WILD-TYPE  89  20  19
D20V5, multiclass
    clus
vv   AMP PEAK 20(20Q11.21) MUTATED AMP PEAK 20(20Q11.21) WILD-TYPE
  N0                           173                              89
  N1                            85                              20
  N2                            63                              19
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V6, binary
                                 cls
clus                                0   1
  AMP PEAK 20(20Q11.21) MUTATED   227  55
  AMP PEAK 20(20Q11.21) WILD-TYPE 101   9
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 20(20Q11.21) MUTATED    227   55
  AMP PEAK 20(20Q11.21) WILD-TYPE  101    9
   clus
vv  AMP PEAK 20(20Q11.21) MUTATED AMP PEAK 20(20Q11.21) WILD-TYPE
  0                           227                             101
  1                            55                               9
[1] 2 2
[1] FALSE
D20V7, binary
                                 cls
clus                                0   1
  AMP PEAK 20(20Q11.21) MUTATED   146 175
  AMP PEAK 20(20Q11.21) WILD-TYPE  67  61
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 20(20Q11.21) MUTATED    146  175
  AMP PEAK 20(20Q11.21) WILD-TYPE   67   61
        clus
vv       AMP PEAK 20(20Q11.21) MUTATED AMP PEAK 20(20Q11.21) WILD-TYPE
  FEMALE                           146                              67
  MALE                             175                              61
[1] 2 2
[1] FALSE
D20V8, binary
                                 cls
clus                                0   1
  AMP PEAK 20(20Q11.21) MUTATED   266   7
  AMP PEAK 20(20Q11.21) WILD-TYPE 104   2
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 20(20Q11.21) MUTATED    266    7
  AMP PEAK 20(20Q11.21) WILD-TYPE  104    2
     clus
vv    AMP PEAK 20(20Q11.21) MUTATED AMP PEAK 20(20Q11.21) WILD-TYPE
  NO                            266                             104
  YES                             7                               2
[1] 2 2
[1] FALSE
D20V9, binary
                                 cls
clus                                0   1
  AMP PEAK 20(20Q11.21) MUTATED   291  26
  AMP PEAK 20(20Q11.21) WILD-TYPE  91  36
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 20(20Q11.21) MUTATED    291   26
  AMP PEAK 20(20Q11.21) WILD-TYPE   91   36
                               clus
vv                              AMP PEAK 20(20Q11.21) MUTATED
  COLON ADENOCARCINOMA                                    291
  COLON MUCINOUS ADENOCARCINOMA                            26
                               clus
vv                              AMP PEAK 20(20Q11.21) WILD-TYPE
  COLON ADENOCARCINOMA                                       91
  COLON MUCINOUS ADENOCARCINOMA                              36
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  AMP PEAK 20(20Q11.21) MUTATED   229   3  21  14
  AMP PEAK 20(20Q11.21) WILD-TYPE  94   1   4  11
D20V10, multiclass
    clus
vv   AMP PEAK 20(20Q11.21) MUTATED AMP PEAK 20(20Q11.21) WILD-TYPE
  R0                           229                              94
  R1                             3                               1
  R2                            21                               4
  RX                            14                              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"
D20V11, continuous
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 20(20Q11.21) MUTATED                                  1     7
  AMP PEAK 20(20Q11.21) WILD-TYPE                                0     4
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 20(20Q11.21) MUTATED                          42   154
  AMP PEAK 20(20Q11.21) WILD-TYPE                        17    58
D20V12, multiclass
                                  clus
vv                                 AMP PEAK 20(20Q11.21) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        7
  BLACK OR AFRICAN AMERICAN                                   42
  WHITE                                                      154
                                  clus
vv                                 AMP PEAK 20(20Q11.21) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               0
  ASIAN                                                          4
  BLACK OR AFRICAN AMERICAN                                     17
  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"
D20V13, binary
                                 cls
clus                                0   1
  AMP PEAK 20(20Q11.21) MUTATED     3 193
  AMP PEAK 20(20Q11.21) WILD-TYPE   1  76
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 20(20Q11.21) MUTATED      3  193
  AMP PEAK 20(20Q11.21) WILD-TYPE    1   76
                        clus
vv                       AMP PEAK 20(20Q11.21) MUTATED
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           193
                        clus
vv                       AMP PEAK 20(20Q11.21) WILD-TYPE
  HISPANIC OR LATINO                                   1
  NOT HISPANIC OR LATINO                              76
[1] 2 2
[1] FALSE

Clustering(21) Variable = AMP PEAK 21(20Q12) MUTATION ANALYSIS
D21V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 21(20Q12) MUTATED   244  69
  AMP PEAK 21(20Q12) WILD-TYPE  91  32
  AMP PEAK 21(20Q12) MUTATED AMP PEAK 21(20Q12) WILD-TYPE 
                         313                          123 
  AMP PEAK 21(20Q12) MUTATED AMP PEAK 21(20Q12) WILD-TYPE 
                          69                           32 
$`AMP PEAK 21(20Q12) MUTATED`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 
       24.33        45.60        13.94        14.53        24.16         1.02 
TCGA-AA-3506 TCGA-AA-3524 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3552 TCGA-AA-3556 
       58.03        36.03        19.07        34.03        13.02        23.01 
TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 
       19.99        19.99         6.05        19.00        36.00        85.05 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3939 TCGA-AA-3972 TCGA-AA-3976 
       14.93        31.07        24.03        12.99        50.99        26.01 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AD-6548 TCGA-AD-6888 
       24.00        19.07        38.04        21.99        21.37        15.52 
TCGA-AD-6895 TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6294 
       25.08       106.75         1.94        49.08         5.88        28.21 
TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6625 TCGA-NH-A8F7 TCGA-3L-AA1B 
       23.51        63.62        35.93        91.79        17.85        15.62 
TCGA-4N-A93T TCGA-5M-AAT4 TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 
        4.80         1.61        39.45        43.76        43.76        43.43 
TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 
       44.91        35.11        16.57        37.25        37.02        34.65 
TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 
       36.53        32.45        32.91        30.44        29.19        23.61 
TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6142 
       32.71        29.16        27.09        22.52        24.13        25.08 
TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6782 
       25.18        20.61        21.76        24.69        23.87        20.28 
TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3494 
       61.84        56.25         9.63         5.03         7.04         1.02 
TCGA-AA-3495 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3526 
       37.05         6.97         1.02        38.99         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3660 
       33.99        21.01        24.00        20.98        13.94        78.08 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01        50.04        47.05        47.01        15.02 
TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
       37.05         5.03        10.06        35.05         0.99        25.02 
TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        36.95        37.02         0.00        17.03        10.06 
TCGA-AA-3851 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3866 TCGA-AA-3869 
       33.07        32.05         0.99        31.07        17.03        27.02 
TCGA-AA-3875 TCGA-AA-3941 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       18.05        24.00        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-A004 
       16.08        13.05        34.06        27.02         7.96        13.94 
TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       19.00        34.03        18.05         4.01        27.02        42.02 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01G 
       17.03        14.99        15.02        15.02        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A01Z 
       31.00        31.00         1.02        33.04        26.01        37.02 
TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O 
       51.98         2.96        39.98         2.01         5.03         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6890 TCGA-AD-6899 
       41.00        39.98        40.96        12.16        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AU-3779 
       22.42        27.42        26.47        16.44         0.46        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-A54L TCGA-AY-A69D 
       16.31         0.95        33.01         0.20        17.26        17.85 
TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4616 
       19.33        18.84       109.28         1.41         5.65         5.13 
TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6603 
       22.36        65.00        62.79        49.41        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5797 
        5.23         3.19        12.69        12.36        12.46        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.59        12.20        14.30        17.56       148.01        85.45 
TCGA-CK-5914 TCGA-CK-6748 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4750 
       21.99         2.01        20.02        37.02        25.02         8.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 
        5.03        15.02        15.02        17.03        15.02        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       15.02        14.04        11.01        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       10.06        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       20.19        17.75        18.25        25.48        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6898 TCGA-D5-6920 
       17.85         4.80        17.13        12.49         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6929 
       10.13        12.43        14.30         9.04        11.64        13.41 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A1DB 
       92.75        49.91        13.32        12.59         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28E TCGA-DM-A28F 
      131.51       139.17        14.04        26.47       119.93        35.97 
TCGA-DM-A28H TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6463 TCGA-F4-6569 
      117.07        95.18         8.61        31.96        35.74        35.74 
TCGA-F4-6570 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
        6.18         1.55        34.42        41.42        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6295 TCGA-G4-6297 
       13.25         0.53        47.41       133.18         8.35        82.39 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6311 TCGA-G4-6315 
       74.56        65.85        44.68        55.04        39.42        61.91 
TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6626 TCGA-G4-6627 
       36.00        26.43        26.04        13.78        46.75        74.79 
TCGA-NH-A50T TCGA-NH-A50V TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F8 TCGA-QG-A5YV 
       18.18        19.33        15.65        12.79        16.80        42.77 
TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QL-A97D TCGA-RU-A8FL TCGA-SS-A7HO 
       29.46        32.98         8.42        21.90        38.70        60.13 
TCGA-T9-A92H 
       11.90 

$`AMP PEAK 21(20Q12) WILD-TYPE`
TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3525 TCGA-AA-3543 TCGA-AA-3554 
       13.02        24.03        37.05         8.05         0.99        17.95 
TCGA-AA-3672 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3870 TCGA-AA-3950 TCGA-AA-3952 
        0.92        19.04        19.04        29.98        24.00         2.01 
TCGA-AA-A024 TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-6601 TCGA-G4-6321 TCGA-G4-6586 
       39.06        10.88        75.95       100.01        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6628 TCGA-4T-AA8H TCGA-5M-AAT6 TCGA-A6-2672 TCGA-A6-2676 
       26.17        79.69        12.66         9.53        46.65        42.90 
TCGA-A6-2678 TCGA-A6-2684 TCGA-A6-3809 TCGA-A6-5657 TCGA-A6-5661 TCGA-A6-5664 
       42.28        37.05        32.75        31.63        33.53        22.09 
TCGA-A6-5665 TCGA-A6-6141 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 
       22.06         8.38        24.39        20.12        19.66        16.24 
TCGA-A6-A566 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3518 TCGA-AA-3555 
       24.92         3.02        35.01        63.98         1.02        29.95 
TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3710 
       61.02         6.97        54.02        11.01         5.98        26.99 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3854 
        1.02        17.98        15.95         0.00         0.00        36.03 
TCGA-AA-3864 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3977 
       53.00        31.00         2.01        33.01        26.01        25.02 
TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00R TCGA-AA-A010 
       27.02        38.04        30.02        18.05         0.99        34.98 
TCGA-AA-A01D TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01V TCGA-AA-A02R 
       10.98        38.07         1.02        35.01         1.02        22.03 
TCGA-AA-A03F TCGA-AD-6889 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-6197 TCGA-AY-6386 
       18.05        83.24         0.92        27.09        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4615 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6606 TCGA-CA-5796 
       58.39        32.94        88.21         6.77        11.74        12.39 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5916 
       12.76        10.06        70.16        15.62        51.32        21.14 
TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-5861 
       82.95       124.27        23.05        26.04        27.02        15.02 
TCGA-CM-6162 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6680 TCGA-D5-6530 TCGA-D5-6540 
       12.00        12.95        13.05        12.03        20.42        16.14 
TCGA-D5-6541 TCGA-D5-6927 TCGA-D5-6930 TCGA-D5-6931 TCGA-DM-A1D9 TCGA-DM-A1HB 
       15.58         9.44        13.35        12.00       140.38       135.65 
TCGA-DM-A280 TCGA-DM-A28C TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6461 TCGA-F4-6703 
        7.76        81.37        60.79        98.24        11.11        47.87 
TCGA-F4-6856 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6309 TCGA-NH-A50U TCGA-NH-A5IV 
       35.31        67.30        53.62        85.48        10.98        19.33 
TCGA-NH-A6GA TCGA-QG-A5Z2 TCGA-WS-AB45 
        9.93        31.30        70.03 

  AMP PEAK 21(20Q12) MUTATED AMP PEAK 21(20Q12) WILD-TYPE 
                           0                            0 
  AMP PEAK 21(20Q12) MUTATED AMP PEAK 21(20Q12) WILD-TYPE 
                      148.01                       140.38 
  AMP PEAK 21(20Q12) MUTATED AMP PEAK 21(20Q12) WILD-TYPE 
                       21.99                        22.09 
[1] "0.0 - 148.0 (22.0)" "0.0 - 140.4 (22.1)"
[1] "hr=" "1.1"
D21V2, continuous
                              vv
clus                           STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK 21(20Q12) MUTATED        53        1       17        86         4
  AMP PEAK 21(20Q12) WILD-TYPE      21        0       12        46         6
                              vv
clus                           STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 21(20Q12) MUTATED           1        13          8         43
  AMP PEAK 21(20Q12) WILD-TYPE         0         7          0         16
                              vv
clus                           STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 21(20Q12) MUTATED           32       39        16         1
  AMP PEAK 21(20Q12) WILD-TYPE          9        6         1         1
D21V3, multiclass
            clus
vv           AMP PEAK 21(20Q12) MUTATED AMP PEAK 21(20Q12) WILD-TYPE
  STAGE I                            53                           21
  STAGE IA                            1                            0
  STAGE II                           17                           12
  STAGE IIA                          86                           46
  STAGE IIB                           4                            6
  STAGE IIC                           1                            0
  STAGE III                          13                            7
  STAGE IIIA                          8                            0
  STAGE IIIB                         43                           16
  STAGE IIIC                         32                            9
  STAGE IV                           39                            6
  STAGE IVA                          16                            1
  STAGE IVB                           1                            1
[1] 13  2
[1] 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(20Q12) MUTATED     7  58 222  34
  AMP PEAK 21(20Q12) WILD-TYPE   4  19  83  21
D21V4, multiclass
    clus
vv   AMP PEAK 21(20Q12) MUTATED AMP PEAK 21(20Q12) WILD-TYPE
  T1                          7                            4
  T2                         58                           19
  T3                        222                           83
  T4                         34                           21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            N0  N1  N2
  AMP PEAK 21(20Q12) MUTATED   174  85  63
  AMP PEAK 21(20Q12) WILD-TYPE  88  20  19
D21V5, multiclass
    clus
vv   AMP PEAK 21(20Q12) MUTATED AMP PEAK 21(20Q12) WILD-TYPE
  N0                        174                           88
  N1                         85                           20
  N2                         63                           19
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V6, binary
                              cls
clus                             0   1
  AMP PEAK 21(20Q12) MUTATED   227  56
  AMP PEAK 21(20Q12) WILD-TYPE 101   8
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 21(20Q12) MUTATED    227   56
  AMP PEAK 21(20Q12) WILD-TYPE  101    8
   clus
vv  AMP PEAK 21(20Q12) MUTATED AMP PEAK 21(20Q12) WILD-TYPE
  0                        227                          101
  1                         56                            8
[1] 2 2
[1] FALSE
D21V7, binary
                              cls
clus                             0   1
  AMP PEAK 21(20Q12) MUTATED   146 176
  AMP PEAK 21(20Q12) WILD-TYPE  67  60
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 21(20Q12) MUTATED    146  176
  AMP PEAK 21(20Q12) WILD-TYPE   67   60
        clus
vv       AMP PEAK 21(20Q12) MUTATED AMP PEAK 21(20Q12) WILD-TYPE
  FEMALE                        146                           67
  MALE                          176                           60
[1] 2 2
[1] FALSE
D21V8, binary
                              cls
clus                             0   1
  AMP PEAK 21(20Q12) MUTATED   267   7
  AMP PEAK 21(20Q12) WILD-TYPE 103   2
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 21(20Q12) MUTATED    267    7
  AMP PEAK 21(20Q12) WILD-TYPE  103    2
     clus
vv    AMP PEAK 21(20Q12) MUTATED AMP PEAK 21(20Q12) WILD-TYPE
  NO                         267                          103
  YES                          7                            2
[1] 2 2
[1] FALSE
D21V9, binary
                              cls
clus                             0   1
  AMP PEAK 21(20Q12) MUTATED   293  25
  AMP PEAK 21(20Q12) WILD-TYPE  89  37
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 21(20Q12) MUTATED    293   25
  AMP PEAK 21(20Q12) WILD-TYPE   89   37
                               clus
vv                              AMP PEAK 21(20Q12) MUTATED
  COLON ADENOCARCINOMA                                 293
  COLON MUCINOUS ADENOCARCINOMA                         25
                               clus
vv                              AMP PEAK 21(20Q12) WILD-TYPE
  COLON ADENOCARCINOMA                                    89
  COLON MUCINOUS ADENOCARCINOMA                           37
[1] 2 2
[1] FALSE
                              vv
clus                            R0  R1  R2  RX
  AMP PEAK 21(20Q12) MUTATED   230   3  21  14
  AMP PEAK 21(20Q12) WILD-TYPE  93   1   4  11
D21V10, multiclass
    clus
vv   AMP PEAK 21(20Q12) MUTATED AMP PEAK 21(20Q12) WILD-TYPE
  R0                        230                           93
  R1                          3                            1
  R2                         21                            4
  RX                         14                           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"
D21V11, continuous
                              vv
clus                           AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 21(20Q12) MUTATED                                  1     7
  AMP PEAK 21(20Q12) WILD-TYPE                                0     4
                              vv
clus                           BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 21(20Q12) MUTATED                          42   157
  AMP PEAK 21(20Q12) WILD-TYPE                        17    55
D21V12, multiclass
                                  clus
vv                                 AMP PEAK 21(20Q12) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          1
  ASIAN                                                     7
  BLACK OR AFRICAN AMERICAN                                42
  WHITE                                                   157
                                  clus
vv                                 AMP PEAK 21(20Q12) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       4
  BLACK OR AFRICAN AMERICAN                                  17
  WHITE                                                      55
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V13, binary
                              cls
clus                             0   1
  AMP PEAK 21(20Q12) MUTATED     3 196
  AMP PEAK 21(20Q12) WILD-TYPE   1  73
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 21(20Q12) MUTATED      3  196
  AMP PEAK 21(20Q12) WILD-TYPE    1   73
                        clus
vv                       AMP PEAK 21(20Q12) MUTATED
  HISPANIC OR LATINO                              3
  NOT HISPANIC OR LATINO                        196
                        clus
vv                       AMP PEAK 21(20Q12) WILD-TYPE
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           73
[1] 2 2
[1] FALSE

Clustering(22) Variable = AMP PEAK 22(20Q13.12) MUTATION ANALYSIS
D22V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 22(20Q13.12) MUTATED   244  71
  AMP PEAK 22(20Q13.12) WILD-TYPE  91  30
  AMP PEAK 22(20Q13.12) MUTATED AMP PEAK 22(20Q13.12) WILD-TYPE 
                            315                             121 
  AMP PEAK 22(20Q13.12) MUTATED AMP PEAK 22(20Q13.12) WILD-TYPE 
                             71                              30 
$`AMP PEAK 22(20Q13.12) MUTATED`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 
       24.33        45.60        13.94        14.53        24.16         1.02 
TCGA-AA-3506 TCGA-AA-3524 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3552 TCGA-AA-3556 
       58.03        36.03        19.07        34.03        13.02        23.01 
TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 
       19.99        19.99         6.05        19.00        36.00        85.05 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3939 TCGA-AA-3972 TCGA-AA-3976 
       14.93        31.07        24.03        12.99        50.99        26.01 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AD-6548 TCGA-AD-6888 
       24.00        19.07        38.04        21.99        21.37        15.52 
TCGA-AD-6895 TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6294 
       25.08       106.75         1.94        49.08         5.88        28.21 
TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6625 TCGA-NH-A8F7 TCGA-3L-AA1B 
       23.51        63.62        35.93        91.79        17.85        15.62 
TCGA-4N-A93T TCGA-5M-AAT4 TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 
        4.80         1.61        39.45        43.76        43.76        43.43 
TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 
       44.91        35.11        16.57        37.25        37.02        34.65 
TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 
       36.53        32.45        32.91        30.44        29.19        23.61 
TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6142 
       32.71        29.16        27.09        22.52        24.13        25.08 
TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6782 
       25.18        20.61        21.76        24.69        23.87        20.28 
TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3494 
       61.84        56.25         9.63         5.03         7.04         1.02 
TCGA-AA-3495 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3526 
       37.05         6.97         1.02        38.99         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3660 
       33.99        21.01        24.00        20.98        13.94        78.08 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 
       54.02         2.01        14.01        50.04        47.05        47.01 
TCGA-AA-3679 TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
       15.02        37.05         5.03        10.06        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3846 
       25.02        38.99        36.95        37.02         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3866 
       10.06        33.07        32.05         0.99        31.07        17.03 
TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3941 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       27.02        18.05        24.00        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3982 TCGA-AA-3989 
       21.99        16.08        13.05        34.06        27.02         7.96 
TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O 
       13.94        19.00        34.03        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D 
       42.02        17.03        14.99        15.02        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01S TCGA-AA-A01T 
       32.02        12.00        31.00        31.00         1.02        33.04 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        51.98         2.96        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03J TCGA-AD-5900 
        5.03         0.92        41.00        39.98        40.96        12.16 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK 
       24.53         5.79        22.42        27.42        26.47        16.44 
TCGA-AM-5820 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
        0.46        14.50        16.31         0.95        33.01         0.20 
TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4323 TCGA-AZ-4614 
       17.26        17.85        18.84       109.28         1.41         5.65 
TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6600 
        5.13        22.36        65.00        62.79        49.41        12.10 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5256 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 
       12.46        12.59        12.59        12.20        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5914 TCGA-CK-6748 TCGA-CM-4744 TCGA-CM-4746 
      148.01        85.45        21.99         2.01        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       25.02         8.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       30.08        32.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       15.02        14.04        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6676 
       12.99        13.02        15.02        14.04        11.01        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.08        11.01        10.06        45.40        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 
       56.09        55.92        20.19        17.75        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        7.53        12.39        10.13        12.43        14.30         9.04 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       11.64        13.41        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A 
        7.50        44.32       131.51       139.17        14.04        26.47 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28H TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 
      119.93        35.97       117.07        95.18         8.61        31.96 
TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74        35.74         6.18         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 
       43.04        33.67        13.25         0.53        47.41       133.18 
TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 
        8.35        82.39        74.56        65.85        44.68        55.04 
TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 
       39.42        61.91        36.00        26.43        26.04        13.78 
TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50V TCGA-NH-A6GB TCGA-NH-A6GC 
       46.75        74.79        18.18        19.33        15.65        12.79 
TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QL-A97D 
       16.80        42.77        29.46        32.98         8.42        21.90 
TCGA-RU-A8FL TCGA-SS-A7HO TCGA-T9-A92H 
       38.70        60.13        11.90 

$`AMP PEAK 22(20Q13.12) WILD-TYPE`
TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3525 TCGA-AA-3543 TCGA-AA-3554 
       13.02        24.03        37.05         8.05         0.99        17.95 
TCGA-AA-3672 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3870 TCGA-AA-3950 TCGA-AA-3952 
        0.92        19.04        19.04        29.98        24.00         2.01 
TCGA-AA-A024 TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-6601 TCGA-G4-6321 TCGA-G4-6586 
       39.06        10.88        75.95       100.01        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6628 TCGA-4T-AA8H TCGA-5M-AAT6 TCGA-A6-2672 TCGA-A6-2676 
       26.17        79.69        12.66         9.53        46.65        42.90 
TCGA-A6-2678 TCGA-A6-2684 TCGA-A6-3809 TCGA-A6-5657 TCGA-A6-5661 TCGA-A6-5664 
       42.28        37.05        32.75        31.63        33.53        22.09 
TCGA-A6-5665 TCGA-A6-6141 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 
       22.06         8.38        24.39        20.12        19.66        16.24 
TCGA-A6-A566 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3518 TCGA-AA-3555 
       24.92         3.02        35.01        63.98         1.02        29.95 
TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3710 TCGA-AA-3821 
       61.02         6.97        11.01         5.98        26.99         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3864 
       17.98        15.95         0.00         0.00        36.03        53.00 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3977 TCGA-AA-3994 
       31.00         2.01        33.01        26.01        25.02        27.02 
TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00R TCGA-AA-A010 TCGA-AA-A01P 
       38.04        30.02        18.05         0.99        34.98        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01V TCGA-AA-A02R TCGA-AA-A03F TCGA-AD-6889 
        1.02        35.01         1.02        22.03        18.05        83.24 
TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A71X TCGA-AZ-4315 
        0.92        27.09        21.44        17.82        19.33        58.39 
TCGA-AZ-4615 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-CA-5796 TCGA-CA-6717 TCGA-CA-6718 
       32.94        88.21         6.77        12.39        12.76        10.06 
TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 
       70.16        15.62        51.32        21.14        82.95       124.27 
TCGA-CM-4743 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-5861 TCGA-CM-6162 TCGA-CM-6674 
       23.05        26.04        27.02        15.02        12.00        12.95 
TCGA-CM-6675 TCGA-CM-6680 TCGA-D5-6530 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6927 
       13.05        12.03        20.42        16.14        15.58         9.44 
TCGA-D5-6930 TCGA-D5-6931 TCGA-DM-A1D9 TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A28C 
       13.35        12.00       140.38       135.65         7.76        81.37 
TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6461 TCGA-F4-6703 TCGA-F4-6856 TCGA-G4-6302 
       60.79        98.24        11.11        47.87        35.31        67.30 
TCGA-G4-6304 TCGA-G4-6309 TCGA-NH-A50U TCGA-NH-A5IV TCGA-NH-A6GA TCGA-QG-A5Z2 
       53.62        85.48        10.98        19.33         9.93        31.30 
TCGA-WS-AB45 
       70.03 

  AMP PEAK 22(20Q13.12) MUTATED AMP PEAK 22(20Q13.12) WILD-TYPE 
                              0                               0 
  AMP PEAK 22(20Q13.12) MUTATED AMP PEAK 22(20Q13.12) WILD-TYPE 
                         148.01                          140.38 
  AMP PEAK 22(20Q13.12) MUTATED AMP PEAK 22(20Q13.12) WILD-TYPE 
                          21.99                           22.09 
[1] "0.0 - 148.0 (22.0)" "0.0 - 140.4 (22.1)"
[1] "hr=" "1"  
D22V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK 22(20Q13.12) MUTATED        52        1       18        86         4
  AMP PEAK 22(20Q13.12) WILD-TYPE      22        0       11        46         6
                                 vv
clus                              STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 22(20Q13.12) MUTATED           1        13          8         43
  AMP PEAK 22(20Q13.12) WILD-TYPE         0         7          0         16
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 22(20Q13.12) MUTATED           33       40        16         1
  AMP PEAK 22(20Q13.12) WILD-TYPE          8        5         1         1
D22V3, multiclass
            clus
vv           AMP PEAK 22(20Q13.12) MUTATED AMP PEAK 22(20Q13.12) WILD-TYPE
  STAGE I                               52                              22
  STAGE IA                               1                               0
  STAGE II                              18                              11
  STAGE IIA                             86                              46
  STAGE IIB                              4                               6
  STAGE IIC                              1                               0
  STAGE III                             13                               7
  STAGE IIIA                             8                               0
  STAGE IIIB                            43                              16
  STAGE IIIC                            33                               8
  STAGE IV                              40                               5
  STAGE IVA                             16                               1
  STAGE IVB                              1                               1
[1] 13  2
[1] 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(20Q13.12) MUTATED     7  57 224  35
  AMP PEAK 22(20Q13.12) WILD-TYPE   4  20  81  20
D22V4, multiclass
    clus
vv   AMP PEAK 22(20Q13.12) MUTATED AMP PEAK 22(20Q13.12) WILD-TYPE
  T1                             7                               4
  T2                            57                              20
  T3                           224                              81
  T4                            35                              20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               N0  N1  N2
  AMP PEAK 22(20Q13.12) MUTATED   174  85  65
  AMP PEAK 22(20Q13.12) WILD-TYPE  88  20  17
D22V5, multiclass
    clus
vv   AMP PEAK 22(20Q13.12) MUTATED AMP PEAK 22(20Q13.12) WILD-TYPE
  N0                           174                              88
  N1                            85                              20
  N2                            65                              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"
D22V6, binary
                                 cls
clus                                0   1
  AMP PEAK 22(20Q13.12) MUTATED   228  57
  AMP PEAK 22(20Q13.12) WILD-TYPE 100   7
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 22(20Q13.12) MUTATED    228   57
  AMP PEAK 22(20Q13.12) WILD-TYPE  100    7
   clus
vv  AMP PEAK 22(20Q13.12) MUTATED AMP PEAK 22(20Q13.12) WILD-TYPE
  0                           228                             100
  1                            57                               7
[1] 2 2
[1] FALSE
D22V7, binary
                                 cls
clus                                0   1
  AMP PEAK 22(20Q13.12) MUTATED   147 177
  AMP PEAK 22(20Q13.12) WILD-TYPE  66  59
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 22(20Q13.12) MUTATED    147  177
  AMP PEAK 22(20Q13.12) WILD-TYPE   66   59
        clus
vv       AMP PEAK 22(20Q13.12) MUTATED AMP PEAK 22(20Q13.12) WILD-TYPE
  FEMALE                           147                              66
  MALE                             177                              59
[1] 2 2
[1] FALSE
D22V8, binary
                                 cls
clus                                0   1
  AMP PEAK 22(20Q13.12) MUTATED   269   7
  AMP PEAK 22(20Q13.12) WILD-TYPE 101   2
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 22(20Q13.12) MUTATED    269    7
  AMP PEAK 22(20Q13.12) WILD-TYPE  101    2
     clus
vv    AMP PEAK 22(20Q13.12) MUTATED AMP PEAK 22(20Q13.12) WILD-TYPE
  NO                            269                             101
  YES                             7                               2
[1] 2 2
[1] FALSE
D22V9, binary
                                 cls
clus                                0   1
  AMP PEAK 22(20Q13.12) MUTATED   294  26
  AMP PEAK 22(20Q13.12) WILD-TYPE  88  36
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 22(20Q13.12) MUTATED    294   26
  AMP PEAK 22(20Q13.12) WILD-TYPE   88   36
                               clus
vv                              AMP PEAK 22(20Q13.12) MUTATED
  COLON ADENOCARCINOMA                                    294
  COLON MUCINOUS ADENOCARCINOMA                            26
                               clus
vv                              AMP PEAK 22(20Q13.12) WILD-TYPE
  COLON ADENOCARCINOMA                                       88
  COLON MUCINOUS ADENOCARCINOMA                              36
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  AMP PEAK 22(20Q13.12) MUTATED   231   3  21  14
  AMP PEAK 22(20Q13.12) WILD-TYPE  92   1   4  11
D22V10, multiclass
    clus
vv   AMP PEAK 22(20Q13.12) MUTATED AMP PEAK 22(20Q13.12) WILD-TYPE
  R0                           231                              92
  R1                             3                               1
  R2                            21                               4
  RX                            14                              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"
D22V11, continuous
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 22(20Q13.12) MUTATED                                  1     7
  AMP PEAK 22(20Q13.12) WILD-TYPE                                0     4
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 22(20Q13.12) MUTATED                          41   158
  AMP PEAK 22(20Q13.12) WILD-TYPE                        18    54
D22V12, multiclass
                                  clus
vv                                 AMP PEAK 22(20Q13.12) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        7
  BLACK OR AFRICAN AMERICAN                                   41
  WHITE                                                      158
                                  clus
vv                                 AMP PEAK 22(20Q13.12) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               0
  ASIAN                                                          4
  BLACK OR AFRICAN AMERICAN                                     18
  WHITE                                                         54
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V13, binary
                                 cls
clus                                0   1
  AMP PEAK 22(20Q13.12) MUTATED     3 196
  AMP PEAK 22(20Q13.12) WILD-TYPE   1  73
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 22(20Q13.12) MUTATED      3  196
  AMP PEAK 22(20Q13.12) WILD-TYPE    1   73
                        clus
vv                       AMP PEAK 22(20Q13.12) MUTATED
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           196
                        clus
vv                       AMP PEAK 22(20Q13.12) WILD-TYPE
  HISPANIC OR LATINO                                   1
  NOT HISPANIC OR LATINO                              73
[1] 2 2
[1] FALSE

Clustering(23) Variable = DEL PEAK  1(1P36.11) MUTATION ANALYSIS
D23V1, survival
                                sevent
clus2                              0   1
  DEL PEAK  1(1P36.11) MUTATED   118  44
  DEL PEAK  1(1P36.11) WILD-TYPE 217  57
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                           162                            274 
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                            44                             57 
$`DEL PEAK  1(1P36.11) MUTATED`
TCGA-A6-2677 TCGA-A6-2682 TCGA-A6-4105 TCGA-AA-3522 TCGA-AA-3530 TCGA-AA-3531 
       24.33        13.94        14.53        37.05        19.07        34.03 
TCGA-AA-3552 TCGA-AA-3556 TCGA-AA-3562 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 
       13.02        23.01        19.99        19.00        36.00        85.05 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3972 
       31.07        24.03        29.98        12.99         2.01        50.99 
TCGA-AA-3976 TCGA-DM-A285 TCGA-G4-6298 TCGA-G4-6314 TCGA-G4-6625 TCGA-4N-A93T 
       26.01         5.88        23.51        35.93        91.79         4.80 
TCGA-5M-AAT4 TCGA-A6-2674 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-3810 
        1.61        43.76        44.91        35.11        16.57        36.53 
TCGA-A6-4107 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6138 
       32.45        29.19        23.61        32.71        29.16        22.52 
TCGA-A6-6140 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6654 TCGA-A6-A56B TCGA-AA-3488 
       24.13        25.18        21.76        23.87        56.25         5.03 
TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3544 TCGA-AA-3553 TCGA-AA-3666 
       38.99         9.07        19.07        14.01        24.00         2.01 
TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3685 TCGA-AA-3811 TCGA-AA-3819 
       14.01        50.04        47.01        37.05        10.06        25.02 
TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3855 
       38.99        36.95        37.02        10.06        33.07        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3866 TCGA-AA-3930 TCGA-AA-3966 TCGA-AA-3968 
        0.99        31.07        17.03         2.01         2.01        21.99 
TCGA-AA-3973 TCGA-AA-3989 TCGA-AA-A00F TCGA-AA-A00Q TCGA-AA-A017 TCGA-AA-A01C 
       13.05         7.96        34.03        42.02        15.02        15.02 
TCGA-AA-A01F TCGA-AA-A01K TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A02E TCGA-AA-A02F 
       32.02        31.00        33.04        26.01         2.96        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02W TCGA-AA-A03J TCGA-AD-6890 TCGA-AD-6899 
        2.01         5.03        41.00        40.96        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AU-3779 TCGA-AY-4070 
       22.42        26.47        16.44         0.46        14.50        16.31 
TCGA-AY-A69D TCGA-AZ-4614 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-6600 
       17.85         5.65         5.13        22.36        65.00        12.10 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 
       29.56         5.23         3.19        12.69        12.36        12.46 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-5914 TCGA-CK-6748 
       12.59        12.59        12.20        14.30        21.99         2.01 
TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5862 
       25.02         8.02        13.02        22.03        30.08         5.03 
TCGA-CM-5864 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 
       15.02        14.04        29.03        13.02        15.02        11.01 
TCGA-CM-6676 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5540 TCGA-D5-6529 
       11.08        10.06        12.03        45.40        56.09        20.19 
TCGA-D5-6531 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6541 
       17.75        25.48        43.27        15.12        17.85        15.58 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A1D4 TCGA-DM-A1D6 
       12.43        14.30        13.41        11.38        92.75        49.91 
TCGA-DM-A1DB TCGA-DM-A282 TCGA-DM-A28A TCGA-DM-A28H TCGA-DM-A28M TCGA-F4-6460 
       44.32       139.17        26.47       117.07        95.18        31.96 
TCGA-F4-6461 TCGA-F4-6704 TCGA-F4-6806 TCGA-F4-6809 TCGA-F4-6855 TCGA-G4-6295 
       11.11         1.55        41.42        13.25        47.41         8.35 
TCGA-G4-6297 TCGA-G4-6303 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6626 TCGA-NH-A50T 
       82.39        65.85        61.91        36.00        46.75        18.18 
TCGA-NH-A50U TCGA-NH-A6GA TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-SS-A7HO TCGA-T9-A92H 
       10.98         9.93        16.80        42.77        60.13        11.90 

$`DEL PEAK  1(1P36.11) WILD-TYPE`
TCGA-A6-2681 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3506 TCGA-AA-3516 TCGA-AA-3520 
       45.60        24.16         1.02        58.03        13.02        24.03 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3543 TCGA-AA-3554 TCGA-AA-3560 TCGA-AA-3662 
       36.03         8.05         0.99        17.95        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3950 TCGA-AA-3979 
        0.92        19.04        19.04        14.93        24.00        24.00 
TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 
       19.07        38.04        21.99        39.06        21.37        15.52 
TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 
       25.08        10.88        75.95       106.75       100.01         1.94 
TCGA-CK-5912 TCGA-G4-6294 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       49.08        28.21        63.62        22.09        35.80        26.17 
TCGA-G4-6628 TCGA-NH-A8F7 TCGA-3L-AA1B TCGA-4T-AA8H TCGA-5M-AAT6 TCGA-5M-AATE 
       79.69        17.85        15.62        12.66         9.53        39.45 
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2684 
       43.76        46.65        43.43        42.90        42.28        37.05 
TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-5656 TCGA-A6-5657 
       37.25        37.02        34.65        32.75        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6141 
       30.44        33.53        22.09        22.06        27.09         8.38 
TCGA-A6-6142 TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 
       25.08        20.61        24.69        24.39        20.12        19.66 
TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A5ZU TCGA-AA-3489 
       20.28        16.24        24.92        61.84         9.63         7.04 
TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
        3.02         1.02        37.05        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3518 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        1.02         1.02         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       12.99        33.99        21.01        29.95        20.98        13.94 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3675 TCGA-AA-3679 
       61.02        78.08         6.97        54.02        47.05        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3818 
       11.01         5.98         5.03        26.99        35.05         0.99 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3850 
        1.02        17.98        15.95         0.00        17.03         0.00 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
        0.00        36.03        53.00        27.02        18.05        31.00 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3971 
       24.00        33.01        26.01        20.98        34.03        16.08 
TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       34.06        25.02        27.02        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O 
       19.00        30.02        18.05        18.05         4.01        27.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A01D TCGA-AA-A01G 
        0.99        17.03        14.99        34.98        10.98        12.00 
TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V 
       31.00        38.07         1.02        35.01         1.02         1.02 
TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F 
       37.02        51.98         0.92        22.03        39.98        18.05 
TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6963 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4071 
       12.16        83.24        27.42         0.92        27.09         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A71X 
       33.01         0.20        21.44        17.82        17.26        19.33 
TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-5403 
       18.84       109.28        58.39         1.41        32.94        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6606 TCGA-CA-5796 TCGA-CA-6717 
       88.21        49.41         6.77        11.74        12.39        12.76 
TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 
       10.06        17.56       148.01        85.45        70.16        15.62 
TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       51.32        21.14        82.95       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5860 
       37.02        26.04        27.02        29.06        22.98        32.02 
TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6165 
       15.02        15.02        17.03        15.02        12.00        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 
       21.99        14.99        12.99        14.04        12.95        13.05 
TCGA-CM-6677 TCGA-CM-6678 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6530 
       11.08        11.01        54.61        19.59        55.92        20.42 
TCGA-D5-6532 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6898 
       18.25         4.80        17.13        12.49        16.14         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 
       12.39        10.13         9.04         9.44        11.64        13.35 
TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       12.00        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A1HB 
       13.32        12.59       140.38         7.50       131.51       135.65 
TCGA-DM-A280 TCGA-DM-A288 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
        7.76        14.04        81.37       119.93        35.97        60.79 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        35.74        35.74         6.18        47.87 
TCGA-F4-6805 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6854 TCGA-F4-6856 TCGA-G4-6293 
       34.42        43.04        33.67         0.53        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        67.30        53.62        44.68        55.04        85.48 
TCGA-G4-6311 TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6627 TCGA-NH-A50V 
       39.42        26.43        26.04        13.78        74.79        19.33 
TCGA-NH-A5IV TCGA-NH-A6GB TCGA-NH-A6GC TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 
       19.33        15.65        12.79        29.46        32.98         8.42 
TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-RU-A8FL TCGA-WS-AB45 
       31.30        21.90        38.70        70.03 

  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                          0.46                           0.00 
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                        139.17                         148.01 
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                         21.99                          22.09 
[1] "0.5 - 139.2 (22.0)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.5"
D23V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK  1(1P36.11) MUTATED        21        0        6        46         2
  DEL PEAK  1(1P36.11) WILD-TYPE      53        1       23        86         8
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  1(1P36.11) MUTATED           1         7          4         18
  DEL PEAK  1(1P36.11) WILD-TYPE         0        13          4         41
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK  1(1P36.11) MUTATED           18       30        10         0
  DEL PEAK  1(1P36.11) WILD-TYPE         23       15         7         2
D23V3, multiclass
            clus
vv           DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  STAGE I                              21                             53
  STAGE IA                              0                              1
  STAGE II                              6                             23
  STAGE IIA                            46                             86
  STAGE IIB                             2                              8
  STAGE IIC                             1                              0
  STAGE III                             7                             13
  STAGE IIIA                            4                              4
  STAGE IIIB                           18                             41
  STAGE IIIC                           18                             23
  STAGE IV                             30                             15
  STAGE IVA                            10                              7
  STAGE IVB                             0                              2
[1] 13  2
[1] 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(1P36.11) MUTATED     3  26 115  23
  DEL PEAK  1(1P36.11) WILD-TYPE   8  51 190  32
D23V4, multiclass
    clus
vv   DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  T1                            3                              8
  T2                           26                             51
  T3                          115                            190
  T4                           23                             32
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2
  DEL PEAK  1(1P36.11) MUTATED    84  43  40
  DEL PEAK  1(1P36.11) WILD-TYPE 178  62  42
D23V5, multiclass
    clus
vv   DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  N0                           84                            178
  N1                           43                             62
  N2                           40                             42
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V6, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.11) MUTATED   109  40
  DEL PEAK  1(1P36.11) WILD-TYPE 219  24
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.11) MUTATED    109   40
  DEL PEAK  1(1P36.11) WILD-TYPE  219   24
   clus
vv  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  0                          109                            219
  1                           40                             24
[1] 2 2
[1] FALSE
D23V7, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.11) MUTATED    71  96
  DEL PEAK  1(1P36.11) WILD-TYPE 142 140
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.11) MUTATED     71   96
  DEL PEAK  1(1P36.11) WILD-TYPE  142  140
        clus
vv       DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  FEMALE                           71                            142
  MALE                             96                            140
[1] 2 2
[1] FALSE
D23V8, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.11) MUTATED   140   2
  DEL PEAK  1(1P36.11) WILD-TYPE 230   7
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.11) MUTATED    140    2
  DEL PEAK  1(1P36.11) WILD-TYPE  230    7
     clus
vv    DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  NO                           140                            230
  YES                            2                              7
[1] 2 2
[1] FALSE
D23V9, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.11) MUTATED   155  11
  DEL PEAK  1(1P36.11) WILD-TYPE 227  51
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.11) MUTATED    155   11
  DEL PEAK  1(1P36.11) WILD-TYPE  227   51
                               clus
vv                              DEL PEAK  1(1P36.11) MUTATED
  COLON ADENOCARCINOMA                                   155
  COLON MUCINOUS ADENOCARCINOMA                           11
                               clus
vv                              DEL PEAK  1(1P36.11) WILD-TYPE
  COLON ADENOCARCINOMA                                     227
  COLON MUCINOUS ADENOCARCINOMA                             51
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK  1(1P36.11) MUTATED   112   2  14  11
  DEL PEAK  1(1P36.11) WILD-TYPE 211   2  11  14
D23V10, multiclass
    clus
vv   DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  R0                          112                            211
  R1                            2                              2
  R2                           14                             11
  RX                           11                             14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  1(1P36.11) MUTATED                                  1     7
  DEL PEAK  1(1P36.11) WILD-TYPE                                0     4
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  1(1P36.11) MUTATED                          19    79
  DEL PEAK  1(1P36.11) WILD-TYPE                        40   133
D23V12, multiclass
                                  clus
vv                                 DEL PEAK  1(1P36.11) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       7
  BLACK OR AFRICAN AMERICAN                                  19
  WHITE                                                      79
                                  clus
vv                                 DEL PEAK  1(1P36.11) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         4
  BLACK OR AFRICAN AMERICAN                                    40
  WHITE                                                       133
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V13, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.11) MUTATED     2 100
  DEL PEAK  1(1P36.11) WILD-TYPE   2 169
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.11) MUTATED      2  100
  DEL PEAK  1(1P36.11) WILD-TYPE    2  169
                        clus
vv                       DEL PEAK  1(1P36.11) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                          100
                        clus
vv                       DEL PEAK  1(1P36.11) WILD-TYPE
  HISPANIC OR LATINO                                  2
  NOT HISPANIC OR LATINO                            169
[1] 2 2
[1] FALSE

Clustering(24) Variable = DEL PEAK  2(1P33) MUTATION ANALYSIS
D24V1, survival
                             sevent
clus2                           0   1
  DEL PEAK  2(1P33) MUTATED    82  37
  DEL PEAK  2(1P33) WILD-TYPE 253  64
  DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE 
                        119                         317 
  DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE 
                         37                          64 
$`DEL PEAK  2(1P33) MUTATED`
TCGA-A6-4105 TCGA-AA-3522 TCGA-AA-3525 TCGA-AA-3562 TCGA-AA-3688 TCGA-AA-3697 
       14.53        37.05         8.05        19.99        19.00        85.05 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3939 TCGA-G4-6298 TCGA-G4-6314 TCGA-G4-6625 
       31.07        24.03        12.99        23.51        35.93        91.79 
TCGA-4N-A93T TCGA-5M-AAT4 TCGA-A6-2674 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2685 
        4.80         1.61        43.76        35.11        16.57        37.25 
TCGA-A6-2686 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5667 
       37.02        36.53        32.45        29.19        23.61        29.16 
TCGA-A6-6138 TCGA-A6-6651 TCGA-A6-6654 TCGA-AA-3488 TCGA-AA-3517 TCGA-AA-3519 
       22.52        21.76        23.87         5.03        38.99         9.07 
TCGA-AA-3549 TCGA-AA-3673 TCGA-AA-3685 TCGA-AA-3811 TCGA-AA-3837 TCGA-AA-3841 
       21.01        50.04        37.05        10.06        38.99        36.95 
TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3855 TCGA-AA-3866 
       37.02         0.00        10.06        33.07        32.05        17.03 
TCGA-AA-3930 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3973 TCGA-AA-3989 TCGA-AA-A00F 
        2.01         2.01        21.99        13.05         7.96        34.03 
TCGA-AA-A00Q TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01K TCGA-AA-A01T TCGA-AA-A01X 
       42.02        15.02        32.02        31.00        33.04        26.01 
TCGA-AA-A02E TCGA-AA-A02H TCGA-AA-A02R TCGA-AA-A02W TCGA-AD-6890 TCGA-AD-6899 
        2.96         2.01        22.03        41.00        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-A69D 
       22.42        26.47        16.44        14.50        16.31        17.85 
TCGA-AZ-4614 TCGA-AZ-4616 TCGA-AZ-5403 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 
        5.65         5.13        62.79        12.10        29.56         5.23 
TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-6716 TCGA-CK-6748 
        3.19        12.69        12.36        12.46        12.20         2.01 
TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-6163 
        8.02        13.02        22.03         5.03        15.02        14.04 
TCGA-CM-6164 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6679 
       29.03        13.02        15.02        11.08        11.08        10.06 
TCGA-D5-5540 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6924 TCGA-D5-6929 
       56.09        25.48        15.12        17.85        14.30        13.41 
TCGA-D5-6932 TCGA-DM-A0XF TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A288 TCGA-DM-A28A 
       11.38        38.20        92.75        49.91        14.04        26.47 
TCGA-DM-A28F TCGA-F4-6460 TCGA-F4-6704 TCGA-F4-6855 TCGA-G4-6295 TCGA-G4-6297 
       35.97        31.96         1.55        47.41         8.35        82.39 
TCGA-G4-6303 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6626 TCGA-NH-A50T TCGA-NH-A50U 
       65.85        61.91        36.00        46.75        18.18        10.98 
TCGA-NH-A6GA TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-SS-A7HO TCGA-T9-A92H 
        9.93        16.80        42.77        60.13        11.90 

$`DEL PEAK  2(1P33) WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3506 
       24.33        45.60        13.94        24.16         1.02        58.03 
TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       13.02        24.03        36.03        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3662 TCGA-AA-3672 
       13.02        17.95        23.01        19.99         6.05         0.92 
TCGA-AA-3692 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3870 TCGA-AA-3950 
       36.00        19.04        19.04        14.93        29.98        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 
       75.95       106.75       100.01         1.94        49.08         5.88 
TCGA-G4-6294 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 
       28.21        63.62        22.09        35.80        26.17        79.69 
TCGA-NH-A8F7 TCGA-3L-AA1B TCGA-4T-AA8H TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2671 
       17.85        15.62        12.66         9.53        39.45        43.76 
TCGA-A6-2672 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2684 
       46.65        43.43        42.90        42.28        44.91        37.05 
TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 
       34.65        32.75        32.91        31.63        30.44        33.53 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        24.13         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 
       25.08        25.18        20.61        24.69        24.39        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B 
       19.66        20.28        16.24        24.92        61.84        56.25 
TCGA-A6-A5ZU TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 
        9.63         7.04         3.02         1.02        37.05        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3518 TCGA-AA-3526 TCGA-AA-3529 
       63.98         6.97         1.02         1.02        19.07         0.00 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 
       29.00        29.00        26.01        12.99        14.01        33.99 
TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        61.02        78.08 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3675 TCGA-AA-3678 
        6.97        54.02         2.01        14.01        47.05        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3812 
       15.02        11.01         5.98         5.03        26.99        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3846 
        0.99        25.02         1.02        17.98        15.95        17.03 
TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 
        0.00         0.00        36.03         0.99        31.07        53.00 
TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       27.02        18.05        31.00        24.00        33.01        26.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3982 
       20.98        34.03        16.08        34.06        25.02        27.02 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J 
       27.02        13.94        38.04        19.00        30.02        18.05 
TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       18.05         4.01        27.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P 
       34.98        15.02        10.98        12.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A029 
        1.02        35.01         1.02         1.02        37.02        51.98 
TCGA-AA-A02F TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       39.98         5.03         0.92        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6963 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 
       12.16        83.24        27.42         0.46         0.92        27.09 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L 
        0.95        33.01         0.20        21.44        17.82        17.26 
TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 
       19.33        18.84       109.28        58.39         1.41        32.94 
TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6606 
       22.36        65.00        88.21        49.41         6.77        11.74 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.39        12.59        12.59        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 
       17.56       148.01        85.45        70.16        15.62        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.99        21.14        82.95       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-5341 TCGA-CM-5348 
       37.02        25.02        26.04        27.02        29.06        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5868 TCGA-CM-6161 
       30.08        32.02        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6171 
       12.00        16.04        21.99        14.99        12.99        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-5537 
       11.01        12.95        13.05        11.01        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 
       54.61        19.59        55.92        20.19        20.42        17.75 
TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       18.25        43.27         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 
       15.58         7.53        12.39        10.13        12.43         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 
        9.44        11.64        13.35        12.00        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A1D0 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       24.43       130.65        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A28C 
       44.32       131.51       135.65         7.76       139.17        81.37 
TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 
      119.93        60.79       117.07        98.24        95.18         8.61 
TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 
       11.11        35.74        35.74         6.18        47.87        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6856 
       41.42        43.04        33.67        13.25         0.53        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        67.30        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6627 
       85.48        39.42        26.43        26.04        13.78        74.79 
TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GB TCGA-NH-A6GC TCGA-QG-A5YW TCGA-QG-A5YX 
       19.33        19.33        15.65        12.79        29.46        32.98 
TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-RU-A8FL TCGA-WS-AB45 
        8.42        31.30        21.90        38.70        70.03 

  DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE 
                          0                           0 
  DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE 
                      92.75                      148.01 
  DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE 
                      21.01                       22.98 
[1] "0.0 - 92.8 (21.0)"  "0.0 - 148.0 (23.0)"
[1] "hr=" "1.8"
D24V2, continuous
                             vv
clus                          STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK  2(1P33) MUTATED        12        0        6        35         1
  DEL PEAK  2(1P33) WILD-TYPE      62        1       23        97         9
                             vv
clus                          STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  2(1P33) MUTATED           0         5          3         15
  DEL PEAK  2(1P33) WILD-TYPE         1        15          5         44
                             vv
clus                          STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK  2(1P33) MUTATED           15       23         4         0
  DEL PEAK  2(1P33) WILD-TYPE         26       22        13         2
D24V3, multiclass
            clus
vv           DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE
  STAGE I                           12                          62
  STAGE IA                           0                           1
  STAGE II                           6                          23
  STAGE IIA                         35                          97
  STAGE IIB                          1                           9
  STAGE IIC                          0                           1
  STAGE III                          5                          15
  STAGE IIIA                         3                           5
  STAGE IIIB                        15                          44
  STAGE IIIC                        15                          26
  STAGE IV                          23                          22
  STAGE IVA                          4                          13
  STAGE IVB                          0                           2
[1] 13  2
[1] 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(1P33) MUTATED     3  15  87  18
  DEL PEAK  2(1P33) WILD-TYPE   8  62 218  37
D24V4, multiclass
    clus
vv   DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE
  T1                         3                           8
  T2                        15                          62
  T3                        87                         218
  T4                        18                          37
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           N0  N1  N2
  DEL PEAK  2(1P33) MUTATED    60  33  30
  DEL PEAK  2(1P33) WILD-TYPE 202  72  52
D24V5, multiclass
    clus
vv   DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE
  N0                        60                         202
  N1                        33                          72
  N2                        30                          52
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V6, binary
                             cls
clus                            0   1
  DEL PEAK  2(1P33) MUTATED    80  27
  DEL PEAK  2(1P33) WILD-TYPE 248  37
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  2(1P33) MUTATED     80   27
  DEL PEAK  2(1P33) WILD-TYPE  248   37
   clus
vv  DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE
  0                        80                         248
  1                        27                          37
[1] 2 2
[1] FALSE
D24V7, binary
                             cls
clus                            0   1
  DEL PEAK  2(1P33) MUTATED    54  69
  DEL PEAK  2(1P33) WILD-TYPE 159 167
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  2(1P33) MUTATED     54   69
  DEL PEAK  2(1P33) WILD-TYPE  159  167
        clus
vv       DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE
  FEMALE                        54                         159
  MALE                          69                         167
[1] 2 2
[1] FALSE
D24V8, binary
                             cls
clus                            0   1
  DEL PEAK  2(1P33) MUTATED   104   2
  DEL PEAK  2(1P33) WILD-TYPE 266   7
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  2(1P33) MUTATED    104    2
  DEL PEAK  2(1P33) WILD-TYPE  266    7
     clus
vv    DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE
  NO                        104                         266
  YES                         2                           7
[1] 2 2
[1] FALSE
D24V9, binary
                             cls
clus                            0   1
  DEL PEAK  2(1P33) MUTATED   113   9
  DEL PEAK  2(1P33) WILD-TYPE 269  53
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  2(1P33) MUTATED    113    9
  DEL PEAK  2(1P33) WILD-TYPE  269   53
                               clus
vv                              DEL PEAK  2(1P33) MUTATED
  COLON ADENOCARCINOMA                                113
  COLON MUCINOUS ADENOCARCINOMA                         9
                               clus
vv                              DEL PEAK  2(1P33) WILD-TYPE
  COLON ADENOCARCINOMA                                  269
  COLON MUCINOUS ADENOCARCINOMA                          53
[1] 2 2
[1] FALSE
                             vv
clus                           R0  R1  R2  RX
  DEL PEAK  2(1P33) MUTATED    81   2  10   7
  DEL PEAK  2(1P33) WILD-TYPE 242   2  15  18
D24V10, multiclass
    clus
vv   DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE
  R0                        81                         242
  R1                         2                           2
  R2                        10                          15
  RX                         7                          18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V11, continuous
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  2(1P33) MUTATED                                  1     4
  DEL PEAK  2(1P33) WILD-TYPE                                0     7
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  2(1P33) MUTATED                          19    57
  DEL PEAK  2(1P33) WILD-TYPE                        40   155
D24V12, multiclass
                                  clus
vv                                 DEL PEAK  2(1P33) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         1
  ASIAN                                                    4
  BLACK OR AFRICAN AMERICAN                               19
  WHITE                                                   57
                                  clus
vv                                 DEL PEAK  2(1P33) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      7
  BLACK OR AFRICAN AMERICAN                                 40
  WHITE                                                    155
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V13, binary
                             cls
clus                            0   1
  DEL PEAK  2(1P33) MUTATED     2  75
  DEL PEAK  2(1P33) WILD-TYPE   2 194
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  2(1P33) MUTATED      2   75
  DEL PEAK  2(1P33) WILD-TYPE    2  194
                        clus
vv                       DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE
  HISPANIC OR LATINO                             2                           2
  NOT HISPANIC OR LATINO                        75                         194
[1] 2 2
[1] FALSE

Clustering(25) Variable = DEL PEAK  3(1P13.1) MUTATION ANALYSIS
D25V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  3(1P13.1) MUTATED    83  31
  DEL PEAK  3(1P13.1) WILD-TYPE 252  70
  DEL PEAK  3(1P13.1) MUTATED DEL PEAK  3(1P13.1) WILD-TYPE 
                          114                           322 
  DEL PEAK  3(1P13.1) MUTATED DEL PEAK  3(1P13.1) WILD-TYPE 
                           31                            70 
$`DEL PEAK  3(1P13.1) MUTATED`
TCGA-A6-4105 TCGA-AA-3522 TCGA-AA-3562 TCGA-AA-3688 TCGA-AA-3860 TCGA-AA-3867 
       14.53        37.05        19.99        19.00        31.07        24.03 
TCGA-AA-3939 TCGA-AA-3952 TCGA-DM-A285 TCGA-G4-6298 TCGA-G4-6625 TCGA-4N-A93T 
       12.99         2.01         5.88        23.51        91.79         4.80 
TCGA-5M-AAT4 TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2685 
        1.61        43.76        43.76        35.11        16.57        37.25 
TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-6138 TCGA-A6-6651 
       36.53        32.45        29.19        23.61        22.52        21.76 
TCGA-A6-6654 TCGA-A6-A56B TCGA-AA-3488 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3549 
       23.87        56.25         5.03        38.99         9.07        21.01 
TCGA-AA-3561 TCGA-AA-3673 TCGA-AA-3685 TCGA-AA-3811 TCGA-AA-3837 TCGA-AA-3842 
       13.94        50.04        37.05        10.06        38.99        37.02 
TCGA-AA-3848 TCGA-AA-3855 TCGA-AA-3866 TCGA-AA-3930 TCGA-AA-3966 TCGA-AA-3968 
       10.06        32.05        17.03         2.01         2.01        21.99 
TCGA-AA-3973 TCGA-AA-3989 TCGA-AA-A00A TCGA-AA-A00Q TCGA-AA-A01C TCGA-AA-A01F 
       13.05         7.96        38.04        42.02        15.02        32.02 
TCGA-AA-A01K TCGA-AA-A01Q TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A02E TCGA-AA-A02H 
       31.00         1.02        33.04        26.01         2.96         2.01 
TCGA-AA-A02W TCGA-AA-A03J TCGA-AD-6890 TCGA-AD-6901 TCGA-AD-6965 TCGA-AD-A5EK 
       41.00        40.96        24.53        22.42        26.47        16.44 
TCGA-AM-5821 TCGA-AU-3779 TCGA-AY-A69D TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4684 
        0.92        14.50        17.85        32.94         5.13        65.00 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 
       12.10        29.56         5.23         3.19        12.69        12.36 
TCGA-CA-5256 TCGA-CA-6716 TCGA-CK-6748 TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5344 
       12.46        12.20         2.01         8.02        13.02        22.03 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6676 TCGA-CM-6679 
       14.04        29.03        13.02        15.02        11.08        10.06 
TCGA-D5-5540 TCGA-D5-6531 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6924 TCGA-D5-6929 
       56.09        17.75        25.48        15.12        14.30        13.41 
TCGA-D5-6932 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1HA TCGA-DM-A288 TCGA-DM-A28A 
       11.38        92.75        49.91       131.51        14.04        26.47 
TCGA-F4-6460 TCGA-F4-6704 TCGA-F4-6807 TCGA-F4-6855 TCGA-G4-6295 TCGA-G4-6297 
       31.96         1.55        43.04        47.41         8.35        82.39 
TCGA-G4-6303 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6322 TCGA-G4-6626 TCGA-NH-A50T 
       65.85        61.91        36.00        26.04        46.75        18.18 
TCGA-NH-A50U TCGA-NH-A6GA TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-SS-A7HO TCGA-T9-A92H 
       10.98         9.93        16.80        42.77        60.13        11.90 

$`DEL PEAK  3(1P13.1) WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3506 
       24.33        45.60        13.94        24.16         1.02        58.03 
TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 
       13.02        24.03        36.03         8.05        19.07        34.03 
TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3662 
        0.99        13.02        17.95        23.01        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
        0.92        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3870 TCGA-AA-3950 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 
       29.98        24.00        50.99        26.01        24.00        19.07 
TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 
       38.04        21.99        39.06        21.37        15.52        25.08 
TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 
       10.88        75.95       106.75       100.01         1.94        49.08 
TCGA-G4-6294 TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       28.21        63.62        35.93        22.09        35.80        26.17 
TCGA-G4-6628 TCGA-NH-A8F7 TCGA-3L-AA1B TCGA-4T-AA8H TCGA-5M-AAT6 TCGA-5M-AATE 
       79.69        17.85        15.62        12.66         9.53        39.45 
TCGA-A6-2672 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2684 
       46.65        43.43        42.90        42.28        44.91        37.05 
TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       37.02        34.65        32.75        32.91        31.63        30.44 
TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 
       33.53        22.09        22.06        32.71        29.16        27.09 
TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6652 
       24.13         8.38        25.08        25.18        20.61        24.69 
TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 
       24.39        20.12        19.66        20.28        16.24        24.92 
TCGA-A6-A567 TCGA-A6-A5ZU TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 
       61.84         9.63         7.04         3.02         1.02        37.05 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3518 TCGA-AA-3526 
       35.01        63.98         6.97         1.02         1.02        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3655 TCGA-AA-3660 
       33.99        24.00        29.95        20.98        61.02        78.08 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3675 TCGA-AA-3678 
        6.97        54.02         2.01        14.01        47.05        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3812 
       15.02        11.01         5.98         5.03        26.99        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3841 
        0.99        25.02         1.02        17.98        15.95        36.95 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
        0.00        17.03         0.00        33.07         0.00        36.03 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
        0.99        31.07        53.00        27.02        18.05        31.00 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3971 
       24.00        33.01        26.01        20.98        34.03        16.08 
TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D 
       34.06        25.02        27.02        27.02        13.94        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V 
       12.00        31.00        38.07        35.01         1.02         1.02 
TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R 
       37.02        51.98        39.98         5.03         0.92        22.03 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6899 TCGA-AD-6963 
       39.98        18.05        12.16        83.24         5.79        27.42 
TCGA-AM-5820 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
        0.46        27.09        16.31         0.95        33.01         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 
       21.44        17.82        17.26        19.33        18.84       109.28 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
       58.39         1.41         5.65        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6606 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
       49.41         6.77        11.74        12.39        12.59        12.59 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       70.16        15.62        51.32        21.99        21.14        82.95 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 
      124.27        23.05        20.02        37.02        25.02        26.04 
TCGA-CM-4751 TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       27.02        29.06        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6171 TCGA-CM-6172 
       16.04        21.99        14.99        12.99        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-5537 
       12.95        13.05        11.08        11.01        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6532 
       54.61        19.59        55.92        20.19        20.42        18.25 
TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       43.27        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 
       15.58         7.53        12.39        10.13        12.43         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 
        9.44        11.64        13.35        12.00        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
       24.43        38.20       130.65        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A28C 
        7.50        44.32       135.65         7.76       139.17        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M 
      119.93        35.97        60.79       117.07        98.24        95.18 
TCGA-F4-6459 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
        8.61        11.11        35.74        35.74         6.18        47.87 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6856 
       34.42        41.42        33.67        13.25         0.53        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        67.30        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6320 TCGA-G4-6323 TCGA-G4-6627 TCGA-NH-A50V 
       85.48        39.42        26.43        13.78        74.79        19.33 
TCGA-NH-A5IV TCGA-NH-A6GB TCGA-NH-A6GC TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 
       19.33        15.65        12.79        29.46        32.98         8.42 
TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-RU-A8FL TCGA-WS-AB45 
       31.30        21.90        38.70        70.03 

  DEL PEAK  3(1P13.1) MUTATED DEL PEAK  3(1P13.1) WILD-TYPE 
                         0.92                          0.00 
  DEL PEAK  3(1P13.1) MUTATED DEL PEAK  3(1P13.1) WILD-TYPE 
                       131.51                        148.01 
  DEL PEAK  3(1P13.1) MUTATED DEL PEAK  3(1P13.1) WILD-TYPE 
                       21.385                        22.225 
[1] "0.9 - 131.5 (21.4)" "0.0 - 148.0 (22.2)"
[1] "hr=" "1.4"
D25V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK  3(1P13.1) MUTATED        12        0        5        32         1
  DEL PEAK  3(1P13.1) WILD-TYPE      62        1       24       100         9
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  3(1P13.1) MUTATED           0         5          3         15
  DEL PEAK  3(1P13.1) WILD-TYPE         1        15          5         44
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK  3(1P13.1) MUTATED           14       24         3         0
  DEL PEAK  3(1P13.1) WILD-TYPE         27       21        14         2
D25V3, multiclass
            clus
vv           DEL PEAK  3(1P13.1) MUTATED DEL PEAK  3(1P13.1) WILD-TYPE
  STAGE I                             12                            62
  STAGE IA                             0                             1
  STAGE II                             5                            24
  STAGE IIA                           32                           100
  STAGE IIB                            1                             9
  STAGE IIC                            0                             1
  STAGE III                            5                            15
  STAGE IIIA                           3                             5
  STAGE IIIB                          15                            44
  STAGE IIIC                          14                            27
  STAGE IV                            24                            21
  STAGE IVA                            3                            14
  STAGE IVB                            0                             2
[1] 13  2
[1] 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(1P13.1) MUTATED     3  15  84  16
  DEL PEAK  3(1P13.1) WILD-TYPE   8  62 221  39
D25V4, multiclass
    clus
vv   DEL PEAK  3(1P13.1) MUTATED DEL PEAK  3(1P13.1) WILD-TYPE
  T1                           3                             8
  T2                          15                            62
  T3                          84                           221
  T4                          16                            39
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2
  DEL PEAK  3(1P13.1) MUTATED    56  31  31
  DEL PEAK  3(1P13.1) WILD-TYPE 206  74  51
D25V5, multiclass
    clus
vv   DEL PEAK  3(1P13.1) MUTATED DEL PEAK  3(1P13.1) WILD-TYPE
  N0                          56                           206
  N1                          31                            74
  N2                          31                            51
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V6, binary
                               cls
clus                              0   1
  DEL PEAK  3(1P13.1) MUTATED    77  27
  DEL PEAK  3(1P13.1) WILD-TYPE 251  37
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(1P13.1) MUTATED     77   27
  DEL PEAK  3(1P13.1) WILD-TYPE  251   37
   clus
vv  DEL PEAK  3(1P13.1) MUTATED DEL PEAK  3(1P13.1) WILD-TYPE
  0                          77                           251
  1                          27                            37
[1] 2 2
[1] FALSE
D25V7, binary
                               cls
clus                              0   1
  DEL PEAK  3(1P13.1) MUTATED    50  68
  DEL PEAK  3(1P13.1) WILD-TYPE 163 168
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(1P13.1) MUTATED     50   68
  DEL PEAK  3(1P13.1) WILD-TYPE  163  168
        clus
vv       DEL PEAK  3(1P13.1) MUTATED DEL PEAK  3(1P13.1) WILD-TYPE
  FEMALE                          50                           163
  MALE                            68                           168
[1] 2 2
[1] FALSE
D25V8, binary
                               cls
clus                              0   1
  DEL PEAK  3(1P13.1) MUTATED    98   2
  DEL PEAK  3(1P13.1) WILD-TYPE 272   7
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(1P13.1) MUTATED     98    2
  DEL PEAK  3(1P13.1) WILD-TYPE  272    7
     clus
vv    DEL PEAK  3(1P13.1) MUTATED DEL PEAK  3(1P13.1) WILD-TYPE
  NO                           98                           272
  YES                           2                             7
[1] 2 2
[1] FALSE
D25V9, binary
                               cls
clus                              0   1
  DEL PEAK  3(1P13.1) MUTATED   108  10
  DEL PEAK  3(1P13.1) WILD-TYPE 274  52
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(1P13.1) MUTATED    108   10
  DEL PEAK  3(1P13.1) WILD-TYPE  274   52
                               clus
vv                              DEL PEAK  3(1P13.1) MUTATED
  COLON ADENOCARCINOMA                                  108
  COLON MUCINOUS ADENOCARCINOMA                          10
                               clus
vv                              DEL PEAK  3(1P13.1) WILD-TYPE
  COLON ADENOCARCINOMA                                    274
  COLON MUCINOUS ADENOCARCINOMA                            52
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  3(1P13.1) MUTATED    77   1  10   8
  DEL PEAK  3(1P13.1) WILD-TYPE 246   3  15  17
D25V10, multiclass
    clus
vv   DEL PEAK  3(1P13.1) MUTATED DEL PEAK  3(1P13.1) WILD-TYPE
  R0                          77                           246
  R1                           1                             3
  R2                          10                            15
  RX                           8                            17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V11, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  3(1P13.1) MUTATED                                  1     4
  DEL PEAK  3(1P13.1) WILD-TYPE                                0     7
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  3(1P13.1) MUTATED                          19    54
  DEL PEAK  3(1P13.1) WILD-TYPE                        40   158
D25V12, multiclass
                                  clus
vv                                 DEL PEAK  3(1P13.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      4
  BLACK OR AFRICAN AMERICAN                                 19
  WHITE                                                     54
                                  clus
vv                                 DEL PEAK  3(1P13.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        7
  BLACK OR AFRICAN AMERICAN                                   40
  WHITE                                                      158
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V13, binary
                               cls
clus                              0   1
  DEL PEAK  3(1P13.1) MUTATED     2  73
  DEL PEAK  3(1P13.1) WILD-TYPE   2 196
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(1P13.1) MUTATED      2   73
  DEL PEAK  3(1P13.1) WILD-TYPE    2  196
                        clus
vv                       DEL PEAK  3(1P13.1) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          73
                        clus
vv                       DEL PEAK  3(1P13.1) WILD-TYPE
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                           196
[1] 2 2
[1] FALSE

Clustering(26) Variable = DEL PEAK  4(2P21) MUTATION ANALYSIS
D26V1, survival
                             sevent
clus2                           0   1
  DEL PEAK  4(2P21) MUTATED    14   3
  DEL PEAK  4(2P21) WILD-TYPE 321  98
  DEL PEAK  4(2P21) MUTATED DEL PEAK  4(2P21) WILD-TYPE 
                         17                         419 
  DEL PEAK  4(2P21) MUTATED DEL PEAK  4(2P21) WILD-TYPE 
                          3                          98 
$`DEL PEAK  4(2P21) MUTATED`
TCGA-AA-3496 TCGA-AA-3560 TCGA-AA-3939 TCGA-AA-3952 TCGA-AZ-4313 TCGA-5M-AAT4 
        1.02        19.99        12.99         2.01        75.95         1.61 
TCGA-A6-2678 TCGA-AA-3511 TCGA-AA-3842 TCGA-AA-A01K TCGA-AA-A01S TCGA-CM-4746 
       42.28         6.97        37.02        31.00         1.02        37.02 
TCGA-CM-5341 TCGA-D5-6534 TCGA-D5-6932 TCGA-F4-6461 TCGA-NH-A50V 
       29.06        43.27        11.38        11.11        19.33 

$`DEL PEAK  4(2P21) WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3506 
       24.33        45.60        13.94        14.53        24.16        58.03 
TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 
       13.02        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3562 
       34.03         0.99        13.02        17.95        23.01        19.99 
TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 
        6.05         0.92        19.00        36.00        85.05        19.04 
TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3950 
       19.04        14.93        31.07        24.03        29.98        24.00 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6298 
      100.01         1.94        49.08         5.88        28.21        23.51 
TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       63.62        35.93        22.09        35.80        26.17        91.79 
TCGA-G4-6628 TCGA-NH-A8F7 TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT6 
       79.69        17.85        15.62         4.80        12.66         9.53 
TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 
       39.45        43.76        46.65        43.76        43.43        42.90 
TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 
       44.91        35.11        16.57        37.05        37.25        37.02 
TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 
       34.65        32.75        36.53        32.45        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       30.44        29.19        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 
       32.71        29.16        27.09        22.52        24.13         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        20.61        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 
       23.87        20.12        19.66        20.28        16.24        24.92 
TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 
       61.84        56.25         9.63         5.03         7.04         3.02 
TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3517 
        1.02        37.05        35.01        63.98         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 
       26.01        12.99        14.01        33.99        21.01        24.00 
TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 
       54.02         2.01        14.01        50.04        47.05        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         5.03        26.99 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       10.06        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       15.95        38.99        36.95         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       31.07        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       27.02         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P 
       15.02        10.98        32.02        12.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
        1.02        35.01        33.04         1.02        26.01        37.02 
TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O 
       51.98         2.96        39.98         2.01         5.03         0.92 
TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
       22.03        41.00        39.98        18.05        40.96        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       16.44         0.46         0.92        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L 
        0.95        33.01         0.20        21.44        17.82        17.26 
TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 
       17.85        19.33        18.84       109.28        58.39         1.41 
TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 
        5.65        32.94         5.13        22.36        65.00        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 
       88.21        49.41         6.77        12.10        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 
       11.74         3.19        12.69        12.36        12.46        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 
       17.56       148.01        85.45        70.16        15.62        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14        82.95         2.01       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 
       20.02        25.02        26.04         8.02        27.02        13.02 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 
       19.59        56.09        55.92        20.19        20.42        17.75 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       18.25        25.48        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       13.35        12.00        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 
        7.50        44.32       131.51       135.65         7.76       139.17 
TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
       14.04        26.47        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6463 
      117.07        98.24        95.18         8.61        31.96        35.74 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       43.04        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 
      133.18         8.35        82.39        74.56        67.30        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        39.42        61.91 
TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6626 TCGA-G4-6627 
       36.00        26.43        26.04        13.78        46.75        74.79 
TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC 
       18.18        10.98        19.33         9.93        15.65        12.79 
TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 
       16.80        42.77        29.46        32.98         8.42        31.30 
TCGA-QL-A97D TCGA-RU-A8FL TCGA-SS-A7HO TCGA-T9-A92H TCGA-WS-AB45 
       21.90        38.70        60.13        11.90        70.03 

  DEL PEAK  4(2P21) MUTATED DEL PEAK  4(2P21) WILD-TYPE 
                       1.02                        0.00 
  DEL PEAK  4(2P21) MUTATED DEL PEAK  4(2P21) WILD-TYPE 
                      75.95                      148.01 
  DEL PEAK  4(2P21) MUTATED DEL PEAK  4(2P21) WILD-TYPE 
                      19.33                       22.09 
[1] "1.0 - 76.0 (19.3)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1"  
D26V2, continuous
                             vv
clus                          STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK  4(2P21) MUTATED         2        0        2         3         0
  DEL PEAK  4(2P21) WILD-TYPE      72        1       27       129        10
                             vv
clus                          STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  4(2P21) MUTATED           0         1          2          2
  DEL PEAK  4(2P21) WILD-TYPE         1        19          6         57
                             vv
clus                          STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK  4(2P21) MUTATED            4        1         0         0
  DEL PEAK  4(2P21) WILD-TYPE         37       44        17         2
D26V3, multiclass
            clus
vv           DEL PEAK  4(2P21) MUTATED DEL PEAK  4(2P21) WILD-TYPE
  STAGE I                            2                          72
  STAGE IA                           0                           1
  STAGE II                           2                          27
  STAGE IIA                          3                         129
  STAGE IIB                          0                          10
  STAGE IIC                          0                           1
  STAGE III                          1                          19
  STAGE IIIA                         2                           6
  STAGE IIIB                         2                          57
  STAGE IIIC                         4                          37
  STAGE IV                           1                          44
  STAGE IVA                          0                          17
  STAGE IVB                          0                           2
[1] 13  2
[1] 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(2P21) MUTATED     1   3  11   2
  DEL PEAK  4(2P21) WILD-TYPE  10  74 294  53
D26V4, multiclass
    clus
vv   DEL PEAK  4(2P21) MUTATED DEL PEAK  4(2P21) WILD-TYPE
  T1                         1                          10
  T2                         3                          74
  T3                        11                         294
  T4                         2                          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"
                             vv
clus                           N0  N1  N2
  DEL PEAK  4(2P21) MUTATED     8   4   5
  DEL PEAK  4(2P21) WILD-TYPE 254 101  77
D26V5, multiclass
    clus
vv   DEL PEAK  4(2P21) MUTATED DEL PEAK  4(2P21) WILD-TYPE
  N0                         8                         254
  N1                         4                         101
  N2                         5                          77
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V6, binary
                             cls
clus                            0   1
  DEL PEAK  4(2P21) MUTATED    16   1
  DEL PEAK  4(2P21) WILD-TYPE 312  63
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  4(2P21) MUTATED     16    1
  DEL PEAK  4(2P21) WILD-TYPE  312   63
   clus
vv  DEL PEAK  4(2P21) MUTATED DEL PEAK  4(2P21) WILD-TYPE
  0                        16                         312
  1                         1                          63
[1] 2 2
[1] FALSE
D26V7, binary
                             cls
clus                            0   1
  DEL PEAK  4(2P21) MUTATED     9   8
  DEL PEAK  4(2P21) WILD-TYPE 204 228
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  4(2P21) MUTATED      9    8
  DEL PEAK  4(2P21) WILD-TYPE  204  228
        clus
vv       DEL PEAK  4(2P21) MUTATED DEL PEAK  4(2P21) WILD-TYPE
  FEMALE                         9                         204
  MALE                           8                         228
[1] 2 2
[1] FALSE
D26V8, binary
                             cls
clus                            0   1
  DEL PEAK  4(2P21) MUTATED    14   0
  DEL PEAK  4(2P21) WILD-TYPE 356   9
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  4(2P21) MUTATED     14    0
  DEL PEAK  4(2P21) WILD-TYPE  356    9
     clus
vv    DEL PEAK  4(2P21) MUTATED DEL PEAK  4(2P21) WILD-TYPE
  NO                         14                         356
  YES                         0                           9
[1] 2 2
[1] FALSE
D26V9, binary
                             cls
clus                            0   1
  DEL PEAK  4(2P21) MUTATED    16   1
  DEL PEAK  4(2P21) WILD-TYPE 366  61
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  4(2P21) MUTATED     16    1
  DEL PEAK  4(2P21) WILD-TYPE  366   61
                               clus
vv                              DEL PEAK  4(2P21) MUTATED
  COLON ADENOCARCINOMA                                 16
  COLON MUCINOUS ADENOCARCINOMA                         1
                               clus
vv                              DEL PEAK  4(2P21) WILD-TYPE
  COLON ADENOCARCINOMA                                  366
  COLON MUCINOUS ADENOCARCINOMA                          61
[1] 2 2
[1] FALSE
                             vv
clus                           R0  R1  R2  RX
  DEL PEAK  4(2P21) MUTATED    16   0   0   0
  DEL PEAK  4(2P21) WILD-TYPE 307   4  25  25
D26V10, multiclass
    clus
vv   DEL PEAK  4(2P21) MUTATED DEL PEAK  4(2P21) WILD-TYPE
  R0                        16                         307
  R1                         0                           4
  R2                         0                          25
  RX                         0                          25
[1] 4 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, continuous
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  4(2P21) MUTATED                                  0     0
  DEL PEAK  4(2P21) WILD-TYPE                                1    11
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  4(2P21) MUTATED                           3     6
  DEL PEAK  4(2P21) WILD-TYPE                        56   206
D26V12, multiclass
                                  clus
vv                                 DEL PEAK  4(2P21) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         0
  ASIAN                                                    0
  BLACK OR AFRICAN AMERICAN                                3
  WHITE                                                    6
                                  clus
vv                                 DEL PEAK  4(2P21) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                     11
  BLACK OR AFRICAN AMERICAN                                 56
  WHITE                                                    206
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V13, binary
                             cls
clus                            0   1
  DEL PEAK  4(2P21) MUTATED     1   8
  DEL PEAK  4(2P21) WILD-TYPE   3 261
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  4(2P21) MUTATED      1    8
  DEL PEAK  4(2P21) WILD-TYPE    3  261
                        clus
vv                       DEL PEAK  4(2P21) MUTATED DEL PEAK  4(2P21) WILD-TYPE
  HISPANIC OR LATINO                             1                           3
  NOT HISPANIC OR LATINO                         8                         261
[1] 2 2
[1] FALSE

Clustering(27) Variable = DEL PEAK  5(2Q22.1) MUTATION ANALYSIS
D27V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  5(2Q22.1) MUTATED    16   7
  DEL PEAK  5(2Q22.1) WILD-TYPE 319  94
  DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE 
                           23                           413 
  DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE 
                            7                            94 
$`DEL PEAK  5(2Q22.1) MUTATED`
TCGA-AA-3522 TCGA-AA-3560 TCGA-AA-3939 TCGA-A6-2678 TCGA-A6-3810 TCGA-A6-6651 
       37.05        19.99        12.99        42.28        36.53        21.76 
TCGA-A6-A566 TCGA-AA-3511 TCGA-AA-3666 TCGA-AA-3679 TCGA-AA-3811 TCGA-AA-3842 
       24.92         6.97         2.01        15.02        10.06        37.02 
TCGA-AA-3848 TCGA-AA-3941 TCGA-AZ-4308 TCGA-CA-5254 TCGA-CA-5797 TCGA-DM-A1D6 
       10.06        24.00       109.28        12.69        12.59        49.91 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A28H TCGA-F4-6704 TCGA-G4-6626 
       44.32       131.51       117.07         1.55        46.75 

$`DEL PEAK  5(2Q22.1) WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 
       24.33        45.60        13.94        14.53        24.16         1.02 
TCGA-AA-3506 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 
       58.03        13.02        24.03        36.03         8.05        19.07 
TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3562 
       34.03         0.99        13.02        17.95        23.01        19.99 
TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 
        6.05         0.92        19.00        36.00        85.05        19.04 
TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3950 
       19.04        14.93        31.07        24.03        29.98        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 
       75.95       106.75       100.01         1.94        49.08         5.88 
TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6321 TCGA-G4-6586 
       28.21        23.51        63.62        35.93        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-NH-A8F7 TCGA-3L-AA1B TCGA-4N-A93T 
       26.17        91.79        79.69        17.85        15.62         4.80 
TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2672 
       12.66         1.61         9.53        39.45        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 
       43.76        43.43        42.90        44.91        35.11        16.57 
TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-4107 
       37.05        37.25        37.02        34.65        32.75        32.45 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 
       22.09        22.06        32.71        29.16        27.09        22.52 
TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6652 
       24.13         8.38        25.08        25.18        20.61        24.69 
TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 
       24.39        23.87        20.12        19.66        20.28        16.24 
TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 
       61.84        56.25         9.63         5.03         7.04         3.02 
TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3517 
        1.02        37.05        35.01        63.98         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 
       26.01        12.99        14.01        33.99        21.01        24.00 
TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         6.97 
TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3680 
       54.02        14.01        50.04        47.05        47.01        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3818 
        5.98        37.05         5.03        26.99        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 
       25.02         1.02        17.98        15.95        38.99        36.95 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
        0.00        17.03         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
       32.05         0.99        31.07        53.00        17.03        27.02 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       18.05        31.00         2.01        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       25.02        27.02         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N 
       19.00        30.02        34.03        18.05        18.05         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       15.02        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F 
        1.02        26.01        37.02        51.98         2.96        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03         0.92        22.03        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 
       22.42        27.42        26.47        16.44         0.46         0.92 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK 
       21.44        17.82        17.26        17.85        19.33        18.84 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 
       58.39         1.41         5.65        32.94         5.13        22.36 
TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       65.00        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5255 TCGA-CA-5256 
       29.56         5.23        11.74         3.19        12.36        12.46 
TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.39        12.59        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 
       17.56       148.01        85.45        70.16        15.62        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14        82.95         2.01       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 
       20.02        37.02        25.02        26.04         8.02        27.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00        14.04        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       20.42        17.75        18.25        25.48        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        7.53        12.39        10.13        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HB TCGA-DM-A280 
       13.32        12.59       140.38         7.50       135.65         7.76 
TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      139.17        14.04        26.47        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 
       60.79        98.24        95.18         8.61        31.96        11.11 
TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 
       35.74        35.74         6.18        47.87        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       43.04        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 
      133.18         8.35        82.39        74.56        67.30        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        39.42        61.91 
TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6627 TCGA-NH-A50T 
       36.00        26.43        26.04        13.78        74.79        18.18 
TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC 
       10.98        19.33        19.33         9.93        15.65        12.79 
TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 
       16.80        42.77        29.46        32.98         8.42        31.30 
TCGA-QL-A97D TCGA-RU-A8FL TCGA-SS-A7HO TCGA-T9-A92H TCGA-WS-AB45 
       21.90        38.70        60.13        11.90        70.03 

  DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE 
                         1.55                          0.00 
  DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE 
                       131.51                        148.01 
  DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE 
                        24.00                         22.03 
[1] "1.6 - 131.5 (24.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.1"
D27V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK  5(2Q22.1) MUTATED         0        0        1         8         0
  DEL PEAK  5(2Q22.1) WILD-TYPE      74        1       28       124        10
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  5(2Q22.1) MUTATED           0         2          1          4
  DEL PEAK  5(2Q22.1) WILD-TYPE         1        18          7         55
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK  5(2Q22.1) MUTATED            5        2         1         0
  DEL PEAK  5(2Q22.1) WILD-TYPE         36       43        16         2
D27V3, multiclass
            clus
vv           DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE
  STAGE I                              0                            74
  STAGE IA                             0                             1
  STAGE II                             1                            28
  STAGE IIA                            8                           124
  STAGE IIB                            0                            10
  STAGE IIC                            0                             1
  STAGE III                            2                            18
  STAGE IIIA                           1                             7
  STAGE IIIB                           4                            55
  STAGE IIIC                           5                            36
  STAGE IV                             2                            43
  STAGE IVA                            1                            16
  STAGE IVB                            0                             2
[1] 13  2
[1] 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(2Q22.1) MUTATED     0   1  19   4
  DEL PEAK  5(2Q22.1) WILD-TYPE  11  76 286  51
D27V4, multiclass
    clus
vv   DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE
  T1                           0                            11
  T2                           1                            76
  T3                          19                           286
  T4                           4                            51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2
  DEL PEAK  5(2Q22.1) MUTATED     9   8   7
  DEL PEAK  5(2Q22.1) WILD-TYPE 253  97  75
D27V5, multiclass
    clus
vv   DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE
  N0                           9                           253
  N1                           8                            97
  N2                           7                            75
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V6, binary
                               cls
clus                              0   1
  DEL PEAK  5(2Q22.1) MUTATED    19   3
  DEL PEAK  5(2Q22.1) WILD-TYPE 309  61
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2Q22.1) MUTATED     19    3
  DEL PEAK  5(2Q22.1) WILD-TYPE  309   61
   clus
vv  DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE
  0                          19                           309
  1                           3                            61
[1] 2 2
[1] FALSE
D27V7, binary
                               cls
clus                              0   1
  DEL PEAK  5(2Q22.1) MUTATED    10  14
  DEL PEAK  5(2Q22.1) WILD-TYPE 203 222
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2Q22.1) MUTATED     10   14
  DEL PEAK  5(2Q22.1) WILD-TYPE  203  222
        clus
vv       DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE
  FEMALE                          10                           203
  MALE                            14                           222
[1] 2 2
[1] FALSE
D27V8, binary
                               cls
clus                              0   1
  DEL PEAK  5(2Q22.1) MUTATED    17   0
  DEL PEAK  5(2Q22.1) WILD-TYPE 353   9
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2Q22.1) MUTATED     17    0
  DEL PEAK  5(2Q22.1) WILD-TYPE  353    9
     clus
vv    DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE
  NO                           17                           353
  YES                           0                             9
[1] 2 2
[1] FALSE
D27V9, binary
                               cls
clus                              0   1
  DEL PEAK  5(2Q22.1) MUTATED    21   3
  DEL PEAK  5(2Q22.1) WILD-TYPE 361  59
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2Q22.1) MUTATED     21    3
  DEL PEAK  5(2Q22.1) WILD-TYPE  361   59
                               clus
vv                              DEL PEAK  5(2Q22.1) MUTATED
  COLON ADENOCARCINOMA                                   21
  COLON MUCINOUS ADENOCARCINOMA                           3
                               clus
vv                              DEL PEAK  5(2Q22.1) WILD-TYPE
  COLON ADENOCARCINOMA                                    361
  COLON MUCINOUS ADENOCARCINOMA                            59
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  5(2Q22.1) MUTATED    16   0   2   1
  DEL PEAK  5(2Q22.1) WILD-TYPE 307   4  23  24
D27V10, multiclass
    clus
vv   DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE
  R0                          16                           307
  R1                           0                             4
  R2                           2                            23
  RX                           1                            24
[1] 4 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, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  5(2Q22.1) MUTATED                                  1     2
  DEL PEAK  5(2Q22.1) WILD-TYPE                                0     9
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  5(2Q22.1) MUTATED                           1     9
  DEL PEAK  5(2Q22.1) WILD-TYPE                        58   203
D27V12, multiclass
                                  clus
vv                                 DEL PEAK  5(2Q22.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      2
  BLACK OR AFRICAN AMERICAN                                  1
  WHITE                                                      9
                                  clus
vv                                 DEL PEAK  5(2Q22.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        9
  BLACK OR AFRICAN AMERICAN                                   58
  WHITE                                                      203
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V13, binary
                               cls
clus                              0   1
  DEL PEAK  5(2Q22.1) MUTATED     0  13
  DEL PEAK  5(2Q22.1) WILD-TYPE   4 256
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2Q22.1) MUTATED      0   13
  DEL PEAK  5(2Q22.1) WILD-TYPE    4  256
                        clus
vv                       DEL PEAK  5(2Q22.1) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                          13
                        clus
vv                       DEL PEAK  5(2Q22.1) WILD-TYPE
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           256
[1] 2 2
[1] FALSE

Clustering(28) Variable = DEL PEAK  6(3P26.1) MUTATION ANALYSIS
D28V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  6(3P26.1) MUTATED    53  17
  DEL PEAK  6(3P26.1) WILD-TYPE 282  84
  DEL PEAK  6(3P26.1) MUTATED DEL PEAK  6(3P26.1) WILD-TYPE 
                           70                           366 
  DEL PEAK  6(3P26.1) MUTATED DEL PEAK  6(3P26.1) WILD-TYPE 
                           17                            84 
$`DEL PEAK  6(3P26.1) MUTATED`
TCGA-A6-4105 TCGA-AA-3662 TCGA-AA-3697 TCGA-AA-3860 TCGA-AA-3870 TCGA-AA-3939 
       14.53         6.05        85.05        31.07        29.98        12.99 
TCGA-AA-3972 TCGA-AA-3979 TCGA-5M-AAT4 TCGA-A6-2675 TCGA-A6-2683 TCGA-A6-3807 
       50.99        24.00         1.61        43.43        16.57        34.65 
TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 
       36.53        32.45        29.16        27.09        22.52        25.08 
TCGA-A6-6651 TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3511 TCGA-AA-3517 TCGA-AA-3519 
       21.76         9.63         5.03         6.97        38.99         9.07 
TCGA-AA-3532 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3811 TCGA-AA-3855 TCGA-AA-3866 
       29.00        15.02        11.01        10.06        32.05        17.03 
TCGA-AA-3930 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00O 
        2.01         2.01        21.99         7.96        13.94        27.02 
TCGA-AA-A01F TCGA-AA-A01K TCGA-AA-A02H TCGA-AD-A5EK TCGA-AY-6196 TCGA-AZ-4614 
       32.02        31.00         2.01        16.44         0.20         5.65 
TCGA-AZ-4616 TCGA-AZ-6600 TCGA-AZ-6607 TCGA-CA-5797 TCGA-CA-6716 TCGA-CK-6748 
        5.13        12.10         3.19        12.59        12.20         2.01 
TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5862 TCGA-CM-6163 
        8.02        13.02        29.06        22.03         5.03        14.04 
TCGA-CM-6677 TCGA-CM-6678 TCGA-D5-6529 TCGA-D5-6531 TCGA-D5-6533 TCGA-D5-6534 
       11.08        11.01        20.19        17.75        25.48        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A1DA TCGA-F4-6460 
       15.12        17.85        13.41        11.38         7.50        31.96 
TCGA-NH-A6GA TCGA-QG-A5YV TCGA-RU-A8FL TCGA-T9-A92H 
        9.93        42.77        38.70        11.90 

$`DEL PEAK  6(3P26.1) WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3506 
       24.33        45.60        13.94        24.16         1.02        58.03 
TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 
       13.02        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 
       34.03         0.99        13.02        17.95        23.01        19.99 
TCGA-AA-3562 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3713 TCGA-AA-3715 
       19.99         0.92        19.00        36.00        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3867 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3976 TCGA-AA-3986 
       14.93        24.03        24.00         2.01        26.01        19.07 
TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 
       38.04        21.99        39.06        21.37        15.52        25.08 
TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 
       10.88        75.95       106.75       100.01         1.94        49.08 
TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6321 
        5.88        28.21        23.51        63.62        35.93        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-NH-A8F7 TCGA-3L-AA1B 
       35.80        26.17        91.79        79.69        17.85        15.62 
TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2672 
        4.80        12.66         9.53        39.45        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2684 
       43.76        42.90        42.28        44.91        35.11        37.05 
TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3809 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       37.25        37.02        32.75        32.91        31.63        30.44 
TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 
       29.19        33.53        23.61        22.09        22.06        32.71 
TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6653 
       24.13         8.38        25.18        20.61        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 
       23.87        20.12        19.66        20.28        16.24        24.92 
TCGA-A6-A567 TCGA-A6-A56B TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 
       61.84        56.25         7.04         3.02         1.02        37.05 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3518 TCGA-AA-3526 TCGA-AA-3529 
       35.01        63.98         1.02         1.02        19.07         0.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       29.00        26.01        12.99        14.01        33.99        21.01 
TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        61.02        78.08 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3675 
        6.97        54.02         2.01        14.01        50.04        47.05 
TCGA-AA-3678 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3812 
       47.01         5.98        37.05         5.03        26.99        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       36.95        37.02         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 
       33.07         0.00        36.03         0.99        31.07        53.00 
TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       27.02        18.05        31.00        24.00        33.01        26.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
       20.98        34.03        16.08        13.05        34.06        25.02 
TCGA-AA-3982 TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        27.02        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        18.05         4.01        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01G 
       14.99        34.98        15.02        15.02        10.98        12.00 
TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F 
        1.02        26.01        37.02        51.98         2.96        39.98 
TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03         0.92        22.03        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 
       27.42        26.47         0.46         0.92        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L 
       16.31         0.95        33.01        21.44        17.82        17.26 
TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 
       17.85        19.33        18.84       109.28        58.39         1.41 
TCGA-AZ-4615 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
       32.94        22.36        65.00        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-CA-5254 TCGA-CA-5255 
        6.77        29.56         5.23        11.74        12.69        12.36 
TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.46        12.39        12.59        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 
       17.56       148.01        85.45        70.16        15.62        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.99        21.14        82.95       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-5348 TCGA-CM-5349 
       37.02        25.02        26.04        27.02        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       32.02        15.02        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
       12.00        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.08        10.06        12.03        45.40        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6537 TCGA-D5-6538 
       56.09        55.92        20.42        18.25         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 
       12.43        14.30         9.04         9.44        11.64        13.35 
TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       12.00        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB 
       92.75        49.91        13.32        12.59       140.38        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A 
      131.51       135.65         7.76       139.17        14.04        26.47 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 
       95.18         8.61        11.11        35.74        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6295 
       13.25         0.53        47.41        35.31       133.18         8.35 
TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       82.39        74.56        67.30        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 
       55.04        85.48        39.42        61.91        36.00        26.43 
TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50U 
       26.04        13.78        46.75        74.79        18.18        10.98 
TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F8 TCGA-QG-A5YW 
       19.33        19.33        15.65        12.79        16.80        29.46 
TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-SS-A7HO TCGA-WS-AB45 
       32.98         8.42        31.30        21.90        60.13        70.03 

  DEL PEAK  6(3P26.1) MUTATED DEL PEAK  6(3P26.1) WILD-TYPE 
                          0.2                           0.0 
  DEL PEAK  6(3P26.1) MUTATED DEL PEAK  6(3P26.1) WILD-TYPE 
                        85.05                        148.01 
  DEL PEAK  6(3P26.1) MUTATED DEL PEAK  6(3P26.1) WILD-TYPE 
                        15.07                         23.74 
[1] "0.2 - 85.0 (15.1)"  "0.0 - 148.0 (23.7)"
[1] "hr=" "1.6"
D28V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK  6(3P26.1) MUTATED         6        0        2        19         0
  DEL PEAK  6(3P26.1) WILD-TYPE      68        1       27       113        10
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  6(3P26.1) MUTATED           0         3          2         11
  DEL PEAK  6(3P26.1) WILD-TYPE         1        17          6         48
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK  6(3P26.1) MUTATED            7       16         4         0
  DEL PEAK  6(3P26.1) WILD-TYPE         34       29        13         2
D28V3, multiclass
            clus
vv           DEL PEAK  6(3P26.1) MUTATED DEL PEAK  6(3P26.1) WILD-TYPE
  STAGE I                              6                            68
  STAGE IA                             0                             1
  STAGE II                             2                            27
  STAGE IIA                           19                           113
  STAGE IIB                            0                            10
  STAGE IIC                            0                             1
  STAGE III                            3                            17
  STAGE IIIA                           2                             6
  STAGE IIIB                          11                            48
  STAGE IIIC                           7                            34
  STAGE IV                            16                            29
  STAGE IVA                            4                            13
  STAGE IVB                            0                             2
[1] 13  2
[1] 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(3P26.1) MUTATED     2   6  52  11
  DEL PEAK  6(3P26.1) WILD-TYPE   9  71 253  44
D28V4, multiclass
    clus
vv   DEL PEAK  6(3P26.1) MUTATED DEL PEAK  6(3P26.1) WILD-TYPE
  T1                           2                             9
  T2                           6                            71
  T3                          52                           253
  T4                          11                            44
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2
  DEL PEAK  6(3P26.1) MUTATED    30  22  19
  DEL PEAK  6(3P26.1) WILD-TYPE 232  83  63
D28V5, multiclass
    clus
vv   DEL PEAK  6(3P26.1) MUTATED DEL PEAK  6(3P26.1) WILD-TYPE
  N0                          30                           232
  N1                          22                            83
  N2                          19                            63
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V6, binary
                               cls
clus                              0   1
  DEL PEAK  6(3P26.1) MUTATED    42  20
  DEL PEAK  6(3P26.1) WILD-TYPE 286  44
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(3P26.1) MUTATED     42   20
  DEL PEAK  6(3P26.1) WILD-TYPE  286   44
   clus
vv  DEL PEAK  6(3P26.1) MUTATED DEL PEAK  6(3P26.1) WILD-TYPE
  0                          42                           286
  1                          20                            44
[1] 2 2
[1] FALSE
D28V7, binary
                               cls
clus                              0   1
  DEL PEAK  6(3P26.1) MUTATED    32  39
  DEL PEAK  6(3P26.1) WILD-TYPE 181 197
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(3P26.1) MUTATED     32   39
  DEL PEAK  6(3P26.1) WILD-TYPE  181  197
        clus
vv       DEL PEAK  6(3P26.1) MUTATED DEL PEAK  6(3P26.1) WILD-TYPE
  FEMALE                          32                           181
  MALE                            39                           197
[1] 2 2
[1] FALSE
D28V8, binary
                               cls
clus                              0   1
  DEL PEAK  6(3P26.1) MUTATED    64   0
  DEL PEAK  6(3P26.1) WILD-TYPE 306   9
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(3P26.1) MUTATED     64    0
  DEL PEAK  6(3P26.1) WILD-TYPE  306    9
     clus
vv    DEL PEAK  6(3P26.1) MUTATED DEL PEAK  6(3P26.1) WILD-TYPE
  NO                           64                           306
  YES                           0                             9
[1] 2 2
[1] FALSE
D28V9, binary
                               cls
clus                              0   1
  DEL PEAK  6(3P26.1) MUTATED    67   4
  DEL PEAK  6(3P26.1) WILD-TYPE 315  58
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(3P26.1) MUTATED     67    4
  DEL PEAK  6(3P26.1) WILD-TYPE  315   58
                               clus
vv                              DEL PEAK  6(3P26.1) MUTATED
  COLON ADENOCARCINOMA                                   67
  COLON MUCINOUS ADENOCARCINOMA                           4
                               clus
vv                              DEL PEAK  6(3P26.1) WILD-TYPE
  COLON ADENOCARCINOMA                                    315
  COLON MUCINOUS ADENOCARCINOMA                            58
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  6(3P26.1) MUTATED    49   0   8   4
  DEL PEAK  6(3P26.1) WILD-TYPE 274   4  17  21
D28V10, multiclass
    clus
vv   DEL PEAK  6(3P26.1) MUTATED DEL PEAK  6(3P26.1) WILD-TYPE
  R0                          49                           274
  R1                           0                             4
  R2                           8                            17
  RX                           4                            21
[1] 4 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, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  6(3P26.1) MUTATED                                  0     2
  DEL PEAK  6(3P26.1) WILD-TYPE                                1     9
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  6(3P26.1) MUTATED                           9    33
  DEL PEAK  6(3P26.1) WILD-TYPE                        50   179
D28V12, multiclass
                                  clus
vv                                 DEL PEAK  6(3P26.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      2
  BLACK OR AFRICAN AMERICAN                                  9
  WHITE                                                     33
                                  clus
vv                                 DEL PEAK  6(3P26.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        9
  BLACK OR AFRICAN AMERICAN                                   50
  WHITE                                                      179
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V13, binary
                               cls
clus                              0   1
  DEL PEAK  6(3P26.1) MUTATED     2  42
  DEL PEAK  6(3P26.1) WILD-TYPE   2 227
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(3P26.1) MUTATED      2   42
  DEL PEAK  6(3P26.1) WILD-TYPE    2  227
                        clus
vv                       DEL PEAK  6(3P26.1) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          42
                        clus
vv                       DEL PEAK  6(3P26.1) WILD-TYPE
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                           227
[1] 2 2
[1] FALSE

Clustering(29) Variable = DEL PEAK  7(3P14.2) MUTATION ANALYSIS
D29V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  7(3P14.2) MUTATED    64  20
  DEL PEAK  7(3P14.2) WILD-TYPE 271  81
  DEL PEAK  7(3P14.2) MUTATED DEL PEAK  7(3P14.2) WILD-TYPE 
                           84                           352 
  DEL PEAK  7(3P14.2) MUTATED DEL PEAK  7(3P14.2) WILD-TYPE 
                           20                            81 
$`DEL PEAK  7(3P14.2) MUTATED`
TCGA-A6-4105 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3697 TCGA-AA-3860 TCGA-AA-3939 
       14.53         6.05         0.92        85.05        31.07        12.99 
TCGA-AA-3979 TCGA-AA-A00L TCGA-AD-6548 TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-A6-2683 
       24.00        38.04        21.37        12.66         1.61        16.57 
TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5667 TCGA-A6-6138 
       37.02        34.65        36.53        32.45        29.16        22.52 
TCGA-A6-6142 TCGA-A6-6651 TCGA-A6-6780 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 
       25.08        21.76        20.12        56.25         9.63         5.03 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3664 TCGA-AA-3680 TCGA-AA-3685 
       38.99         1.02         9.07        54.02        11.01        37.05 
TCGA-AA-3811 TCGA-AA-3855 TCGA-AA-3866 TCGA-AA-3930 TCGA-AA-3966 TCGA-AA-3968 
       10.06        32.05        17.03         2.01         2.01        21.99 
TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00J TCGA-AA-A00O TCGA-AA-A00R 
       27.02         7.96        13.94        18.05        27.02         0.99 
TCGA-AA-A01F TCGA-AA-A01K TCGA-AA-A02W TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-A5EK 
       32.02        31.00        41.00        24.53         5.79        16.44 
TCGA-AM-5820 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-6196 TCGA-AZ-4308 TCGA-AZ-4614 
        0.46        14.50        16.31         0.20       109.28         5.65 
TCGA-AZ-6600 TCGA-CA-5797 TCGA-CA-6716 TCGA-CK-6748 TCGA-CM-4750 TCGA-CM-5862 
       12.10        12.59        12.20         2.01         8.02         5.03 
TCGA-CM-6163 TCGA-CM-6171 TCGA-CM-6675 TCGA-CM-6677 TCGA-CM-6678 TCGA-D5-6529 
       14.04        14.04        13.05        11.08        11.01        20.19 
TCGA-D5-6531 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6929 TCGA-D5-6932 
       17.75        25.48        43.27        17.85        13.41        11.38 
TCGA-DM-A0X9 TCGA-DM-A1DA TCGA-DM-A28F TCGA-DM-A28H TCGA-F4-6460 TCGA-G4-6317 
      119.70         7.50        35.97       117.07        31.96        36.00 
TCGA-NH-A6GA TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-RU-A8FL TCGA-T9-A92H TCGA-WS-AB45 
        9.93        16.80        42.77        38.70        11.90        70.03 

$`DEL PEAK  7(3P14.2) WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3506 
       24.33        45.60        13.94        24.16         1.02        58.03 
TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 
       13.02        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 
       34.03         0.99        13.02        17.95        23.01        19.99 
TCGA-AA-3562 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.99        19.00        36.00        19.04        19.04        14.93 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 
       24.03        29.98        24.00         2.01        50.99        26.01 
TCGA-AA-3986 TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       19.07        21.99        39.06        15.52        25.08        10.88 
TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 
       75.95       106.75       100.01         1.94        49.08         5.88 
TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6321 TCGA-G4-6586 
       28.21        23.51        63.62        35.93        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-NH-A8F7 TCGA-3L-AA1B TCGA-4N-A93T 
       26.17        91.79        79.69        17.85        15.62         4.80 
TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 
        9.53        39.45        43.76        46.65        43.76        43.43 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2684 TCGA-A6-2685 
       42.90        42.28        44.91        35.11        37.05        37.25 
TCGA-A6-3809 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 
       32.75        32.91        31.63        30.44        29.19        33.53 
TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6140 
       23.61        22.09        22.06        32.71        27.09        24.13 
TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
        8.38        25.18        20.61        24.69        24.39        23.87 
TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-AA-3489 
       19.66        20.28        16.24        24.92        61.84         7.04 
TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
        3.02         1.02        37.05        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        1.02        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3666 
       20.98        13.94        61.02        78.08         6.97         2.01 
TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3681 
       14.01        50.04        47.05        47.01        15.02         5.98 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
        5.03        26.99        35.05         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3845 
       17.98        15.95        38.99        36.95        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
        0.99        31.07        53.00        27.02        18.05        31.00 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3971 
       24.00        33.01        26.01        20.98        34.03        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00D 
       13.05        34.06        25.02        27.02        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00Q TCGA-AA-A00U 
       30.02        34.03        18.05         4.01        42.02        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01G 
       14.99        34.98        15.02        15.02        10.98        12.00 
TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F 
        1.02        26.01        37.02        51.98         2.96        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F 
        2.01         5.03         0.92        22.03        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       40.96        12.16        83.24        22.42        27.42        26.47 
TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
        0.92        27.09         0.95        33.01        21.44        17.82 
TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4315 TCGA-AZ-4323 
       17.26        17.85        19.33        18.84        58.39         1.41 
TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 
       32.94         5.13        22.36        65.00        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       49.41         6.77        29.56         5.23        11.74         3.19 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6717 
       12.69        12.36        12.46        12.39        12.59        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 
       10.06        14.30        17.56       148.01        85.45        70.16 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 
       15.62        51.32        21.99        21.14        82.95       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 
       23.05        20.02        37.02        25.02        26.04        27.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
       15.02        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6676 TCGA-CM-6679 TCGA-CM-6680 
       15.02        11.01        12.95        11.08        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6530 
       45.40        54.61        19.59        56.09        55.92        20.42 
TCGA-D5-6532 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       18.25        15.12         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         7.53        12.39        10.13        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 
        9.04         9.44        11.64        13.35        12.00        10.26 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 
       12.59       140.38        44.32       131.51       135.65         7.76 
TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G 
      139.17        14.04        26.47        81.37       119.93        60.79 
TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 
       98.24        95.18         8.61        11.11        35.74        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 
        8.35        82.39        74.56        67.30        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6320 
       44.68        55.04        85.48        39.42        61.91        26.43 
TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50U 
       26.04        13.78        46.75        74.79        18.18        10.98 
TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GB TCGA-NH-A6GC TCGA-QG-A5YW TCGA-QG-A5YX 
       19.33        19.33        15.65        12.79        29.46        32.98 
TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-SS-A7HO 
        8.42        31.30        21.90        60.13 

  DEL PEAK  7(3P14.2) MUTATED DEL PEAK  7(3P14.2) WILD-TYPE 
                          0.2                           0.0 
  DEL PEAK  7(3P14.2) MUTATED DEL PEAK  7(3P14.2) WILD-TYPE 
                       119.70                        148.01 
  DEL PEAK  7(3P14.2) MUTATED DEL PEAK  7(3P14.2) WILD-TYPE 
                       16.915                        23.560 
[1] "0.2 - 119.7 (16.9)" "0.0 - 148.0 (23.6)"
[1] "hr=" "1.3"
D29V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK  7(3P14.2) MUTATED        10        0        3        25         0
  DEL PEAK  7(3P14.2) WILD-TYPE      64        1       26       107        10
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  7(3P14.2) MUTATED           0         4          1         13
  DEL PEAK  7(3P14.2) WILD-TYPE         1        16          7         46
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK  7(3P14.2) MUTATED           11       12         5         1
  DEL PEAK  7(3P14.2) WILD-TYPE         30       33        12         1
D29V3, multiclass
            clus
vv           DEL PEAK  7(3P14.2) MUTATED DEL PEAK  7(3P14.2) WILD-TYPE
  STAGE I                             10                            64
  STAGE IA                             0                             1
  STAGE II                             3                            26
  STAGE IIA                           25                           107
  STAGE IIB                            0                            10
  STAGE IIC                            0                             1
  STAGE III                            4                            16
  STAGE IIIA                           1                             7
  STAGE IIIB                          13                            46
  STAGE IIIC                          11                            30
  STAGE IV                            12                            33
  STAGE IVA                            5                            12
  STAGE IVB                            1                             1
[1] 13  2
[1] 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(3P14.2) MUTATED     3   9  61  14
  DEL PEAK  7(3P14.2) WILD-TYPE   8  68 244  41
D29V4, multiclass
    clus
vv   DEL PEAK  7(3P14.2) MUTATED DEL PEAK  7(3P14.2) WILD-TYPE
  T1                           3                             8
  T2                           9                            68
  T3                          61                           244
  T4                          14                            41
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2
  DEL PEAK  7(3P14.2) MUTATED    42  23  22
  DEL PEAK  7(3P14.2) WILD-TYPE 220  82  60
D29V5, multiclass
    clus
vv   DEL PEAK  7(3P14.2) MUTATED DEL PEAK  7(3P14.2) WILD-TYPE
  N0                          42                           220
  N1                          23                            82
  N2                          22                            60
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V6, binary
                               cls
clus                              0   1
  DEL PEAK  7(3P14.2) MUTATED    56  18
  DEL PEAK  7(3P14.2) WILD-TYPE 272  46
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(3P14.2) MUTATED     56   18
  DEL PEAK  7(3P14.2) WILD-TYPE  272   46
   clus
vv  DEL PEAK  7(3P14.2) MUTATED DEL PEAK  7(3P14.2) WILD-TYPE
  0                          56                           272
  1                          18                            46
[1] 2 2
[1] FALSE
D29V7, binary
                               cls
clus                              0   1
  DEL PEAK  7(3P14.2) MUTATED    43  44
  DEL PEAK  7(3P14.2) WILD-TYPE 170 192
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(3P14.2) MUTATED     43   44
  DEL PEAK  7(3P14.2) WILD-TYPE  170  192
        clus
vv       DEL PEAK  7(3P14.2) MUTATED DEL PEAK  7(3P14.2) WILD-TYPE
  FEMALE                          43                           170
  MALE                            44                           192
[1] 2 2
[1] FALSE
D29V8, binary
                               cls
clus                              0   1
  DEL PEAK  7(3P14.2) MUTATED    74   0
  DEL PEAK  7(3P14.2) WILD-TYPE 296   9
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(3P14.2) MUTATED     74    0
  DEL PEAK  7(3P14.2) WILD-TYPE  296    9
     clus
vv    DEL PEAK  7(3P14.2) MUTATED DEL PEAK  7(3P14.2) WILD-TYPE
  NO                           74                           296
  YES                           0                             9
[1] 2 2
[1] FALSE
D29V9, binary
                               cls
clus                              0   1
  DEL PEAK  7(3P14.2) MUTATED    78   9
  DEL PEAK  7(3P14.2) WILD-TYPE 304  53
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(3P14.2) MUTATED     78    9
  DEL PEAK  7(3P14.2) WILD-TYPE  304   53
                               clus
vv                              DEL PEAK  7(3P14.2) MUTATED
  COLON ADENOCARCINOMA                                   78
  COLON MUCINOUS ADENOCARCINOMA                           9
                               clus
vv                              DEL PEAK  7(3P14.2) WILD-TYPE
  COLON ADENOCARCINOMA                                    304
  COLON MUCINOUS ADENOCARCINOMA                            53
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  7(3P14.2) MUTATED    62   1   6   4
  DEL PEAK  7(3P14.2) WILD-TYPE 261   3  19  21
D29V10, multiclass
    clus
vv   DEL PEAK  7(3P14.2) MUTATED DEL PEAK  7(3P14.2) WILD-TYPE
  R0                          62                           261
  R1                           1                             3
  R2                           6                            19
  RX                           4                            21
[1] 4 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, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  7(3P14.2) MUTATED                                  0     2
  DEL PEAK  7(3P14.2) WILD-TYPE                                1     9
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  7(3P14.2) MUTATED                          14    39
  DEL PEAK  7(3P14.2) WILD-TYPE                        45   173
D29V12, multiclass
                                  clus
vv                                 DEL PEAK  7(3P14.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      2
  BLACK OR AFRICAN AMERICAN                                 14
  WHITE                                                     39
                                  clus
vv                                 DEL PEAK  7(3P14.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        9
  BLACK OR AFRICAN AMERICAN                                   45
  WHITE                                                      173
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V13, binary
                               cls
clus                              0   1
  DEL PEAK  7(3P14.2) MUTATED     1  52
  DEL PEAK  7(3P14.2) WILD-TYPE   3 217
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(3P14.2) MUTATED      1   52
  DEL PEAK  7(3P14.2) WILD-TYPE    3  217
                        clus
vv                       DEL PEAK  7(3P14.2) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          52
                        clus
vv                       DEL PEAK  7(3P14.2) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           217
[1] 2 2
[1] FALSE

Clustering(30) Variable = DEL PEAK  8(3Q26.31) MUTATION ANALYSIS
D30V1, survival
                                sevent
clus2                              0   1
  DEL PEAK  8(3Q26.31) MUTATED    36  10
  DEL PEAK  8(3Q26.31) WILD-TYPE 299  91
  DEL PEAK  8(3Q26.31) MUTATED DEL PEAK  8(3Q26.31) WILD-TYPE 
                            46                            390 
  DEL PEAK  8(3Q26.31) MUTATED DEL PEAK  8(3Q26.31) WILD-TYPE 
                            10                             91 
$`DEL PEAK  8(3Q26.31) MUTATED`
TCGA-A6-4105 TCGA-AA-3662 TCGA-AA-3697 TCGA-AA-3939 TCGA-AD-6548 TCGA-A6-2683 
       14.53         6.05        85.05        12.99        21.37        16.57 
TCGA-A6-2685 TCGA-A6-3807 TCGA-A6-4107 TCGA-AA-3517 TCGA-AA-3529 TCGA-AA-3811 
       37.25        34.65        32.45        38.99         0.00        10.06 
TCGA-AA-3855 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00O 
       32.05         2.01        21.99         7.96        13.94        27.02 
TCGA-AA-A01F TCGA-AA-A01T TCGA-AD-6899 TCGA-AD-A5EK TCGA-AY-5543 TCGA-AZ-6600 
       32.02        33.04         5.79        16.44        33.01        12.10 
TCGA-CA-6716 TCGA-CM-4752 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-6677 TCGA-CM-6678 
       12.20        13.02        15.02         5.03        11.08        11.01 
TCGA-D5-5540 TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6929 
       56.09        20.19        25.48        43.27        17.85        13.41 
TCGA-D5-6932 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A28F TCGA-G4-6297 TCGA-G4-6317 
       11.38         7.50       131.51        35.97        82.39        36.00 
TCGA-NH-A6GB TCGA-QG-A5YV TCGA-RU-A8FL TCGA-T9-A92H 
       15.65        42.77        38.70        11.90 

$`DEL PEAK  8(3Q26.31) WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3506 
       24.33        45.60        13.94        24.16         1.02        58.03 
TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 
       13.02        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 
       34.03         0.99        13.02        17.95        23.01        19.99 
TCGA-AA-3562 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3713 TCGA-AA-3715 
       19.99         0.92        19.00        36.00        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3950 TCGA-AA-3952 
       14.93        31.07        24.03        29.98        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 
       39.06        15.52        25.08        10.88        75.95       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6298 
      100.01         1.94        49.08         5.88        28.21        23.51 
TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       63.62        35.93        22.09        35.80        26.17        91.79 
TCGA-G4-6628 TCGA-NH-A8F7 TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 
       79.69        17.85        15.62         4.80        12.66         1.61 
TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 
        9.53        39.45        43.76        46.65        43.76        43.43 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2684 TCGA-A6-2686 
       42.90        42.28        44.91        35.11        37.05        37.02 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 
       33.53        23.61        22.09        22.06        32.71        29.16 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       27.09        22.52        24.13         8.38        25.08        25.18 
TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       20.61        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B 
       19.66        20.28        16.24        24.92        61.84        56.25 
TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 
        9.63         5.03         7.04         3.02         1.02        37.05 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3518 TCGA-AA-3519 
       35.01        63.98         6.97         1.02         1.02         9.07 
TCGA-AA-3526 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
       19.07        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       61.02        78.08         6.97        54.02         2.01        14.01 
TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
       50.04        47.05        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
       37.05         5.03        26.99        35.05         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 
        1.02        17.98        15.95        38.99        36.95        37.02 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
       36.03         0.99        31.07        53.00        17.03        27.02 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       18.05        31.00         2.01        24.00        33.01        26.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
       20.98        34.03        16.08        13.05        34.06        25.02 
TCGA-AA-3982 TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        27.02        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        18.05         4.01        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01G 
       14.99        34.98        15.02        15.02        10.98        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F 
        1.02        26.01        37.02        51.98         2.96        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03         0.92        22.03        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6901 
       18.05        40.96        12.16        83.24        24.53        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 
       27.42        26.47         0.46         0.92        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L 
       16.31         0.95         0.20        21.44        17.82        17.26 
TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 
       17.85        19.33        18.84       109.28        58.39         1.41 
TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 
        5.65        32.94         5.13        22.36        65.00        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       88.21        49.41         6.77        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 
        3.19        12.69        12.36        12.46        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        70.16        15.62        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-5341 TCGA-CM-5344 
       25.02        26.04         8.02        27.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       22.98        30.08        32.02        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       12.95        13.05        11.08        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 
       54.61        19.59        55.92        20.42        17.75        18.25 
TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       15.12         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        7.53        12.39        10.13        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 
        9.44        11.64        13.35        12.00        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 
       12.59       140.38        44.32       135.65         7.76       139.17 
TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H 
       14.04        26.47        81.37       119.93        60.79       117.07 
TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 
       98.24        95.18         8.61        31.96        11.11        35.74 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       43.04        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6295 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 
      133.18         8.35        74.56        67.30        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6320 
       44.68        55.04        85.48        39.42        61.91        26.43 
TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50U 
       26.04        13.78        46.75        74.79        18.18        10.98 
TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GC TCGA-NH-A8F8 TCGA-QG-A5YW 
       19.33        19.33         9.93        12.79        16.80        29.46 
TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-SS-A7HO TCGA-WS-AB45 
       32.98         8.42        31.30        21.90        60.13        70.03 

  DEL PEAK  8(3Q26.31) MUTATED DEL PEAK  8(3Q26.31) WILD-TYPE 
                             0                              0 
  DEL PEAK  8(3Q26.31) MUTATED DEL PEAK  8(3Q26.31) WILD-TYPE 
                        131.51                         148.01 
  DEL PEAK  8(3Q26.31) MUTATED DEL PEAK  8(3Q26.31) WILD-TYPE 
                         17.21                          22.39 
[1] "0.0 - 131.5 (17.2)" "0.0 - 148.0 (22.4)"
[1] "hr=" "1"  
D30V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK  8(3Q26.31) MUTATED         4        0        1        16         0
  DEL PEAK  8(3Q26.31) WILD-TYPE      70        1       28       116        10
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  8(3Q26.31) MUTATED           0         2          0          4
  DEL PEAK  8(3Q26.31) WILD-TYPE         1        18          8         55
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK  8(3Q26.31) MUTATED            9        6         3         0
  DEL PEAK  8(3Q26.31) WILD-TYPE         32       39        14         2
D30V3, multiclass
            clus
vv           DEL PEAK  8(3Q26.31) MUTATED DEL PEAK  8(3Q26.31) WILD-TYPE
  STAGE I                               4                             70
  STAGE IA                              0                              1
  STAGE II                              1                             28
  STAGE IIA                            16                            116
  STAGE IIB                             0                             10
  STAGE IIC                             0                              1
  STAGE III                             2                             18
  STAGE IIIA                            0                              8
  STAGE IIIB                            4                             55
  STAGE IIIC                            9                             32
  STAGE IV                              6                             39
  STAGE IVA                             3                             14
  STAGE IVB                             0                              2
[1] 13  2
[1] 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(3Q26.31) MUTATED     0   4  35   7
  DEL PEAK  8(3Q26.31) WILD-TYPE  11  73 270  48
D30V4, multiclass
    clus
vv   DEL PEAK  8(3Q26.31) MUTATED DEL PEAK  8(3Q26.31) WILD-TYPE
  T1                            0                             11
  T2                            4                             73
  T3                           35                            270
  T4                            7                             48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2
  DEL PEAK  8(3Q26.31) MUTATED    23  10  13
  DEL PEAK  8(3Q26.31) WILD-TYPE 239  95  69
D30V5, multiclass
    clus
vv   DEL PEAK  8(3Q26.31) MUTATED DEL PEAK  8(3Q26.31) WILD-TYPE
  N0                           23                            239
  N1                           10                             95
  N2                           13                             69
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V6, binary
                                cls
clus                               0   1
  DEL PEAK  8(3Q26.31) MUTATED    31   9
  DEL PEAK  8(3Q26.31) WILD-TYPE 297  55
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  8(3Q26.31) MUTATED     31    9
  DEL PEAK  8(3Q26.31) WILD-TYPE  297   55
   clus
vv  DEL PEAK  8(3Q26.31) MUTATED DEL PEAK  8(3Q26.31) WILD-TYPE
  0                           31                            297
  1                            9                             55
[1] 2 2
[1] FALSE
D30V7, binary
                                cls
clus                               0   1
  DEL PEAK  8(3Q26.31) MUTATED    24  22
  DEL PEAK  8(3Q26.31) WILD-TYPE 189 214
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  8(3Q26.31) MUTATED     24   22
  DEL PEAK  8(3Q26.31) WILD-TYPE  189  214
        clus
vv       DEL PEAK  8(3Q26.31) MUTATED DEL PEAK  8(3Q26.31) WILD-TYPE
  FEMALE                           24                            189
  MALE                             22                            214
[1] 2 2
[1] FALSE
D30V8, binary
                                cls
clus                               0   1
  DEL PEAK  8(3Q26.31) MUTATED    41   0
  DEL PEAK  8(3Q26.31) WILD-TYPE 329   9
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  8(3Q26.31) MUTATED     41    0
  DEL PEAK  8(3Q26.31) WILD-TYPE  329    9
     clus
vv    DEL PEAK  8(3Q26.31) MUTATED DEL PEAK  8(3Q26.31) WILD-TYPE
  NO                            41                            329
  YES                            0                              9
[1] 2 2
[1] FALSE
D30V9, binary
                                cls
clus                               0   1
  DEL PEAK  8(3Q26.31) MUTATED    43   3
  DEL PEAK  8(3Q26.31) WILD-TYPE 339  59
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  8(3Q26.31) MUTATED     43    3
  DEL PEAK  8(3Q26.31) WILD-TYPE  339   59
                               clus
vv                              DEL PEAK  8(3Q26.31) MUTATED
  COLON ADENOCARCINOMA                                    43
  COLON MUCINOUS ADENOCARCINOMA                            3
                               clus
vv                              DEL PEAK  8(3Q26.31) WILD-TYPE
  COLON ADENOCARCINOMA                                     339
  COLON MUCINOUS ADENOCARCINOMA                             59
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK  8(3Q26.31) MUTATED    36   0   2   1
  DEL PEAK  8(3Q26.31) WILD-TYPE 287   4  23  24
D30V10, multiclass
    clus
vv   DEL PEAK  8(3Q26.31) MUTATED DEL PEAK  8(3Q26.31) WILD-TYPE
  R0                           36                            287
  R1                            0                              4
  R2                            2                             23
  RX                            1                             24
[1] 4 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, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  8(3Q26.31) MUTATED                                  0     1
  DEL PEAK  8(3Q26.31) WILD-TYPE                                1    10
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  8(3Q26.31) MUTATED                           9    22
  DEL PEAK  8(3Q26.31) WILD-TYPE                        50   190
D30V12, multiclass
                                  clus
vv                                 DEL PEAK  8(3Q26.31) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       1
  BLACK OR AFRICAN AMERICAN                                   9
  WHITE                                                      22
                                  clus
vv                                 DEL PEAK  8(3Q26.31) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        10
  BLACK OR AFRICAN AMERICAN                                    50
  WHITE                                                       190
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V13, binary
                                cls
clus                               0   1
  DEL PEAK  8(3Q26.31) MUTATED     0  31
  DEL PEAK  8(3Q26.31) WILD-TYPE   4 238
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  8(3Q26.31) MUTATED      0   31
  DEL PEAK  8(3Q26.31) WILD-TYPE    4  238
                        clus
vv                       DEL PEAK  8(3Q26.31) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           31
                        clus
vv                       DEL PEAK  8(3Q26.31) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            238
[1] 2 2
[1] FALSE

Clustering(31) Variable = DEL PEAK  9(4P16.2) MUTATION ANALYSIS
D31V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  9(4P16.2) MUTATED    96  37
  DEL PEAK  9(4P16.2) WILD-TYPE 239  64
  DEL PEAK  9(4P16.2) MUTATED DEL PEAK  9(4P16.2) WILD-TYPE 
                          133                           303 
  DEL PEAK  9(4P16.2) MUTATED DEL PEAK  9(4P16.2) WILD-TYPE 
                           37                            64 
$`DEL PEAK  9(4P16.2) MUTATED`
TCGA-A6-2682 TCGA-A6-4105 TCGA-AA-3522 TCGA-AA-3531 TCGA-AA-3552 TCGA-AA-3562 
       13.94        14.53        37.05        34.03        13.02        19.99 
TCGA-AA-3662 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 
        6.05        36.00        85.05        31.07        24.03        29.98 
TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-CK-5912 TCGA-DM-A285 
       12.99         2.01        50.99        26.01        49.08         5.88 
TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6625 TCGA-4N-A93T TCGA-5M-AAT4 TCGA-5M-AATE 
       23.51        63.62        91.79         4.80         1.61        39.45 
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2684 
       43.76        43.76        44.91        35.11        16.57        37.05 
TCGA-A6-2686 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5659 TCGA-A6-5667 TCGA-A6-6648 
       37.02        36.53        32.45        30.44        29.16        25.18 
TCGA-A6-6651 TCGA-A6-6654 TCGA-A6-6782 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU 
       21.76        23.87        20.28        61.84        56.25         9.63 
TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3517 TCGA-AA-3542 TCGA-AA-3549 TCGA-AA-3664 
        5.03         7.04        38.99        12.99        21.01        54.02 
TCGA-AA-3666 TCGA-AA-3673 TCGA-AA-3679 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 
        2.01        50.04        15.02        38.99        36.95        37.02 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       17.03        10.06        33.07        32.05         0.99        31.07 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3930 TCGA-AA-3955 TCGA-AA-3966 TCGA-AA-3968 
       53.00        17.03         2.01        20.98         2.01        21.99 
TCGA-AA-A00F TCGA-AA-A00Q TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01K TCGA-AA-A01T 
       34.03        42.02        15.02        32.02        31.00        33.04 
TCGA-AA-A01X TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02W TCGA-AD-6899 
       26.01         2.96        39.98         2.01        41.00         5.79 
TCGA-AD-6901 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       22.42        26.47        14.50         0.95        33.01         0.20 
TCGA-AY-A69D TCGA-AZ-4614 TCGA-AZ-4616 TCGA-AZ-4684 TCGA-AZ-6600 TCGA-AZ-6603 
       17.85         5.65         5.13        65.00        12.10        29.56 
TCGA-AZ-6607 TCGA-CA-5256 TCGA-CA-5797 TCGA-CM-4750 TCGA-CM-5341 TCGA-CM-5344 
        3.19        12.46        12.59         8.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6169 
       22.98        15.02        17.03        14.04        29.03        13.02 
TCGA-CM-6170 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-D5-5537 TCGA-D5-5540 
       15.02        11.08        11.01        10.06        45.40        56.09 
TCGA-D5-6529 TCGA-D5-6531 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6932 
       20.19        17.75        14.30         9.04        13.41        11.38 
TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A288 TCGA-DM-A28A TCGA-F4-6704 TCGA-F4-6807 
       12.59         7.50        14.04        26.47         1.55        43.04 
TCGA-F4-6808 TCGA-F4-6855 TCGA-G4-6295 TCGA-G4-6315 TCGA-G4-6626 TCGA-NH-A50T 
       33.67        47.41         8.35        61.91        46.75        18.18 
TCGA-NH-A50U TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QL-A97D TCGA-SS-A7HO 
       10.98        16.80        42.77        29.46        21.90        60.13 
TCGA-T9-A92H 
       11.90 

$`DEL PEAK  9(4P16.2) WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3506 TCGA-AA-3516 
       24.33        45.60        24.16         1.02        58.03        13.02 
TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3543 TCGA-AA-3554 
       24.03        36.03         8.05        19.07         0.99        17.95 
TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3713 TCGA-AA-3715 
       23.01        19.99         0.92        19.00        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3950 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       14.93        24.00        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 
       39.06        21.37        15.52        25.08        10.88        75.95 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-G4-6294 TCGA-G4-6314 TCGA-G4-6321 
      106.75       100.01         1.94        28.21        35.93        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 TCGA-NH-A8F7 TCGA-3L-AA1B TCGA-4T-AA8H 
       35.80        26.17        79.69        17.85        15.62        12.66 
TCGA-5M-AAT6 TCGA-A6-2672 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2685 
        9.53        46.65        43.43        42.90        42.28        37.25 
TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 
       34.65        32.75        32.91        31.63        29.19        33.53 
TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 
       23.61        22.09        22.06        32.71        27.09        22.52 
TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6653 
       24.13         8.38        25.08        20.61        24.69        24.39 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 TCGA-AA-3492 TCGA-AA-3494 
       20.12        19.66        16.24        24.92         3.02         1.02 
TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3518 
       37.05        35.01        63.98         6.97         1.02         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       14.01        33.99        24.00        29.95        20.98        13.94 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3667 TCGA-AA-3675 TCGA-AA-3678 
       61.02        78.08         6.97        14.01        47.05        47.01 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        26.99        10.06 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3845 TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3869 TCGA-AA-3875 
        0.00         0.00         0.00        36.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3956 TCGA-AA-3971 
       31.00        24.00        33.01        26.01        34.03        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       13.05        34.06        25.02        27.02         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K 
       13.94        38.04        19.00        30.02        18.05        18.05 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 
        4.01        27.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q 
       15.02        10.98        12.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02J 
       35.01         1.02         1.02        37.02        51.98         5.03 
TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        22.03        39.98        18.05        40.96        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6963 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 
       83.24        24.53        27.42        16.44         0.46         0.92 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A71X 
       27.09        16.31        21.44        17.82        17.26        19.33 
TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4682 
       18.84       109.28        58.39         1.41        32.94        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6605 TCGA-AZ-6606 
       62.79        88.21        49.41         6.77         5.23        11.74 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
       12.69        12.36        12.39        12.59        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 
       10.06        14.30        17.56       148.01        85.45        70.16 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 
      124.27        23.05        20.02        37.02        25.02        26.04 
TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       27.02        13.02        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       15.02        15.02        12.00        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       12.99        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6680 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6530 TCGA-D5-6532 
       12.03        54.61        19.59        55.92        20.42        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 
       12.43         9.44        11.64        13.35        12.00        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 
       13.32       140.38        44.32       131.51       135.65         7.76 
TCGA-DM-A282 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
      139.17        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 
       98.24        95.18         8.61        31.96        11.11        35.74 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6809 
       35.74         6.18        47.87        34.42        41.42        13.25 
TCGA-F4-6854 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6302 
        0.53        35.31       133.18        82.39        74.56        67.30 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 
       65.85        53.62        44.68        55.04        85.48        39.42 
TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6627 TCGA-NH-A50V 
       36.00        26.43        26.04        13.78        74.79        19.33 
TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-QG-A5YX TCGA-QG-A5Z1 
       19.33         9.93        15.65        12.79        32.98         8.42 
TCGA-QG-A5Z2 TCGA-RU-A8FL TCGA-WS-AB45 
       31.30        38.70        70.03 

  DEL PEAK  9(4P16.2) MUTATED DEL PEAK  9(4P16.2) WILD-TYPE 
                          0.2                           0.0 
  DEL PEAK  9(4P16.2) MUTATED DEL PEAK  9(4P16.2) WILD-TYPE 
                        91.79                        148.01 
  DEL PEAK  9(4P16.2) MUTATED DEL PEAK  9(4P16.2) WILD-TYPE 
                        21.99                         22.09 
[1] "0.2 - 91.8 (22.0)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.6"
D31V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK  9(4P16.2) MUTATED        16        0        7        33         3
  DEL PEAK  9(4P16.2) WILD-TYPE      58        1       22        99         7
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  9(4P16.2) MUTATED           0         4          5         16
  DEL PEAK  9(4P16.2) WILD-TYPE         1        16          3         43
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK  9(4P16.2) MUTATED           17       27         7         0
  DEL PEAK  9(4P16.2) WILD-TYPE         24       18        10         2
D31V3, multiclass
            clus
vv           DEL PEAK  9(4P16.2) MUTATED DEL PEAK  9(4P16.2) WILD-TYPE
  STAGE I                             16                            58
  STAGE IA                             0                             1
  STAGE II                             7                            22
  STAGE IIA                           33                            99
  STAGE IIB                            3                             7
  STAGE IIC                            0                             1
  STAGE III                            4                            16
  STAGE IIIA                           5                             3
  STAGE IIIB                          16                            43
  STAGE IIIC                          17                            24
  STAGE IV                            27                            18
  STAGE IVA                            7                            10
  STAGE IVB                            0                             2
[1] 13  2
[1] 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(4P16.2) MUTATED     4  20  93  21
  DEL PEAK  9(4P16.2) WILD-TYPE   7  57 212  34
D31V4, multiclass
    clus
vv   DEL PEAK  9(4P16.2) MUTATED DEL PEAK  9(4P16.2) WILD-TYPE
  T1                           4                             7
  T2                          20                            57
  T3                          93                           212
  T4                          21                            34
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2
  DEL PEAK  9(4P16.2) MUTATED    63  39  36
  DEL PEAK  9(4P16.2) WILD-TYPE 199  66  46
D31V5, multiclass
    clus
vv   DEL PEAK  9(4P16.2) MUTATED DEL PEAK  9(4P16.2) WILD-TYPE
  N0                          63                           199
  N1                          39                            66
  N2                          36                            46
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V6, binary
                               cls
clus                              0   1
  DEL PEAK  9(4P16.2) MUTATED    85  34
  DEL PEAK  9(4P16.2) WILD-TYPE 243  30
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(4P16.2) MUTATED     85   34
  DEL PEAK  9(4P16.2) WILD-TYPE  243   30
   clus
vv  DEL PEAK  9(4P16.2) MUTATED DEL PEAK  9(4P16.2) WILD-TYPE
  0                          85                           243
  1                          34                            30
[1] 2 2
[1] FALSE
D31V7, binary
                               cls
clus                              0   1
  DEL PEAK  9(4P16.2) MUTATED    61  77
  DEL PEAK  9(4P16.2) WILD-TYPE 152 159
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(4P16.2) MUTATED     61   77
  DEL PEAK  9(4P16.2) WILD-TYPE  152  159
        clus
vv       DEL PEAK  9(4P16.2) MUTATED DEL PEAK  9(4P16.2) WILD-TYPE
  FEMALE                          61                           152
  MALE                            77                           159
[1] 2 2
[1] FALSE
D31V8, binary
                               cls
clus                              0   1
  DEL PEAK  9(4P16.2) MUTATED   114   4
  DEL PEAK  9(4P16.2) WILD-TYPE 256   5
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(4P16.2) MUTATED    114    4
  DEL PEAK  9(4P16.2) WILD-TYPE  256    5
     clus
vv    DEL PEAK  9(4P16.2) MUTATED DEL PEAK  9(4P16.2) WILD-TYPE
  NO                          114                           256
  YES                           4                             5
[1] 2 2
[1] FALSE
D31V9, binary
                               cls
clus                              0   1
  DEL PEAK  9(4P16.2) MUTATED   126  11
  DEL PEAK  9(4P16.2) WILD-TYPE 256  51
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(4P16.2) MUTATED    126   11
  DEL PEAK  9(4P16.2) WILD-TYPE  256   51
                               clus
vv                              DEL PEAK  9(4P16.2) MUTATED
  COLON ADENOCARCINOMA                                  126
  COLON MUCINOUS ADENOCARCINOMA                          11
                               clus
vv                              DEL PEAK  9(4P16.2) WILD-TYPE
  COLON ADENOCARCINOMA                                    256
  COLON MUCINOUS ADENOCARCINOMA                            51
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  9(4P16.2) MUTATED    98   1  13   5
  DEL PEAK  9(4P16.2) WILD-TYPE 225   3  12  20
D31V10, multiclass
    clus
vv   DEL PEAK  9(4P16.2) MUTATED DEL PEAK  9(4P16.2) WILD-TYPE
  R0                          98                           225
  R1                           1                             3
  R2                          13                            12
  RX                           5                            20
[1] 4 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, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  9(4P16.2) MUTATED                                  1     2
  DEL PEAK  9(4P16.2) WILD-TYPE                                0     9
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  9(4P16.2) MUTATED                          20    62
  DEL PEAK  9(4P16.2) WILD-TYPE                        39   150
D31V12, multiclass
                                  clus
vv                                 DEL PEAK  9(4P16.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      2
  BLACK OR AFRICAN AMERICAN                                 20
  WHITE                                                     62
                                  clus
vv                                 DEL PEAK  9(4P16.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        9
  BLACK OR AFRICAN AMERICAN                                   39
  WHITE                                                      150
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V13, binary
                               cls
clus                              0   1
  DEL PEAK  9(4P16.2) MUTATED     3  77
  DEL PEAK  9(4P16.2) WILD-TYPE   1 192
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(4P16.2) MUTATED      3   77
  DEL PEAK  9(4P16.2) WILD-TYPE    1  192
                        clus
vv                       DEL PEAK  9(4P16.2) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                          77
                        clus
vv                       DEL PEAK  9(4P16.2) WILD-TYPE
  HISPANIC OR LATINO                                 1
  NOT HISPANIC OR LATINO                           192
[1] 2 2
[1] FALSE

Clustering(32) Variable = DEL PEAK 10(4Q22.1) MUTATION ANALYSIS
D32V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 10(4Q22.1) MUTATED   106  41
  DEL PEAK 10(4Q22.1) WILD-TYPE 229  60
  DEL PEAK 10(4Q22.1) MUTATED DEL PEAK 10(4Q22.1) WILD-TYPE 
                          147                           289 
  DEL PEAK 10(4Q22.1) MUTATED DEL PEAK 10(4Q22.1) WILD-TYPE 
                           41                            60 
$`DEL PEAK 10(4Q22.1) MUTATED`
TCGA-A6-2682 TCGA-A6-6649 TCGA-AA-3522 TCGA-AA-3531 TCGA-AA-3552 TCGA-AA-3562 
       13.94        24.16        37.05        34.03        13.02        19.99 
TCGA-AA-3662 TCGA-AA-3692 TCGA-AA-3715 TCGA-AA-3860 TCGA-AA-3952 TCGA-AA-3972 
        6.05        36.00        19.04        31.07         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AZ-4681 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6294 
       26.01        24.00       106.75        49.08         5.88        28.21 
TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6625 TCGA-4N-A93T TCGA-5M-AAT4 TCGA-5M-AATE 
       23.51        63.62        91.79         4.80         1.61        39.45 
TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2684 
       43.76        43.43        44.91        35.11        16.57        37.05 
TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5660 TCGA-A6-5667 TCGA-A6-6650 
       34.65        36.53        32.45        29.19        29.16        20.61 
TCGA-A6-6651 TCGA-A6-6654 TCGA-A6-6782 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU 
       21.76        23.87        20.28        61.84        56.25         9.63 
TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3517 TCGA-AA-3529 
        5.03         7.04        63.98         6.97        38.99         0.00 
TCGA-AA-3532 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3666 TCGA-AA-3673 TCGA-AA-3685 
       29.00        33.99        21.01         2.01        50.04        37.05 
TCGA-AA-3811 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3846 TCGA-AA-3848 
       10.06        38.99        36.95        37.02        17.03        10.06 
TCGA-AA-3851 TCGA-AA-3856 TCGA-AA-3866 TCGA-AA-3930 TCGA-AA-3955 TCGA-AA-3956 
       33.07         0.99        17.03         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3982 TCGA-AA-A00F TCGA-AA-A00Q TCGA-AA-A00U 
        2.01        21.99        27.02        34.03        42.02        17.03 
TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01X TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02W 
       15.02        32.02        26.01         2.96        39.98        41.00 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 
        5.79        22.42        26.47        14.50        16.31         0.95 
TCGA-AY-6196 TCGA-AY-A69D TCGA-AY-A8YK TCGA-AZ-4616 TCGA-AZ-4684 TCGA-AZ-6600 
        0.20        17.85        18.84         5.13        65.00        12.10 
TCGA-AZ-6603 TCGA-CA-5256 TCGA-CA-5797 TCGA-CA-6719 TCGA-CK-4948 TCGA-CM-4744 
       29.56        12.46        12.59        14.30       148.01        20.02 
TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5862 TCGA-CM-5864 
        8.02        13.02        29.06        22.03         5.03        15.02 
TCGA-CM-5868 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 
       17.03        14.04        29.03        13.02        15.02        11.01 
TCGA-CM-6675 TCGA-CM-6677 TCGA-CM-6678 TCGA-D5-5537 TCGA-D5-5540 TCGA-D5-6529 
       13.05        11.08        11.01        45.40        56.09        20.19 
TCGA-D5-6531 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6924 TCGA-D5-6926 
       17.75        25.48        43.27        15.12        14.30         9.04 
TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 TCGA-DM-A0XD TCGA-DM-A1D8 TCGA-DM-A1DA 
       13.41        12.00        11.38        24.43        12.59         7.50 
TCGA-DM-A1DB TCGA-DM-A288 TCGA-DM-A28F TCGA-F4-6460 TCGA-F4-6807 TCGA-F4-6808 
       44.32        14.04        35.97        31.96        43.04        33.67 
TCGA-F4-6855 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6315 TCGA-G4-6626 TCGA-NH-A50T 
       47.41         8.35        82.39        61.91        46.75        18.18 
TCGA-NH-A50U TCGA-NH-A6GA TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QL-A97D 
       10.98         9.93        16.80        42.77        29.46        21.90 
TCGA-RU-A8FL TCGA-SS-A7HO TCGA-T9-A92H 
       38.70        60.13        11.90 

$`DEL PEAK 10(4Q22.1) WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-4105 TCGA-AA-3496 TCGA-AA-3506 TCGA-AA-3516 
       24.33        45.60        14.53         1.02        58.03        13.02 
TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3543 TCGA-AA-3554 
       24.03        36.03         8.05        19.07         0.99        17.95 
TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3697 TCGA-AA-3713 
       23.01        19.99         0.92        19.00        85.05        19.04 
TCGA-AA-3844 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3986 
       14.93        24.03        29.98        12.99        24.00        19.07 
TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 
       38.04        21.99        39.06        21.37        15.52        25.08 
TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-G4-6314 TCGA-G4-6321 
       10.88        75.95       100.01         1.94        35.93        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 TCGA-NH-A8F7 TCGA-3L-AA1B TCGA-4T-AA8H 
       35.80        26.17        79.69        17.85        15.62        12.66 
TCGA-5M-AAT6 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2685 
        9.53        43.76        46.65        42.90        42.28        37.25 
TCGA-A6-2686 TCGA-A6-3809 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 
       37.02        32.75        32.91        31.63        30.44        33.53 
TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 
       23.61        22.09        22.06        32.71        27.09        22.52 
TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6652 TCGA-A6-6653 
       24.13         8.38        25.08        25.18        24.69        24.39 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 TCGA-AA-3492 TCGA-AA-3494 
       20.12        19.66        16.24        24.92         3.02         1.02 
TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3514 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
       37.05        35.01         1.02         1.02         9.07        19.07 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3553 TCGA-AA-3555 
       29.00        26.01        12.99        14.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         6.97        54.02 
TCGA-AA-3667 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
       14.01        47.05        47.01        15.02        11.01         5.98 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
        5.03        26.99        35.05         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3845 TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3854 
       17.98        15.95         0.00         0.00         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       32.05        31.07        53.00        27.02        18.05        31.00 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       24.00        33.01        26.01        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       25.02         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R 
       30.02        18.05        18.05         4.01        27.02         0.99 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I 
       14.99        34.98        15.02        10.98        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O 
        1.02        37.02        51.98         2.01         5.03         0.92 
TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6889 
       22.03        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6963 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 
       24.53        27.42        16.44         0.46         0.92        27.09 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A71X TCGA-AZ-4308 
       33.01        21.44        17.82        17.26        19.33       109.28 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.65        32.94        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       88.21        49.41         6.77         5.23        11.74         3.19 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
       12.69        12.36        12.39        12.59        12.20        12.76 
TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 
       10.06        17.56        85.45        70.16        15.62        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14        82.95         2.01       124.27        23.05 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-5348 TCGA-CM-5349 
       37.02        25.02        26.04        27.02        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6165 
       32.02        15.02        15.02        15.02        12.00        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6676 
       21.99        14.99        12.99        14.04        12.95        11.08 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6530 
       10.06        12.03        54.61        19.59        55.92        20.42 
TCGA-D5-6532 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       18.25        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6927 
       15.58         7.53        12.39        10.13        12.43         9.44 
TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XF TCGA-DM-A1D0 
       11.64        13.35        10.26       119.70        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1HA TCGA-DM-A1HB 
       92.75        49.91        13.32       140.38       131.51       135.65 
TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G 
        7.76       139.17        26.47        81.37       119.93        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6461 TCGA-F4-6463 
      117.07        98.24        95.18         8.61        11.11        35.74 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6302 
       13.25         0.53        35.31       133.18        74.56        67.30 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 
       65.85        53.62        44.68        55.04        85.48        39.42 
TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6627 TCGA-NH-A50V 
       36.00        26.43        26.04        13.78        74.79        19.33 
TCGA-NH-A5IV TCGA-NH-A6GB TCGA-NH-A6GC TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 
       19.33        15.65        12.79        32.98         8.42        31.30 
TCGA-WS-AB45 
       70.03 

  DEL PEAK 10(4Q22.1) MUTATED DEL PEAK 10(4Q22.1) WILD-TYPE 
                            0                             0 
  DEL PEAK 10(4Q22.1) MUTATED DEL PEAK 10(4Q22.1) WILD-TYPE 
                       148.01                        140.38 
  DEL PEAK 10(4Q22.1) MUTATED DEL PEAK 10(4Q22.1) WILD-TYPE 
                        21.90                         22.09 
[1] "0.0 - 148.0 (21.9)" "0.0 - 140.4 (22.1)"
[1] "hr=" "1.5"
D32V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 10(4Q22.1) MUTATED        14        0        8        40         3
  DEL PEAK 10(4Q22.1) WILD-TYPE      60        1       21        92         7
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 10(4Q22.1) MUTATED           0         4          5         23
  DEL PEAK 10(4Q22.1) WILD-TYPE         1        16          3         36
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 10(4Q22.1) MUTATED           20       22         6         1
  DEL PEAK 10(4Q22.1) WILD-TYPE         21       23        11         1
D32V3, multiclass
            clus
vv           DEL PEAK 10(4Q22.1) MUTATED DEL PEAK 10(4Q22.1) WILD-TYPE
  STAGE I                             14                            60
  STAGE IA                             0                             1
  STAGE II                             8                            21
  STAGE IIA                           40                            92
  STAGE IIB                            3                             7
  STAGE IIC                            0                             1
  STAGE III                            4                            16
  STAGE IIIA                           5                             3
  STAGE IIIB                          23                            36
  STAGE IIIC                          20                            21
  STAGE IV                            22                            23
  STAGE IVA                            6                            11
  STAGE IVB                            1                             1
[1] 13  2
[1] 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(4Q22.1) MUTATED     4  18 106  22
  DEL PEAK 10(4Q22.1) WILD-TYPE   7  59 199  33
D32V4, multiclass
    clus
vv   DEL PEAK 10(4Q22.1) MUTATED DEL PEAK 10(4Q22.1) WILD-TYPE
  T1                           4                             7
  T2                          18                            59
  T3                         106                           199
  T4                          22                            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"
                               vv
clus                             N0  N1  N2
  DEL PEAK 10(4Q22.1) MUTATED    69  44  37
  DEL PEAK 10(4Q22.1) WILD-TYPE 193  61  45
D32V5, multiclass
    clus
vv   DEL PEAK 10(4Q22.1) MUTATED DEL PEAK 10(4Q22.1) WILD-TYPE
  N0                          69                           193
  N1                          44                            61
  N2                          37                            45
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V6, binary
                               cls
clus                              0   1
  DEL PEAK 10(4Q22.1) MUTATED    99  29
  DEL PEAK 10(4Q22.1) WILD-TYPE 229  35
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(4Q22.1) MUTATED     99   29
  DEL PEAK 10(4Q22.1) WILD-TYPE  229   35
   clus
vv  DEL PEAK 10(4Q22.1) MUTATED DEL PEAK 10(4Q22.1) WILD-TYPE
  0                          99                           229
  1                          29                            35
[1] 2 2
[1] FALSE
D32V7, binary
                               cls
clus                              0   1
  DEL PEAK 10(4Q22.1) MUTATED    66  84
  DEL PEAK 10(4Q22.1) WILD-TYPE 147 152
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(4Q22.1) MUTATED     66   84
  DEL PEAK 10(4Q22.1) WILD-TYPE  147  152
        clus
vv       DEL PEAK 10(4Q22.1) MUTATED DEL PEAK 10(4Q22.1) WILD-TYPE
  FEMALE                          66                           147
  MALE                            84                           152
[1] 2 2
[1] FALSE
D32V8, binary
                               cls
clus                              0   1
  DEL PEAK 10(4Q22.1) MUTATED   128   4
  DEL PEAK 10(4Q22.1) WILD-TYPE 242   5
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(4Q22.1) MUTATED    128    4
  DEL PEAK 10(4Q22.1) WILD-TYPE  242    5
     clus
vv    DEL PEAK 10(4Q22.1) MUTATED DEL PEAK 10(4Q22.1) WILD-TYPE
  NO                          128                           242
  YES                           4                             5
[1] 2 2
[1] FALSE
D32V9, binary
                               cls
clus                              0   1
  DEL PEAK 10(4Q22.1) MUTATED   138  11
  DEL PEAK 10(4Q22.1) WILD-TYPE 244  51
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(4Q22.1) MUTATED    138   11
  DEL PEAK 10(4Q22.1) WILD-TYPE  244   51
                               clus
vv                              DEL PEAK 10(4Q22.1) MUTATED
  COLON ADENOCARCINOMA                                  138
  COLON MUCINOUS ADENOCARCINOMA                          11
                               clus
vv                              DEL PEAK 10(4Q22.1) WILD-TYPE
  COLON ADENOCARCINOMA                                    244
  COLON MUCINOUS ADENOCARCINOMA                            51
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 10(4Q22.1) MUTATED   108   2   9   7
  DEL PEAK 10(4Q22.1) WILD-TYPE 215   2  16  18
D32V10, multiclass
    clus
vv   DEL PEAK 10(4Q22.1) MUTATED DEL PEAK 10(4Q22.1) WILD-TYPE
  R0                         108                           215
  R1                           2                             2
  R2                           9                            16
  RX                           7                            18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V11, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 10(4Q22.1) MUTATED                                  0     3
  DEL PEAK 10(4Q22.1) WILD-TYPE                                1     8
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 10(4Q22.1) MUTATED                          27    70
  DEL PEAK 10(4Q22.1) WILD-TYPE                        32   142
D32V12, multiclass
                                  clus
vv                                 DEL PEAK 10(4Q22.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      3
  BLACK OR AFRICAN AMERICAN                                 27
  WHITE                                                     70
                                  clus
vv                                 DEL PEAK 10(4Q22.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        8
  BLACK OR AFRICAN AMERICAN                                   32
  WHITE                                                      142
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V13, binary
                               cls
clus                              0   1
  DEL PEAK 10(4Q22.1) MUTATED     3  92
  DEL PEAK 10(4Q22.1) WILD-TYPE   1 177
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(4Q22.1) MUTATED      3   92
  DEL PEAK 10(4Q22.1) WILD-TYPE    1  177
                        clus
vv                       DEL PEAK 10(4Q22.1) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                          92
                        clus
vv                       DEL PEAK 10(4Q22.1) WILD-TYPE
  HISPANIC OR LATINO                                 1
  NOT HISPANIC OR LATINO                           177
[1] 2 2
[1] FALSE

Clustering(33) Variable = DEL PEAK 11(4Q35.1) MUTATION ANALYSIS
D33V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 11(4Q35.1) MUTATED   115  38
  DEL PEAK 11(4Q35.1) WILD-TYPE 220  63
  DEL PEAK 11(4Q35.1) MUTATED DEL PEAK 11(4Q35.1) WILD-TYPE 
                          153                           283 
  DEL PEAK 11(4Q35.1) MUTATED DEL PEAK 11(4Q35.1) WILD-TYPE 
                           38                            63 
$`DEL PEAK 11(4Q35.1) MUTATED`
TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-6649 TCGA-AA-3522 TCGA-AA-3531 TCGA-AA-3552 
       45.60        13.94        24.16        37.05        34.03        13.02 
TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3860 TCGA-AA-3972 
       19.99         6.05        36.00        85.05        31.07        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-A00L TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6298 
       26.01        24.00        38.04        49.08         5.88        23.51 
TCGA-G4-6310 TCGA-G4-6625 TCGA-4N-A93T TCGA-5M-AAT4 TCGA-5M-AATE TCGA-A6-2674 
       63.62        91.79         4.80         1.61        39.45        43.76 
TCGA-A6-2675 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-3807 
       43.43        35.11        16.57        37.05        37.25        34.65 
TCGA-A6-4107 TCGA-A6-5660 TCGA-A6-5667 TCGA-A6-6140 TCGA-A6-6142 TCGA-A6-6650 
       32.45        29.19        29.16        24.13        25.08        20.61 
TCGA-A6-6651 TCGA-A6-6654 TCGA-A6-6782 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU 
       21.76        23.87        20.28        61.84        56.25         9.63 
TCGA-AA-3488 TCGA-AA-3511 TCGA-AA-3517 TCGA-AA-3532 TCGA-AA-3538 TCGA-AA-3544 
        5.03         6.97        38.99        29.00        26.01        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3673 
       33.99        21.01        78.08        54.02         2.01        50.04 
TCGA-AA-3685 TCGA-AA-3811 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3846 
       37.05        10.06        38.99        36.95        37.02        17.03 
TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3866 TCGA-AA-3930 
       10.06        33.07        36.03         0.99        17.03         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3989 
       20.98        34.03         2.01        21.99        16.08         7.96 
TCGA-AA-A00F TCGA-AA-A00Q TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01K TCGA-AA-A01R 
       34.03        42.02        15.02        32.02        31.00        35.01 
TCGA-AA-A01S TCGA-AA-A01X TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02W 
        1.02        26.01         2.96        39.98         2.01        41.00 
TCGA-AD-6901 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-A69D 
       22.42        26.47        14.50        16.31         0.95        17.85 
TCGA-AZ-4308 TCGA-AZ-4614 TCGA-AZ-4616 TCGA-AZ-4684 TCGA-AZ-6600 TCGA-AZ-6603 
      109.28         5.65         5.13        65.00        12.10        29.56 
TCGA-CA-5254 TCGA-CA-5256 TCGA-CA-6718 TCGA-CA-6719 TCGA-CM-4750 TCGA-CM-4752 
       12.69        12.46        10.06        14.30         8.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       29.06        22.03        30.08         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 
       17.03        14.04        29.03        13.02        15.02        11.01 
TCGA-CM-6677 TCGA-CM-6678 TCGA-D5-5537 TCGA-D5-5540 TCGA-D5-6529 TCGA-D5-6531 
       11.08        11.01        45.40        56.09        20.19        17.75 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6898 TCGA-D5-6926 TCGA-D5-6929 
       25.48        43.27        17.85         7.53         9.04        13.41 
TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A288 
       13.32       140.38         7.50        44.32       131.51        14.04 
TCGA-DM-A28A TCGA-F4-6460 TCGA-F4-6704 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6855 
       26.47        31.96         1.55        43.04        33.67        47.41 
TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6315 TCGA-G4-6626 TCGA-NH-A50T TCGA-NH-A50U 
        8.35        82.39        61.91        46.75        18.18        10.98 
TCGA-NH-A6GA TCGA-NH-A6GC TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QL-A97D 
        9.93        12.79        16.80        42.77        29.46        21.90 
TCGA-RU-A8FL TCGA-SS-A7HO TCGA-T9-A92H 
       38.70        60.13        11.90 

$`DEL PEAK 11(4Q35.1) WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-AA-3496 TCGA-AA-3506 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53         1.02        58.03        13.02        24.03 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3543 TCGA-AA-3554 TCGA-AA-3556 
       36.03         8.05        19.07         0.99        17.95        23.01 
TCGA-AA-3560 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.99         0.92        19.00        19.04        19.04        14.93 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3986 
       24.03        29.98        12.99        24.00         2.01        19.07 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-G4-6294 TCGA-G4-6314 
       75.95       106.75       100.01         1.94        28.21        35.93 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 TCGA-NH-A8F7 TCGA-3L-AA1B 
       22.09        35.80        26.17        79.69        17.85        15.62 
TCGA-4T-AA8H TCGA-5M-AAT6 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2678 
       12.66         9.53        43.76        46.65        42.90        42.28 
TCGA-A6-2679 TCGA-A6-2686 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 
       44.91        37.02        32.75        36.53        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 
       30.44        33.53        23.61        22.09        22.06        32.71 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6652 TCGA-A6-6653 
       27.09        22.52         8.38        25.18        24.69        24.39 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 TCGA-AA-3489 TCGA-AA-3492 
       20.12        19.66        16.24        24.92         7.04         3.02 
TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3518 
        1.02        37.05        35.01        63.98         1.02         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3534 TCGA-AA-3542 TCGA-AA-3553 
        9.07        19.07         0.00        29.00        12.99        24.00 
TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3667 
       29.95        20.98        13.94        61.02         6.97        14.01 
TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3696 
       47.05        47.01        15.02        11.01         5.98         5.03 
TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       26.99        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3845 TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3855 TCGA-AA-3858 
       15.95         0.00         0.00         0.00        32.05        31.07 
TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3941 TCGA-AA-3947 
       53.00        27.02        18.05        31.00        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3994 
       26.01        13.05        34.06        25.02        27.02        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K 
       13.94        38.04        19.00        30.02        18.05        18.05 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 
        4.01        27.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q 
       15.02        10.98        12.00        31.00        38.07         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02J TCGA-AA-A02O 
       33.04         1.02        37.02        51.98         5.03         0.92 
TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6889 
       22.03        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 
       24.53         5.79        27.42        16.44         0.46         0.92 
TCGA-AU-6004 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L 
       27.09        33.01         0.20        21.44        17.82        17.26 
TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4682 
       19.33        18.84        58.39         1.41        32.94        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6605 TCGA-AZ-6606 
       62.79        88.21        49.41         6.77         5.23        11.74 
TCGA-AZ-6607 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        3.19        12.36        12.39        12.59        12.59        12.20 
TCGA-CA-6717 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 
       12.76        17.56       148.01        85.45        70.16        15.62 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 
       23.05        20.02        37.02        25.02        26.04        27.02 
TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6165 
       22.98        32.02        15.02        15.02        12.00        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 
       21.99        14.99        12.99        14.04        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5541 
       11.08        10.06        12.03        54.61        19.59        55.92 
TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       20.42        18.25        15.12         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       16.14        15.58        12.39        10.13        12.43        14.30 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
        9.44        11.64        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D8 TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A28C TCGA-DM-A28E 
       12.59       135.65         7.76       139.17        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 
       35.97        60.79       117.07        98.24        95.18         8.61 
TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 
       11.11        35.74        35.74         6.18        47.87        34.42 
TCGA-F4-6806 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       41.42        13.25         0.53        35.31       133.18        74.56 
TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       67.30        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6311 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6627 
       39.42        36.00        26.43        26.04        13.78        74.79 
TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GB TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 
       19.33        19.33        15.65        32.98         8.42        31.30 
TCGA-WS-AB45 
       70.03 

  DEL PEAK 11(4Q35.1) MUTATED DEL PEAK 11(4Q35.1) WILD-TYPE 
                         0.95                          0.00 
  DEL PEAK 11(4Q35.1) MUTATED DEL PEAK 11(4Q35.1) WILD-TYPE 
                       140.38                        148.01 
  DEL PEAK 11(4Q35.1) MUTATED DEL PEAK 11(4Q35.1) WILD-TYPE 
                        23.87                         21.99 
[1] "0.9 - 140.4 (23.9)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.2"
D33V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 11(4Q35.1) MUTATED        17        0        8        44         2
  DEL PEAK 11(4Q35.1) WILD-TYPE      57        1       21        88         8
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 11(4Q35.1) MUTATED           0         6          5         21
  DEL PEAK 11(4Q35.1) WILD-TYPE         1        14          3         38
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 11(4Q35.1) MUTATED           19       24         7         1
  DEL PEAK 11(4Q35.1) WILD-TYPE         22       21        10         1
D33V3, multiclass
            clus
vv           DEL PEAK 11(4Q35.1) MUTATED DEL PEAK 11(4Q35.1) WILD-TYPE
  STAGE I                             17                            57
  STAGE IA                             0                             1
  STAGE II                             8                            21
  STAGE IIA                           44                            88
  STAGE IIB                            2                             8
  STAGE IIC                            0                             1
  STAGE III                            6                            14
  STAGE IIIA                           5                             3
  STAGE IIIB                          21                            38
  STAGE IIIC                          19                            22
  STAGE IV                            24                            21
  STAGE IVA                            7                            10
  STAGE IVB                            1                             1
[1] 13  2
[1] 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(4Q35.1) MUTATED     4  21 109  23
  DEL PEAK 11(4Q35.1) WILD-TYPE   7  56 196  32
D33V4, multiclass
    clus
vv   DEL PEAK 11(4Q35.1) MUTATED DEL PEAK 11(4Q35.1) WILD-TYPE
  T1                           4                             7
  T2                          21                            56
  T3                         109                           196
  T4                          23                            32
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2
  DEL PEAK 11(4Q35.1) MUTATED    75  44  38
  DEL PEAK 11(4Q35.1) WILD-TYPE 187  61  44
D33V5, multiclass
    clus
vv   DEL PEAK 11(4Q35.1) MUTATED DEL PEAK 11(4Q35.1) WILD-TYPE
  N0                          75                           187
  N1                          44                            61
  N2                          38                            44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V6, binary
                               cls
clus                              0   1
  DEL PEAK 11(4Q35.1) MUTATED   107  32
  DEL PEAK 11(4Q35.1) WILD-TYPE 221  32
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(4Q35.1) MUTATED    107   32
  DEL PEAK 11(4Q35.1) WILD-TYPE  221   32
   clus
vv  DEL PEAK 11(4Q35.1) MUTATED DEL PEAK 11(4Q35.1) WILD-TYPE
  0                         107                           221
  1                          32                            32
[1] 2 2
[1] FALSE
D33V7, binary
                               cls
clus                              0   1
  DEL PEAK 11(4Q35.1) MUTATED    79  78
  DEL PEAK 11(4Q35.1) WILD-TYPE 134 158
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(4Q35.1) MUTATED     79   78
  DEL PEAK 11(4Q35.1) WILD-TYPE  134  158
        clus
vv       DEL PEAK 11(4Q35.1) MUTATED DEL PEAK 11(4Q35.1) WILD-TYPE
  FEMALE                          79                           134
  MALE                            78                           158
[1] 2 2
[1] FALSE
D33V8, binary
                               cls
clus                              0   1
  DEL PEAK 11(4Q35.1) MUTATED   132   5
  DEL PEAK 11(4Q35.1) WILD-TYPE 238   4
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(4Q35.1) MUTATED    132    5
  DEL PEAK 11(4Q35.1) WILD-TYPE  238    4
     clus
vv    DEL PEAK 11(4Q35.1) MUTATED DEL PEAK 11(4Q35.1) WILD-TYPE
  NO                          132                           238
  YES                           5                             4
[1] 2 2
[1] FALSE
D33V9, binary
                               cls
clus                              0   1
  DEL PEAK 11(4Q35.1) MUTATED   140  15
  DEL PEAK 11(4Q35.1) WILD-TYPE 242  47
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(4Q35.1) MUTATED    140   15
  DEL PEAK 11(4Q35.1) WILD-TYPE  242   47
                               clus
vv                              DEL PEAK 11(4Q35.1) MUTATED
  COLON ADENOCARCINOMA                                  140
  COLON MUCINOUS ADENOCARCINOMA                          15
                               clus
vv                              DEL PEAK 11(4Q35.1) WILD-TYPE
  COLON ADENOCARCINOMA                                    242
  COLON MUCINOUS ADENOCARCINOMA                            47
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 11(4Q35.1) MUTATED   110   2  12   8
  DEL PEAK 11(4Q35.1) WILD-TYPE 213   2  13  17
D33V10, multiclass
    clus
vv   DEL PEAK 11(4Q35.1) MUTATED DEL PEAK 11(4Q35.1) WILD-TYPE
  R0                         110                           213
  R1                           2                             2
  R2                          12                            13
  RX                           8                            17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V11, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 11(4Q35.1) MUTATED                                  1     4
  DEL PEAK 11(4Q35.1) WILD-TYPE                                0     7
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 11(4Q35.1) MUTATED                          27    68
  DEL PEAK 11(4Q35.1) WILD-TYPE                        32   144
D33V12, multiclass
                                  clus
vv                                 DEL PEAK 11(4Q35.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      4
  BLACK OR AFRICAN AMERICAN                                 27
  WHITE                                                     68
                                  clus
vv                                 DEL PEAK 11(4Q35.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        7
  BLACK OR AFRICAN AMERICAN                                   32
  WHITE                                                      144
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V13, binary
                               cls
clus                              0   1
  DEL PEAK 11(4Q35.1) MUTATED     3  93
  DEL PEAK 11(4Q35.1) WILD-TYPE   1 176
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(4Q35.1) MUTATED      3   93
  DEL PEAK 11(4Q35.1) WILD-TYPE    1  176
                        clus
vv                       DEL PEAK 11(4Q35.1) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                          93
                        clus
vv                       DEL PEAK 11(4Q35.1) WILD-TYPE
  HISPANIC OR LATINO                                 1
  NOT HISPANIC OR LATINO                           176
[1] 2 2
[1] FALSE

Clustering(34) Variable = DEL PEAK 12(5Q12.1) MUTATION ANALYSIS
D34V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 12(5Q12.1) MUTATED    75  28
  DEL PEAK 12(5Q12.1) WILD-TYPE 260  73
  DEL PEAK 12(5Q12.1) MUTATED DEL PEAK 12(5Q12.1) WILD-TYPE 
                          103                           333 
  DEL PEAK 12(5Q12.1) MUTATED DEL PEAK 12(5Q12.1) WILD-TYPE 
                           28                            73 
$`DEL PEAK 12(5Q12.1) MUTATED`
TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3552 TCGA-AA-3562 TCGA-AA-3688 
       13.94        14.53        24.16        13.02        19.99        19.00 
TCGA-AA-3697 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3952 TCGA-AZ-6608 TCGA-CK-5912 
       85.05        31.07        24.03         2.01         1.94        49.08 
TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6625 TCGA-5M-AAT4 TCGA-5M-AATE TCGA-A6-2671 
        5.88        63.62        91.79         1.61        39.45        43.76 
TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2683 TCGA-A6-2686 TCGA-A6-3807 
       43.76        43.43        42.90        16.57        37.02        34.65 
TCGA-A6-3810 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-6137 TCGA-A6-6142 TCGA-A6-6648 
       36.53        30.44        29.19        27.09        25.08        25.18 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3502 
       21.76        24.69        23.87         9.63         5.03        35.01 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3553 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3685 
       26.01        12.99        24.00        50.04        47.01        37.05 
TCGA-AA-3811 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3851 TCGA-AA-3856 TCGA-AA-3858 
       10.06        36.95        37.02        33.07         0.99        31.07 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-A00F TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A01D 
        2.01        21.99        34.03        27.02        42.02        10.98 
TCGA-AA-A01T TCGA-AA-A02E TCGA-AA-A02H TCGA-AA-A02W TCGA-AD-6901 TCGA-AD-6963 
       33.04         2.96         2.01        41.00        22.42        27.42 
TCGA-AD-6965 TCGA-AY-4070 TCGA-AY-6196 TCGA-AY-A54L TCGA-AY-A71X TCGA-AZ-4614 
       26.47        16.31         0.20        17.26        19.33         5.65 
TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-CA-5797 TCGA-CA-6719 
       65.00        62.79        29.56         5.23        12.59        14.30 
TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5862 
       25.02         8.02        13.02        29.06        22.03         5.03 
TCGA-CM-5864 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6169 TCGA-D5-6531 TCGA-D5-6536 
       15.02        14.04        29.03        13.02        17.75        17.85 
TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 TCGA-DM-A1DB TCGA-DM-A1HA 
        7.53        10.13        12.43         9.04        44.32       131.51 
TCGA-F4-6459 TCGA-F4-6704 TCGA-F4-6808 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6317 
        8.61         1.55        33.67         8.35        82.39        36.00 
TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A6GC TCGA-QG-A5YV TCGA-QG-A5Z1 TCGA-QL-A97D 
       18.18        10.98        12.79        42.77         8.42        21.90 
TCGA-RU-A8FL 
       38.70 

$`DEL PEAK 12(5Q12.1) WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-AA-3496 TCGA-AA-3506 TCGA-AA-3516 TCGA-AA-3520 
       24.33        45.60         1.02        58.03        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3692 
       17.95        23.01        19.99         6.05         0.92        36.00 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       19.04        19.04        14.93        29.98        12.99        24.00 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 
       39.06        21.37        15.52        25.08        10.88        75.95 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6314 TCGA-G4-6321 
      106.75       100.01        28.21        23.51        35.93        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 TCGA-NH-A8F7 TCGA-3L-AA1B TCGA-4N-A93T 
       35.80        26.17        79.69        17.85        15.62         4.80 
TCGA-4T-AA8H TCGA-5M-AAT6 TCGA-A6-2672 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 
       12.66         9.53        46.65        42.28        44.91        35.11 
TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-3809 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 
       37.05        37.25        32.75        32.45        32.91        31.63 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 
       33.53        23.61        22.09        22.06        32.71        29.16 
TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6650 TCGA-A6-6653 TCGA-A6-6780 
       22.52        24.13         8.38        20.61        24.39        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B 
       19.66        20.28        16.24        24.92        61.84        56.25 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3510 TCGA-AA-3511 
        7.04         3.02         1.02        37.05        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3555 
       29.00        29.00        14.01        33.99        21.01        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3675 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        2.01        14.01        47.05        15.02        11.01         5.98 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
        5.03        26.99        35.05         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       17.98        15.95        38.99         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3864 TCGA-AA-3866 
        0.00         0.00        36.03        32.05        53.00        17.03 
TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       26.01        20.98        34.03        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       25.02        27.02         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00R 
       19.00        30.02        18.05        18.05         4.01         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01F 
       17.03        14.99        34.98        15.02        15.02        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02F 
        1.02         1.02        26.01        37.02        51.98        39.98 
TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
        5.03         0.92        22.03        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-A5EK TCGA-AM-5820 
       12.16        83.24        24.53         5.79        16.44         0.46 
TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
        0.92        14.50        27.09         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AY-A69D TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 
       17.82        17.85        18.84       109.28        58.39         1.41 
TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       32.94         5.13        22.36        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 
       12.10        11.74         3.19        12.69        12.36        12.46 
TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 
       12.39        12.59        12.20        12.76        10.06        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        70.16        15.62        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       37.02        26.04        27.02        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6165 
       15.02        15.02        17.03        15.02        12.00        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       21.99        14.99        12.99        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       20.19        20.42        18.25        25.48        43.27        15.12 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 
        4.80        17.13        12.49        16.14        15.58        12.39 
TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
       14.30         9.44        11.64        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C 
      135.65         7.76       139.17        14.04        26.47        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M 
      119.93        35.97        60.79       117.07        98.24        95.18 
TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       31.96        11.11        35.74        35.74         6.18        47.87 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       34.42        41.42        43.04        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 
       35.31       133.18        74.56        67.30        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6320 
       44.68        55.04        85.48        39.42        61.91        26.43 
TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50V TCGA-NH-A5IV 
       26.04        13.78        46.75        74.79        19.33        19.33 
TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A8F8 TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z2 
        9.93        15.65        16.80        29.46        32.98        31.30 
TCGA-SS-A7HO TCGA-T9-A92H TCGA-WS-AB45 
       60.13        11.90        70.03 

  DEL PEAK 12(5Q12.1) MUTATED DEL PEAK 12(5Q12.1) WILD-TYPE 
                          0.2                           0.0 
  DEL PEAK 12(5Q12.1) MUTATED DEL PEAK 12(5Q12.1) WILD-TYPE 
                       131.51                        148.01 
  DEL PEAK 12(5Q12.1) MUTATED DEL PEAK 12(5Q12.1) WILD-TYPE 
                        23.87                         21.99 
[1] "0.2 - 131.5 (23.9)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.4"
D34V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 12(5Q12.1) MUTATED        17        0        5        19         1
  DEL PEAK 12(5Q12.1) WILD-TYPE      57        1       24       113         9
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 12(5Q12.1) MUTATED           0         3          5         14
  DEL PEAK 12(5Q12.1) WILD-TYPE         1        17          3         45
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 12(5Q12.1) MUTATED           16       13         8         1
  DEL PEAK 12(5Q12.1) WILD-TYPE         25       32         9         1
D34V3, multiclass
            clus
vv           DEL PEAK 12(5Q12.1) MUTATED DEL PEAK 12(5Q12.1) WILD-TYPE
  STAGE I                             17                            57
  STAGE IA                             0                             1
  STAGE II                             5                            24
  STAGE IIA                           19                           113
  STAGE IIB                            1                             9
  STAGE IIC                            0                             1
  STAGE III                            3                            17
  STAGE IIIA                           5                             3
  STAGE IIIB                          14                            45
  STAGE IIIC                          16                            25
  STAGE IV                            13                            32
  STAGE IVA                            8                             9
  STAGE IVB                            1                             1
[1] 13  2
[1] 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(5Q12.1) MUTATED     3  20  69  13
  DEL PEAK 12(5Q12.1) WILD-TYPE   8  57 236  42
D34V4, multiclass
    clus
vv   DEL PEAK 12(5Q12.1) MUTATED DEL PEAK 12(5Q12.1) WILD-TYPE
  T1                           3                             8
  T2                          20                            57
  T3                          69                           236
  T4                          13                            42
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2
  DEL PEAK 12(5Q12.1) MUTATED    49  29  27
  DEL PEAK 12(5Q12.1) WILD-TYPE 213  76  55
D34V5, multiclass
    clus
vv   DEL PEAK 12(5Q12.1) MUTATED DEL PEAK 12(5Q12.1) WILD-TYPE
  N0                          49                           213
  N1                          29                            76
  N2                          27                            55
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V6, binary
                               cls
clus                              0   1
  DEL PEAK 12(5Q12.1) MUTATED    67  22
  DEL PEAK 12(5Q12.1) WILD-TYPE 261  42
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(5Q12.1) MUTATED     67   22
  DEL PEAK 12(5Q12.1) WILD-TYPE  261   42
   clus
vv  DEL PEAK 12(5Q12.1) MUTATED DEL PEAK 12(5Q12.1) WILD-TYPE
  0                          67                           261
  1                          22                            42
[1] 2 2
[1] FALSE
D34V7, binary
                               cls
clus                              0   1
  DEL PEAK 12(5Q12.1) MUTATED    44  61
  DEL PEAK 12(5Q12.1) WILD-TYPE 169 175
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(5Q12.1) MUTATED     44   61
  DEL PEAK 12(5Q12.1) WILD-TYPE  169  175
        clus
vv       DEL PEAK 12(5Q12.1) MUTATED DEL PEAK 12(5Q12.1) WILD-TYPE
  FEMALE                          44                           169
  MALE                            61                           175
[1] 2 2
[1] FALSE
D34V8, binary
                               cls
clus                              0   1
  DEL PEAK 12(5Q12.1) MUTATED    90   2
  DEL PEAK 12(5Q12.1) WILD-TYPE 280   7
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(5Q12.1) MUTATED     90    2
  DEL PEAK 12(5Q12.1) WILD-TYPE  280    7
     clus
vv    DEL PEAK 12(5Q12.1) MUTATED DEL PEAK 12(5Q12.1) WILD-TYPE
  NO                           90                           280
  YES                           2                             7
[1] 2 2
[1] FALSE
D34V9, binary
                               cls
clus                              0   1
  DEL PEAK 12(5Q12.1) MUTATED    97   8
  DEL PEAK 12(5Q12.1) WILD-TYPE 285  54
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(5Q12.1) MUTATED     97    8
  DEL PEAK 12(5Q12.1) WILD-TYPE  285   54
                               clus
vv                              DEL PEAK 12(5Q12.1) MUTATED
  COLON ADENOCARCINOMA                                   97
  COLON MUCINOUS ADENOCARCINOMA                           8
                               clus
vv                              DEL PEAK 12(5Q12.1) WILD-TYPE
  COLON ADENOCARCINOMA                                    285
  COLON MUCINOUS ADENOCARCINOMA                            54
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 12(5Q12.1) MUTATED    71   2   6   4
  DEL PEAK 12(5Q12.1) WILD-TYPE 252   2  19  21
D34V10, multiclass
    clus
vv   DEL PEAK 12(5Q12.1) MUTATED DEL PEAK 12(5Q12.1) WILD-TYPE
  R0                          71                           252
  R1                           2                             2
  R2                           6                            19
  RX                           4                            21
[1] 4 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, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 12(5Q12.1) MUTATED                                  1     2
  DEL PEAK 12(5Q12.1) WILD-TYPE                                0     9
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 12(5Q12.1) MUTATED                          17    53
  DEL PEAK 12(5Q12.1) WILD-TYPE                        42   159
D34V12, multiclass
                                  clus
vv                                 DEL PEAK 12(5Q12.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      2
  BLACK OR AFRICAN AMERICAN                                 17
  WHITE                                                     53
                                  clus
vv                                 DEL PEAK 12(5Q12.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        9
  BLACK OR AFRICAN AMERICAN                                   42
  WHITE                                                      159
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V13, binary
                               cls
clus                              0   1
  DEL PEAK 12(5Q12.1) MUTATED     3  66
  DEL PEAK 12(5Q12.1) WILD-TYPE   1 203
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(5Q12.1) MUTATED      3   66
  DEL PEAK 12(5Q12.1) WILD-TYPE    1  203
                        clus
vv                       DEL PEAK 12(5Q12.1) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                          66
                        clus
vv                       DEL PEAK 12(5Q12.1) WILD-TYPE
  HISPANIC OR LATINO                                 1
  NOT HISPANIC OR LATINO                           203
[1] 2 2
[1] FALSE

Clustering(35) Variable = DEL PEAK 13(5Q21.1) MUTATION ANALYSIS
D35V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 13(5Q21.1) MUTATED    90  34
  DEL PEAK 13(5Q21.1) WILD-TYPE 245  67
  DEL PEAK 13(5Q21.1) MUTATED DEL PEAK 13(5Q21.1) WILD-TYPE 
                          124                           312 
  DEL PEAK 13(5Q21.1) MUTATED DEL PEAK 13(5Q21.1) WILD-TYPE 
                           34                            67 
$`DEL PEAK 13(5Q21.1) MUTATED`
TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3522 TCGA-AA-3530 
       13.94        14.53        24.16         1.02        37.05        19.07 
TCGA-AA-3552 TCGA-AA-3556 TCGA-AA-3562 TCGA-AA-3688 TCGA-AA-3697 TCGA-AA-3860 
       13.02        23.01        19.99        19.00        85.05        31.07 
TCGA-AA-3867 TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
       24.03       106.75         1.94        49.08         5.88        63.62 
TCGA-G4-6625 TCGA-5M-AAT4 TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2683 
       91.79         1.61        39.45        43.76        43.76        16.57 
TCGA-A6-2686 TCGA-A6-3810 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-6137 TCGA-A6-6140 
       37.02        36.53        30.44        29.19        27.09        24.13 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6654 TCGA-A6-A5ZU TCGA-AA-3488 
       25.08        25.18        21.76        23.87         9.63         5.03 
TCGA-AA-3518 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3553 TCGA-AA-3655 TCGA-AA-3673 
        1.02        26.01        12.99        24.00        61.02        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3811 TCGA-AA-3841 TCGA-AA-3842 
       47.01        15.02        11.01        10.06        36.95        37.02 
TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3866 TCGA-AA-3941 
       10.06        33.07         0.99        31.07        17.03        24.00 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3994 TCGA-AA-A00F TCGA-AA-A00O TCGA-AA-A00Q 
        2.01        21.99        27.02        34.03        27.02        42.02 
TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01T TCGA-AA-A02E TCGA-AA-A02H TCGA-AA-A02J 
       15.02        10.98        33.04         2.96         2.01         5.03 
TCGA-AA-A02W TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AY-4070 TCGA-AY-6196 
       41.00        22.42        27.42        26.47        16.31         0.20 
TCGA-AY-A71X TCGA-AZ-4614 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6603 TCGA-AZ-6605 
       19.33         5.65        65.00        62.79        29.56         5.23 
TCGA-CA-5797 TCGA-CA-6719 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4752 
       12.59        14.30        25.02        26.04         8.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-6163 TCGA-CM-6164 
       29.06        22.03         5.03        15.02        14.04        29.03 
TCGA-CM-6169 TCGA-CM-6675 TCGA-D5-5539 TCGA-D5-6530 TCGA-D5-6535 TCGA-D5-6536 
       13.02        13.05        19.59        20.42        15.12        17.85 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A1D4 
       10.13        12.43         9.04        13.41        11.38        92.75 
TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A280 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28H 
      140.38        44.32         7.76        14.04        26.47       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6704 TCGA-F4-6808 TCGA-G4-6295 
       98.24         8.61        31.96         1.55        33.67         8.35 
TCGA-G4-6297 TCGA-G4-6317 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A6GC TCGA-QG-A5YV 
       82.39        36.00        18.18        10.98        12.79        42.77 
TCGA-QG-A5YW TCGA-QG-A5Z1 TCGA-QL-A97D TCGA-RU-A8FL 
       29.46         8.42        21.90        38.70 

$`DEL PEAK 13(5Q21.1) WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-AA-3506 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3524 
       24.33        45.60        58.03        13.02        24.03        36.03 
TCGA-AA-3525 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3554 TCGA-AA-3560 TCGA-AA-3662 
        8.05        34.03         0.99        17.95        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3692 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3870 
        0.92        36.00        19.04        19.04        14.93        29.98 
TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 
       12.99        24.00         2.01        50.99        26.01        24.00 
TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 
       19.07        38.04        21.99        39.06        21.37        15.52 
TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-6601 TCGA-G4-6294 TCGA-G4-6298 
       25.08        10.88        75.95       100.01        28.21        23.51 
TCGA-G4-6314 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 TCGA-NH-A8F7 
       35.93        22.09        35.80        26.17        79.69        17.85 
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT6 TCGA-A6-2672 TCGA-A6-2675 
       15.62         4.80        12.66         9.53        46.65        43.43 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2684 TCGA-A6-2685 
       42.90        42.28        44.91        35.11        37.05        37.25 
TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5661 
       34.65        32.75        32.45        32.91        31.63        33.53 
TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6138 
       23.61        22.09        22.06        32.71        29.16        22.52 
TCGA-A6-6141 TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 
        8.38        20.61        24.69        24.39        20.12        19.66 
TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-AA-3489 
       20.28        16.24        24.92        61.84        56.25         7.04 
TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
        3.02         1.02        37.05        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
        1.02        38.99         9.07        19.07         0.00        29.00 
TCGA-AA-3534 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3555 TCGA-AA-3558 
       29.00        14.01        33.99        21.01        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       13.94        78.08         6.97        54.02         2.01        14.01 
TCGA-AA-3675 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3812 
       47.05         5.98        37.05         5.03        26.99        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
        0.00        17.03         0.00         0.00        36.03        32.05 
TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 
       53.00        27.02        18.05        31.00         2.01        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       26.01        20.98        34.03        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       25.02        27.02         7.96        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00R TCGA-AA-A00U 
       30.02        18.05        18.05         4.01         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       14.99        34.98        15.02        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V 
       31.00        38.07         1.02        35.01         1.02         1.02 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02O TCGA-AA-A02R 
       26.01        37.02        51.98        39.98         0.92        22.03 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 
        5.79        16.44         0.46         0.92        14.50        27.09 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D 
        0.95        33.01        21.44        17.82        17.26        17.85 
TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4616 
       18.84       109.28        58.39         1.41        32.94         5.13 
TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6606 
       22.36        88.21        49.41         6.77        12.10        11.74 
TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-6715 
        3.19        12.69        12.36        12.46        12.39        12.59 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.20        12.76        10.06        17.56       148.01        85.45 
TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       70.16        15.62        51.32        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4751 
        2.01       124.27        23.05        20.02        37.02        27.02 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5868 
       22.98        30.08        32.02        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
       15.02        12.00        16.04        21.99        14.99        12.99 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6676 TCGA-CM-6677 
       15.02        14.04        11.01        12.95        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 
       11.01        10.06        12.03        45.40        54.61        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       55.92        20.19        17.75        18.25        25.48        43.27 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 
       12.39        14.30         9.44        11.64        13.35        12.00 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D6 
       10.26       119.70        24.43        38.20       130.65        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
       13.32        12.59         7.50       131.51       135.65       139.17 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28M TCGA-F4-6461 
       81.37       119.93        35.97        60.79        95.18        11.11 
TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 
       35.74        35.74         6.18        47.87        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       43.04        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
       74.56        67.30        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 
       85.48        39.42        61.91        26.43        26.04        13.78 
TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB 
       46.75        74.79        19.33        19.33         9.93        15.65 
TCGA-NH-A8F8 TCGA-QG-A5YX TCGA-QG-A5Z2 TCGA-SS-A7HO TCGA-T9-A92H TCGA-WS-AB45 
       16.80        32.98        31.30        60.13        11.90        70.03 

  DEL PEAK 13(5Q21.1) MUTATED DEL PEAK 13(5Q21.1) WILD-TYPE 
                          0.2                           0.0 
  DEL PEAK 13(5Q21.1) MUTATED DEL PEAK 13(5Q21.1) WILD-TYPE 
                       140.38                        148.01 
  DEL PEAK 13(5Q21.1) MUTATED DEL PEAK 13(5Q21.1) WILD-TYPE 
                       22.010                        22.075 
[1] "0.2 - 140.4 (22.0)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.4"
D35V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 13(5Q21.1) MUTATED        18        0        6        26         0
  DEL PEAK 13(5Q21.1) WILD-TYPE      56        1       23       106        10
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 13(5Q21.1) MUTATED           0         3          7         18
  DEL PEAK 13(5Q21.1) WILD-TYPE         1        17          1         41
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 13(5Q21.1) MUTATED           18       17         8         2
  DEL PEAK 13(5Q21.1) WILD-TYPE         23       28         9         0
D35V3, multiclass
            clus
vv           DEL PEAK 13(5Q21.1) MUTATED DEL PEAK 13(5Q21.1) WILD-TYPE
  STAGE I                             18                            56
  STAGE IA                             0                             1
  STAGE II                             6                            23
  STAGE IIA                           26                           106
  STAGE IIB                            0                            10
  STAGE IIC                            0                             1
  STAGE III                            3                            17
  STAGE IIIA                           7                             1
  STAGE IIIB                          18                            41
  STAGE IIIC                          18                            23
  STAGE IV                            17                            28
  STAGE IVA                            8                             9
  STAGE IVB                            2                             0
[1] 13  2
[1] 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(5Q21.1) MUTATED     3  22  86  15
  DEL PEAK 13(5Q21.1) WILD-TYPE   8  55 219  40
D35V4, multiclass
    clus
vv   DEL PEAK 13(5Q21.1) MUTATED DEL PEAK 13(5Q21.1) WILD-TYPE
  T1                           3                             8
  T2                          22                            55
  T3                          86                           219
  T4                          15                            40
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2
  DEL PEAK 13(5Q21.1) MUTATED    57  37  32
  DEL PEAK 13(5Q21.1) WILD-TYPE 205  68  50
D35V5, multiclass
    clus
vv   DEL PEAK 13(5Q21.1) MUTATED DEL PEAK 13(5Q21.1) WILD-TYPE
  N0                          57                           205
  N1                          37                            68
  N2                          32                            50
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V6, binary
                               cls
clus                              0   1
  DEL PEAK 13(5Q21.1) MUTATED    82  27
  DEL PEAK 13(5Q21.1) WILD-TYPE 246  37
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(5Q21.1) MUTATED     82   27
  DEL PEAK 13(5Q21.1) WILD-TYPE  246   37
   clus
vv  DEL PEAK 13(5Q21.1) MUTATED DEL PEAK 13(5Q21.1) WILD-TYPE
  0                          82                           246
  1                          27                            37
[1] 2 2
[1] FALSE
D35V7, binary
                               cls
clus                              0   1
  DEL PEAK 13(5Q21.1) MUTATED    54  72
  DEL PEAK 13(5Q21.1) WILD-TYPE 159 164
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(5Q21.1) MUTATED     54   72
  DEL PEAK 13(5Q21.1) WILD-TYPE  159  164
        clus
vv       DEL PEAK 13(5Q21.1) MUTATED DEL PEAK 13(5Q21.1) WILD-TYPE
  FEMALE                          54                           159
  MALE                            72                           164
[1] 2 2
[1] FALSE
D35V8, binary
                               cls
clus                              0   1
  DEL PEAK 13(5Q21.1) MUTATED   103   2
  DEL PEAK 13(5Q21.1) WILD-TYPE 267   7
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(5Q21.1) MUTATED    103    2
  DEL PEAK 13(5Q21.1) WILD-TYPE  267    7
     clus
vv    DEL PEAK 13(5Q21.1) MUTATED DEL PEAK 13(5Q21.1) WILD-TYPE
  NO                          103                           267
  YES                           2                             7
[1] 2 2
[1] FALSE
D35V9, binary
                               cls
clus                              0   1
  DEL PEAK 13(5Q21.1) MUTATED   110  15
  DEL PEAK 13(5Q21.1) WILD-TYPE 272  47
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(5Q21.1) MUTATED    110   15
  DEL PEAK 13(5Q21.1) WILD-TYPE  272   47
                               clus
vv                              DEL PEAK 13(5Q21.1) MUTATED
  COLON ADENOCARCINOMA                                  110
  COLON MUCINOUS ADENOCARCINOMA                          15
                               clus
vv                              DEL PEAK 13(5Q21.1) WILD-TYPE
  COLON ADENOCARCINOMA                                    272
  COLON MUCINOUS ADENOCARCINOMA                            47
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 13(5Q21.1) MUTATED    82   2   9   5
  DEL PEAK 13(5Q21.1) WILD-TYPE 241   2  16  20
D35V10, multiclass
    clus
vv   DEL PEAK 13(5Q21.1) MUTATED DEL PEAK 13(5Q21.1) WILD-TYPE
  R0                          82                           241
  R1                           2                             2
  R2                           9                            16
  RX                           5                            20
[1] 4 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, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 13(5Q21.1) MUTATED                                  1     2
  DEL PEAK 13(5Q21.1) WILD-TYPE                                0     9
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 13(5Q21.1) MUTATED                          17    63
  DEL PEAK 13(5Q21.1) WILD-TYPE                        42   149
D35V12, multiclass
                                  clus
vv                                 DEL PEAK 13(5Q21.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      2
  BLACK OR AFRICAN AMERICAN                                 17
  WHITE                                                     63
                                  clus
vv                                 DEL PEAK 13(5Q21.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        9
  BLACK OR AFRICAN AMERICAN                                   42
  WHITE                                                      149
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V13, binary
                               cls
clus                              0   1
  DEL PEAK 13(5Q21.1) MUTATED     3  77
  DEL PEAK 13(5Q21.1) WILD-TYPE   1 192
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(5Q21.1) MUTATED      3   77
  DEL PEAK 13(5Q21.1) WILD-TYPE    1  192
                        clus
vv                       DEL PEAK 13(5Q21.1) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                          77
                        clus
vv                       DEL PEAK 13(5Q21.1) WILD-TYPE
  HISPANIC OR LATINO                                 1
  NOT HISPANIC OR LATINO                           192
[1] 2 2
[1] FALSE

Clustering(36) Variable = DEL PEAK 14(5Q22.2) MUTATION ANALYSIS
D36V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 14(5Q22.2) MUTATED    89  35
  DEL PEAK 14(5Q22.2) WILD-TYPE 246  66
  DEL PEAK 14(5Q22.2) MUTATED DEL PEAK 14(5Q22.2) WILD-TYPE 
                          124                           312 
  DEL PEAK 14(5Q22.2) MUTATED DEL PEAK 14(5Q22.2) WILD-TYPE 
                           35                            66 
$`DEL PEAK 14(5Q22.2) MUTATED`
TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3522 TCGA-AA-3530 
       13.94        14.53        24.16         1.02        37.05        19.07 
TCGA-AA-3552 TCGA-AA-3562 TCGA-AA-3688 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3867 
       13.02        19.99        19.00        85.05        19.04        24.03 
TCGA-AA-3986 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 
       19.07        10.88       106.75         1.94        49.08         5.88 
TCGA-G4-6310 TCGA-G4-6625 TCGA-5M-AAT4 TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2674 
       63.62        91.79         1.61        39.45        43.76        43.76 
TCGA-A6-2683 TCGA-A6-2686 TCGA-A6-3810 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-6137 
       16.57        37.02        36.53        30.44        29.19        27.09 
TCGA-A6-6140 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6654 TCGA-A6-A5ZU 
       24.13        25.08        25.18        21.76        23.87         9.63 
TCGA-AA-3488 TCGA-AA-3494 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3553 TCGA-AA-3655 
        5.03         1.02        26.01        12.99        24.00        61.02 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3811 TCGA-AA-3841 TCGA-AA-3842 
       50.04        47.01        15.02        10.06        36.95        37.02 
TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3866 TCGA-AA-3941 
       10.06        33.07         0.99        31.07        17.03        24.00 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-A00F TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A01C 
        2.01        21.99        34.03        27.02        42.02        15.02 
TCGA-AA-A01D TCGA-AA-A01T TCGA-AA-A02E TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02W 
       10.98        33.04         2.96         2.01         5.03        41.00 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AY-4070 TCGA-AY-6196 TCGA-AY-6197 
       22.42        27.42        26.47        16.31         0.20        21.44 
TCGA-AY-A71X TCGA-AZ-4614 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6599 TCGA-AZ-6603 
       19.33         5.65        65.00        62.79         6.77        29.56 
TCGA-AZ-6605 TCGA-CA-5256 TCGA-CA-5797 TCGA-CA-6719 TCGA-CK-6751 TCGA-CM-4747 
        5.23        12.46        12.59        14.30       124.27        25.02 
TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5862 TCGA-CM-5864 
       26.04         8.02        13.02        22.03         5.03        15.02 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6169 TCGA-CM-6677 TCGA-D5-5539 TCGA-D5-6535 
       14.04        29.03        13.02        11.08        19.59        15.12 
TCGA-D5-6536 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6932 
       17.85        10.13        12.43         9.04        13.41        11.38 
TCGA-DM-A1D4 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A280 TCGA-DM-A28A TCGA-DM-A28G 
       92.75       140.38        44.32         7.76        26.47        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6704 TCGA-F4-6808 
      117.07        98.24         8.61        31.96         1.55        33.67 
TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6317 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A6GC 
        8.35        82.39        36.00        18.18        10.98        12.79 
TCGA-QG-A5YV TCGA-QG-A5Z1 TCGA-QL-A97D TCGA-RU-A8FL 
       42.77         8.42        21.90        38.70 

$`DEL PEAK 14(5Q22.2) WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-AA-3506 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3524 
       24.33        45.60        58.03        13.02        24.03        36.03 
TCGA-AA-3525 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 
        8.05        34.03         0.99        17.95        23.01        19.99 
TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3692 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 
        6.05         0.92        36.00        19.04        14.93        31.07 
TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 
       29.98        12.99        24.00         2.01        50.99        26.01 
TCGA-AA-3979 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 
       24.00        38.04        21.99        39.06        21.37        15.52 
TCGA-AD-6895 TCGA-AZ-4313 TCGA-AZ-6601 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6314 
       25.08        75.95       100.01        28.21        23.51        35.93 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 TCGA-NH-A8F7 TCGA-3L-AA1B 
       22.09        35.80        26.17        79.69        17.85        15.62 
TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT6 TCGA-A6-2672 TCGA-A6-2675 TCGA-A6-2676 
        4.80        12.66         9.53        46.65        43.43        42.90 
TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-3807 
       42.28        44.91        35.11        37.05        37.25        34.65 
TCGA-A6-3809 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5661 TCGA-A6-5662 
       32.75        32.45        32.91        31.63        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        29.16        22.52         8.38 
TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       20.61        24.69        24.39        20.12        19.66        20.28 
TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-AA-3489 TCGA-AA-3492 
       16.24        24.92        61.84        56.25         7.04         3.02 
TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
       37.05        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        29.00        29.00 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       14.01        33.99        21.01        29.95        20.98        13.94 
TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3675 
       78.08         6.97        54.02         2.01        14.01        47.05 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3812 
       11.01         5.98        37.05         5.03        26.99        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
        0.00        17.03         0.00         0.00        36.03        32.05 
TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 
       53.00        27.02        18.05        31.00         2.01        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       26.01        20.98        34.03        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       25.02        27.02         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00R 
       19.00        30.02        18.05        18.05         4.01         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01F TCGA-AA-A01G 
       17.03        14.99        34.98        15.02        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02O 
        1.02        26.01        37.02        51.98        39.98         0.92 
TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6889 
       22.03        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 
       24.53         5.79        16.44         0.46         0.92        14.50 
TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D 
       27.09         0.95        33.01        17.82        17.26        17.85 
TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4616 
       18.84       109.28        58.39         1.41        32.94         5.13 
TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6606 TCGA-AZ-6607 
       22.36        88.21        49.41        12.10        11.74         3.19 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
       12.69        12.36        12.39        12.59        12.20        12.76 
TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 
       10.06        17.56       148.01        85.45        70.16        15.62 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CM-4743 
       51.32        21.99        21.14        82.95         2.01        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4751 TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5349 
       20.02        37.02        27.02        29.06        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
       32.02        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6170 TCGA-CM-6171 
       16.04        21.99        14.99        12.99        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6678 TCGA-CM-6679 
       11.01        12.95        13.05        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       12.03        45.40        54.61        56.09        55.92        20.19 
TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6537 
       20.42        17.75        18.25        25.48        43.27         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 
       14.30         9.44        11.64        13.35        12.00        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1D7 
      119.70        24.43        38.20       130.65        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A288 
       12.59         7.50       131.51       135.65       139.17        14.04 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28M TCGA-F4-6461 TCGA-F4-6463 
       81.37       119.93        35.97        95.18        11.11        35.74 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       35.74         6.18        47.87        34.42        41.42        43.04 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       67.30        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6626 
       39.42        61.91        26.43        26.04        13.78        46.75 
TCGA-G4-6627 TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A8F8 
       74.79        19.33        19.33         9.93        15.65        16.80 
TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z2 TCGA-SS-A7HO TCGA-T9-A92H TCGA-WS-AB45 
       29.46        32.98        31.30        60.13        11.90        70.03 

  DEL PEAK 14(5Q22.2) MUTATED DEL PEAK 14(5Q22.2) WILD-TYPE 
                          0.2                           0.0 
  DEL PEAK 14(5Q22.2) MUTATED DEL PEAK 14(5Q22.2) WILD-TYPE 
                       140.38                        148.01 
  DEL PEAK 14(5Q22.2) MUTATED DEL PEAK 14(5Q22.2) WILD-TYPE 
                        21.60                         22.44 
[1] "0.2 - 140.4 (21.6)" "0.0 - 148.0 (22.4)"
[1] "hr=" "1.4"
D36V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 14(5Q22.2) MUTATED        19        0        7        29         0
  DEL PEAK 14(5Q22.2) WILD-TYPE      55        1       22       103        10
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 14(5Q22.2) MUTATED           0         4          6         16
  DEL PEAK 14(5Q22.2) WILD-TYPE         1        16          2         43
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 14(5Q22.2) MUTATED           16       19         8         1
  DEL PEAK 14(5Q22.2) WILD-TYPE         25       26         9         1
D36V3, multiclass
            clus
vv           DEL PEAK 14(5Q22.2) MUTATED DEL PEAK 14(5Q22.2) WILD-TYPE
  STAGE I                             19                            55
  STAGE IA                             0                             1
  STAGE II                             7                            22
  STAGE IIA                           29                           103
  STAGE IIB                            0                            10
  STAGE IIC                            0                             1
  STAGE III                            4                            16
  STAGE IIIA                           6                             2
  STAGE IIIB                          16                            43
  STAGE IIIC                          16                            25
  STAGE IV                            19                            26
  STAGE IVA                            8                             9
  STAGE IVB                            1                             1
[1] 13  2
[1] 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(5Q22.2) MUTATED     3  22  89  15
  DEL PEAK 14(5Q22.2) WILD-TYPE   8  55 216  40
D36V4, multiclass
    clus
vv   DEL PEAK 14(5Q22.2) MUTATED DEL PEAK 14(5Q22.2) WILD-TYPE
  T1                           3                             8
  T2                          22                            55
  T3                          89                           216
  T4                          15                            40
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2
  DEL PEAK 14(5Q22.2) MUTATED    64  34  31
  DEL PEAK 14(5Q22.2) WILD-TYPE 198  71  51
D36V5, multiclass
    clus
vv   DEL PEAK 14(5Q22.2) MUTATED DEL PEAK 14(5Q22.2) WILD-TYPE
  N0                          64                           198
  N1                          34                            71
  N2                          31                            51
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V6, binary
                               cls
clus                              0   1
  DEL PEAK 14(5Q22.2) MUTATED    81  28
  DEL PEAK 14(5Q22.2) WILD-TYPE 247  36
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(5Q22.2) MUTATED     81   28
  DEL PEAK 14(5Q22.2) WILD-TYPE  247   36
   clus
vv  DEL PEAK 14(5Q22.2) MUTATED DEL PEAK 14(5Q22.2) WILD-TYPE
  0                          81                           247
  1                          28                            36
[1] 2 2
[1] FALSE
D36V7, binary
                               cls
clus                              0   1
  DEL PEAK 14(5Q22.2) MUTATED    53  76
  DEL PEAK 14(5Q22.2) WILD-TYPE 160 160
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(5Q22.2) MUTATED     53   76
  DEL PEAK 14(5Q22.2) WILD-TYPE  160  160
        clus
vv       DEL PEAK 14(5Q22.2) MUTATED DEL PEAK 14(5Q22.2) WILD-TYPE
  FEMALE                          53                           160
  MALE                            76                           160
[1] 2 2
[1] FALSE
D36V8, binary
                               cls
clus                              0   1
  DEL PEAK 14(5Q22.2) MUTATED   102   3
  DEL PEAK 14(5Q22.2) WILD-TYPE 268   6
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(5Q22.2) MUTATED    102    3
  DEL PEAK 14(5Q22.2) WILD-TYPE  268    6
     clus
vv    DEL PEAK 14(5Q22.2) MUTATED DEL PEAK 14(5Q22.2) WILD-TYPE
  NO                          102                           268
  YES                           3                             6
[1] 2 2
[1] FALSE
D36V9, binary
                               cls
clus                              0   1
  DEL PEAK 14(5Q22.2) MUTATED   116  13
  DEL PEAK 14(5Q22.2) WILD-TYPE 266  49
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(5Q22.2) MUTATED    116   13
  DEL PEAK 14(5Q22.2) WILD-TYPE  266   49
                               clus
vv                              DEL PEAK 14(5Q22.2) MUTATED
  COLON ADENOCARCINOMA                                  116
  COLON MUCINOUS ADENOCARCINOMA                          13
                               clus
vv                              DEL PEAK 14(5Q22.2) WILD-TYPE
  COLON ADENOCARCINOMA                                    266
  COLON MUCINOUS ADENOCARCINOMA                            49
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 14(5Q22.2) MUTATED    80   2  11   6
  DEL PEAK 14(5Q22.2) WILD-TYPE 243   2  14  19
D36V10, multiclass
    clus
vv   DEL PEAK 14(5Q22.2) MUTATED DEL PEAK 14(5Q22.2) WILD-TYPE
  R0                          80                           243
  R1                           2                             2
  R2                          11                            14
  RX                           6                            19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V11, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 14(5Q22.2) MUTATED                                  1     3
  DEL PEAK 14(5Q22.2) WILD-TYPE                                0     8
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 14(5Q22.2) MUTATED                          15    66
  DEL PEAK 14(5Q22.2) WILD-TYPE                        44   146
D36V12, multiclass
                                  clus
vv                                 DEL PEAK 14(5Q22.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      3
  BLACK OR AFRICAN AMERICAN                                 15
  WHITE                                                     66
                                  clus
vv                                 DEL PEAK 14(5Q22.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        8
  BLACK OR AFRICAN AMERICAN                                   44
  WHITE                                                      146
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V13, binary
                               cls
clus                              0   1
  DEL PEAK 14(5Q22.2) MUTATED     3  78
  DEL PEAK 14(5Q22.2) WILD-TYPE   1 191
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(5Q22.2) MUTATED      3   78
  DEL PEAK 14(5Q22.2) WILD-TYPE    1  191
                        clus
vv                       DEL PEAK 14(5Q22.2) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                          78
                        clus
vv                       DEL PEAK 14(5Q22.2) WILD-TYPE
  HISPANIC OR LATINO                                 1
  NOT HISPANIC OR LATINO                           191
[1] 2 2
[1] FALSE

Clustering(37) Variable = DEL PEAK 15(6P25.3) MUTATION ANALYSIS
D37V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 15(6P25.3) MUTATED    40  14
  DEL PEAK 15(6P25.3) WILD-TYPE 295  87
  DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE 
                           54                           382 
  DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE 
                           14                            87 
$`DEL PEAK 15(6P25.3) MUTATED`
TCGA-A6-6649 TCGA-AA-3692 TCGA-AA-3715 TCGA-AA-3870 TCGA-AA-3939 TCGA-AD-6895 
       24.16        36.00        19.04        29.98        12.99        25.08 
TCGA-AD-6964 TCGA-A6-2671 TCGA-A6-2683 TCGA-A6-2686 TCGA-A6-6648 TCGA-A6-6782 
       10.88        43.76        16.57        37.02        25.18        20.28 
TCGA-AA-3518 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3666 TCGA-AA-3685 
        1.02        13.94        61.02         6.97         2.01        37.05 
TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3875 TCGA-AA-3941 
       38.99        36.95        31.07        53.00        18.05        24.00 
TCGA-AA-3966 TCGA-AA-A004 TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00O TCGA-AA-A01P 
        2.01        13.94        30.02        18.05        27.02        38.07 
TCGA-AA-A01X TCGA-AA-A02O TCGA-AD-6899 TCGA-AD-A5EK TCGA-AZ-4614 TCGA-AZ-6607 
       26.01         0.92         5.79        16.44         5.65         3.19 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-6676 
       12.69        12.36        12.46        29.06        22.98        11.08 
TCGA-CM-6678 TCGA-D5-5537 TCGA-D5-6529 TCGA-D5-6531 TCGA-D5-6536 TCGA-D5-6898 
       11.01        45.40        20.19        17.75        17.85         7.53 
TCGA-DM-A1D7 TCGA-DM-A28A TCGA-DM-A28H TCGA-F4-6808 TCGA-G4-6317 TCGA-T9-A92H 
       13.32        26.47       117.07        33.67        36.00        11.90 

$`DEL PEAK 15(6P25.3) WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-4105 TCGA-AA-3496 TCGA-AA-3506 
       24.33        45.60        13.94        14.53         1.02        58.03 
TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 
       13.02        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 
       34.03         0.99        13.02        17.95        23.01        19.99 
TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3697 TCGA-AA-3713 
       19.99         6.05         0.92        19.00        85.05        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       14.93        31.07        24.03        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 
       21.37        15.52        75.95       106.75       100.01         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6314 
       49.08         5.88        28.21        23.51        63.62        35.93 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-NH-A8F7 
       22.09        35.80        26.17        91.79        79.69        17.85 
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-5M-AATE 
       15.62         4.80        12.66         1.61         9.53        39.45 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 
       46.65        43.76        43.43        42.90        42.28        44.91 
TCGA-A6-2680 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-3810 
       35.11        37.05        37.25        34.65        32.75        36.53 
TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 
       32.45        32.91        31.63        30.44        29.19        33.53 
TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 
       23.61        22.09        22.06        32.71        29.16        27.09 
TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6650 TCGA-A6-6651 
       22.52        24.13         8.38        25.08        20.61        21.76 
TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 
       24.69        24.39        23.87        20.12        19.66        16.24 
TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 
       24.92        61.84        56.25         9.63         5.03         7.04 
TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
        3.02         1.02        37.05        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
        1.02        38.99         9.07        19.07         0.00        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       29.00        26.01        12.99        14.01        33.99        21.01 
TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3667 
       24.00        29.95        20.98        78.08        54.02        14.01 
TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
       50.04        47.05        47.01        15.02        11.01         5.98 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
        5.03        26.99        10.06        35.05         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3846 
        1.02        17.98        15.95        37.02         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 
        0.99        17.03        27.02        31.00         2.01        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 
       26.01        20.98        34.03        21.99        16.08        13.05 
TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A00A 
       34.06        25.02        27.02         7.96        27.02        38.04 
TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00Q TCGA-AA-A00R 
       19.00        34.03        18.05         4.01        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D 
       17.03        14.99        34.98        15.02        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01Q TCGA-AA-A01R 
       32.02        12.00        31.00        31.00         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02E 
        1.02        33.04         1.02        37.02        51.98         2.96 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y 
       39.98         2.01         5.03        22.03        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6901 
       18.05        40.96        12.16        83.24        24.53        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 
       27.42        26.47         0.46         0.92        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        21.44        17.82 
TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4315 
       17.26        17.85        19.33        18.84       109.28        58.39 
TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 
        1.41        32.94         5.13        22.36        65.00        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 
       88.21        49.41         6.77        12.10        29.56         5.23 
TCGA-AZ-6606 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
       11.74        12.39        12.59        12.59        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 
       10.06        14.30        17.56       148.01        85.45        70.16 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 
      124.27        23.05        20.02        37.02        25.02        26.04 
TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5860 
        8.02        27.02        13.02        22.03        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00        14.04        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6677 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5538 TCGA-D5-5539 
       13.05        11.08        10.06        12.03        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.42        18.25        25.48        43.27 
TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       15.12         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
        7.76       139.17        14.04        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 
       60.79        98.24        95.18         8.61        31.96        11.11 
TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       35.74        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       41.42        43.04        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 
      133.18         8.35        82.39        74.56        67.30        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        39.42        61.91 
TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T 
       26.43        26.04        13.78        46.75        74.79        18.18 
TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC 
       10.98        19.33        19.33         9.93        15.65        12.79 
TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 
       16.80        42.77        29.46        32.98         8.42        31.30 
TCGA-QL-A97D TCGA-RU-A8FL TCGA-SS-A7HO TCGA-WS-AB45 
       21.90        38.70        60.13        70.03 

  DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE 
                         0.92                          0.00 
  DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE 
                       117.07                        148.01 
  DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE 
                       19.615                        22.090 
[1] "0.9 - 117.1 (19.6)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.4"
D37V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 15(6P25.3) MUTATED         7        0        6        18         1
  DEL PEAK 15(6P25.3) WILD-TYPE      67        1       23       114         9
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 15(6P25.3) MUTATED           0         3          1          4
  DEL PEAK 15(6P25.3) WILD-TYPE         1        17          7         55
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 15(6P25.3) MUTATED            5        5         4         0
  DEL PEAK 15(6P25.3) WILD-TYPE         36       40        13         2
D37V3, multiclass
            clus
vv           DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE
  STAGE I                              7                            67
  STAGE IA                             0                             1
  STAGE II                             6                            23
  STAGE IIA                           18                           114
  STAGE IIB                            1                             9
  STAGE IIC                            0                             1
  STAGE III                            3                            17
  STAGE IIIA                           1                             7
  STAGE IIIB                           4                            55
  STAGE IIIC                           5                            36
  STAGE IV                             5                            40
  STAGE IVA                            4                            13
  STAGE IVB                            0                             2
[1] 13  2
[1] 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(6P25.3) MUTATED     2   7  37   9
  DEL PEAK 15(6P25.3) WILD-TYPE   9  70 268  46
D37V4, multiclass
    clus
vv   DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE
  T1                           2                             9
  T2                           7                            70
  T3                          37                           268
  T4                           9                            46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2
  DEL PEAK 15(6P25.3) MUTATED    33  11  11
  DEL PEAK 15(6P25.3) WILD-TYPE 229  94  71
D37V5, multiclass
    clus
vv   DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE
  N0                          33                           229
  N1                          11                            94
  N2                          11                            71
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V6, binary
                               cls
clus                              0   1
  DEL PEAK 15(6P25.3) MUTATED    39   9
  DEL PEAK 15(6P25.3) WILD-TYPE 289  55
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(6P25.3) MUTATED     39    9
  DEL PEAK 15(6P25.3) WILD-TYPE  289   55
   clus
vv  DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE
  0                          39                           289
  1                           9                            55
[1] 2 2
[1] FALSE
D37V7, binary
                               cls
clus                              0   1
  DEL PEAK 15(6P25.3) MUTATED    19  36
  DEL PEAK 15(6P25.3) WILD-TYPE 194 200
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(6P25.3) MUTATED     19   36
  DEL PEAK 15(6P25.3) WILD-TYPE  194  200
        clus
vv       DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE
  FEMALE                          19                           194
  MALE                            36                           200
[1] 2 2
[1] FALSE
D37V8, binary
                               cls
clus                              0   1
  DEL PEAK 15(6P25.3) MUTATED    44   2
  DEL PEAK 15(6P25.3) WILD-TYPE 326   7
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(6P25.3) MUTATED     44    2
  DEL PEAK 15(6P25.3) WILD-TYPE  326    7
     clus
vv    DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE
  NO                           44                           326
  YES                           2                             7
[1] 2 2
[1] FALSE
D37V9, binary
                               cls
clus                              0   1
  DEL PEAK 15(6P25.3) MUTATED    49   5
  DEL PEAK 15(6P25.3) WILD-TYPE 333  57
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(6P25.3) MUTATED     49    5
  DEL PEAK 15(6P25.3) WILD-TYPE  333   57
                               clus
vv                              DEL PEAK 15(6P25.3) MUTATED
  COLON ADENOCARCINOMA                                   49
  COLON MUCINOUS ADENOCARCINOMA                           5
                               clus
vv                              DEL PEAK 15(6P25.3) WILD-TYPE
  COLON ADENOCARCINOMA                                    333
  COLON MUCINOUS ADENOCARCINOMA                            57
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 15(6P25.3) MUTATED    39   0   1   5
  DEL PEAK 15(6P25.3) WILD-TYPE 284   4  24  20
D37V10, multiclass
    clus
vv   DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE
  R0                          39                           284
  R1                           0                             4
  R2                           1                            24
  RX                           5                            20
[1] 4 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, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 15(6P25.3) MUTATED                                  0     3
  DEL PEAK 15(6P25.3) WILD-TYPE                                1     8
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 15(6P25.3) MUTATED                           2    26
  DEL PEAK 15(6P25.3) WILD-TYPE                        57   186
D37V12, multiclass
                                  clus
vv                                 DEL PEAK 15(6P25.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      3
  BLACK OR AFRICAN AMERICAN                                  2
  WHITE                                                     26
                                  clus
vv                                 DEL PEAK 15(6P25.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        8
  BLACK OR AFRICAN AMERICAN                                   57
  WHITE                                                      186
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V13, binary
                               cls
clus                              0   1
  DEL PEAK 15(6P25.3) MUTATED     0  29
  DEL PEAK 15(6P25.3) WILD-TYPE   4 240
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(6P25.3) MUTATED      0   29
  DEL PEAK 15(6P25.3) WILD-TYPE    4  240
                        clus
vv                       DEL PEAK 15(6P25.3) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                          29
                        clus
vv                       DEL PEAK 15(6P25.3) WILD-TYPE
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           240
[1] 2 2
[1] FALSE

Clustering(38) Variable = DEL PEAK 16(6Q26) MUTATION ANALYSIS
D38V1, survival
                             sevent
clus2                           0   1
  DEL PEAK 16(6Q26) MUTATED    40  19
  DEL PEAK 16(6Q26) WILD-TYPE 295  82
  DEL PEAK 16(6Q26) MUTATED DEL PEAK 16(6Q26) WILD-TYPE 
                         59                         377 
  DEL PEAK 16(6Q26) MUTATED DEL PEAK 16(6Q26) WILD-TYPE 
                         19                          82 
$`DEL PEAK 16(6Q26) MUTATED`
TCGA-A6-2681 TCGA-A6-6649 TCGA-AA-3552 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 
       45.60        24.16        13.02        36.00        85.05        19.04 
TCGA-AA-3860 TCGA-AA-3939 TCGA-AA-3952 TCGA-A6-2671 TCGA-A6-2678 TCGA-A6-4107 
       31.07        12.99         2.01        43.76        42.28        32.45 
TCGA-A6-6138 TCGA-A6-6782 TCGA-AA-3488 TCGA-AA-3655 TCGA-AA-3664 TCGA-AA-3666 
       22.52        20.28         5.03        61.02        54.02         2.01 
TCGA-AA-3680 TCGA-AA-3685 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3854 TCGA-AA-3875 
       11.01        37.05        38.99        36.95        36.03        18.05 
TCGA-AA-3941 TCGA-AA-A00J TCGA-AA-A00U TCGA-AA-A01D TCGA-AA-A01T TCGA-AA-A01X 
       24.00        18.05        17.03        10.98        33.04        26.01 
TCGA-AA-A02E TCGA-AA-A02H TCGA-AD-6899 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AY-4070 
        2.96         2.01         5.79        16.44         0.46        16.31 
TCGA-AY-6196 TCGA-AY-A8YK TCGA-AZ-4616 TCGA-AZ-6598 TCGA-AZ-6607 TCGA-CA-5254 
        0.20        18.84         5.13        49.41         3.19        12.69 
TCGA-CA-5255 TCGA-CA-5256 TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6678 
       12.36        12.46        11.01        13.05        11.08        11.01 
TCGA-D5-5537 TCGA-D5-6529 TCGA-D5-6531 TCGA-D5-6535 TCGA-D5-6898 TCGA-DM-A1D7 
       45.40        20.19        17.75        15.12         7.53        13.32 
TCGA-DM-A1HA TCGA-F4-6704 TCGA-F4-6808 TCGA-G4-6297 TCGA-NH-A6GA 
      131.51         1.55        33.67        82.39         9.93 

$`DEL PEAK 16(6Q26) WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2682 TCGA-A6-4105 TCGA-AA-3496 TCGA-AA-3506 TCGA-AA-3516 
       24.33        13.94        14.53         1.02        58.03        13.02 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 
       24.03        37.05        36.03         8.05        19.07        34.03 
TCGA-AA-3543 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
        0.99        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3713 TCGA-AA-3844 TCGA-AA-3867 TCGA-AA-3870 
        0.92        19.00        19.04        14.93        24.03        29.98 
TCGA-AA-3950 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
       24.00        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 
       75.95       106.75       100.01         1.94        49.08         5.88 
TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6321 TCGA-G4-6586 
       28.21        23.51        63.62        35.93        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-NH-A8F7 TCGA-3L-AA1B TCGA-4N-A93T 
       26.17        91.79        79.69        17.85        15.62         4.80 
TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2672 TCGA-A6-2674 
       12.66         1.61         9.53        39.45        46.65        43.76 
TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2684 
       43.43        42.90        44.91        35.11        16.57        37.05 
TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 
       37.25        37.02        34.65        32.75        36.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6141 
       22.06        32.71        29.16        27.09        24.13         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        20.61        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 
       23.87        20.12        19.66        16.24        24.92        61.84 
TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 
       56.25         9.63         7.04         3.02         1.02        37.05 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3667 TCGA-AA-3673 
       20.98        13.94        78.08         6.97        14.01        50.04 
TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3681 TCGA-AA-3696 TCGA-AA-3710 
       47.05        47.01        15.02         5.98         5.03        26.99 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       10.06        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       15.95        37.02         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 
       33.07         0.00        32.05         0.99        31.07        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 
       17.03        27.02        31.00         2.01        33.01        26.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 
       20.98        34.03         2.01        21.99        16.08        13.05 
TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       34.06        25.02        27.02         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00N 
       38.04        19.00        30.02        34.03        18.05         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       27.02        42.02         0.99        14.99        34.98        15.02 
TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       15.02        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A029 
        1.02        35.01         1.02         1.02        37.02        51.98 
TCGA-AA-A02F TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y 
       39.98         5.03         0.92        22.03        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6901 
       18.05        40.96        12.16        83.24        24.53        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4071 
       27.42        26.47         0.92        14.50        27.09         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X 
       33.01        21.44        17.82        17.26        17.85        19.33 
TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4682 
      109.28        58.39         1.41         5.65        32.94        22.36 
TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 
       65.00        62.79        88.21         6.77        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        5.23        11.74        12.39        12.59        12.59        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       70.16        15.62        51.32        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       26.04         8.02        27.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6677 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5538 
       14.04        12.95        11.08        10.06        12.03        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.42        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       43.27        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
       15.58        12.39        10.13        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HB 
       49.91        12.59       140.38         7.50        44.32       135.65 
TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E 
        7.76       139.17        14.04        26.47        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 
       35.97        60.79       117.07        98.24        95.18         8.61 
TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       31.96        11.11        35.74        35.74         6.18        47.87 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       34.42        41.42        43.04        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6295 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 
       35.31       133.18         8.35        74.56        67.30        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        39.42        61.91 
TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6626 TCGA-G4-6627 
       36.00        26.43        26.04        13.78        46.75        74.79 
TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GB TCGA-NH-A6GC 
       18.18        10.98        19.33        19.33        15.65        12.79 
TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 
       16.80        42.77        29.46        32.98         8.42        31.30 
TCGA-QL-A97D TCGA-RU-A8FL TCGA-SS-A7HO TCGA-T9-A92H TCGA-WS-AB45 
       21.90        38.70        60.13        11.90        70.03 

  DEL PEAK 16(6Q26) MUTATED DEL PEAK 16(6Q26) WILD-TYPE 
                        0.2                         0.0 
  DEL PEAK 16(6Q26) MUTATED DEL PEAK 16(6Q26) WILD-TYPE 
                     131.51                      148.01 
  DEL PEAK 16(6Q26) MUTATED DEL PEAK 16(6Q26) WILD-TYPE 
                      17.75                       23.01 
[1] "0.2 - 131.5 (17.8)" "0.0 - 148.0 (23.0)"
[1] "hr=" "1.8"
D38V2, continuous
                             vv
clus                          STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 16(6Q26) MUTATED         8        0        7        11         1
  DEL PEAK 16(6Q26) WILD-TYPE      66        1       22       121         9
                             vv
clus                          STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 16(6Q26) MUTATED           0         3          0          8
  DEL PEAK 16(6Q26) WILD-TYPE         1        17          8         51
                             vv
clus                          STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 16(6Q26) MUTATED            9        9         4         1
  DEL PEAK 16(6Q26) WILD-TYPE         32       36        13         1
D38V3, multiclass
            clus
vv           DEL PEAK 16(6Q26) MUTATED DEL PEAK 16(6Q26) WILD-TYPE
  STAGE I                            8                          66
  STAGE IA                           0                           1
  STAGE II                           7                          22
  STAGE IIA                         11                         121
  STAGE IIB                          1                           9
  STAGE IIC                          0                           1
  STAGE III                          3                          17
  STAGE IIIA                         0                           8
  STAGE IIIB                         8                          51
  STAGE IIIC                         9                          32
  STAGE IV                           9                          36
  STAGE IVA                          4                          13
  STAGE IVB                          1                           1
[1] 13  2
[1] 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(6Q26) MUTATED     2   7  43   9
  DEL PEAK 16(6Q26) WILD-TYPE   9  70 262  46
D38V4, multiclass
    clus
vv   DEL PEAK 16(6Q26) MUTATED DEL PEAK 16(6Q26) WILD-TYPE
  T1                         2                           9
  T2                         7                          70
  T3                        43                         262
  T4                         9                          46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           N0  N1  N2
  DEL PEAK 16(6Q26) MUTATED    26  14  21
  DEL PEAK 16(6Q26) WILD-TYPE 236  91  61
D38V5, multiclass
    clus
vv   DEL PEAK 16(6Q26) MUTATED DEL PEAK 16(6Q26) WILD-TYPE
  N0                        26                         236
  N1                        14                          91
  N2                        21                          61
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V6, binary
                             cls
clus                            0   1
  DEL PEAK 16(6Q26) MUTATED    37  14
  DEL PEAK 16(6Q26) WILD-TYPE 291  50
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 16(6Q26) MUTATED     37   14
  DEL PEAK 16(6Q26) WILD-TYPE  291   50
   clus
vv  DEL PEAK 16(6Q26) MUTATED DEL PEAK 16(6Q26) WILD-TYPE
  0                        37                         291
  1                        14                          50
[1] 2 2
[1] FALSE
D38V7, binary
                             cls
clus                            0   1
  DEL PEAK 16(6Q26) MUTATED    27  34
  DEL PEAK 16(6Q26) WILD-TYPE 186 202
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 16(6Q26) MUTATED     27   34
  DEL PEAK 16(6Q26) WILD-TYPE  186  202
        clus
vv       DEL PEAK 16(6Q26) MUTATED DEL PEAK 16(6Q26) WILD-TYPE
  FEMALE                        27                         186
  MALE                          34                         202
[1] 2 2
[1] FALSE
D38V8, binary
                             cls
clus                            0   1
  DEL PEAK 16(6Q26) MUTATED    47   2
  DEL PEAK 16(6Q26) WILD-TYPE 323   7
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 16(6Q26) MUTATED     47    2
  DEL PEAK 16(6Q26) WILD-TYPE  323    7
     clus
vv    DEL PEAK 16(6Q26) MUTATED DEL PEAK 16(6Q26) WILD-TYPE
  NO                         47                         323
  YES                         2                           7
[1] 2 2
[1] FALSE
D38V9, binary
                             cls
clus                            0   1
  DEL PEAK 16(6Q26) MUTATED    52   8
  DEL PEAK 16(6Q26) WILD-TYPE 330  54
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 16(6Q26) MUTATED     52    8
  DEL PEAK 16(6Q26) WILD-TYPE  330   54
                               clus
vv                              DEL PEAK 16(6Q26) MUTATED
  COLON ADENOCARCINOMA                                 52
  COLON MUCINOUS ADENOCARCINOMA                         8
                               clus
vv                              DEL PEAK 16(6Q26) WILD-TYPE
  COLON ADENOCARCINOMA                                  330
  COLON MUCINOUS ADENOCARCINOMA                          54
[1] 2 2
[1] FALSE
                             vv
clus                           R0  R1  R2  RX
  DEL PEAK 16(6Q26) MUTATED    40   1   5   6
  DEL PEAK 16(6Q26) WILD-TYPE 283   3  20  19
D38V10, multiclass
    clus
vv   DEL PEAK 16(6Q26) MUTATED DEL PEAK 16(6Q26) WILD-TYPE
  R0                        40                         283
  R1                         1                           3
  R2                         5                          20
  RX                         6                          19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V11, continuous
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 16(6Q26) MUTATED                                  1     3
  DEL PEAK 16(6Q26) WILD-TYPE                                0     8
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 16(6Q26) MUTATED                           5    26
  DEL PEAK 16(6Q26) WILD-TYPE                        54   186
D38V12, multiclass
                                  clus
vv                                 DEL PEAK 16(6Q26) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         1
  ASIAN                                                    3
  BLACK OR AFRICAN AMERICAN                                5
  WHITE                                                   26
                                  clus
vv                                 DEL PEAK 16(6Q26) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      8
  BLACK OR AFRICAN AMERICAN                                 54
  WHITE                                                    186
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V13, binary
                             cls
clus                            0   1
  DEL PEAK 16(6Q26) MUTATED     0  33
  DEL PEAK 16(6Q26) WILD-TYPE   4 236
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 16(6Q26) MUTATED      0   33
  DEL PEAK 16(6Q26) WILD-TYPE    4  236
                        clus
vv                       DEL PEAK 16(6Q26) MUTATED DEL PEAK 16(6Q26) WILD-TYPE
  HISPANIC OR LATINO                             0                           4
  NOT HISPANIC OR LATINO                        33                         236
[1] 2 2
[1] FALSE

Clustering(39) Variable = DEL PEAK 17(7Q31.1) MUTATION ANALYSIS
D39V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 17(7Q31.1) MUTATED     9   3
  DEL PEAK 17(7Q31.1) WILD-TYPE 326  98
  DEL PEAK 17(7Q31.1) MUTATED DEL PEAK 17(7Q31.1) WILD-TYPE 
                           12                           424 
  DEL PEAK 17(7Q31.1) MUTATED DEL PEAK 17(7Q31.1) WILD-TYPE 
                            3                            98 
$`DEL PEAK 17(7Q31.1) MUTATED`
TCGA-AA-A00L TCGA-AD-6548 TCGA-5M-AAT4 TCGA-A6-3807 TCGA-AA-A01R TCGA-AU-3779 
       38.04        21.37         1.61        34.65        35.01        14.50 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5862 TCGA-CM-6170 TCGA-D5-6932 TCGA-DM-A0XD 
       29.06        22.03         5.03        15.02        11.38        24.43 

$`DEL PEAK 17(7Q31.1) WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 
       24.33        45.60        13.94        14.53        24.16         1.02 
TCGA-AA-3506 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
       58.03        13.02        24.03        37.05        36.03         8.05 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 
       19.07        34.03         0.99        13.02        17.95        23.01 
TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 
       19.99        19.99         6.05         0.92        19.00        36.00 
TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 
       85.05        19.04        19.04        14.93        31.07        24.03 
TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 
       29.98        12.99        24.00         2.01        50.99        26.01 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6888 TCGA-AD-6895 
       24.00        19.07        21.99        39.06        15.52        25.08 
TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 
       10.88        75.95       106.75       100.01         1.94        49.08 
TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6321 
        5.88        28.21        23.51        63.62        35.93        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-NH-A8F7 TCGA-3L-AA1B 
       35.80        26.17        91.79        79.69        17.85        15.62 
TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2672 
        4.80        12.66         9.53        39.45        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 
       43.76        43.43        42.90        42.28        44.91        35.11 
TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3809 TCGA-A6-3810 
       16.57        37.05        37.25        37.02        32.75        36.53 
TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 
       32.45        32.91        31.63        30.44        29.19        33.53 
TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 
       23.61        22.09        22.06        32.71        29.16        27.09 
TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 
       22.52        24.13         8.38        25.08        25.18        20.61 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU 
       20.28        16.24        24.92        61.84        56.25         9.63 
TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 
        5.03         7.04         3.02         1.02        37.05        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
       63.98         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        61.02        78.08         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01        50.04        47.05        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         5.03        26.99        10.06        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       36.95        37.02         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3982 
       21.99        16.08        13.05        34.06        25.02        27.02 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C 
        0.99        17.03        14.99        34.98        15.02        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
        1.02         1.02        33.04         1.02        26.01        37.02 
TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O 
       51.98         2.96        39.98         2.01         5.03         0.92 
TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
       22.03        41.00        39.98        18.05        40.96        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       16.44         0.46         0.92        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D 
       33.01         0.20        21.44        17.82        17.26        17.85 
TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 
       19.33        18.84       109.28        58.39         1.41         5.65 
TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 
       32.94         5.13        22.36        65.00        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       49.41         6.77        12.10        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 
        3.19        12.69        12.36        12.46        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        70.16        15.62        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 
       37.02        25.02        26.04         8.02        27.02        13.02 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5864 
       22.98        30.08        32.02        15.02        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6171 TCGA-CM-6172 
       21.99        14.99        12.99        13.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       20.19        20.42        17.75        18.25        25.48        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         7.53        12.39        10.13        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64        13.41        13.35        12.00 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
       10.26       119.70        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C 
      135.65         7.76       139.17        14.04        26.47        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M 
      119.93        35.97        60.79       117.07        98.24        95.18 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 
        8.61        31.96        11.11        35.74        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6295 
       13.25         0.53        47.41        35.31       133.18         8.35 
TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       82.39        74.56        67.30        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 
       55.04        85.48        39.42        61.91        36.00        26.43 
TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50U 
       26.04        13.78        46.75        74.79        18.18        10.98 
TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F8 
       19.33        19.33         9.93        15.65        12.79        16.80 
TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D 
       42.77        29.46        32.98         8.42        31.30        21.90 
TCGA-RU-A8FL TCGA-SS-A7HO TCGA-T9-A92H TCGA-WS-AB45 
       38.70        60.13        11.90        70.03 

  DEL PEAK 17(7Q31.1) MUTATED DEL PEAK 17(7Q31.1) WILD-TYPE 
                         1.61                          0.00 
  DEL PEAK 17(7Q31.1) MUTATED DEL PEAK 17(7Q31.1) WILD-TYPE 
                        38.04                        148.01 
  DEL PEAK 17(7Q31.1) MUTATED DEL PEAK 17(7Q31.1) WILD-TYPE 
                       21.700                        22.075 
[1] "1.6 - 38.0 (21.7)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.5"
D39V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 17(7Q31.1) MUTATED         2        0        0         5         0
  DEL PEAK 17(7Q31.1) WILD-TYPE      72        1       29       127        10
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 17(7Q31.1) MUTATED           0         1          1          1
  DEL PEAK 17(7Q31.1) WILD-TYPE         1        19          7         58
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 17(7Q31.1) MUTATED            1        1         1         0
  DEL PEAK 17(7Q31.1) WILD-TYPE         40       44        16         2
D39V3, multiclass
            clus
vv           DEL PEAK 17(7Q31.1) MUTATED DEL PEAK 17(7Q31.1) WILD-TYPE
  STAGE I                              2                            72
  STAGE IA                             0                             1
  STAGE II                             0                            29
  STAGE IIA                            5                           127
  STAGE IIB                            0                            10
  STAGE IIC                            0                             1
  STAGE III                            1                            19
  STAGE IIIA                           1                             7
  STAGE IIIB                           1                            58
  STAGE IIIC                           1                            40
  STAGE IV                             1                            44
  STAGE IVA                            1                            16
  STAGE IVB                            0                             2
[1] 13  2
[1] 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(7Q31.1) MUTATED     0   3  10   0
  DEL PEAK 17(7Q31.1) WILD-TYPE  11  74 295  55
D39V4, multiclass
    clus
vv   DEL PEAK 17(7Q31.1) MUTATED DEL PEAK 17(7Q31.1) WILD-TYPE
  T1                           0                            11
  T2                           3                            74
  T3                          10                           295
  T4                           0                            55
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2
  DEL PEAK 17(7Q31.1) MUTATED     8   3   2
  DEL PEAK 17(7Q31.1) WILD-TYPE 254 102  80
D39V5, multiclass
    clus
vv   DEL PEAK 17(7Q31.1) MUTATED DEL PEAK 17(7Q31.1) WILD-TYPE
  N0                           8                           254
  N1                           3                           102
  N2                           2                            80
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V6, binary
                               cls
clus                              0   1
  DEL PEAK 17(7Q31.1) MUTATED    11   2
  DEL PEAK 17(7Q31.1) WILD-TYPE 317  62
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 17(7Q31.1) MUTATED     11    2
  DEL PEAK 17(7Q31.1) WILD-TYPE  317   62
   clus
vv  DEL PEAK 17(7Q31.1) MUTATED DEL PEAK 17(7Q31.1) WILD-TYPE
  0                          11                           317
  1                           2                            62
[1] 2 2
[1] FALSE
D39V7, binary
                               cls
clus                              0   1
  DEL PEAK 17(7Q31.1) MUTATED     7   6
  DEL PEAK 17(7Q31.1) WILD-TYPE 206 230
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 17(7Q31.1) MUTATED      7    6
  DEL PEAK 17(7Q31.1) WILD-TYPE  206  230
        clus
vv       DEL PEAK 17(7Q31.1) MUTATED DEL PEAK 17(7Q31.1) WILD-TYPE
  FEMALE                           7                           206
  MALE                             6                           230
[1] 2 2
[1] FALSE
D39V8, binary
                               cls
clus                              0   1
  DEL PEAK 17(7Q31.1) MUTATED    10   1
  DEL PEAK 17(7Q31.1) WILD-TYPE 360   8
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 17(7Q31.1) MUTATED     10    1
  DEL PEAK 17(7Q31.1) WILD-TYPE  360    8
     clus
vv    DEL PEAK 17(7Q31.1) MUTATED DEL PEAK 17(7Q31.1) WILD-TYPE
  NO                           10                           360
  YES                           1                             8
[1] 2 2
[1] FALSE
D39V9, binary
                               cls
clus                              0   1
  DEL PEAK 17(7Q31.1) MUTATED    12   1
  DEL PEAK 17(7Q31.1) WILD-TYPE 370  61
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 17(7Q31.1) MUTATED     12    1
  DEL PEAK 17(7Q31.1) WILD-TYPE  370   61
                               clus
vv                              DEL PEAK 17(7Q31.1) MUTATED
  COLON ADENOCARCINOMA                                   12
  COLON MUCINOUS ADENOCARCINOMA                           1
                               clus
vv                              DEL PEAK 17(7Q31.1) WILD-TYPE
  COLON ADENOCARCINOMA                                    370
  COLON MUCINOUS ADENOCARCINOMA                            61
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 17(7Q31.1) MUTATED    12   0   0   0
  DEL PEAK 17(7Q31.1) WILD-TYPE 311   4  25  25
D39V10, multiclass
    clus
vv   DEL PEAK 17(7Q31.1) MUTATED DEL PEAK 17(7Q31.1) WILD-TYPE
  R0                          12                           311
  R1                           0                             4
  R2                           0                            25
  RX                           0                            25
[1] 4 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, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 17(7Q31.1) MUTATED                                  0     0
  DEL PEAK 17(7Q31.1) WILD-TYPE                                1    11
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 17(7Q31.1) MUTATED                           1     9
  DEL PEAK 17(7Q31.1) WILD-TYPE                        58   203
D39V12, multiclass
                                  clus
vv                                 DEL PEAK 17(7Q31.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      0
  BLACK OR AFRICAN AMERICAN                                  1
  WHITE                                                      9
                                  clus
vv                                 DEL PEAK 17(7Q31.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                       11
  BLACK OR AFRICAN AMERICAN                                   58
  WHITE                                                      203
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V13, binary
                               cls
clus                              0   1
  DEL PEAK 17(7Q31.1) MUTATED     2   8
  DEL PEAK 17(7Q31.1) WILD-TYPE   2 261
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 17(7Q31.1) MUTATED      2    8
  DEL PEAK 17(7Q31.1) WILD-TYPE    2  261
                        clus
vv                       DEL PEAK 17(7Q31.1) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                           8
                        clus
vv                       DEL PEAK 17(7Q31.1) WILD-TYPE
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                           261
[1] 2 2
[1] FALSE

Clustering(40) Variable = DEL PEAK 18(8P23.2) MUTATION ANALYSIS
D40V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 18(8P23.2) MUTATED   138  48
  DEL PEAK 18(8P23.2) WILD-TYPE 197  53
  DEL PEAK 18(8P23.2) MUTATED DEL PEAK 18(8P23.2) WILD-TYPE 
                          186                           250 
  DEL PEAK 18(8P23.2) MUTATED DEL PEAK 18(8P23.2) WILD-TYPE 
                           48                            53 
$`DEL PEAK 18(8P23.2) MUTATED`
TCGA-A6-2677 TCGA-A6-2681 TCGA-AA-3496 TCGA-AA-3520 TCGA-AA-3531 TCGA-AA-3543 
       24.33        45.60         1.02        24.03        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3688 
       13.02        23.01        19.99        19.99         6.05        19.00 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3952 
       36.00        85.05        31.07        24.03        29.98         2.01 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AD-6888 TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 
       26.01        24.00        15.52       106.75         1.94        49.08 
TCGA-DM-A285 TCGA-G4-6298 TCGA-G4-6314 TCGA-G4-6586 TCGA-G4-6625 TCGA-4N-A93T 
        5.88        23.51        35.93        35.80        91.79         4.80 
TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2678 
        1.61         9.53        43.76        43.76        43.43        42.28 
TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-5656 
       44.91        35.11        16.57        34.65        36.53        32.91 
TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6140 
       31.63        29.19        23.61        29.16        27.09        24.13 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6782 
       25.08        25.18        20.61        24.69        23.87        20.28 
TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3494 TCGA-AA-3495 
       61.84        56.25         9.63         5.03         1.02        37.05 
TCGA-AA-3517 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
       38.99         0.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3660 TCGA-AA-3666 TCGA-AA-3667 
       33.99        21.01        24.00        78.08         2.01        14.01 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3842 TCGA-AA-3851 
       47.01        15.02         5.98        37.05        37.02        33.07 
TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3930 
       36.03         0.99        31.07        17.03        27.02         2.01 
TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3975 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-A00D 
       34.03        16.08        34.06        27.02         7.96        19.00 
TCGA-AA-A00F TCGA-AA-A00U TCGA-AA-A017 TCGA-AA-A01G TCGA-AA-A01K TCGA-AA-A01S 
       34.03        17.03        15.02        12.00        31.00         1.02 
TCGA-AA-A01T TCGA-AA-A01Z TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02J TCGA-AA-A02W 
       33.04        37.02         2.96        39.98         5.03        41.00 
TCGA-AA-A03J TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6965 TCGA-AY-4070 TCGA-AY-5543 
       40.96         5.79        22.42        26.47        16.31        33.01 
TCGA-AY-6196 TCGA-AY-A69D TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4614 TCGA-AZ-4684 
        0.20        17.85        18.84       109.28         5.65        65.00 
TCGA-AZ-5403 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       62.79        12.10        29.56         5.23        11.74         3.19 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6719 TCGA-CK-4952 TCGA-CM-4751 TCGA-CM-4752 
       12.59        12.59        14.30        15.62        27.02        13.02 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5868 
       22.03        22.98        30.08        32.02         5.03        17.03 
TCGA-CM-6163 TCGA-CM-6166 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6675 TCGA-CM-6676 
       14.04        21.99        13.02        15.02        13.05        11.08 
TCGA-CM-6679 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6531 TCGA-D5-6533 
       10.06        54.61        56.09        55.92        17.75        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6922 
       43.27        15.12        12.49        15.58         7.53        10.13 
TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.43         9.04        13.41        11.38        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1HA TCGA-DM-A28A 
      130.65        49.91        13.32       140.38       131.51        26.47 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-F4-6460 TCGA-F4-6463 TCGA-F4-6704 
       35.97        60.79       117.07        31.96        35.74         1.55 
TCGA-F4-6805 TCGA-F4-6854 TCGA-G4-6295 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 
       34.42         0.53         8.35        74.56        65.85        44.68 
TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-NH-A50U TCGA-NH-A50V 
       39.42        61.91        36.00        26.43        10.98        19.33 
TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A8F8 TCGA-QG-A5Z1 TCGA-QL-A97D TCGA-RU-A8FL 
        9.93        15.65        16.80         8.42        21.90        38.70 

$`DEL PEAK 18(8P23.2) WILD-TYPE`
TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3506 TCGA-AA-3516 TCGA-AA-3522 
       13.94        14.53        24.16        58.03        13.02        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3554 TCGA-AA-3672 TCGA-AA-3713 
       36.03         8.05        19.07        17.95         0.92        19.04 
TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3972 TCGA-AA-3986 
       19.04        14.93        12.99        24.00        50.99        19.07 
TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6895 TCGA-AD-6964 
       38.04        21.99        39.06        21.37        25.08        10.88 
TCGA-AZ-4313 TCGA-AZ-6601 TCGA-G4-6294 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6588 
       75.95       100.01        28.21        63.62        22.09        26.17 
TCGA-G4-6628 TCGA-NH-A8F7 TCGA-3L-AA1B TCGA-4T-AA8H TCGA-5M-AATE TCGA-A6-2672 
       79.69        17.85        15.62        12.66        39.45        46.65 
TCGA-A6-2676 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3809 TCGA-A6-4107 
       42.90        37.05        37.25        37.02        32.75        32.45 
TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6138 
       30.44        33.53        22.09        22.06        32.71        22.52 
TCGA-A6-6141 TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 
        8.38        21.76        24.39        20.12        19.66        16.24 
TCGA-A6-A566 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
       24.92         7.04         3.02        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3534 TCGA-AA-3555 
        1.02         1.02         9.07        19.07        29.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3673 
       20.98        13.94        61.02         6.97        54.02        50.04 
TCGA-AA-3675 TCGA-AA-3680 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
       47.05        11.01         5.03        26.99        10.06        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3841 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3852 
       36.95         0.00        17.03        10.06         0.00         0.00 
TCGA-AA-3855 TCGA-AA-3864 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3941 TCGA-AA-3947 
       32.05        53.00        18.05        31.00        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3973 TCGA-AA-3977 
       26.01        20.98         2.01        21.99        13.05        25.02 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K 
       27.02        13.94        38.04        30.02        18.05        18.05 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00W TCGA-AA-A010 
        4.01        27.02        42.02         0.99        14.99        34.98 
TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q 
       15.02        10.98        32.02        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A029 TCGA-AA-A02H TCGA-AA-A02O 
       35.01         1.02        26.01        51.98         2.01         0.92 
TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 
       22.03        39.98        18.05        12.16        83.24        24.53 
TCGA-AD-6963 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 
       27.42        16.44         0.46         0.92        14.50        27.09 
TCGA-AY-4071 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A71X TCGA-AZ-4315 
        0.95        21.44        17.82        17.26        19.33        58.39 
TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6598 
        1.41        32.94         5.13        22.36        88.21        49.41 
TCGA-AZ-6599 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-6716 
        6.77        12.69        12.36        12.46        12.39        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 
       12.76        10.06        17.56       148.01        85.45        70.16 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 
       23.05        20.02        37.02        25.02        26.04         8.02 
TCGA-CM-5341 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6162 
       29.06        15.02        15.02        15.02        15.02        12.00 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6171 TCGA-CM-6172 
       29.03        16.04        14.99        12.99        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5539 
       12.95        11.08        11.01        12.03        45.40        19.59 
TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       20.19        20.42        18.25        17.85         4.80        17.13 
TCGA-D5-6540 TCGA-D5-6920 TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 
       16.14        12.39        14.30         9.44        11.64        13.35 
TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A1D4 TCGA-DM-A1D8 TCGA-DM-A1DA 
       12.00        10.26       119.70        92.75        12.59         7.50 
TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28C 
       44.32       135.65         7.76       139.17        14.04        81.37 
TCGA-DM-A28E TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6461 TCGA-F4-6569 
      119.93        98.24        95.18         8.61        11.11        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        6.18        47.87        41.42        43.04        33.67        13.25 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6297 TCGA-G4-6302 TCGA-G4-6304 
       47.41        35.31       133.18        82.39        67.30        53.62 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6626 TCGA-G4-6627 
       55.04        85.48        26.04        13.78        46.75        74.79 
TCGA-NH-A50T TCGA-NH-A5IV TCGA-NH-A6GC TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX 
       18.18        19.33        12.79        42.77        29.46        32.98 
TCGA-QG-A5Z2 TCGA-SS-A7HO TCGA-T9-A92H TCGA-WS-AB45 
       31.30        60.13        11.90        70.03 

  DEL PEAK 18(8P23.2) MUTATED DEL PEAK 18(8P23.2) WILD-TYPE 
                            0                             0 
  DEL PEAK 18(8P23.2) MUTATED DEL PEAK 18(8P23.2) WILD-TYPE 
                       140.38                        148.01 
  DEL PEAK 18(8P23.2) MUTATED DEL PEAK 18(8P23.2) WILD-TYPE 
                       24.000                        21.255 
[1] "0.0 - 140.4 (24.0)" "0.0 - 148.0 (21.3)"
[1] "hr=" "1.3"
D40V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 18(8P23.2) MUTATED        24        0        9        39         2
  DEL PEAK 18(8P23.2) WILD-TYPE      50        1       20        93         8
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 18(8P23.2) MUTATED           0         8          4         28
  DEL PEAK 18(8P23.2) WILD-TYPE         1        12          4         31
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 18(8P23.2) MUTATED           26       31        11         1
  DEL PEAK 18(8P23.2) WILD-TYPE         15       14         6         1
D40V3, multiclass
            clus
vv           DEL PEAK 18(8P23.2) MUTATED DEL PEAK 18(8P23.2) WILD-TYPE
  STAGE I                             24                            50
  STAGE IA                             0                             1
  STAGE II                             9                            20
  STAGE IIA                           39                            93
  STAGE IIB                            2                             8
  STAGE IIC                            0                             1
  STAGE III                            8                            12
  STAGE IIIA                           4                             4
  STAGE IIIB                          28                            31
  STAGE IIIC                          26                            15
  STAGE IV                            31                            14
  STAGE IVA                           11                             6
  STAGE IVB                            1                             1
[1] 13  2
[1] 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(8P23.2) MUTATED     1  29 135  23
  DEL PEAK 18(8P23.2) WILD-TYPE  10  48 170  32
D40V4, multiclass
    clus
vv   DEL PEAK 18(8P23.2) MUTATED DEL PEAK 18(8P23.2) WILD-TYPE
  T1                           1                            10
  T2                          29                            48
  T3                         135                           170
  T4                          23                            32
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2
  DEL PEAK 18(8P23.2) MUTATED    85  52  51
  DEL PEAK 18(8P23.2) WILD-TYPE 177  53  31
D40V5, multiclass
    clus
vv   DEL PEAK 18(8P23.2) MUTATED DEL PEAK 18(8P23.2) WILD-TYPE
  N0                          85                           177
  N1                          52                            53
  N2                          51                            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"
D40V6, binary
                               cls
clus                              0   1
  DEL PEAK 18(8P23.2) MUTATED   124  43
  DEL PEAK 18(8P23.2) WILD-TYPE 204  21
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 18(8P23.2) MUTATED    124   43
  DEL PEAK 18(8P23.2) WILD-TYPE  204   21
   clus
vv  DEL PEAK 18(8P23.2) MUTATED DEL PEAK 18(8P23.2) WILD-TYPE
  0                         124                           204
  1                          43                            21
[1] 2 2
[1] FALSE
D40V7, binary
                               cls
clus                              0   1
  DEL PEAK 18(8P23.2) MUTATED    76 112
  DEL PEAK 18(8P23.2) WILD-TYPE 137 124
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 18(8P23.2) MUTATED     76  112
  DEL PEAK 18(8P23.2) WILD-TYPE  137  124
        clus
vv       DEL PEAK 18(8P23.2) MUTATED DEL PEAK 18(8P23.2) WILD-TYPE
  FEMALE                          76                           137
  MALE                           112                           124
[1] 2 2
[1] FALSE
D40V8, binary
                               cls
clus                              0   1
  DEL PEAK 18(8P23.2) MUTATED   157   3
  DEL PEAK 18(8P23.2) WILD-TYPE 213   6
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 18(8P23.2) MUTATED    157    3
  DEL PEAK 18(8P23.2) WILD-TYPE  213    6
     clus
vv    DEL PEAK 18(8P23.2) MUTATED DEL PEAK 18(8P23.2) WILD-TYPE
  NO                          157                           213
  YES                           3                             6
[1] 2 2
[1] FALSE
D40V9, binary
                               cls
clus                              0   1
  DEL PEAK 18(8P23.2) MUTATED   170  15
  DEL PEAK 18(8P23.2) WILD-TYPE 212  47
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 18(8P23.2) MUTATED    170   15
  DEL PEAK 18(8P23.2) WILD-TYPE  212   47
                               clus
vv                              DEL PEAK 18(8P23.2) MUTATED
  COLON ADENOCARCINOMA                                  170
  COLON MUCINOUS ADENOCARCINOMA                          15
                               clus
vv                              DEL PEAK 18(8P23.2) WILD-TYPE
  COLON ADENOCARCINOMA                                    212
  COLON MUCINOUS ADENOCARCINOMA                            47
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 18(8P23.2) MUTATED   127   2  16   6
  DEL PEAK 18(8P23.2) WILD-TYPE 196   2   9  19
D40V10, multiclass
    clus
vv   DEL PEAK 18(8P23.2) MUTATED DEL PEAK 18(8P23.2) WILD-TYPE
  R0                         127                           196
  R1                           2                             2
  R2                          16                             9
  RX                           6                            19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V11, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 18(8P23.2) MUTATED                                  1     3
  DEL PEAK 18(8P23.2) WILD-TYPE                                0     8
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 18(8P23.2) MUTATED                          28    90
  DEL PEAK 18(8P23.2) WILD-TYPE                        31   122
D40V12, multiclass
                                  clus
vv                                 DEL PEAK 18(8P23.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      3
  BLACK OR AFRICAN AMERICAN                                 28
  WHITE                                                     90
                                  clus
vv                                 DEL PEAK 18(8P23.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        8
  BLACK OR AFRICAN AMERICAN                                   31
  WHITE                                                      122
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V13, binary
                               cls
clus                              0   1
  DEL PEAK 18(8P23.2) MUTATED     3 115
  DEL PEAK 18(8P23.2) WILD-TYPE   1 154
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 18(8P23.2) MUTATED      3  115
  DEL PEAK 18(8P23.2) WILD-TYPE    1  154
                        clus
vv                       DEL PEAK 18(8P23.2) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                         115
                        clus
vv                       DEL PEAK 18(8P23.2) WILD-TYPE
  HISPANIC OR LATINO                                 1
  NOT HISPANIC OR LATINO                           154
[1] 2 2
[1] FALSE

Clustering(41) Variable = DEL PEAK 19(8P22) MUTATION ANALYSIS
D41V1, survival
                             sevent
clus2                           0   1
  DEL PEAK 19(8P22) MUTATED   144  55
  DEL PEAK 19(8P22) WILD-TYPE 191  46
  DEL PEAK 19(8P22) MUTATED DEL PEAK 19(8P22) WILD-TYPE 
                        199                         237 
  DEL PEAK 19(8P22) MUTATED DEL PEAK 19(8P22) WILD-TYPE 
                         55                          46 
$`DEL PEAK 19(8P22) MUTATED`
TCGA-A6-2677 TCGA-A6-2681 TCGA-AA-3496 TCGA-AA-3520 TCGA-AA-3531 TCGA-AA-3552 
       24.33        45.60         1.02        24.03        34.03        13.02 
TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3688 TCGA-AA-3692 
       23.01        19.99        19.99         6.05        19.00        36.00 
TCGA-AA-3697 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3976 TCGA-AA-3979 
       85.05        31.07        24.03        29.98        26.01        24.00 
TCGA-AA-A00L TCGA-AD-6888 TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 
       38.04        15.52       106.75         1.94        49.08         5.88 
TCGA-G4-6298 TCGA-G4-6314 TCGA-G4-6586 TCGA-G4-6625 TCGA-4N-A93T TCGA-5M-AAT4 
       23.51        35.93        35.80        91.79         4.80         1.61 
TCGA-5M-AAT6 TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2678 TCGA-A6-2679 
        9.53        43.76        43.76        43.43        42.28        44.91 
TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 
       35.11        16.57        34.65        36.53        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6140 
       30.44        29.19        23.61        29.16        27.09        24.13 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6782 
       25.08        25.18        20.61        24.69        23.87        20.28 
TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3494 TCGA-AA-3495 
       61.84        56.25         9.63         5.03         1.02        37.05 
TCGA-AA-3517 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
       38.99         0.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 
       33.99        21.01        24.00        78.08        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       14.01        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3842 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3858 
       37.02        10.06        33.07        36.03         0.99        31.07 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3930 TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3975 
       17.03        27.02         2.01        34.03        16.08        34.06 
TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00U TCGA-AA-A017 
       27.02         7.96        19.00        34.03        17.03        15.02 
TCGA-AA-A01G TCGA-AA-A01K TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01Z TCGA-AA-A02E 
       12.00        31.00         1.02        33.04        37.02         2.96 
TCGA-AA-A02J TCGA-AA-A02W TCGA-AA-A03J TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6965 
        5.03        41.00        40.96         5.79        22.42        26.47 
TCGA-AM-5820 TCGA-AY-4070 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-A69D TCGA-AY-A71X 
        0.46        16.31        33.01         0.20        17.85        19.33 
TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4614 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 
       18.84       109.28         5.65        22.36        65.00        62.79 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5797 
       12.10        29.56         5.23        11.74         3.19        12.59 
TCGA-CA-6715 TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4952 TCGA-CM-4751 TCGA-CM-4752 
       12.59        14.30       148.01        15.62        27.02        13.02 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5868 
       22.03        22.98        30.08        32.02         5.03        17.03 
TCGA-CM-6163 TCGA-CM-6166 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6675 
       14.04        21.99        13.02        15.02        11.01        13.05 
TCGA-CM-6676 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6531 
       11.08        54.61        19.59        56.09        55.92        17.75 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 
       25.48        43.27        15.12        12.49        15.58         7.53 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A0XD 
       10.13        12.43         9.04        13.41        11.38        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1DB 
       38.20       130.65        49.91        13.32       140.38        44.32 
TCGA-DM-A1HA TCGA-DM-A28A TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-F4-6459 
      131.51        26.47        35.97        60.79       117.07         8.61 
TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6809 
       31.96        11.11        35.74         1.55        34.42        13.25 
TCGA-F4-6854 TCGA-G4-6295 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6311 
        0.53         8.35        74.56        65.85        44.68        39.42 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6626 TCGA-NH-A50U 
       61.91        36.00        26.43        26.04        46.75        10.98 
TCGA-NH-A50V TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A8F8 TCGA-QG-A5Z1 TCGA-QL-A97D 
       19.33         9.93        15.65        16.80         8.42        21.90 
TCGA-RU-A8FL 
       38.70 

$`DEL PEAK 19(8P22) WILD-TYPE`
TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3506 TCGA-AA-3516 TCGA-AA-3522 
       13.94        14.53        24.16        58.03        13.02        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3543 TCGA-AA-3554 TCGA-AA-3672 
       36.03         8.05        19.07         0.99        17.95         0.92 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       19.04        19.04        14.93        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3986 TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6895 
       50.99        19.07        21.99        39.06        21.37        25.08 
TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-6601 TCGA-G4-6294 TCGA-G4-6310 TCGA-G4-6321 
       10.88        75.95       100.01        28.21        63.62        22.09 
TCGA-G4-6588 TCGA-G4-6628 TCGA-NH-A8F7 TCGA-3L-AA1B TCGA-4T-AA8H TCGA-5M-AATE 
       26.17        79.69        17.85        15.62        12.66        39.45 
TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3809 
       46.65        42.90        37.05        37.25        37.02        32.75 
TCGA-A6-4107 TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6138 
       32.45        33.53        22.09        22.06        32.71        22.52 
TCGA-A6-6141 TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 
        8.38        21.76        24.39        20.12        19.66        16.24 
TCGA-A6-A566 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
       24.92         7.04         3.02        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3534 TCGA-AA-3555 
        1.02         1.02         9.07        19.07        29.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3673 TCGA-AA-3675 
       20.98        13.94        61.02         6.97        50.04        47.05 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
        5.03        26.99        10.06        35.05         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3845 
        1.02        17.98        15.95        38.99        36.95         0.00 
TCGA-AA-3846 TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3855 TCGA-AA-3864 TCGA-AA-3875 
       17.03         0.00         0.00        32.05        53.00        18.05 
TCGA-AA-3877 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3966 
       31.00        24.00        33.01        26.01        20.98         2.01 
TCGA-AA-3968 TCGA-AA-3973 TCGA-AA-3977 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       21.99        13.05        25.02        27.02        13.94        38.04 
TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       30.02        18.05        18.05         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F 
        0.99        14.99        34.98        15.02        10.98        32.02 
TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01V TCGA-AA-A01X 
       31.00        38.07         1.02        35.01         1.02        26.01 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y 
       51.98        39.98         2.01         0.92        22.03        39.98 
TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6963 TCGA-AD-A5EK 
       18.05        12.16        83.24        24.53        27.42        16.44 
TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-6197 TCGA-AY-6386 
        0.92        14.50        27.09         0.95        21.44        17.82 
TCGA-AY-A54L TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-5407 
       17.26        58.39         1.41        32.94         5.13        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 
       49.41         6.77        12.69        12.36        12.46        12.39 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 
       12.20        12.76        10.06        17.56        85.45        70.16 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 
       23.05        20.02        37.02        25.02        26.04         8.02 
TCGA-CM-5341 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6162 
       29.06        15.02        15.02        15.02        15.02        12.00 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6171 TCGA-CM-6674 
       29.03        16.04        14.99        12.99        14.04        12.95 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-6529 
       11.08        11.01        10.06        12.03        45.40        20.19 
TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 
       20.42        18.25        17.85         4.80        17.13        16.14 
TCGA-D5-6920 TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 
       12.39        14.30         9.44        11.64        13.35        12.00 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A1D4 TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A1HB 
       10.26       119.70        92.75        12.59         7.50       135.65 
TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28K 
        7.76       139.17        14.04        81.37       119.93        98.24 
TCGA-DM-A28M TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6806 TCGA-F4-6807 
       95.18        35.74         6.18        47.87        41.42        43.04 
TCGA-F4-6808 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6297 TCGA-G4-6302 
       33.67        47.41        35.31       133.18        82.39        67.30 
TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6323 TCGA-G4-6627 TCGA-NH-A50T 
       53.62        55.04        85.48        13.78        74.79        18.18 
TCGA-NH-A5IV TCGA-NH-A6GC TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z2 
       19.33        12.79        42.77        29.46        32.98        31.30 
TCGA-SS-A7HO TCGA-T9-A92H TCGA-WS-AB45 
       60.13        11.90        70.03 

  DEL PEAK 19(8P22) MUTATED DEL PEAK 19(8P22) WILD-TYPE 
                          0                           0 
  DEL PEAK 19(8P22) MUTATED DEL PEAK 19(8P22) WILD-TYPE 
                     148.01                      139.17 
  DEL PEAK 19(8P22) MUTATED DEL PEAK 19(8P22) WILD-TYPE 
                      24.00                       21.14 
[1] "0.0 - 148.0 (24.0)" "0.0 - 139.2 (21.1)"
[1] "hr=" "1.5"
D41V2, continuous
                             vv
clus                          STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 19(8P22) MUTATED        25        0       10        41         2
  DEL PEAK 19(8P22) WILD-TYPE      49        1       19        91         8
                             vv
clus                          STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 19(8P22) MUTATED           0         9          5         31
  DEL PEAK 19(8P22) WILD-TYPE         1        11          3         28
                             vv
clus                          STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 19(8P22) MUTATED           27       31        14         1
  DEL PEAK 19(8P22) WILD-TYPE         14       14         3         1
D41V3, multiclass
            clus
vv           DEL PEAK 19(8P22) MUTATED DEL PEAK 19(8P22) WILD-TYPE
  STAGE I                           25                          49
  STAGE IA                           0                           1
  STAGE II                          10                          19
  STAGE IIA                         41                          91
  STAGE IIB                          2                           8
  STAGE IIC                          0                           1
  STAGE III                          9                          11
  STAGE IIIA                         5                           3
  STAGE IIIB                        31                          28
  STAGE IIIC                        27                          14
  STAGE IV                          31                          14
  STAGE IVA                         14                           3
  STAGE IVB                          1                           1
[1] 13  2
[1] 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(8P22) MUTATED     1  30 144  26
  DEL PEAK 19(8P22) WILD-TYPE  10  47 161  29
D41V4, multiclass
    clus
vv   DEL PEAK 19(8P22) MUTATED DEL PEAK 19(8P22) WILD-TYPE
  T1                         1                          10
  T2                        30                          47
  T3                       144                         161
  T4                        26                          29
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           N0  N1  N2
  DEL PEAK 19(8P22) MUTATED    90  56  55
  DEL PEAK 19(8P22) WILD-TYPE 172  49  27
D41V5, multiclass
    clus
vv   DEL PEAK 19(8P22) MUTATED DEL PEAK 19(8P22) WILD-TYPE
  N0                        90                         172
  N1                        56                          49
  N2                        55                          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"
D41V6, binary
                             cls
clus                            0   1
  DEL PEAK 19(8P22) MUTATED   133  46
  DEL PEAK 19(8P22) WILD-TYPE 195  18
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 19(8P22) MUTATED    133   46
  DEL PEAK 19(8P22) WILD-TYPE  195   18
   clus
vv  DEL PEAK 19(8P22) MUTATED DEL PEAK 19(8P22) WILD-TYPE
  0                       133                         195
  1                        46                          18
[1] 2 2
[1] FALSE
D41V7, binary
                             cls
clus                            0   1
  DEL PEAK 19(8P22) MUTATED    85 116
  DEL PEAK 19(8P22) WILD-TYPE 128 120
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 19(8P22) MUTATED     85  116
  DEL PEAK 19(8P22) WILD-TYPE  128  120
        clus
vv       DEL PEAK 19(8P22) MUTATED DEL PEAK 19(8P22) WILD-TYPE
  FEMALE                        85                         128
  MALE                         116                         120
[1] 2 2
[1] FALSE
D41V8, binary
                             cls
clus                            0   1
  DEL PEAK 19(8P22) MUTATED   169   3
  DEL PEAK 19(8P22) WILD-TYPE 201   6
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 19(8P22) MUTATED    169    3
  DEL PEAK 19(8P22) WILD-TYPE  201    6
     clus
vv    DEL PEAK 19(8P22) MUTATED DEL PEAK 19(8P22) WILD-TYPE
  NO                        169                         201
  YES                         3                           6
[1] 2 2
[1] FALSE
D41V9, binary
                             cls
clus                            0   1
  DEL PEAK 19(8P22) MUTATED   182  16
  DEL PEAK 19(8P22) WILD-TYPE 200  46
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 19(8P22) MUTATED    182   16
  DEL PEAK 19(8P22) WILD-TYPE  200   46
                               clus
vv                              DEL PEAK 19(8P22) MUTATED
  COLON ADENOCARCINOMA                                182
  COLON MUCINOUS ADENOCARCINOMA                        16
                               clus
vv                              DEL PEAK 19(8P22) WILD-TYPE
  COLON ADENOCARCINOMA                                  200
  COLON MUCINOUS ADENOCARCINOMA                          46
[1] 2 2
[1] FALSE
                             vv
clus                           R0  R1  R2  RX
  DEL PEAK 19(8P22) MUTATED   139   2  16   6
  DEL PEAK 19(8P22) WILD-TYPE 184   2   9  19
D41V10, multiclass
    clus
vv   DEL PEAK 19(8P22) MUTATED DEL PEAK 19(8P22) WILD-TYPE
  R0                       139                         184
  R1                         2                           2
  R2                        16                           9
  RX                         6                          19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V11, continuous
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 19(8P22) MUTATED                                  1     3
  DEL PEAK 19(8P22) WILD-TYPE                                0     8
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 19(8P22) MUTATED                          29   101
  DEL PEAK 19(8P22) WILD-TYPE                        30   111
D41V12, multiclass
                                  clus
vv                                 DEL PEAK 19(8P22) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         1
  ASIAN                                                    3
  BLACK OR AFRICAN AMERICAN                               29
  WHITE                                                  101
                                  clus
vv                                 DEL PEAK 19(8P22) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      8
  BLACK OR AFRICAN AMERICAN                                 30
  WHITE                                                    111
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V13, binary
                             cls
clus                            0   1
  DEL PEAK 19(8P22) MUTATED     3 127
  DEL PEAK 19(8P22) WILD-TYPE   1 142
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 19(8P22) MUTATED      3  127
  DEL PEAK 19(8P22) WILD-TYPE    1  142
                        clus
vv                       DEL PEAK 19(8P22) MUTATED DEL PEAK 19(8P22) WILD-TYPE
  HISPANIC OR LATINO                             3                           1
  NOT HISPANIC OR LATINO                       127                         142
[1] 2 2
[1] FALSE

Clustering(42) Variable = DEL PEAK 20(8Q11.1) MUTATION ANALYSIS
D42V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 20(8Q11.1) MUTATED    23   7
  DEL PEAK 20(8Q11.1) WILD-TYPE 312  94
  DEL PEAK 20(8Q11.1) MUTATED DEL PEAK 20(8Q11.1) WILD-TYPE 
                           30                           406 
  DEL PEAK 20(8Q11.1) MUTATED DEL PEAK 20(8Q11.1) WILD-TYPE 
                            7                            94 
$`DEL PEAK 20(8Q11.1) MUTATED`
TCGA-A6-2677 TCGA-AA-3531 TCGA-G4-6298 TCGA-G4-6625 TCGA-A6-2678 TCGA-A6-2679 
       24.33        34.03        23.51        91.79        42.28        44.91 
TCGA-A6-2683 TCGA-A6-3810 TCGA-A6-6650 TCGA-A6-6654 TCGA-AA-3517 TCGA-AA-3544 
       16.57        36.53        20.61        23.87        38.99        14.01 
TCGA-AA-3666 TCGA-AA-3681 TCGA-AA-3842 TCGA-AA-3989 TCGA-AA-A01D TCGA-AA-A01K 
        2.01         5.98        37.02         7.96        10.98        31.00 
TCGA-AA-A02F TCGA-AY-6196 TCGA-AY-A69D TCGA-AY-A8YK TCGA-CM-4746 TCGA-CM-5868 
       39.98         0.20        17.85        18.84        37.02        17.03 
TCGA-CM-6675 TCGA-D5-5540 TCGA-D5-6531 TCGA-DM-A1D6 TCGA-DM-A1HA TCGA-F4-6704 
       13.05        56.09        17.75        49.91       131.51         1.55 

$`DEL PEAK 20(8Q11.1) WILD-TYPE`
TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3506 
       45.60        13.94        14.53        24.16         1.02        58.03 
TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 
       13.02        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 
        0.99        13.02        17.95        23.01        19.99        19.99 
TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 
        6.05         0.92        19.00        36.00        85.05        19.04 
TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 
       19.04        14.93        31.07        24.03        29.98        12.99 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 
       24.00         2.01        50.99        26.01        24.00        19.07 
TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 
       38.04        21.99        39.06        21.37        15.52        25.08 
TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 
       10.88        75.95       106.75       100.01         1.94        49.08 
TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6321 TCGA-G4-6586 
        5.88        28.21        63.62        35.93        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6628 TCGA-NH-A8F7 TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H 
       26.17        79.69        17.85        15.62         4.80        12.66 
TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
        1.61         9.53        39.45        43.76        46.65        43.76 
TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2680 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 
       43.43        42.90        35.11        37.05        37.25        37.02 
TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       34.65        32.75        32.45        32.91        31.63        30.44 
TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 
       29.19        33.53        23.61        22.09        22.06        32.71 
TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 
       29.16        27.09        22.52        24.13         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 
       25.18        21.76        24.69        24.39        20.12        19.66 
TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU 
       20.28        16.24        24.92        61.84        56.25         9.63 
TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 
        5.03         7.04         3.02         1.02        37.05        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
       63.98         6.97         1.02         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3548 
        0.00        29.00        29.00        26.01        12.99        33.99 
TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        61.02 
TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3675 
       78.08         6.97        54.02        14.01        50.04        47.05 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3710 
       47.01        15.02        11.01        37.05         5.03        26.99 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       10.06        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       15.95        38.99        36.95         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       31.07        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
TCGA-AA-3982 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
       27.02        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C 
        0.99        17.03        14.99        34.98        15.02        15.02 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       32.02        12.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 
        1.02        33.04         1.02        26.01        37.02        51.98 
TCGA-AA-A02E TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W 
        2.96         2.01         5.03         0.92        22.03        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 
        5.79        22.42        27.42        26.47        16.44         0.46 
TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.92        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A71X TCGA-AZ-4308 TCGA-AZ-4315 
       21.44        17.82        17.26        19.33       109.28        58.39 
TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-4684 
        1.41         5.65        32.94         5.13        22.36        65.00 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 
       62.79        88.21        49.41         6.77        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 
        5.23        11.74         3.19        12.69        12.36        12.46 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 
       14.30        17.56       148.01        85.45        70.16        15.62 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 
       23.05        20.02        25.02        26.04         8.02        27.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6162 
       15.02         5.03        15.02        15.02        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6676 
       13.02        15.02        14.04        11.01        12.95        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6533 
       19.59        55.92        20.19        20.42        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
      130.65        92.75        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A 
       44.32       135.65         7.76       139.17        14.04        26.47 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 
       95.18         8.61        31.96        11.11        35.74        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
        6.18        47.87        34.42        41.42        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6295 
       13.25         0.53        47.41        35.31       133.18         8.35 
TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       82.39        74.56        67.30        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 
       55.04        85.48        39.42        61.91        36.00        26.43 
TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50U 
       26.04        13.78        46.75        74.79        18.18        10.98 
TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F8 
       19.33        19.33         9.93        15.65        12.79        16.80 
TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D 
       42.77        29.46        32.98         8.42        31.30        21.90 
TCGA-RU-A8FL TCGA-SS-A7HO TCGA-T9-A92H TCGA-WS-AB45 
       38.70        60.13        11.90        70.03 

  DEL PEAK 20(8Q11.1) MUTATED DEL PEAK 20(8Q11.1) WILD-TYPE 
                          0.2                           0.0 
  DEL PEAK 20(8Q11.1) MUTATED DEL PEAK 20(8Q11.1) WILD-TYPE 
                       131.51                        148.01 
  DEL PEAK 20(8Q11.1) MUTATED DEL PEAK 20(8Q11.1) WILD-TYPE 
                        23.69                         22.03 
[1] "0.2 - 131.5 (23.7)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1"  
D42V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 20(8Q11.1) MUTATED         2        0        0         9         1
  DEL PEAK 20(8Q11.1) WILD-TYPE      72        1       29       123         9
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 20(8Q11.1) MUTATED           0         2          1          3
  DEL PEAK 20(8Q11.1) WILD-TYPE         1        18          7         56
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 20(8Q11.1) MUTATED            6        3         2         1
  DEL PEAK 20(8Q11.1) WILD-TYPE         35       42        15         1
D42V3, multiclass
            clus
vv           DEL PEAK 20(8Q11.1) MUTATED DEL PEAK 20(8Q11.1) WILD-TYPE
  STAGE I                              2                            72
  STAGE IA                             0                             1
  STAGE II                             0                            29
  STAGE IIA                            9                           123
  STAGE IIB                            1                             9
  STAGE IIC                            0                             1
  STAGE III                            2                            18
  STAGE IIIA                           1                             7
  STAGE IIIB                           3                            56
  STAGE IIIC                           6                            35
  STAGE IV                             3                            42
  STAGE IVA                            2                            15
  STAGE IVB                            1                             1
[1] 13  2
[1] 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(8Q11.1) MUTATED     0   3  24   3
  DEL PEAK 20(8Q11.1) WILD-TYPE  11  74 281  52
D42V4, multiclass
    clus
vv   DEL PEAK 20(8Q11.1) MUTATED DEL PEAK 20(8Q11.1) WILD-TYPE
  T1                           0                            11
  T2                           3                            74
  T3                          24                           281
  T4                           3                            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"
                               vv
clus                             N0  N1  N2
  DEL PEAK 20(8Q11.1) MUTATED    13   8   9
  DEL PEAK 20(8Q11.1) WILD-TYPE 249  97  73
D42V5, multiclass
    clus
vv   DEL PEAK 20(8Q11.1) MUTATED DEL PEAK 20(8Q11.1) WILD-TYPE
  N0                          13                           249
  N1                           8                            97
  N2                           9                            73
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V6, binary
                               cls
clus                              0   1
  DEL PEAK 20(8Q11.1) MUTATED    20   6
  DEL PEAK 20(8Q11.1) WILD-TYPE 308  58
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 20(8Q11.1) MUTATED     20    6
  DEL PEAK 20(8Q11.1) WILD-TYPE  308   58
   clus
vv  DEL PEAK 20(8Q11.1) MUTATED DEL PEAK 20(8Q11.1) WILD-TYPE
  0                          20                           308
  1                           6                            58
[1] 2 2
[1] FALSE
D42V7, binary
                               cls
clus                              0   1
  DEL PEAK 20(8Q11.1) MUTATED    14  16
  DEL PEAK 20(8Q11.1) WILD-TYPE 199 220
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 20(8Q11.1) MUTATED     14   16
  DEL PEAK 20(8Q11.1) WILD-TYPE  199  220
        clus
vv       DEL PEAK 20(8Q11.1) MUTATED DEL PEAK 20(8Q11.1) WILD-TYPE
  FEMALE                          14                           199
  MALE                            16                           220
[1] 2 2
[1] FALSE
D42V8, binary
                               cls
clus                              0   1
  DEL PEAK 20(8Q11.1) MUTATED    25   0
  DEL PEAK 20(8Q11.1) WILD-TYPE 345   9
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 20(8Q11.1) MUTATED     25    0
  DEL PEAK 20(8Q11.1) WILD-TYPE  345    9
     clus
vv    DEL PEAK 20(8Q11.1) MUTATED DEL PEAK 20(8Q11.1) WILD-TYPE
  NO                           25                           345
  YES                           0                             9
[1] 2 2
[1] FALSE
D42V9, binary
                               cls
clus                              0   1
  DEL PEAK 20(8Q11.1) MUTATED    26   4
  DEL PEAK 20(8Q11.1) WILD-TYPE 356  58
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 20(8Q11.1) MUTATED     26    4
  DEL PEAK 20(8Q11.1) WILD-TYPE  356   58
                               clus
vv                              DEL PEAK 20(8Q11.1) MUTATED
  COLON ADENOCARCINOMA                                   26
  COLON MUCINOUS ADENOCARCINOMA                           4
                               clus
vv                              DEL PEAK 20(8Q11.1) WILD-TYPE
  COLON ADENOCARCINOMA                                    356
  COLON MUCINOUS ADENOCARCINOMA                            58
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 20(8Q11.1) MUTATED    24   0   2   0
  DEL PEAK 20(8Q11.1) WILD-TYPE 299   4  23  25
D42V10, multiclass
    clus
vv   DEL PEAK 20(8Q11.1) MUTATED DEL PEAK 20(8Q11.1) WILD-TYPE
  R0                          24                           299
  R1                           0                             4
  R2                           2                            23
  RX                           0                            25
[1] 4 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, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 20(8Q11.1) MUTATED                                  1     0
  DEL PEAK 20(8Q11.1) WILD-TYPE                                0    11
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 20(8Q11.1) MUTATED                           6    13
  DEL PEAK 20(8Q11.1) WILD-TYPE                        53   199
D42V12, multiclass
                                  clus
vv                                 DEL PEAK 20(8Q11.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      0
  BLACK OR AFRICAN AMERICAN                                  6
  WHITE                                                     13
                                  clus
vv                                 DEL PEAK 20(8Q11.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                       11
  BLACK OR AFRICAN AMERICAN                                   53
  WHITE                                                      199
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V13, binary
                               cls
clus                              0   1
  DEL PEAK 20(8Q11.1) MUTATED     0  20
  DEL PEAK 20(8Q11.1) WILD-TYPE   4 249
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 20(8Q11.1) MUTATED      0   20
  DEL PEAK 20(8Q11.1) WILD-TYPE    4  249
                        clus
vv                       DEL PEAK 20(8Q11.1) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                          20
                        clus
vv                       DEL PEAK 20(8Q11.1) WILD-TYPE
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           249
[1] 2 2
[1] FALSE

Clustering(43) Variable = DEL PEAK 21(9P21.3) MUTATION ANALYSIS
D43V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 21(9P21.3) MUTATED    46  11
  DEL PEAK 21(9P21.3) WILD-TYPE 289  90
  DEL PEAK 21(9P21.3) MUTATED DEL PEAK 21(9P21.3) WILD-TYPE 
                           57                           379 
  DEL PEAK 21(9P21.3) MUTATED DEL PEAK 21(9P21.3) WILD-TYPE 
                           11                            90 
$`DEL PEAK 21(9P21.3) MUTATED`
TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3506 TCGA-AA-3562 TCGA-AA-3697 TCGA-AA-3867 
       14.53        24.16        58.03        19.99        85.05        24.03 
TCGA-AA-3939 TCGA-AA-3972 TCGA-AD-6888 TCGA-AZ-6608 TCGA-5M-AATE TCGA-A6-2675 
       12.99        50.99        15.52         1.94        39.45        43.43 
TCGA-A6-3810 TCGA-A6-5667 TCGA-A6-6651 TCGA-A6-A567 TCGA-AA-3511 TCGA-AA-3517 
       36.53        29.16        21.76        61.84         6.97        38.99 
TCGA-AA-3538 TCGA-AA-3553 TCGA-AA-3685 TCGA-AA-3842 TCGA-AA-3855 TCGA-AA-3941 
       26.01        24.00        37.05        37.02        32.05        24.00 
TCGA-AA-3955 TCGA-AA-A004 TCGA-AA-A01F TCGA-AA-A01K TCGA-AA-A01S TCGA-AA-A03J 
       20.98        13.94        32.02        31.00         1.02        40.96 
TCGA-AD-6965 TCGA-AY-4070 TCGA-AY-A69D TCGA-AZ-4614 TCGA-AZ-6605 TCGA-AZ-6607 
       26.47        16.31        17.85         5.65         5.23         3.19 
TCGA-CA-5254 TCGA-CA-5797 TCGA-CA-6716 TCGA-CM-4750 TCGA-CM-5348 TCGA-CM-6169 
       12.69        12.59        12.20         8.02        22.98        13.02 
TCGA-CM-6170 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6678 TCGA-CM-6679 TCGA-D5-6529 
       15.02        13.05        11.08        11.01        10.06        20.19 
TCGA-D5-6534 TCGA-D5-6898 TCGA-DM-A0XF TCGA-DM-A288 TCGA-F4-6808 TCGA-G4-6295 
       43.27         7.53        38.20        14.04        33.67         8.35 
TCGA-G4-6297 TCGA-NH-A6GA TCGA-T9-A92H 
       82.39         9.93        11.90 

$`DEL PEAK 21(9P21.3) WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        45.60        13.94         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3662 TCGA-AA-3672 
       13.02        17.95        23.01        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 
       19.00        36.00        19.04        19.04        14.93        31.07 
TCGA-AA-3870 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 
       29.98        24.00         2.01        26.01        24.00        19.07 
TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6895 TCGA-AD-6964 
       38.04        21.99        39.06        21.37        25.08        10.88 
TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6294 
       75.95       106.75       100.01        49.08         5.88        28.21 
TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       23.51        63.62        35.93        22.09        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-NH-A8F7 TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H 
       91.79        79.69        17.85        15.62         4.80        12.66 
TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
        1.61         9.53        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 
       42.28        44.91        35.11        16.57        37.05        37.25 
TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 
       37.02        34.65        32.75        32.45        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       30.44        29.19        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 
       32.71        27.09        22.52        24.13         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       25.18        20.61        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A56B TCGA-A6-A5ZU 
       19.66        20.28        16.24        24.92        56.25         9.63 
TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 
        5.03         7.04         3.02         1.02        37.05        35.01 
TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
       63.98         1.02         1.02         9.07        19.07         0.00 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       29.00        29.00        12.99        14.01        33.99        21.01 
TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 
       54.02         2.01        14.01        50.04        47.05        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 
       15.02        11.01         5.98         5.03        26.99        10.06 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       38.99        36.95         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 
       33.07         0.00        36.03         0.99        31.07        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 
       17.03        27.02        18.05        31.00         2.01        33.01 
TCGA-AA-3949 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 
       26.01        34.03         2.01        21.99        16.08        13.05 
TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A00A 
       34.06        25.02        27.02         7.96        27.02        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N 
       19.00        30.02        34.03        18.05        18.05         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P 
       15.02        15.02        10.98        12.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
        1.02        35.01        33.04         1.02        26.01        37.02 
TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O 
       51.98         2.96        39.98         2.01         5.03         0.92 
TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6889 
       22.03        41.00        39.98        18.05        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-A5EK TCGA-AM-5820 
       24.53         5.79        22.42        27.42        16.44         0.46 
TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
        0.92        14.50        27.09         0.95        33.01         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 
       21.44        17.82        17.26        19.33        18.84       109.28 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-4684 
       58.39         1.41        32.94         5.13        22.36        65.00 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 
       62.79        88.21        49.41         6.77        12.10        29.56 
TCGA-AZ-6606 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6717 
       11.74        12.36        12.46        12.39        12.59        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 
       10.06        14.30        17.56       148.01        85.45        70.16 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 
      124.27        23.05        20.02        37.02        25.02        26.04 
TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5860 
       27.02        13.02        29.06        22.03        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00        14.04        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6677 TCGA-CM-6680 
       12.99        14.04        11.01        12.95        11.08        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6530 
       45.40        54.61        19.59        56.09        55.92        20.42 
TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       17.75        18.25        25.48        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6922 
       17.13        12.49        16.14        15.58        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 
        7.50        44.32       131.51       135.65         7.76       139.17 
TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
       26.47        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 
       98.24        95.18         8.61        31.96        11.11        35.74 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       43.04        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
       74.56        67.30        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6322 
       85.48        39.42        61.91        36.00        26.43        26.04 
TCGA-G4-6323 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V 
       13.78        46.75        74.79        18.18        10.98        19.33 
TCGA-NH-A5IV TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW 
       19.33        15.65        12.79        16.80        42.77        29.46 
TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-RU-A8FL TCGA-SS-A7HO 
       32.98         8.42        31.30        21.90        38.70        60.13 
TCGA-WS-AB45 
       70.03 

  DEL PEAK 21(9P21.3) MUTATED DEL PEAK 21(9P21.3) WILD-TYPE 
                         1.02                          0.00 
  DEL PEAK 21(9P21.3) MUTATED DEL PEAK 21(9P21.3) WILD-TYPE 
                        85.05                        148.01 
  DEL PEAK 21(9P21.3) MUTATED DEL PEAK 21(9P21.3) WILD-TYPE 
                        20.19                         22.09 
[1] "1.0 - 85.0 (20.2)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.1"
D43V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 21(9P21.3) MUTATED        10        0        4        17         0
  DEL PEAK 21(9P21.3) WILD-TYPE      64        1       25       115        10
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 21(9P21.3) MUTATED           0         2          3          8
  DEL PEAK 21(9P21.3) WILD-TYPE         1        18          5         51
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 21(9P21.3) MUTATED            7        6         3         1
  DEL PEAK 21(9P21.3) WILD-TYPE         34       39        14         1
D43V3, multiclass
            clus
vv           DEL PEAK 21(9P21.3) MUTATED DEL PEAK 21(9P21.3) WILD-TYPE
  STAGE I                             10                            64
  STAGE IA                             0                             1
  STAGE II                             4                            25
  STAGE IIA                           17                           115
  STAGE IIB                            0                            10
  STAGE IIC                            0                             1
  STAGE III                            2                            18
  STAGE IIIA                           3                             5
  STAGE IIIB                           8                            51
  STAGE IIIC                           7                            34
  STAGE IV                             6                            39
  STAGE IVA                            3                            14
  STAGE IVB                            1                             1
[1] 13  2
[1] 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(9P21.3) MUTATED     2  12  38   9
  DEL PEAK 21(9P21.3) WILD-TYPE   9  65 267  46
D43V4, multiclass
    clus
vv   DEL PEAK 21(9P21.3) MUTATED DEL PEAK 21(9P21.3) WILD-TYPE
  T1                           2                             9
  T2                          12                            65
  T3                          38                           267
  T4                           9                            46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2
  DEL PEAK 21(9P21.3) MUTATED    31  16  14
  DEL PEAK 21(9P21.3) WILD-TYPE 231  89  68
D43V5, multiclass
    clus
vv   DEL PEAK 21(9P21.3) MUTATED DEL PEAK 21(9P21.3) WILD-TYPE
  N0                          31                           231
  N1                          16                            89
  N2                          14                            68
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V6, binary
                               cls
clus                              0   1
  DEL PEAK 21(9P21.3) MUTATED    46  10
  DEL PEAK 21(9P21.3) WILD-TYPE 282  54
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 21(9P21.3) MUTATED     46   10
  DEL PEAK 21(9P21.3) WILD-TYPE  282   54
   clus
vv  DEL PEAK 21(9P21.3) MUTATED DEL PEAK 21(9P21.3) WILD-TYPE
  0                          46                           282
  1                          10                            54
[1] 2 2
[1] FALSE
D43V7, binary
                               cls
clus                              0   1
  DEL PEAK 21(9P21.3) MUTATED    23  38
  DEL PEAK 21(9P21.3) WILD-TYPE 190 198
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 21(9P21.3) MUTATED     23   38
  DEL PEAK 21(9P21.3) WILD-TYPE  190  198
        clus
vv       DEL PEAK 21(9P21.3) MUTATED DEL PEAK 21(9P21.3) WILD-TYPE
  FEMALE                          23                           190
  MALE                            38                           198
[1] 2 2
[1] FALSE
D43V8, binary
                               cls
clus                              0   1
  DEL PEAK 21(9P21.3) MUTATED    54   0
  DEL PEAK 21(9P21.3) WILD-TYPE 316   9
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 21(9P21.3) MUTATED     54    0
  DEL PEAK 21(9P21.3) WILD-TYPE  316    9
     clus
vv    DEL PEAK 21(9P21.3) MUTATED DEL PEAK 21(9P21.3) WILD-TYPE
  NO                           54                           316
  YES                           0                             9
[1] 2 2
[1] FALSE
D43V9, binary
                               cls
clus                              0   1
  DEL PEAK 21(9P21.3) MUTATED    58   2
  DEL PEAK 21(9P21.3) WILD-TYPE 324  60
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 21(9P21.3) MUTATED     58    2
  DEL PEAK 21(9P21.3) WILD-TYPE  324   60
                               clus
vv                              DEL PEAK 21(9P21.3) MUTATED
  COLON ADENOCARCINOMA                                   58
  COLON MUCINOUS ADENOCARCINOMA                           2
                               clus
vv                              DEL PEAK 21(9P21.3) WILD-TYPE
  COLON ADENOCARCINOMA                                    324
  COLON MUCINOUS ADENOCARCINOMA                            60
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 21(9P21.3) MUTATED    43   2   3   3
  DEL PEAK 21(9P21.3) WILD-TYPE 280   2  22  22
D43V10, multiclass
    clus
vv   DEL PEAK 21(9P21.3) MUTATED DEL PEAK 21(9P21.3) WILD-TYPE
  R0                          43                           280
  R1                           2                             2
  R2                           3                            22
  RX                           3                            22
[1] 4 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, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 21(9P21.3) MUTATED                                  0     3
  DEL PEAK 21(9P21.3) WILD-TYPE                                1     8
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 21(9P21.3) MUTATED                           8    27
  DEL PEAK 21(9P21.3) WILD-TYPE                        51   185
D43V12, multiclass
                                  clus
vv                                 DEL PEAK 21(9P21.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      3
  BLACK OR AFRICAN AMERICAN                                  8
  WHITE                                                     27
                                  clus
vv                                 DEL PEAK 21(9P21.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        8
  BLACK OR AFRICAN AMERICAN                                   51
  WHITE                                                      185
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V13, binary
                               cls
clus                              0   1
  DEL PEAK 21(9P21.3) MUTATED     1  36
  DEL PEAK 21(9P21.3) WILD-TYPE   3 233
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 21(9P21.3) MUTATED      1   36
  DEL PEAK 21(9P21.3) WILD-TYPE    3  233
                        clus
vv                       DEL PEAK 21(9P21.3) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          36
                        clus
vv                       DEL PEAK 21(9P21.3) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           233
[1] 2 2
[1] FALSE

Clustering(44) Variable = DEL PEAK 22(10P15.3) MUTATION ANALYSIS
D44V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 22(10P15.3) MUTATED    60  17
  DEL PEAK 22(10P15.3) WILD-TYPE 275  84
  DEL PEAK 22(10P15.3) MUTATED DEL PEAK 22(10P15.3) WILD-TYPE 
                            77                            359 
  DEL PEAK 22(10P15.3) MUTATED DEL PEAK 22(10P15.3) WILD-TYPE 
                            17                             84 
$`DEL PEAK 22(10P15.3) MUTATED`
TCGA-A6-2677 TCGA-A6-2681 TCGA-AA-3552 TCGA-AA-3562 TCGA-AA-3692 TCGA-AA-3697 
       24.33        45.60        13.02        19.99        36.00        85.05 
TCGA-AA-3867 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3979 TCGA-AA-A00Z TCGA-G4-6314 
       24.03         2.01        50.99        24.00        21.99        35.93 
TCGA-A6-2674 TCGA-A6-2680 TCGA-A6-5659 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6138 
       43.76        35.11        30.44        32.71        29.16        22.52 
TCGA-A6-6648 TCGA-A6-6654 TCGA-A6-A567 TCGA-A6-A5ZU TCGA-AA-3494 TCGA-AA-3511 
       25.18        23.87        61.84         9.63         1.02         6.97 
TCGA-AA-3664 TCGA-AA-3673 TCGA-AA-3685 TCGA-AA-3848 TCGA-AA-3858 TCGA-AA-3866 
       54.02        50.04        37.05        10.06        31.07        17.03 
TCGA-AA-3989 TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00Q TCGA-AA-A01D TCGA-AA-A01X 
        7.96        34.03        18.05        42.02        10.98        26.01 
TCGA-AA-A02W TCGA-AD-6901 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AU-3779 TCGA-AY-6196 
       41.00        22.42        16.44         0.46        14.50         0.20 
TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4616 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6603 
        1.41         5.65         5.13        65.00        62.79        29.56 
TCGA-AZ-6607 TCGA-CA-5797 TCGA-CA-6716 TCGA-CA-6719 TCGA-CM-4750 TCGA-CM-5341 
        3.19        12.59        12.20        14.30         8.02        29.06 
TCGA-CM-5344 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6164 TCGA-CM-6169 TCGA-CM-6170 
       22.03        15.02        15.02        29.03        13.02        15.02 
TCGA-CM-6676 TCGA-CM-6677 TCGA-D5-6531 TCGA-D5-6535 TCGA-D5-6898 TCGA-D5-6922 
       11.08        11.08        17.75        15.12         7.53        10.13 
TCGA-D5-6926 TCGA-D5-6929 TCGA-G4-6297 TCGA-G4-6303 TCGA-G4-6307 TCGA-G4-6315 
        9.04        13.41        82.39        65.85        55.04        61.91 
TCGA-G4-6322 TCGA-G4-6626 TCGA-NH-A6GC TCGA-RU-A8FL TCGA-SS-A7HO 
       26.04        46.75        12.79        38.70        60.13 

$`DEL PEAK 22(10P15.3) WILD-TYPE`
TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3506 TCGA-AA-3516 
       13.94        14.53        24.16         1.02        58.03        13.02 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 
       24.03        37.05        36.03         8.05        19.07        34.03 
TCGA-AA-3543 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3662 TCGA-AA-3672 
        0.99        17.95        23.01        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3870 
       19.00        19.04        19.04        14.93        31.07        29.98 
TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3976 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A024 
       12.99        24.00        26.01        19.07        38.04        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 
       21.37        15.52        25.08        10.88        75.95       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6298 
      100.01         1.94        49.08         5.88        28.21        23.51 
TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 
       63.62        22.09        35.80        26.17        91.79        79.69 
TCGA-NH-A8F7 TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 
       17.85        15.62         4.80        12.66         1.61         9.53 
TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2678 
       39.45        43.76        46.65        43.43        42.90        42.28 
TCGA-A6-2679 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 
       44.91        16.57        37.05        37.25        37.02        34.65 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 
       32.75        36.53        32.45        32.91        31.63        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6140 
       33.53        23.61        22.09        22.06        27.09        24.13 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        20.61        21.76        24.69        24.39 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A56B 
       20.12        19.66        20.28        16.24        24.92        56.25 
TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 
        5.03         7.04         3.02        37.05        35.01        63.98 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 
       29.00        29.00        26.01        12.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        61.02 
TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3675 TCGA-AA-3678 
       78.08         6.97         2.01        14.01        47.05        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 
       15.02        11.01         5.98         5.03        26.99        10.06 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3850 
       38.99        36.95        37.02         0.00        17.03         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3864 
       33.07         0.00        36.03        32.05         0.99        53.00 
TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3994 TCGA-AA-A004 
       13.05        34.06        25.02        27.02        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O 
       38.04        19.00        30.02        18.05         4.01        27.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C 
        0.99        17.03        14.99        34.98        15.02        15.02 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A029 
       35.01         1.02        33.04         1.02        37.02        51.98 
TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R 
        2.96        39.98         2.01         5.03         0.92        22.03 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6965 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4070 
        5.79        27.42        26.47         0.92        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D 
        0.95        33.01        21.44        17.82        17.26        17.85 
TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4615 TCGA-AZ-4682 
       19.33        18.84       109.28        58.39        32.94        22.36 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6605 TCGA-AZ-6606 
       88.21        49.41         6.77        12.10         5.23        11.74 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6717 
       12.69        12.36        12.46        12.39        12.59        12.76 
TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 
       10.06        17.56       148.01        85.45        70.16        15.62 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 
       23.05        20.02        37.02        25.02        26.04        27.02 
TCGA-CM-4752 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       13.02        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6165 TCGA-CM-6166 
       17.03        15.02        12.00        14.04        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       14.99        12.99        14.04        11.01        12.95        13.05 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6533 
       56.09        55.92        20.19        20.42        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       43.27        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6928 
       15.58        12.39        12.43        14.30         9.44        11.64 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 
      140.38         7.50        44.32       131.51       135.65         7.76 
TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      139.17        14.04        26.47        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 
       60.79       117.07        98.24        95.18         8.61        31.96 
TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
       11.11        35.74        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6295 TCGA-G4-6299 TCGA-G4-6302 
       47.41        35.31       133.18         8.35        74.56        67.30 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6317 TCGA-G4-6320 
       53.62        44.68        85.48        39.42        36.00        26.43 
TCGA-G4-6323 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV 
       13.78        74.79        18.18        10.98        19.33        19.33 
TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX 
        9.93        15.65        16.80        42.77        29.46        32.98 
TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-T9-A92H TCGA-WS-AB45 
        8.42        31.30        21.90        11.90        70.03 

  DEL PEAK 22(10P15.3) MUTATED DEL PEAK 22(10P15.3) WILD-TYPE 
                           0.2                            0.0 
  DEL PEAK 22(10P15.3) MUTATED DEL PEAK 22(10P15.3) WILD-TYPE 
                         85.05                         148.01 
  DEL PEAK 22(10P15.3) MUTATED DEL PEAK 22(10P15.3) WILD-TYPE 
                         22.42                          22.03 
[1] "0.2 - 85.0 (22.4)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1"  
D44V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 22(10P15.3) MUTATED        10        0        7        12         1
  DEL PEAK 22(10P15.3) WILD-TYPE      64        1       22       120         9
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 22(10P15.3) MUTATED           1         1          3         12
  DEL PEAK 22(10P15.3) WILD-TYPE         0        19          5         47
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 22(10P15.3) MUTATED            8       16         4         1
  DEL PEAK 22(10P15.3) WILD-TYPE         33       29        13         1
D44V3, multiclass
            clus
vv           DEL PEAK 22(10P15.3) MUTATED DEL PEAK 22(10P15.3) WILD-TYPE
  STAGE I                              10                             64
  STAGE IA                              0                              1
  STAGE II                              7                             22
  STAGE IIA                            12                            120
  STAGE IIB                             1                              9
  STAGE IIC                             1                              0
  STAGE III                             1                             19
  STAGE IIIA                            3                              5
  STAGE IIIB                           12                             47
  STAGE IIIC                            8                             33
  STAGE IV                             16                             29
  STAGE IVA                             4                             13
  STAGE IVB                             1                              1
[1] 13  2
[1] 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(10P15.3) MUTATED     1  13  53  11
  DEL PEAK 22(10P15.3) WILD-TYPE  10  64 252  44
D44V4, multiclass
    clus
vv   DEL PEAK 22(10P15.3) MUTATED DEL PEAK 22(10P15.3) WILD-TYPE
  T1                            1                             10
  T2                           13                             64
  T3                           53                            252
  T4                           11                             44
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2
  DEL PEAK 22(10P15.3) MUTATED    34  23  21
  DEL PEAK 22(10P15.3) WILD-TYPE 228  82  61
D44V5, multiclass
    clus
vv   DEL PEAK 22(10P15.3) MUTATED DEL PEAK 22(10P15.3) WILD-TYPE
  N0                           34                            228
  N1                           23                             82
  N2                           21                             61
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V6, binary
                                cls
clus                               0   1
  DEL PEAK 22(10P15.3) MUTATED    48  21
  DEL PEAK 22(10P15.3) WILD-TYPE 280  43
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 22(10P15.3) MUTATED     48   21
  DEL PEAK 22(10P15.3) WILD-TYPE  280   43
   clus
vv  DEL PEAK 22(10P15.3) MUTATED DEL PEAK 22(10P15.3) WILD-TYPE
  0                           48                            280
  1                           21                             43
[1] 2 2
[1] FALSE
D44V7, binary
                                cls
clus                               0   1
  DEL PEAK 22(10P15.3) MUTATED    36  42
  DEL PEAK 22(10P15.3) WILD-TYPE 177 194
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 22(10P15.3) MUTATED     36   42
  DEL PEAK 22(10P15.3) WILD-TYPE  177  194
        clus
vv       DEL PEAK 22(10P15.3) MUTATED DEL PEAK 22(10P15.3) WILD-TYPE
  FEMALE                           36                            177
  MALE                             42                            194
[1] 2 2
[1] FALSE
D44V8, binary
                                cls
clus                               0   1
  DEL PEAK 22(10P15.3) MUTATED    71   2
  DEL PEAK 22(10P15.3) WILD-TYPE 299   7
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 22(10P15.3) MUTATED     71    2
  DEL PEAK 22(10P15.3) WILD-TYPE  299    7
     clus
vv    DEL PEAK 22(10P15.3) MUTATED DEL PEAK 22(10P15.3) WILD-TYPE
  NO                            71                            299
  YES                            2                              7
[1] 2 2
[1] FALSE
D44V9, binary
                                cls
clus                               0   1
  DEL PEAK 22(10P15.3) MUTATED    70   8
  DEL PEAK 22(10P15.3) WILD-TYPE 312  54
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 22(10P15.3) MUTATED     70    8
  DEL PEAK 22(10P15.3) WILD-TYPE  312   54
                               clus
vv                              DEL PEAK 22(10P15.3) MUTATED
  COLON ADENOCARCINOMA                                    70
  COLON MUCINOUS ADENOCARCINOMA                            8
                               clus
vv                              DEL PEAK 22(10P15.3) WILD-TYPE
  COLON ADENOCARCINOMA                                     312
  COLON MUCINOUS ADENOCARCINOMA                             54
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 22(10P15.3) MUTATED    55   0   6   5
  DEL PEAK 22(10P15.3) WILD-TYPE 268   4  19  20
D44V10, multiclass
    clus
vv   DEL PEAK 22(10P15.3) MUTATED DEL PEAK 22(10P15.3) WILD-TYPE
  R0                           55                            268
  R1                            0                              4
  R2                            6                             19
  RX                            5                             20
[1] 4 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, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 22(10P15.3) MUTATED                                  0     3
  DEL PEAK 22(10P15.3) WILD-TYPE                                1     8
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 22(10P15.3) MUTATED                           8    42
  DEL PEAK 22(10P15.3) WILD-TYPE                        51   170
D44V12, multiclass
                                  clus
vv                                 DEL PEAK 22(10P15.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       3
  BLACK OR AFRICAN AMERICAN                                   8
  WHITE                                                      42
                                  clus
vv                                 DEL PEAK 22(10P15.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         8
  BLACK OR AFRICAN AMERICAN                                    51
  WHITE                                                       170
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V13, binary
                                cls
clus                               0   1
  DEL PEAK 22(10P15.3) MUTATED     1  50
  DEL PEAK 22(10P15.3) WILD-TYPE   3 219
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 22(10P15.3) MUTATED      1   50
  DEL PEAK 22(10P15.3) WILD-TYPE    3  219
                        clus
vv                       DEL PEAK 22(10P15.3) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           50
                        clus
vv                       DEL PEAK 22(10P15.3) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            219
[1] 2 2
[1] FALSE

Clustering(45) Variable = DEL PEAK 23(10Q21.1) MUTATION ANALYSIS
D45V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 23(10Q21.1) MUTATED    73  22
  DEL PEAK 23(10Q21.1) WILD-TYPE 262  79
  DEL PEAK 23(10Q21.1) MUTATED DEL PEAK 23(10Q21.1) WILD-TYPE 
                            95                            341 
  DEL PEAK 23(10Q21.1) MUTATED DEL PEAK 23(10Q21.1) WILD-TYPE 
                            22                             79 
$`DEL PEAK 23(10Q21.1) MUTATED`
TCGA-A6-2677 TCGA-A6-2681 TCGA-AA-3552 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3692 
       24.33        45.60        13.02        19.99         6.05        36.00 
TCGA-AA-3697 TCGA-AA-3867 TCGA-AA-3952 TCGA-AA-3972 TCGA-G4-6314 TCGA-G4-6625 
       85.05        24.03         2.01        50.99        35.93        91.79 
TCGA-NH-A8F7 TCGA-5M-AAT4 TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2680 TCGA-A6-3807 
       17.85         1.61        39.45        43.76        35.11        34.65 
TCGA-A6-4107 TCGA-A6-5659 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6138 TCGA-A6-6648 
       32.45        30.44        32.71        29.16        22.52        25.18 
TCGA-A6-6650 TCGA-A6-6654 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3494 
       20.61        23.87        61.84        56.25         9.63         1.02 
TCGA-AA-3511 TCGA-AA-3517 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3673 TCGA-AA-3685 
        6.97        38.99        33.99        21.01        50.04        37.05 
TCGA-AA-3848 TCGA-AA-3858 TCGA-AA-3866 TCGA-AA-3968 TCGA-AA-3989 TCGA-AA-A00F 
       10.06        31.07        17.03        21.99         7.96        34.03 
TCGA-AA-A00Q TCGA-AA-A01D TCGA-AA-A01Q TCGA-AA-A01X TCGA-AA-A02F TCGA-AA-A02J 
       42.02        10.98         1.02        26.01        39.98         5.03 
TCGA-AA-A02W TCGA-AD-6890 TCGA-AD-6901 TCGA-AD-A5EK TCGA-AU-3779 TCGA-AY-4070 
       41.00        24.53        22.42        16.44        14.50        16.31 
TCGA-AY-6196 TCGA-AY-A8YK TCGA-AZ-4614 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6603 
        0.20        18.84         5.65        65.00        62.79        29.56 
TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5797 TCGA-CA-6716 TCGA-CA-6719 TCGA-CM-4750 
        3.19        12.69        12.59        12.20        14.30         8.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6164 
       29.06        22.03         5.03        15.02        15.02        29.03 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6676 TCGA-CM-6677 TCGA-D5-6531 TCGA-D5-6534 
       13.02        15.02        11.08        11.08        17.75        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6898 TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6931 
       15.12        17.85         7.53         9.04        13.41        12.00 
TCGA-D5-6932 TCGA-DM-A28F TCGA-DM-A28H TCGA-F4-6461 TCGA-G4-6307 TCGA-G4-6315 
       11.38        35.97       117.07        11.11        55.04        61.91 
TCGA-G4-6322 TCGA-G4-6626 TCGA-NH-A6GC TCGA-RU-A8FL TCGA-SS-A7HO 
       26.04        46.75        12.79        38.70        60.13 

$`DEL PEAK 23(10Q21.1) WILD-TYPE`
TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3506 TCGA-AA-3516 
       13.94        14.53        24.16         1.02        58.03        13.02 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 
       24.03        37.05        36.03         8.05        19.07        34.03 
TCGA-AA-3543 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3672 TCGA-AA-3688 
        0.99        17.95        23.01        19.99         0.92        19.00 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3870 TCGA-AA-3939 
       19.04        19.04        14.93        31.07        29.98        12.99 
TCGA-AA-3950 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       24.00        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 
       39.06        21.37        15.52        25.08        10.88        75.95 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6294 
      106.75       100.01         1.94        49.08         5.88        28.21 
TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 
       23.51        63.62        22.09        35.80        26.17        79.69 
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT6 TCGA-A6-2672 TCGA-A6-2674 
       15.62         4.80        12.66         9.53        46.65        43.76 
TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2683 TCGA-A6-2684 
       43.43        42.90        42.28        44.91        16.57        37.05 
TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 
       37.25        37.02        32.75        36.53        32.91        31.63 
TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 
       29.19        33.53        23.61        22.09        22.06        27.09 
TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       24.13         8.38        25.08        21.76        24.69        24.39 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-AA-3488 
       20.12        19.66        20.28        16.24        24.92         5.03 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3514 
        7.04         3.02        37.05        35.01        63.98         1.02 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       26.01        12.99        14.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        61.02        78.08         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
       14.01        47.05        47.01        15.02        11.01         5.98 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
        5.03        26.99        10.06        35.05         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 
        1.02        17.98        15.95        38.99        36.95        37.02 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
        0.00        17.03         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       32.05         0.99        53.00        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3982 
        2.01        16.08        13.05        34.06        25.02        27.02 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J 
       27.02        13.94        38.04        19.00        30.02        18.05 
TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       18.05         4.01        27.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        15.02        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       31.00        38.07        35.01         1.02        33.04         1.02 
TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02H TCGA-AA-A02O TCGA-AA-A02R 
       37.02        51.98         2.96         2.01         0.92        22.03 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6899 
       39.98        18.05        40.96        12.16        83.24         5.79 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4071 
       27.42        26.47         0.46         0.92        27.09         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X 
       33.01        21.44        17.82        17.26        17.85        19.33 
TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 
      109.28        58.39         1.41        32.94         5.13        22.36 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6605 TCGA-AZ-6606 
       88.21        49.41         6.77        12.10         5.23        11.74 
TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 
       12.36        12.46        12.39        12.59        12.76        10.06 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 
       17.56       148.01        85.45        70.16        15.62        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14        82.95         2.01       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-4752 
       20.02        37.02        25.02        26.04        27.02        13.02 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5868 TCGA-CM-6161 
       22.98        30.08        32.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
       12.00        14.04        16.04        21.99        14.99        12.99 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6678 TCGA-CM-6679 
       14.04        11.01        12.95        13.05        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6537 TCGA-D5-6538 
       20.19        20.42        18.25        25.48         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       12.49        16.14        15.58        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-7000 TCGA-DM-A0X9 
       14.30         9.44        11.64        13.35        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E 
        7.76       139.17        14.04        26.47        81.37       119.93 
TCGA-DM-A28G TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6463 
       60.79        98.24        95.18         8.61        31.96        35.74 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       43.04        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 
      133.18         8.35        82.39        74.56        67.30        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6317 TCGA-G4-6320 
       53.62        44.68        85.48        39.42        36.00        26.43 
TCGA-G4-6323 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV 
       13.78        74.79        18.18        10.98        19.33        19.33 
TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX 
        9.93        15.65        16.80        42.77        29.46        32.98 
TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-T9-A92H TCGA-WS-AB45 
        8.42        31.30        21.90        11.90        70.03 

  DEL PEAK 23(10Q21.1) MUTATED DEL PEAK 23(10Q21.1) WILD-TYPE 
                           0.2                            0.0 
  DEL PEAK 23(10Q21.1) MUTATED DEL PEAK 23(10Q21.1) WILD-TYPE 
                        117.07                         148.01 
  DEL PEAK 23(10Q21.1) MUTATED DEL PEAK 23(10Q21.1) WILD-TYPE 
                         22.03                          22.06 
[1] "0.2 - 117.1 (22.0)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.1"
D45V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 23(10Q21.1) MUTATED        12        0        7        19         1
  DEL PEAK 23(10Q21.1) WILD-TYPE      62        1       22       113         9
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 23(10Q21.1) MUTATED           1         1          2         14
  DEL PEAK 23(10Q21.1) WILD-TYPE         0        19          6         45
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 23(10Q21.1) MUTATED           14       17         5         1
  DEL PEAK 23(10Q21.1) WILD-TYPE         27       28        12         1
D45V3, multiclass
            clus
vv           DEL PEAK 23(10Q21.1) MUTATED DEL PEAK 23(10Q21.1) WILD-TYPE
  STAGE I                              12                             62
  STAGE IA                              0                              1
  STAGE II                              7                             22
  STAGE IIA                            19                            113
  STAGE IIB                             1                              9
  STAGE IIC                             1                              0
  STAGE III                             1                             19
  STAGE IIIA                            2                              6
  STAGE IIIB                           14                             45
  STAGE IIIC                           14                             27
  STAGE IV                             17                             28
  STAGE IVA                             5                             12
  STAGE IVB                             1                              1
[1] 13  2
[1] 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(10Q21.1) MUTATED     2  15  68  12
  DEL PEAK 23(10Q21.1) WILD-TYPE   9  62 237  43
D45V4, multiclass
    clus
vv   DEL PEAK 23(10Q21.1) MUTATED DEL PEAK 23(10Q21.1) WILD-TYPE
  T1                            2                              9
  T2                           15                             62
  T3                           68                            237
  T4                           12                             43
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2
  DEL PEAK 23(10Q21.1) MUTATED    46  25  26
  DEL PEAK 23(10Q21.1) WILD-TYPE 216  80  56
D45V5, multiclass
    clus
vv   DEL PEAK 23(10Q21.1) MUTATED DEL PEAK 23(10Q21.1) WILD-TYPE
  N0                           46                            216
  N1                           25                             80
  N2                           26                             56
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V6, binary
                                cls
clus                               0   1
  DEL PEAK 23(10Q21.1) MUTATED    63  23
  DEL PEAK 23(10Q21.1) WILD-TYPE 265  41
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(10Q21.1) MUTATED     63   23
  DEL PEAK 23(10Q21.1) WILD-TYPE  265   41
   clus
vv  DEL PEAK 23(10Q21.1) MUTATED DEL PEAK 23(10Q21.1) WILD-TYPE
  0                           63                            265
  1                           23                             41
[1] 2 2
[1] FALSE
D45V7, binary
                                cls
clus                               0   1
  DEL PEAK 23(10Q21.1) MUTATED    46  51
  DEL PEAK 23(10Q21.1) WILD-TYPE 167 185
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(10Q21.1) MUTATED     46   51
  DEL PEAK 23(10Q21.1) WILD-TYPE  167  185
        clus
vv       DEL PEAK 23(10Q21.1) MUTATED DEL PEAK 23(10Q21.1) WILD-TYPE
  FEMALE                           46                            167
  MALE                             51                            185
[1] 2 2
[1] FALSE
D45V8, binary
                                cls
clus                               0   1
  DEL PEAK 23(10Q21.1) MUTATED    84   4
  DEL PEAK 23(10Q21.1) WILD-TYPE 286   5
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(10Q21.1) MUTATED     84    4
  DEL PEAK 23(10Q21.1) WILD-TYPE  286    5
     clus
vv    DEL PEAK 23(10Q21.1) MUTATED DEL PEAK 23(10Q21.1) WILD-TYPE
  NO                            84                            286
  YES                            4                              5
[1] 2 2
[1] FALSE
D45V9, binary
                                cls
clus                               0   1
  DEL PEAK 23(10Q21.1) MUTATED    90   7
  DEL PEAK 23(10Q21.1) WILD-TYPE 292  55
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(10Q21.1) MUTATED     90    7
  DEL PEAK 23(10Q21.1) WILD-TYPE  292   55
                               clus
vv                              DEL PEAK 23(10Q21.1) MUTATED
  COLON ADENOCARCINOMA                                    90
  COLON MUCINOUS ADENOCARCINOMA                            7
                               clus
vv                              DEL PEAK 23(10Q21.1) WILD-TYPE
  COLON ADENOCARCINOMA                                     292
  COLON MUCINOUS ADENOCARCINOMA                             55
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 23(10Q21.1) MUTATED    66   1  10   6
  DEL PEAK 23(10Q21.1) WILD-TYPE 257   3  15  19
D45V10, multiclass
    clus
vv   DEL PEAK 23(10Q21.1) MUTATED DEL PEAK 23(10Q21.1) WILD-TYPE
  R0                           66                            257
  R1                            1                              3
  R2                           10                             15
  RX                            6                             19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 23(10Q21.1) MUTATED                                  0     4
  DEL PEAK 23(10Q21.1) WILD-TYPE                                1     7
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 23(10Q21.1) MUTATED                          15    48
  DEL PEAK 23(10Q21.1) WILD-TYPE                        44   164
D45V12, multiclass
                                  clus
vv                                 DEL PEAK 23(10Q21.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       4
  BLACK OR AFRICAN AMERICAN                                  15
  WHITE                                                      48
                                  clus
vv                                 DEL PEAK 23(10Q21.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         7
  BLACK OR AFRICAN AMERICAN                                    44
  WHITE                                                       164
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V13, binary
                                cls
clus                               0   1
  DEL PEAK 23(10Q21.1) MUTATED     3  61
  DEL PEAK 23(10Q21.1) WILD-TYPE   1 208
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(10Q21.1) MUTATED      3   61
  DEL PEAK 23(10Q21.1) WILD-TYPE    1  208
                        clus
vv                       DEL PEAK 23(10Q21.1) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           61
                        clus
vv                       DEL PEAK 23(10Q21.1) WILD-TYPE
  HISPANIC OR LATINO                                  1
  NOT HISPANIC OR LATINO                            208
[1] 2 2
[1] FALSE

Clustering(46) Variable = DEL PEAK 24(10Q23.31) MUTATION ANALYSIS
D46V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 24(10Q23.31) MUTATED    85  21
  DEL PEAK 24(10Q23.31) WILD-TYPE 250  80
  DEL PEAK 24(10Q23.31) MUTATED DEL PEAK 24(10Q23.31) WILD-TYPE 
                            106                             330 
  DEL PEAK 24(10Q23.31) MUTATED DEL PEAK 24(10Q23.31) WILD-TYPE 
                             21                              80 
$`DEL PEAK 24(10Q23.31) MUTATED`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-6649 TCGA-AA-3552 TCGA-AA-3556 
       24.33        45.60        13.94        24.16        13.02        23.01 
TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3860 TCGA-AA-3867 
       19.99         6.05        36.00        85.05        31.07        24.03 
TCGA-AA-3952 TCGA-AA-3972 TCGA-DM-A285 TCGA-NH-A8F7 TCGA-5M-AATE TCGA-A6-2671 
        2.01        50.99         5.88        17.85        39.45        43.76 
TCGA-A6-2678 TCGA-A6-2680 TCGA-A6-4107 TCGA-A6-5659 TCGA-A6-5666 TCGA-A6-5667 
       42.28        35.11        32.45        30.44        32.71        29.16 
TCGA-A6-6138 TCGA-A6-6648 TCGA-A6-6654 TCGA-A6-A567 TCGA-A6-A5ZU TCGA-AA-3494 
       22.52        25.18        23.87        61.84         9.63         1.02 
TCGA-AA-3511 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3548 TCGA-AA-3664 TCGA-AA-3673 
        6.97         9.07        19.07        33.99        54.02        50.04 
TCGA-AA-3680 TCGA-AA-3685 TCGA-AA-3841 TCGA-AA-3851 TCGA-AA-3858 TCGA-AA-3866 
       11.01        37.05        36.95        33.07        31.07        17.03 
TCGA-AA-3989 TCGA-AA-A00F TCGA-AA-A00Q TCGA-AA-A01D TCGA-AA-A01T TCGA-AA-A01X 
        7.96        34.03        42.02        10.98        33.04        26.01 
TCGA-AA-A02F TCGA-AA-A02W TCGA-AD-6901 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AU-3779 
       39.98        41.00        22.42        16.44         0.46        14.50 
TCGA-AY-4070 TCGA-AY-A54L TCGA-AY-A69D TCGA-AZ-4614 TCGA-AZ-4684 TCGA-AZ-5403 
       16.31        17.26        17.85         5.65        65.00        62.79 
TCGA-AZ-6603 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5797 TCGA-CA-6716 TCGA-CA-6719 
       29.56         3.19        12.69        12.59        12.20        14.30 
TCGA-CM-4750 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5862 TCGA-CM-5863 
        8.02        29.06        22.03        30.08         5.03        15.02 
TCGA-CM-5864 TCGA-CM-6164 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6675 TCGA-CM-6676 
       15.02        29.03        13.02        15.02        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6679 TCGA-D5-5539 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6534 
       11.08        10.06        19.59        17.75        18.25        43.27 
TCGA-D5-6536 TCGA-D5-6539 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6926 TCGA-D5-6929 
       17.85        12.49         7.53        10.13         9.04        13.41 
TCGA-DM-A1D0 TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-F4-6461 TCGA-F4-6807 TCGA-F4-6808 
      130.65        13.32       140.38        11.11        43.04        33.67 
TCGA-G4-6307 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6626 
       55.04        61.91        36.00        26.04        13.78        46.75 
TCGA-NH-A6GC TCGA-QG-A5YW TCGA-RU-A8FL TCGA-SS-A7HO 
       12.79        29.46        38.70        60.13 

$`DEL PEAK 24(10Q23.31) WILD-TYPE`
TCGA-A6-4105 TCGA-AA-3496 TCGA-AA-3506 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       14.53         1.02        58.03        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3554 
       36.03         8.05        19.07        34.03         0.99        17.95 
TCGA-AA-3560 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.99         0.92        19.00        19.04        19.04        14.93 
TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 
       29.98        12.99        24.00        26.01        24.00        19.07 
TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 
       38.04        21.99        39.06        21.37        15.52        25.08 
TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 
       10.88        75.95       106.75       100.01         1.94        49.08 
TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6321 TCGA-G4-6586 
       28.21        23.51        63.62        35.93        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H 
       26.17        91.79        79.69        15.62         4.80        12.66 
TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 
        1.61         9.53        46.65        43.76        43.43        42.90 
TCGA-A6-2679 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 
       44.91        16.57        37.05        37.25        37.02        34.65 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 
       32.75        36.53        32.91        31.63        29.19        33.53 
TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6141 
       23.61        22.09        22.06        27.09        24.13         8.38 
TCGA-A6-6142 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 
       25.08        20.61        21.76        24.69        24.39        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A56B TCGA-AA-3488 
       19.66        20.28        16.24        24.92        56.25         5.03 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3514 
        7.04         3.02        37.05        35.01        63.98         1.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
       38.99         1.02         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       12.99        14.01        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3666 TCGA-AA-3667 
       13.94        61.02        78.08         6.97         2.01        14.01 
TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3681 TCGA-AA-3696 TCGA-AA-3710 
       47.05        47.01        15.02         5.98         5.03        26.99 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       10.06        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       15.95        38.99        37.02         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3864 
        0.00         0.00        36.03        32.05         0.99        53.00 
TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3994 TCGA-AA-A004 
       13.05        34.06        25.02        27.02        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N 
       38.04        19.00        30.02        18.05        18.05         4.01 
TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       27.02         0.99        17.03        14.99        34.98        15.02 
TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       15.02        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A029 
        1.02        35.01         1.02         1.02        37.02        51.98 
TCGA-AA-A02E TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y 
        2.96         2.01         5.03         0.92        22.03        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-5543 
       27.42        26.47         0.92        27.09         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 
        0.20        21.44        17.82        19.33        18.84       109.28 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5407 
       58.39         1.41        32.94         5.13        22.36        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-CA-5255 
       49.41         6.77        12.10         5.23        11.74        12.36 
TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 
       12.46        12.39        12.59        12.76        10.06        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        70.16        15.62        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5348 
       37.02        25.02        26.04        27.02        13.02        22.98 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       32.02        15.02        17.03        15.02        12.00        14.04 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6171 TCGA-CM-6172 
       16.04        21.99        14.99        12.99        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 
       12.95        11.01        12.03        45.40        54.61        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6537 
       55.92        20.19        20.42        25.48        15.12         4.80 
TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6923 TCGA-D5-6924 
       17.13        16.14        15.58        12.39        12.43        14.30 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
        9.44        11.64        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D8 
      119.70        24.43        38.20        92.75        49.91        12.59 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 
        7.50        44.32       131.51       135.65         7.76       139.17 
TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
       14.04        26.47        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6463 
      117.07        98.24        95.18         8.61        31.96        35.74 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6295 
       13.25         0.53        47.41        35.31       133.18         8.35 
TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       82.39        74.56        67.30        65.85        53.62        44.68 
TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6320 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50U 
       85.48        39.42        26.43        74.79        18.18        10.98 
TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A8F8 TCGA-QG-A5YV 
       19.33        19.33         9.93        15.65        16.80        42.77 
TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-T9-A92H TCGA-WS-AB45 
       32.98         8.42        31.30        21.90        11.90        70.03 

  DEL PEAK 24(10Q23.31) MUTATED DEL PEAK 24(10Q23.31) WILD-TYPE 
                           0.46                            0.00 
  DEL PEAK 24(10Q23.31) MUTATED DEL PEAK 24(10Q23.31) WILD-TYPE 
                         140.38                          148.01 
  DEL PEAK 24(10Q23.31) MUTATED DEL PEAK 24(10Q23.31) WILD-TYPE 
                          22.47                           22.01 
[1] "0.5 - 140.4 (22.5)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.1"
D46V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 24(10Q23.31) MUTATED        14        1        7        24         1
  DEL PEAK 24(10Q23.31) WILD-TYPE      60        0       22       108         9
                                 vv
clus                              STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 24(10Q23.31) MUTATED           1         3          4         14
  DEL PEAK 24(10Q23.31) WILD-TYPE         0        17          4         45
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 24(10Q23.31) MUTATED           12       17         5         2
  DEL PEAK 24(10Q23.31) WILD-TYPE         29       28        12         0
D46V3, multiclass
            clus
vv           DEL PEAK 24(10Q23.31) MUTATED DEL PEAK 24(10Q23.31) WILD-TYPE
  STAGE I                               14                              60
  STAGE IA                               1                               0
  STAGE II                               7                              22
  STAGE IIA                             24                             108
  STAGE IIB                              1                               9
  STAGE IIC                              1                               0
  STAGE III                              3                              17
  STAGE IIIA                             4                               4
  STAGE IIIB                            14                              45
  STAGE IIIC                            12                              29
  STAGE IV                              17                              28
  STAGE IVA                              5                              12
  STAGE IVB                              2                               0
[1] 13  2
[1] 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(10Q23.31) MUTATED     2  16  75  14
  DEL PEAK 24(10Q23.31) WILD-TYPE   9  61 230  41
D46V4, multiclass
    clus
vv   DEL PEAK 24(10Q23.31) MUTATED DEL PEAK 24(10Q23.31) WILD-TYPE
  T1                             2                               9
  T2                            16                              61
  T3                            75                             230
  T4                            14                              41
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               N0  N1  N2
  DEL PEAK 24(10Q23.31) MUTATED    52  30  26
  DEL PEAK 24(10Q23.31) WILD-TYPE 210  75  56
D46V5, multiclass
    clus
vv   DEL PEAK 24(10Q23.31) MUTATED DEL PEAK 24(10Q23.31) WILD-TYPE
  N0                            52                             210
  N1                            30                              75
  N2                            26                              56
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V6, binary
                                 cls
clus                                0   1
  DEL PEAK 24(10Q23.31) MUTATED    73  24
  DEL PEAK 24(10Q23.31) WILD-TYPE 255  40
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 24(10Q23.31) MUTATED     73   24
  DEL PEAK 24(10Q23.31) WILD-TYPE  255   40
   clus
vv  DEL PEAK 24(10Q23.31) MUTATED DEL PEAK 24(10Q23.31) WILD-TYPE
  0                            73                             255
  1                            24                              40
[1] 2 2
[1] FALSE
D46V7, binary
                                 cls
clus                                0   1
  DEL PEAK 24(10Q23.31) MUTATED    54  54
  DEL PEAK 24(10Q23.31) WILD-TYPE 159 182
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 24(10Q23.31) MUTATED     54   54
  DEL PEAK 24(10Q23.31) WILD-TYPE  159  182
        clus
vv       DEL PEAK 24(10Q23.31) MUTATED DEL PEAK 24(10Q23.31) WILD-TYPE
  FEMALE                            54                             159
  MALE                              54                             182
[1] 2 2
[1] FALSE
D46V8, binary
                                 cls
clus                                0   1
  DEL PEAK 24(10Q23.31) MUTATED    96   3
  DEL PEAK 24(10Q23.31) WILD-TYPE 274   6
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 24(10Q23.31) MUTATED     96    3
  DEL PEAK 24(10Q23.31) WILD-TYPE  274    6
     clus
vv    DEL PEAK 24(10Q23.31) MUTATED DEL PEAK 24(10Q23.31) WILD-TYPE
  NO                             96                             274
  YES                             3                               6
[1] 2 2
[1] FALSE
D46V9, binary
                                 cls
clus                                0   1
  DEL PEAK 24(10Q23.31) MUTATED    97   9
  DEL PEAK 24(10Q23.31) WILD-TYPE 285  53
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 24(10Q23.31) MUTATED     97    9
  DEL PEAK 24(10Q23.31) WILD-TYPE  285   53
                               clus
vv                              DEL PEAK 24(10Q23.31) MUTATED
  COLON ADENOCARCINOMA                                     97
  COLON MUCINOUS ADENOCARCINOMA                             9
                               clus
vv                              DEL PEAK 24(10Q23.31) WILD-TYPE
  COLON ADENOCARCINOMA                                      285
  COLON MUCINOUS ADENOCARCINOMA                              53
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 24(10Q23.31) MUTATED    77   1  10   5
  DEL PEAK 24(10Q23.31) WILD-TYPE 246   3  15  20
D46V10, multiclass
    clus
vv   DEL PEAK 24(10Q23.31) MUTATED DEL PEAK 24(10Q23.31) WILD-TYPE
  R0                            77                             246
  R1                             1                               3
  R2                            10                              15
  RX                             5                              20
[1] 4 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, continuous
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 24(10Q23.31) MUTATED                                  0     4
  DEL PEAK 24(10Q23.31) WILD-TYPE                                1     7
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 24(10Q23.31) MUTATED                          16    55
  DEL PEAK 24(10Q23.31) WILD-TYPE                        43   157
D46V12, multiclass
                                  clus
vv                                 DEL PEAK 24(10Q23.31) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        4
  BLACK OR AFRICAN AMERICAN                                   16
  WHITE                                                       55
                                  clus
vv                                 DEL PEAK 24(10Q23.31) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               1
  ASIAN                                                          7
  BLACK OR AFRICAN AMERICAN                                     43
  WHITE                                                        157
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V13, binary
                                 cls
clus                                0   1
  DEL PEAK 24(10Q23.31) MUTATED     2  70
  DEL PEAK 24(10Q23.31) WILD-TYPE   2 199
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 24(10Q23.31) MUTATED      2   70
  DEL PEAK 24(10Q23.31) WILD-TYPE    2  199
                        clus
vv                       DEL PEAK 24(10Q23.31) MUTATED
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                            70
                        clus
vv                       DEL PEAK 24(10Q23.31) WILD-TYPE
  HISPANIC OR LATINO                                   2
  NOT HISPANIC OR LATINO                             199
[1] 2 2
[1] FALSE

Clustering(47) Variable = DEL PEAK 25(10Q25.2) MUTATION ANALYSIS
D47V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 25(10Q25.2) MUTATED    78  28
  DEL PEAK 25(10Q25.2) WILD-TYPE 257  73
  DEL PEAK 25(10Q25.2) MUTATED DEL PEAK 25(10Q25.2) WILD-TYPE 
                           106                            330 
  DEL PEAK 25(10Q25.2) MUTATED DEL PEAK 25(10Q25.2) WILD-TYPE 
                            28                             73 
$`DEL PEAK 25(10Q25.2) MUTATED`
TCGA-A6-2677 TCGA-A6-2681 TCGA-AA-3522 TCGA-AA-3552 TCGA-AA-3562 TCGA-AA-3662 
       24.33        45.60        37.05        13.02        19.99         6.05 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3867 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-A024 
       36.00        85.05        24.03         2.01        50.99        39.06 
TCGA-DM-A285 TCGA-G4-6625 TCGA-NH-A8F7 TCGA-3L-AA1B TCGA-5M-AATE TCGA-A6-2671 
        5.88        91.79        17.85        15.62        39.45        43.76 
TCGA-A6-2678 TCGA-A6-2680 TCGA-A6-4107 TCGA-A6-5659 TCGA-A6-5666 TCGA-A6-5667 
       42.28        35.11        32.45        30.44        32.71        29.16 
TCGA-A6-6138 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6654 TCGA-A6-A567 TCGA-A6-A56B 
       22.52        25.18        20.61        23.87        61.84        56.25 
TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3494 TCGA-AA-3511 TCGA-AA-3519 TCGA-AA-3532 
        9.63         5.03         1.02         6.97         9.07        29.00 
TCGA-AA-3548 TCGA-AA-3666 TCGA-AA-3673 TCGA-AA-3680 TCGA-AA-3685 TCGA-AA-3696 
       33.99         2.01        50.04        11.01        37.05         5.03 
TCGA-AA-3811 TCGA-AA-3818 TCGA-AA-3841 TCGA-AA-3851 TCGA-AA-3856 TCGA-AA-3866 
       10.06         0.99        36.95        33.07         0.99        17.03 
TCGA-AA-3989 TCGA-AA-A00F TCGA-AA-A00Q TCGA-AA-A01D TCGA-AA-A01T TCGA-AA-A01X 
        7.96        34.03        42.02        10.98        33.04        26.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AD-6901 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AU-3779 
        0.92        41.00        22.42        26.47        16.44        14.50 
TCGA-AY-4070 TCGA-AY-A69D TCGA-AZ-4614 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6603 
       16.31        17.85         5.65        65.00        62.79        29.56 
TCGA-AZ-6607 TCGA-CA-5797 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-6748 TCGA-CM-4747 
        3.19        12.59        12.20        14.30         2.01        25.02 
TCGA-CM-4750 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
        8.02        29.06        22.03         5.03        15.02        15.02 
TCGA-CM-6164 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6679 
       29.03        13.02        15.02        11.08        11.08        10.06 
TCGA-D5-6531 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6926 
       17.75        43.27        17.85         7.53        10.13         9.04 
TCGA-D5-6929 TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1HA TCGA-DM-A28F TCGA-F4-6461 
       13.41        13.32       140.38       131.51        35.97        11.11 
TCGA-F4-6807 TCGA-F4-6808 TCGA-G4-6307 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6322 
       43.04        33.67        55.04        61.91        36.00        26.04 
TCGA-G4-6626 TCGA-NH-A6GC TCGA-RU-A8FL TCGA-SS-A7HO 
       46.75        12.79        38.70        60.13 

$`DEL PEAK 25(10Q25.2) WILD-TYPE`
TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3506 TCGA-AA-3516 
       13.94        14.53        24.16         1.02        58.03        13.02 
TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       24.03        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3713 
       17.95        23.01        19.99         0.92        19.00        19.04 
TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       19.04        14.93        31.07        29.98        12.99        24.00 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AD-6548 
       26.01        24.00        19.07        38.04        21.99        21.37 
TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 
       15.52        25.08        10.88        75.95       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6314 
        1.94        49.08        28.21        23.51        63.62        35.93 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 TCGA-4N-A93T TCGA-4T-AA8H 
       22.09        35.80        26.17        79.69         4.80        12.66 
TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 
        1.61         9.53        46.65        43.76        43.43        42.90 
TCGA-A6-2679 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 
       44.91        16.57        37.05        37.25        37.02        34.65 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 
       32.75        36.53        32.91        31.63        29.19        33.53 
TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6141 
       23.61        22.09        22.06        27.09        24.13         8.38 
TCGA-A6-6142 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 
       25.08        21.76        24.69        24.39        20.12        19.66 
TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3495 
       20.28        16.24        24.92         7.04         3.02        37.05 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3526 
       35.01        63.98         1.02        38.99         1.02        19.07 
TCGA-AA-3529 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3549 
        0.00        29.00        26.01        12.99        14.01        21.01 
TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        61.02        78.08 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 
        6.97        54.02        14.01        47.05        47.01        15.02 
TCGA-AA-3681 TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
        5.98        26.99        35.05        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       15.95        38.99        37.02         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3858 TCGA-AA-3864 
        0.00         0.00        36.03        32.05        31.07        53.00 
TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3994 TCGA-AA-A004 
       13.05        34.06        25.02        27.02        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N 
       38.04        19.00        30.02        18.05        18.05         4.01 
TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       27.02         0.99        17.03        14.99        34.98        15.02 
TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       15.02        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A029 
        1.02        35.01         1.02         1.02        37.02        51.98 
TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02R TCGA-AA-A02Y 
        2.96        39.98         2.01         5.03        22.03        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6963 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-5543 
       27.42         0.46         0.92        27.09         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A71X TCGA-AY-A8YK 
        0.20        21.44        17.82        17.26        19.33        18.84 
TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 
      109.28        58.39         1.41        32.94         5.13        22.36 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6605 TCGA-AZ-6606 
       88.21        49.41         6.77        12.10         5.23        11.74 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6717 
       12.69        12.36        12.46        12.39        12.59        12.76 
TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 
       10.06        17.56       148.01        85.45        70.16        15.62 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 
       51.32        21.99        21.14        82.95       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5348 
       20.02        37.02        26.04        27.02        13.02        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
       30.08        32.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6171 
       14.04        16.04        21.99        14.99        12.99        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-5537 
       11.01        12.95        13.05        11.01        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 
       54.61        19.59        56.09        55.92        20.19        20.42 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       18.25        25.48        15.12         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6927 
       16.14        15.58        12.39        12.43        14.30         9.44 
TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       11.64        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D8 
       24.43        38.20       130.65        92.75        49.91        12.59 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 
        7.50        44.32       135.65         7.76       139.17        14.04 
TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       26.47        81.37       119.93        60.79       117.07        98.24 
TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 
       95.18         8.61        31.96        35.74        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6809 TCGA-F4-6854 
       47.87         1.55        34.42        41.42        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6299 
       47.41        35.31       133.18         8.35        82.39        74.56 
TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6311 
       67.30        65.85        53.62        44.68        85.48        39.42 
TCGA-G4-6320 TCGA-G4-6323 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V 
       26.43        13.78        74.79        18.18        10.98        19.33 
TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW 
       19.33         9.93        15.65        16.80        42.77        29.46 
TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-T9-A92H TCGA-WS-AB45 
       32.98         8.42        31.30        21.90        11.90        70.03 

  DEL PEAK 25(10Q25.2) MUTATED DEL PEAK 25(10Q25.2) WILD-TYPE 
                          0.92                           0.00 
  DEL PEAK 25(10Q25.2) MUTATED DEL PEAK 25(10Q25.2) WILD-TYPE 
                        140.38                         148.01 
  DEL PEAK 25(10Q25.2) MUTATED DEL PEAK 25(10Q25.2) WILD-TYPE 
                         22.47                          22.01 
[1] "0.9 - 140.4 (22.5)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.3"
D47V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 25(10Q25.2) MUTATED        11        0        8        26         1
  DEL PEAK 25(10Q25.2) WILD-TYPE      63        1       21       106         9
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 25(10Q25.2) MUTATED           1         5          3         14
  DEL PEAK 25(10Q25.2) WILD-TYPE         0        15          5         45
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 25(10Q25.2) MUTATED           13       18         5         1
  DEL PEAK 25(10Q25.2) WILD-TYPE         28       27        12         1
D47V3, multiclass
            clus
vv           DEL PEAK 25(10Q25.2) MUTATED DEL PEAK 25(10Q25.2) WILD-TYPE
  STAGE I                              11                             63
  STAGE IA                              0                              1
  STAGE II                              8                             21
  STAGE IIA                            26                            106
  STAGE IIB                             1                              9
  STAGE IIC                             1                              0
  STAGE III                             5                             15
  STAGE IIIA                            3                              5
  STAGE IIIB                           14                             45
  STAGE IIIC                           13                             28
  STAGE IV                             18                             27
  STAGE IVA                             5                             12
  STAGE IVB                             1                              1
[1] 13  2
[1] 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(10Q25.2) MUTATED     2  13  79  14
  DEL PEAK 25(10Q25.2) WILD-TYPE   9  64 226  41
D47V4, multiclass
    clus
vv   DEL PEAK 25(10Q25.2) MUTATED DEL PEAK 25(10Q25.2) WILD-TYPE
  T1                            2                              9
  T2                           13                             64
  T3                           79                            226
  T4                           14                             41
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2
  DEL PEAK 25(10Q25.2) MUTATED    50  31  27
  DEL PEAK 25(10Q25.2) WILD-TYPE 212  74  55
D47V5, multiclass
    clus
vv   DEL PEAK 25(10Q25.2) MUTATED DEL PEAK 25(10Q25.2) WILD-TYPE
  N0                           50                            212
  N1                           31                             74
  N2                           27                             55
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V6, binary
                                cls
clus                               0   1
  DEL PEAK 25(10Q25.2) MUTATED    75  24
  DEL PEAK 25(10Q25.2) WILD-TYPE 253  40
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(10Q25.2) MUTATED     75   24
  DEL PEAK 25(10Q25.2) WILD-TYPE  253   40
   clus
vv  DEL PEAK 25(10Q25.2) MUTATED DEL PEAK 25(10Q25.2) WILD-TYPE
  0                           75                            253
  1                           24                             40
[1] 2 2
[1] FALSE
D47V7, binary
                                cls
clus                               0   1
  DEL PEAK 25(10Q25.2) MUTATED    51  57
  DEL PEAK 25(10Q25.2) WILD-TYPE 162 179
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(10Q25.2) MUTATED     51   57
  DEL PEAK 25(10Q25.2) WILD-TYPE  162  179
        clus
vv       DEL PEAK 25(10Q25.2) MUTATED DEL PEAK 25(10Q25.2) WILD-TYPE
  FEMALE                           51                            162
  MALE                             57                            179
[1] 2 2
[1] FALSE
D47V8, binary
                                cls
clus                               0   1
  DEL PEAK 25(10Q25.2) MUTATED    91   3
  DEL PEAK 25(10Q25.2) WILD-TYPE 279   6
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(10Q25.2) MUTATED     91    3
  DEL PEAK 25(10Q25.2) WILD-TYPE  279    6
     clus
vv    DEL PEAK 25(10Q25.2) MUTATED DEL PEAK 25(10Q25.2) WILD-TYPE
  NO                            91                            279
  YES                            3                              6
[1] 2 2
[1] FALSE
D47V9, binary
                                cls
clus                               0   1
  DEL PEAK 25(10Q25.2) MUTATED    98   9
  DEL PEAK 25(10Q25.2) WILD-TYPE 284  53
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(10Q25.2) MUTATED     98    9
  DEL PEAK 25(10Q25.2) WILD-TYPE  284   53
                               clus
vv                              DEL PEAK 25(10Q25.2) MUTATED
  COLON ADENOCARCINOMA                                    98
  COLON MUCINOUS ADENOCARCINOMA                            9
                               clus
vv                              DEL PEAK 25(10Q25.2) WILD-TYPE
  COLON ADENOCARCINOMA                                     284
  COLON MUCINOUS ADENOCARCINOMA                             53
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 25(10Q25.2) MUTATED    74   2  11   5
  DEL PEAK 25(10Q25.2) WILD-TYPE 249   2  14  20
D47V10, multiclass
    clus
vv   DEL PEAK 25(10Q25.2) MUTATED DEL PEAK 25(10Q25.2) WILD-TYPE
  R0                           74                            249
  R1                            2                              2
  R2                           11                             14
  RX                            5                             20
[1] 4 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, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 25(10Q25.2) MUTATED                                  0     3
  DEL PEAK 25(10Q25.2) WILD-TYPE                                1     8
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 25(10Q25.2) MUTATED                          15    53
  DEL PEAK 25(10Q25.2) WILD-TYPE                        44   159
D47V12, multiclass
                                  clus
vv                                 DEL PEAK 25(10Q25.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       3
  BLACK OR AFRICAN AMERICAN                                  15
  WHITE                                                      53
                                  clus
vv                                 DEL PEAK 25(10Q25.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         8
  BLACK OR AFRICAN AMERICAN                                    44
  WHITE                                                       159
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V13, binary
                                cls
clus                               0   1
  DEL PEAK 25(10Q25.2) MUTATED     2  67
  DEL PEAK 25(10Q25.2) WILD-TYPE   2 202
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(10Q25.2) MUTATED      2   67
  DEL PEAK 25(10Q25.2) WILD-TYPE    2  202
                        clus
vv                       DEL PEAK 25(10Q25.2) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           67
                        clus
vv                       DEL PEAK 25(10Q25.2) WILD-TYPE
  HISPANIC OR LATINO                                  2
  NOT HISPANIC OR LATINO                            202
[1] 2 2
[1] FALSE

Clustering(48) Variable = DEL PEAK 26(12P13.2) MUTATION ANALYSIS
D48V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 26(12P13.2) MUTATED    41  19
  DEL PEAK 26(12P13.2) WILD-TYPE 294  82
  DEL PEAK 26(12P13.2) MUTATED DEL PEAK 26(12P13.2) WILD-TYPE 
                            60                            376 
  DEL PEAK 26(12P13.2) MUTATED DEL PEAK 26(12P13.2) WILD-TYPE 
                            19                             82 
$`DEL PEAK 26(12P13.2) MUTATED`
TCGA-A6-2677 TCGA-A6-2681 TCGA-AA-3552 TCGA-AA-3688 TCGA-AA-3867 TCGA-AA-3952 
       24.33        45.60        13.02        19.00        24.03         2.01 
TCGA-AA-3972 TCGA-CK-5912 TCGA-NH-A8F7 TCGA-4N-A93T TCGA-A6-2671 TCGA-A6-3807 
       50.99        49.08        17.85         4.80        43.76        34.65 
TCGA-A6-3810 TCGA-A6-5659 TCGA-A6-6652 TCGA-A6-6782 TCGA-A6-A567 TCGA-A6-A5ZU 
       36.53        30.44        24.69        20.28        61.84         9.63 
TCGA-AA-3538 TCGA-AA-3548 TCGA-AA-3660 TCGA-AA-3666 TCGA-AA-3673 TCGA-AA-3858 
       26.01        33.99        78.08         2.01        50.04        31.07 
TCGA-AA-3866 TCGA-AA-A01F TCGA-AA-A01T TCGA-AA-A02E TCGA-AD-6899 TCGA-AD-6901 
       17.03        32.02        33.04         2.96         5.79        22.42 
TCGA-AD-A5EK TCGA-AY-4070 TCGA-AZ-6606 TCGA-CA-5256 TCGA-CA-6715 TCGA-CM-4750 
       16.44        16.31        11.74        12.46        12.59         8.02 
TCGA-CM-5862 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6677 
        5.03        14.04        29.03        15.02        11.01        11.08 
TCGA-CM-6679 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6898 TCGA-D5-6929 TCGA-D5-6932 
       10.06        25.48        15.12         7.53        13.41        11.38 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6807 TCGA-G4-6303 
       13.32        12.59        31.96        11.11        43.04        65.85 
TCGA-G4-6315 TCGA-G4-6317 TCGA-NH-A50U TCGA-QL-A97D TCGA-RU-A8FL TCGA-SS-A7HO 
       61.91        36.00        10.98        21.90        38.70        60.13 

$`DEL PEAK 26(12P13.2) WILD-TYPE`
TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3506 TCGA-AA-3516 
       13.94        14.53        24.16         1.02        58.03        13.02 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 
       24.03        37.05        36.03         8.05        19.07        34.03 
TCGA-AA-3543 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
        0.99        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
        0.92        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3976 TCGA-AA-3979 
       31.07        29.98        12.99        24.00        26.01        24.00 
TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 
       19.07        38.04        21.99        39.06        21.37        15.52 
TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 
       25.08        10.88        75.95       106.75       100.01         1.94 
TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6321 
        5.88        28.21        23.51        63.62        35.93        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-3L-AA1B TCGA-4T-AA8H 
       35.80        26.17        91.79        79.69        15.62        12.66 
TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 
        1.61         9.53        39.45        46.65        43.76        43.43 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2684 
       42.90        42.28        44.91        35.11        16.57        37.05 
TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3809 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 
       37.25        37.02        32.75        32.45        32.91        31.63 
TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 
       29.19        33.53        23.61        22.09        22.06        32.71 
TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 
       29.16        27.09        22.52        24.13         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       25.18        20.61        21.76        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A56B TCGA-AA-3488 TCGA-AA-3489 
       19.66        16.24        24.92        56.25         5.03         7.04 
TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
        3.02         1.02        37.05        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3549 TCGA-AA-3553 
       29.00        29.00        12.99        14.01        21.01        24.00 
TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3664 
       29.95        20.98        13.94        61.02         6.97        54.02 
TCGA-AA-3667 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
       14.01        47.05        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
       37.05         5.03        26.99        10.06        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 
       25.02         1.02        17.98        15.95        38.99        36.95 
TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3864 TCGA-AA-3869 
        0.00        36.03        32.05         0.99        53.00        27.02 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       18.05        31.00         2.01        24.00        33.01        26.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 
       20.98        34.03         2.01        21.99        16.08        13.05 
TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       34.06        25.02        27.02         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        15.02        10.98        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V 
       31.00        38.07         1.02        35.01         1.02         1.02 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       26.01        37.02        51.98        39.98         2.01         5.03 
TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
        0.92        22.03        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6963 TCGA-AD-6965 TCGA-AM-5820 
       12.16        83.24        24.53        27.42        26.47         0.46 
TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
        0.92        14.50        27.09         0.95        33.01         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK 
       21.44        17.82        17.26        17.85        19.33        18.84 
TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 
      109.28        58.39         1.41         5.65        32.94         5.13 
TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       22.36        65.00        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 
       12.10        29.56         5.23         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.39        12.59        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 
       17.56       148.01        85.45        70.16        15.62        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14        82.95         2.01       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-4752 
       20.02        37.02        25.02        26.04        27.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6165 
       15.02        15.02        17.03        15.02        12.00        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6171 TCGA-CM-6674 
       21.99        14.99        12.99        13.02        14.04        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       13.05        11.08        11.01        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 
       19.59        56.09        55.92        20.19        20.42        17.75 
TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       18.25        43.27        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       16.14        15.58        12.39        10.13        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 
        9.04         9.44        11.64        13.35        12.00        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 
      140.38         7.50        44.32       131.51       135.65         7.76 
TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      139.17        14.04        26.47        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6463 
       60.79       117.07        98.24        95.18         8.61        35.74 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6306 
        8.35        82.39        74.56        67.30        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 
       55.04        85.48        39.42        26.43        26.04        13.78 
TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA 
       46.75        74.79        18.18        19.33        19.33         9.93 
TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX 
       15.65        12.79        16.80        42.77        29.46        32.98 
TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-T9-A92H TCGA-WS-AB45 
        8.42        31.30        11.90        70.03 

  DEL PEAK 26(12P13.2) MUTATED DEL PEAK 26(12P13.2) WILD-TYPE 
                          2.01                           0.00 
  DEL PEAK 26(12P13.2) MUTATED DEL PEAK 26(12P13.2) WILD-TYPE 
                         78.08                         148.01 
  DEL PEAK 26(12P13.2) MUTATED DEL PEAK 26(12P13.2) WILD-TYPE 
                         19.64                          22.09 
[1] "2.0 - 78.1 (19.6)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.7"
D48V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 26(12P13.2) MUTATED        10        0        2         9         2
  DEL PEAK 26(12P13.2) WILD-TYPE      64        1       27       123         8
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 26(12P13.2) MUTATED           0         2          1          8
  DEL PEAK 26(12P13.2) WILD-TYPE         1        18          7         51
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 26(12P13.2) MUTATED           10       10         3         0
  DEL PEAK 26(12P13.2) WILD-TYPE         31       35        14         2
D48V3, multiclass
            clus
vv           DEL PEAK 26(12P13.2) MUTATED DEL PEAK 26(12P13.2) WILD-TYPE
  STAGE I                              10                             64
  STAGE IA                              0                              1
  STAGE II                              2                             27
  STAGE IIA                             9                            123
  STAGE IIB                             2                              8
  STAGE IIC                             0                              1
  STAGE III                             2                             18
  STAGE IIIA                            1                              7
  STAGE IIIB                            8                             51
  STAGE IIIC                           10                             31
  STAGE IV                             10                             35
  STAGE IVA                             3                             14
  STAGE IVB                             0                              2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 26(12P13.2) MUTATED     2   9  41   8
  DEL PEAK 26(12P13.2) WILD-TYPE   9  68 264  47
D48V4, multiclass
    clus
vv   DEL PEAK 26(12P13.2) MUTATED DEL PEAK 26(12P13.2) WILD-TYPE
  T1                            2                              9
  T2                            9                             68
  T3                           41                            264
  T4                            8                             47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2
  DEL PEAK 26(12P13.2) MUTATED    27  19  14
  DEL PEAK 26(12P13.2) WILD-TYPE 235  86  68
D48V5, multiclass
    clus
vv   DEL PEAK 26(12P13.2) MUTATED DEL PEAK 26(12P13.2) WILD-TYPE
  N0                           27                            235
  N1                           19                             86
  N2                           14                             68
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V6, binary
                                cls
clus                               0   1
  DEL PEAK 26(12P13.2) MUTATED    36  13
  DEL PEAK 26(12P13.2) WILD-TYPE 292  51
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(12P13.2) MUTATED     36   13
  DEL PEAK 26(12P13.2) WILD-TYPE  292   51
   clus
vv  DEL PEAK 26(12P13.2) MUTATED DEL PEAK 26(12P13.2) WILD-TYPE
  0                           36                            292
  1                           13                             51
[1] 2 2
[1] FALSE
D48V7, binary
                                cls
clus                               0   1
  DEL PEAK 26(12P13.2) MUTATED    30  30
  DEL PEAK 26(12P13.2) WILD-TYPE 183 206
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(12P13.2) MUTATED     30   30
  DEL PEAK 26(12P13.2) WILD-TYPE  183  206
        clus
vv       DEL PEAK 26(12P13.2) MUTATED DEL PEAK 26(12P13.2) WILD-TYPE
  FEMALE                           30                            183
  MALE                             30                            206
[1] 2 2
[1] FALSE
D48V8, binary
                                cls
clus                               0   1
  DEL PEAK 26(12P13.2) MUTATED    54   1
  DEL PEAK 26(12P13.2) WILD-TYPE 316   8
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(12P13.2) MUTATED     54    1
  DEL PEAK 26(12P13.2) WILD-TYPE  316    8
     clus
vv    DEL PEAK 26(12P13.2) MUTATED DEL PEAK 26(12P13.2) WILD-TYPE
  NO                            54                            316
  YES                            1                              8
[1] 2 2
[1] FALSE
D48V9, binary
                                cls
clus                               0   1
  DEL PEAK 26(12P13.2) MUTATED    57   2
  DEL PEAK 26(12P13.2) WILD-TYPE 325  60
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(12P13.2) MUTATED     57    2
  DEL PEAK 26(12P13.2) WILD-TYPE  325   60
                               clus
vv                              DEL PEAK 26(12P13.2) MUTATED
  COLON ADENOCARCINOMA                                    57
  COLON MUCINOUS ADENOCARCINOMA                            2
                               clus
vv                              DEL PEAK 26(12P13.2) WILD-TYPE
  COLON ADENOCARCINOMA                                     325
  COLON MUCINOUS ADENOCARCINOMA                             60
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 26(12P13.2) MUTATED    42   1   4   4
  DEL PEAK 26(12P13.2) WILD-TYPE 281   3  21  21
D48V10, multiclass
    clus
vv   DEL PEAK 26(12P13.2) MUTATED DEL PEAK 26(12P13.2) WILD-TYPE
  R0                           42                            281
  R1                            1                              3
  R2                            4                             21
  RX                            4                             21
[1] 4 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, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 26(12P13.2) MUTATED                                  0     2
  DEL PEAK 26(12P13.2) WILD-TYPE                                1     9
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 26(12P13.2) MUTATED                          11    32
  DEL PEAK 26(12P13.2) WILD-TYPE                        48   180
D48V12, multiclass
                                  clus
vv                                 DEL PEAK 26(12P13.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                  11
  WHITE                                                      32
                                  clus
vv                                 DEL PEAK 26(12P13.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         9
  BLACK OR AFRICAN AMERICAN                                    48
  WHITE                                                       180
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V13, binary
                                cls
clus                               0   1
  DEL PEAK 26(12P13.2) MUTATED     0  40
  DEL PEAK 26(12P13.2) WILD-TYPE   4 229
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(12P13.2) MUTATED      0   40
  DEL PEAK 26(12P13.2) WILD-TYPE    4  229
                        clus
vv                       DEL PEAK 26(12P13.2) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           40
                        clus
vv                       DEL PEAK 26(12P13.2) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            229
[1] 2 2
[1] FALSE

Clustering(49) Variable = DEL PEAK 27(13Q14.13) MUTATION ANALYSIS
D49V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 27(13Q14.13) MUTATED    14   4
  DEL PEAK 27(13Q14.13) WILD-TYPE 321  97
  DEL PEAK 27(13Q14.13) MUTATED DEL PEAK 27(13Q14.13) WILD-TYPE 
                             18                             418 
  DEL PEAK 27(13Q14.13) MUTATED DEL PEAK 27(13Q14.13) WILD-TYPE 
                              4                              97 
$`DEL PEAK 27(13Q14.13) MUTATED`
TCGA-AA-3524 TCGA-AA-3556 TCGA-AZ-4681 TCGA-A6-2685 TCGA-AA-3548 TCGA-AA-3664 
       36.03        23.01       106.75        37.25        33.99        54.02 
TCGA-AA-3875 TCGA-AA-3968 TCGA-AY-6196 TCGA-AZ-4315 TCGA-AZ-6607 TCGA-CA-5797 
       18.05        21.99         0.20        58.39         3.19        12.59 
TCGA-CM-6675 TCGA-DM-A1D8 TCGA-F4-6461 TCGA-F4-6704 TCGA-G4-6626 TCGA-RU-A8FL 
       13.05        12.59        11.11         1.55        46.75        38.70 

$`DEL PEAK 27(13Q14.13) WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 
       24.33        45.60        13.94        14.53        24.16         1.02 
TCGA-AA-3506 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3525 TCGA-AA-3530 
       58.03        13.02        24.03        37.05         8.05        19.07 
TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3560 TCGA-AA-3562 
       34.03         0.99        13.02        17.95        19.99        19.99 
TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 
        6.05         0.92        19.00        36.00        85.05        19.04 
TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 
       19.04        14.93        31.07        24.03        29.98        12.99 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 
       24.00         2.01        50.99        26.01        24.00        19.07 
TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 
       38.04        21.99        39.06        21.37        15.52        25.08 
TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 
       10.88        75.95       100.01         1.94        49.08         5.88 
TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6321 TCGA-G4-6586 
       28.21        23.51        63.62        35.93        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-NH-A8F7 TCGA-3L-AA1B TCGA-4N-A93T 
       26.17        91.79        79.69        17.85        15.62         4.80 
TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2672 
       12.66         1.61         9.53        39.45        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 
       43.76        43.43        42.90        42.28        44.91        35.11 
TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-3810 
       16.57        37.05        37.02        34.65        32.75        36.53 
TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 
       32.45        32.91        31.63        30.44        29.19        33.53 
TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 
       23.61        22.09        22.06        32.71        29.16        27.09 
TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 
       22.52        24.13         8.38        25.08        25.18        20.61 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU 
       20.28        16.24        24.92        61.84        56.25         9.63 
TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 
        5.03         7.04         3.02         1.02        37.05        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
       63.98         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       14.01        21.01        24.00        29.95        20.98        13.94 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       61.02        78.08         6.97         2.01        14.01        50.04 
TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       47.05        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
        5.03        26.99        10.06        35.05         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 
        1.02        17.98        15.95        38.99        36.95        37.02 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3866 
       36.03        32.05         0.99        31.07        53.00        17.03 
TCGA-AA-3869 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       27.02        31.00         2.01        24.00        33.01        26.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       20.98        34.03         2.01        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       25.02        27.02         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N 
       19.00        30.02        34.03        18.05        18.05         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       15.02        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F 
        1.02        26.01        37.02        51.98         2.96        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03         0.92        22.03        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 
       22.42        27.42        26.47        16.44         0.46         0.92 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 
       17.82        17.26        17.85        19.33        18.84       109.28 
TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-4684 
        1.41         5.65        32.94         5.13        22.36        65.00 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 
       62.79        88.21        49.41         6.77        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 
        5.23        11.74        12.69        12.36        12.46        12.39 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        70.16        15.62        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 
       37.02        25.02        26.04         8.02        27.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6676 
       13.02        15.02        14.04        11.01        12.95        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 
       19.59        56.09        55.92        20.19        20.42        17.75 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 
      140.38         7.50        44.32       131.51       135.65         7.76 
TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      139.17        14.04        26.47        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 
       60.79       117.07        98.24        95.18         8.61        31.96 
TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 
       35.74        35.74         6.18        47.87        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       43.04        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 
      133.18         8.35        82.39        74.56        67.30        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        39.42        61.91 
TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6627 TCGA-NH-A50T 
       36.00        26.43        26.04        13.78        74.79        18.18 
TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC 
       10.98        19.33        19.33         9.93        15.65        12.79 
TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 
       16.80        42.77        29.46        32.98         8.42        31.30 
TCGA-QL-A97D TCGA-SS-A7HO TCGA-T9-A92H TCGA-WS-AB45 
       21.90        60.13        11.90        70.03 

  DEL PEAK 27(13Q14.13) MUTATED DEL PEAK 27(13Q14.13) WILD-TYPE 
                            0.2                             0.0 
  DEL PEAK 27(13Q14.13) MUTATED DEL PEAK 27(13Q14.13) WILD-TYPE 
                         106.75                          148.01 
  DEL PEAK 27(13Q14.13) MUTATED DEL PEAK 27(13Q14.13) WILD-TYPE 
                         22.500                          22.045 
[1] "0.2 - 106.8 (22.5)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.1"
D49V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 27(13Q14.13) MUTATED         4        0        2         5         0
  DEL PEAK 27(13Q14.13) WILD-TYPE      70        1       27       127        10
                                 vv
clus                              STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 27(13Q14.13) MUTATED           0         0          0          1
  DEL PEAK 27(13Q14.13) WILD-TYPE         1        20          8         58
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 27(13Q14.13) MUTATED            4        1         0         1
  DEL PEAK 27(13Q14.13) WILD-TYPE         37       44        17         1
D49V3, multiclass
            clus
vv           DEL PEAK 27(13Q14.13) MUTATED DEL PEAK 27(13Q14.13) WILD-TYPE
  STAGE I                                4                              70
  STAGE IA                               0                               1
  STAGE II                               2                              27
  STAGE IIA                              5                             127
  STAGE IIB                              0                              10
  STAGE IIC                              0                               1
  STAGE III                              0                              20
  STAGE IIIA                             0                               8
  STAGE IIIB                             1                              58
  STAGE IIIC                             4                              37
  STAGE IV                               1                              44
  STAGE IVA                              0                              17
  STAGE IVB                              1                               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               T1  T2  T3  T4
  DEL PEAK 27(13Q14.13) MUTATED     1   3  13   2
  DEL PEAK 27(13Q14.13) WILD-TYPE  10  74 292  53
D49V4, multiclass
    clus
vv   DEL PEAK 27(13Q14.13) MUTATED DEL PEAK 27(13Q14.13) WILD-TYPE
  T1                             1                              10
  T2                             3                              74
  T3                            13                             292
  T4                             2                              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"
                                 vv
clus                               N0  N1  N2
  DEL PEAK 27(13Q14.13) MUTATED    11   1   7
  DEL PEAK 27(13Q14.13) WILD-TYPE 251 104  75
D49V5, multiclass
    clus
vv   DEL PEAK 27(13Q14.13) MUTATED DEL PEAK 27(13Q14.13) WILD-TYPE
  N0                            11                             251
  N1                             1                             104
  N2                             7                              75
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V6, binary
                                 cls
clus                                0   1
  DEL PEAK 27(13Q14.13) MUTATED    12   2
  DEL PEAK 27(13Q14.13) WILD-TYPE 316  62
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 27(13Q14.13) MUTATED     12    2
  DEL PEAK 27(13Q14.13) WILD-TYPE  316   62
   clus
vv  DEL PEAK 27(13Q14.13) MUTATED DEL PEAK 27(13Q14.13) WILD-TYPE
  0                            12                             316
  1                             2                              62
[1] 2 2
[1] FALSE
D49V7, binary
                                 cls
clus                                0   1
  DEL PEAK 27(13Q14.13) MUTATED     8  11
  DEL PEAK 27(13Q14.13) WILD-TYPE 205 225
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 27(13Q14.13) MUTATED      8   11
  DEL PEAK 27(13Q14.13) WILD-TYPE  205  225
        clus
vv       DEL PEAK 27(13Q14.13) MUTATED DEL PEAK 27(13Q14.13) WILD-TYPE
  FEMALE                             8                             205
  MALE                              11                             225
[1] 2 2
[1] FALSE
D49V8, binary
                                 cls
clus                                0   1
  DEL PEAK 27(13Q14.13) MUTATED    15   0
  DEL PEAK 27(13Q14.13) WILD-TYPE 355   9
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 27(13Q14.13) MUTATED     15    0
  DEL PEAK 27(13Q14.13) WILD-TYPE  355    9
     clus
vv    DEL PEAK 27(13Q14.13) MUTATED DEL PEAK 27(13Q14.13) WILD-TYPE
  NO                             15                             355
  YES                             0                               9
[1] 2 2
[1] FALSE
D49V9, binary
                                 cls
clus                                0   1
  DEL PEAK 27(13Q14.13) MUTATED    16   2
  DEL PEAK 27(13Q14.13) WILD-TYPE 366  60
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 27(13Q14.13) MUTATED     16    2
  DEL PEAK 27(13Q14.13) WILD-TYPE  366   60
                               clus
vv                              DEL PEAK 27(13Q14.13) MUTATED
  COLON ADENOCARCINOMA                                     16
  COLON MUCINOUS ADENOCARCINOMA                             2
                               clus
vv                              DEL PEAK 27(13Q14.13) WILD-TYPE
  COLON ADENOCARCINOMA                                      366
  COLON MUCINOUS ADENOCARCINOMA                              60
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 27(13Q14.13) MUTATED    16   0   0   1
  DEL PEAK 27(13Q14.13) WILD-TYPE 307   4  25  24
D49V10, multiclass
    clus
vv   DEL PEAK 27(13Q14.13) MUTATED DEL PEAK 27(13Q14.13) WILD-TYPE
  R0                            16                             307
  R1                             0                               4
  R2                             0                              25
  RX                             1                              24
[1] 4 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, continuous
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 27(13Q14.13) MUTATED                                  1     1
  DEL PEAK 27(13Q14.13) WILD-TYPE                                0    10
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 27(13Q14.13) MUTATED                           3     8
  DEL PEAK 27(13Q14.13) WILD-TYPE                        56   204
D49V12, multiclass
                                  clus
vv                                 DEL PEAK 27(13Q14.13) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        1
  BLACK OR AFRICAN AMERICAN                                    3
  WHITE                                                        8
                                  clus
vv                                 DEL PEAK 27(13Q14.13) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               0
  ASIAN                                                         10
  BLACK OR AFRICAN AMERICAN                                     56
  WHITE                                                        204
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V13, binary
                                 cls
clus                                0   1
  DEL PEAK 27(13Q14.13) MUTATED     0  13
  DEL PEAK 27(13Q14.13) WILD-TYPE   4 256
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 27(13Q14.13) MUTATED      0   13
  DEL PEAK 27(13Q14.13) WILD-TYPE    4  256
                        clus
vv                       DEL PEAK 27(13Q14.13) MUTATED
  HISPANIC OR LATINO                                 0
  NOT HISPANIC OR LATINO                            13
                        clus
vv                       DEL PEAK 27(13Q14.13) WILD-TYPE
  HISPANIC OR LATINO                                   4
  NOT HISPANIC OR LATINO                             256
[1] 2 2
[1] FALSE

Clustering(50) Variable = DEL PEAK 28(14Q31.1) MUTATION ANALYSIS
D50V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 28(14Q31.1) MUTATED   112  33
  DEL PEAK 28(14Q31.1) WILD-TYPE 223  68
  DEL PEAK 28(14Q31.1) MUTATED DEL PEAK 28(14Q31.1) WILD-TYPE 
                           145                            291 
  DEL PEAK 28(14Q31.1) MUTATED DEL PEAK 28(14Q31.1) WILD-TYPE 
                            33                             68 
$`DEL PEAK 28(14Q31.1) MUTATED`
TCGA-A6-2681 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3520 TCGA-AA-3530 TCGA-AA-3531 
       45.60        14.53        24.16        24.03        19.07        34.03 
TCGA-AA-3552 TCGA-AA-3556 TCGA-AA-3562 TCGA-AA-3688 TCGA-AA-3697 TCGA-AA-3860 
       13.02        23.01        19.99        19.00        85.05        31.07 
TCGA-AA-3867 TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 
       24.03        12.99         2.01        50.99        26.01        24.00 
TCGA-AA-A00L TCGA-AA-A00Z TCGA-AZ-6608 TCGA-CK-5912 TCGA-G4-6625 TCGA-NH-A8F7 
       38.04        21.99         1.94        49.08        91.79        17.85 
TCGA-4N-A93T TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2678 TCGA-A6-2680 TCGA-A6-2683 
        4.80        39.45        43.76        42.28        35.11        16.57 
TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5662 
       34.65        36.53        32.45        32.91        30.44        23.61 
TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6142 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 
       22.52        24.13        25.08        20.61        21.76        24.69 
TCGA-A6-6654 TCGA-A6-6782 TCGA-A6-A567 TCGA-AA-3488 TCGA-AA-3511 TCGA-AA-3517 
       23.87        20.28        61.84         5.03         6.97        38.99 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3542 TCGA-AA-3561 TCGA-AA-3666 TCGA-AA-3667 
        9.07        19.07        12.99        13.94         2.01        14.01 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3685 TCGA-AA-3811 TCGA-AA-3819 
       50.04        47.01        15.02        37.05        10.06        25.02 
TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3846 TCGA-AA-3866 TCGA-AA-3875 TCGA-AA-3930 
       36.95        37.02        17.03        17.03        18.05         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3975 TCGA-AA-3989 TCGA-AA-A00O TCGA-AA-A00Q 
       21.99        16.08        34.06         7.96        27.02        42.02 
TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01F TCGA-AA-A01K TCGA-AA-A01T TCGA-AA-A01X 
       14.99        15.02        32.02        31.00        33.04        26.01 
TCGA-AA-A02E TCGA-AA-A02H TCGA-AA-A03J TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
        2.96         2.01        40.96         5.79        22.42        27.42 
TCGA-AD-A5EK TCGA-AU-3779 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-A69D 
       16.44        14.50         0.95        33.01         0.20        17.85 
TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4682 TCGA-AZ-6603 
       18.84       109.28         1.41         5.65        22.36        29.56 
TCGA-AZ-6605 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-6715 TCGA-CA-6716 TCGA-CK-6748 
        5.23        12.36        12.46        12.59        12.20         2.01 
TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-5868 TCGA-CM-6163 TCGA-CM-6164 
       25.02         8.02        27.02        17.03        14.04        29.03 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6679 TCGA-D5-5537 
       13.02        15.02        13.05        11.08        10.06        45.40 
TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6924 
       54.61        56.09        18.25        25.48        15.12        14.30 
TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A0XF TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1DA 
       13.41        11.38        38.20        13.32       140.38         7.50 
TCGA-DM-A1HA TCGA-DM-A288 TCGA-DM-A28E TCGA-DM-A28F TCGA-F4-6460 TCGA-F4-6806 
      131.51        14.04       119.93        35.97        31.96        41.42 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6315 
       33.67        13.25         0.53         8.35        82.39        61.91 
TCGA-NH-A50T TCGA-NH-A50V TCGA-NH-A6GB TCGA-NH-A8F8 TCGA-RU-A8FL TCGA-SS-A7HO 
       18.18        19.33        15.65        16.80        38.70        60.13 
TCGA-T9-A92H 
       11.90 

$`DEL PEAK 28(14Q31.1) WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2682 TCGA-AA-3496 TCGA-AA-3506 TCGA-AA-3516 TCGA-AA-3522 
       24.33        13.94         1.02        58.03        13.02        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3543 TCGA-AA-3554 TCGA-AA-3560 TCGA-AA-3662 
       36.03         8.05         0.99        17.95        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3692 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3870 
        0.92        36.00        19.04        19.04        14.93        29.98 
TCGA-AA-3950 TCGA-AA-3986 TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 
       24.00        19.07        39.06        21.37        15.52        25.08 
TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-DM-A285 TCGA-G4-6294 
       10.88        75.95       106.75       100.01         5.88        28.21 
TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       23.51        63.62        35.93        22.09        35.80        26.17 
TCGA-G4-6628 TCGA-3L-AA1B TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-A6-2672 
       79.69        15.62        12.66         1.61         9.53        46.65 
TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2679 TCGA-A6-2684 TCGA-A6-2685 
       43.76        43.43        42.90        44.91        37.05        37.25 
TCGA-A6-2686 TCGA-A6-3809 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5664 
       37.02        32.75        31.63        29.19        33.53        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6141 TCGA-A6-6648 
       22.06        32.71        29.16        27.09         8.38        25.18 
TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A56B 
       24.39        20.12        19.66        16.24        24.92        56.25 
TCGA-A6-A5ZU TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 
        9.63         7.04         3.02         1.02        37.05        35.01 
TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3518 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
       63.98         1.02         1.02         0.00        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       26.01        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3675 
       20.98        61.02        78.08         6.97        54.02        47.05 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3818 
       11.01         5.98         5.03        26.99        35.05         0.99 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3845 TCGA-AA-3848 
        1.02        17.98        15.95        38.99         0.00        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3877 TCGA-AA-3941 TCGA-AA-3947 
       31.07        53.00        27.02        31.00        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3973 TCGA-AA-3977 
       26.01        20.98        34.03         2.01        13.05        25.02 
TCGA-AA-3982 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
       27.02        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00R TCGA-AA-A00U 
       34.03        18.05        18.05         4.01         0.99        17.03 
TCGA-AA-A010 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P 
       34.98        15.02        10.98        12.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A029 
        1.02        35.01         1.02         1.02        37.02        51.98 
TCGA-AA-A02F TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y 
       39.98         5.03         0.92        22.03        41.00        39.98 
TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6965 TCGA-AM-5820 
       18.05        12.16        83.24        24.53        26.47         0.46 
TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L 
        0.92        27.09        16.31        21.44        17.82        17.26 
TCGA-AY-A71X TCGA-AZ-4315 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4684 TCGA-AZ-5403 
       19.33        58.39        32.94         5.13        65.00        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6606 TCGA-AZ-6607 
       88.21        49.41         6.77        12.10        11.74         3.19 
TCGA-CA-5254 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.69        12.39        12.59        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 
       17.56       148.01        85.45        70.16        15.62        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.99        21.14        82.95       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        26.04        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
       15.02        12.00        16.04        21.99        14.99        12.99 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6680 
       14.04        11.01        12.95        11.08        11.01        12.03 
TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6534 
       19.59        55.92        20.19        20.42        17.75        43.27 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6927 
        7.53        12.39        10.13        12.43         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       11.64        13.35        12.00        10.26       119.70        24.43 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D8 TCGA-DM-A1DB TCGA-DM-A1HB 
      130.65        92.75        49.91        12.59        44.32       135.65 
TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28G TCGA-DM-A28H 
        7.76       139.17        26.47        81.37        60.79       117.07 
TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 
       98.24        95.18         8.61        11.11        35.74        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6807 TCGA-F4-6855 
        6.18        47.87         1.55        34.42        43.04        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 
       35.31       133.18        74.56        67.30        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6317 TCGA-G4-6320 
       44.68        55.04        85.48        39.42        36.00        26.43 
TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50U TCGA-NH-A5IV 
       26.04        13.78        46.75        74.79        10.98        19.33 
TCGA-NH-A6GA TCGA-NH-A6GC TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 
        9.93        12.79        42.77        29.46        32.98         8.42 
TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-WS-AB45 
       31.30        21.90        70.03 

  DEL PEAK 28(14Q31.1) MUTATED DEL PEAK 28(14Q31.1) WILD-TYPE 
                           0.2                            0.0 
  DEL PEAK 28(14Q31.1) MUTATED DEL PEAK 28(14Q31.1) WILD-TYPE 
                        140.38                         148.01 
  DEL PEAK 28(14Q31.1) MUTATED DEL PEAK 28(14Q31.1) WILD-TYPE 
                         21.76                          22.09 
[1] "0.2 - 140.4 (21.8)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.1"
D50V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 28(14Q31.1) MUTATED        21        0        8        38         2
  DEL PEAK 28(14Q31.1) WILD-TYPE      53        1       21        94         8
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 28(14Q31.1) MUTATED           0         8          4         19
  DEL PEAK 28(14Q31.1) WILD-TYPE         1        12          4         40
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 28(14Q31.1) MUTATED           14       20        10         1
  DEL PEAK 28(14Q31.1) WILD-TYPE         27       25         7         1
D50V3, multiclass
            clus
vv           DEL PEAK 28(14Q31.1) MUTATED DEL PEAK 28(14Q31.1) WILD-TYPE
  STAGE I                              21                             53
  STAGE IA                              0                              1
  STAGE II                              8                             21
  STAGE IIA                            38                             94
  STAGE IIB                             2                              8
  STAGE IIC                             0                              1
  STAGE III                             8                             12
  STAGE IIIA                            4                              4
  STAGE IIIB                           19                             40
  STAGE IIIC                           14                             27
  STAGE IV                             20                             25
  STAGE IVA                            10                              7
  STAGE IVB                             1                              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 28(14Q31.1) MUTATED     6  22 105  16
  DEL PEAK 28(14Q31.1) WILD-TYPE   5  55 200  39
D50V4, multiclass
    clus
vv   DEL PEAK 28(14Q31.1) MUTATED DEL PEAK 28(14Q31.1) WILD-TYPE
  T1                            6                              5
  T2                           22                             55
  T3                          105                            200
  T4                           16                             39
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2
  DEL PEAK 28(14Q31.1) MUTATED    74  42  33
  DEL PEAK 28(14Q31.1) WILD-TYPE 188  63  49
D50V5, multiclass
    clus
vv   DEL PEAK 28(14Q31.1) MUTATED DEL PEAK 28(14Q31.1) WILD-TYPE
  N0                           74                            188
  N1                           42                             63
  N2                           33                             49
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V6, binary
                                cls
clus                               0   1
  DEL PEAK 28(14Q31.1) MUTATED   102  31
  DEL PEAK 28(14Q31.1) WILD-TYPE 226  33
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 28(14Q31.1) MUTATED    102   31
  DEL PEAK 28(14Q31.1) WILD-TYPE  226   33
   clus
vv  DEL PEAK 28(14Q31.1) MUTATED DEL PEAK 28(14Q31.1) WILD-TYPE
  0                          102                            226
  1                           31                             33
[1] 2 2
[1] FALSE
D50V7, binary
                                cls
clus                               0   1
  DEL PEAK 28(14Q31.1) MUTATED    66  83
  DEL PEAK 28(14Q31.1) WILD-TYPE 147 153
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 28(14Q31.1) MUTATED     66   83
  DEL PEAK 28(14Q31.1) WILD-TYPE  147  153
        clus
vv       DEL PEAK 28(14Q31.1) MUTATED DEL PEAK 28(14Q31.1) WILD-TYPE
  FEMALE                           66                            147
  MALE                             83                            153
[1] 2 2
[1] FALSE
D50V8, binary
                                cls
clus                               0   1
  DEL PEAK 28(14Q31.1) MUTATED   129   2
  DEL PEAK 28(14Q31.1) WILD-TYPE 241   7
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 28(14Q31.1) MUTATED    129    2
  DEL PEAK 28(14Q31.1) WILD-TYPE  241    7
     clus
vv    DEL PEAK 28(14Q31.1) MUTATED DEL PEAK 28(14Q31.1) WILD-TYPE
  NO                           129                            241
  YES                            2                              7
[1] 2 2
[1] FALSE
D50V9, binary
                                cls
clus                               0   1
  DEL PEAK 28(14Q31.1) MUTATED   141   4
  DEL PEAK 28(14Q31.1) WILD-TYPE 241  58
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 28(14Q31.1) MUTATED    141    4
  DEL PEAK 28(14Q31.1) WILD-TYPE  241   58
                               clus
vv                              DEL PEAK 28(14Q31.1) MUTATED
  COLON ADENOCARCINOMA                                   141
  COLON MUCINOUS ADENOCARCINOMA                            4
                               clus
vv                              DEL PEAK 28(14Q31.1) WILD-TYPE
  COLON ADENOCARCINOMA                                     241
  COLON MUCINOUS ADENOCARCINOMA                             58
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 28(14Q31.1) MUTATED   101   0  11   8
  DEL PEAK 28(14Q31.1) WILD-TYPE 222   4  14  17
D50V10, multiclass
    clus
vv   DEL PEAK 28(14Q31.1) MUTATED DEL PEAK 28(14Q31.1) WILD-TYPE
  R0                          101                            222
  R1                            0                              4
  R2                           11                             14
  RX                            8                             17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 28(14Q31.1) MUTATED                                  0     4
  DEL PEAK 28(14Q31.1) WILD-TYPE                                1     7
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 28(14Q31.1) MUTATED                          20    68
  DEL PEAK 28(14Q31.1) WILD-TYPE                        39   144
D50V12, multiclass
                                  clus
vv                                 DEL PEAK 28(14Q31.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       4
  BLACK OR AFRICAN AMERICAN                                  20
  WHITE                                                      68
                                  clus
vv                                 DEL PEAK 28(14Q31.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         7
  BLACK OR AFRICAN AMERICAN                                    39
  WHITE                                                       144
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V13, binary
                                cls
clus                               0   1
  DEL PEAK 28(14Q31.1) MUTATED     1  86
  DEL PEAK 28(14Q31.1) WILD-TYPE   3 183
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 28(14Q31.1) MUTATED      1   86
  DEL PEAK 28(14Q31.1) WILD-TYPE    3  183
                        clus
vv                       DEL PEAK 28(14Q31.1) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           86
                        clus
vv                       DEL PEAK 28(14Q31.1) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            183
[1] 2 2
[1] FALSE

Clustering(51) Variable = DEL PEAK 29(15Q11.2) MUTATION ANALYSIS
D51V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 29(15Q11.2) MUTATED   132  38
  DEL PEAK 29(15Q11.2) WILD-TYPE 203  63
  DEL PEAK 29(15Q11.2) MUTATED DEL PEAK 29(15Q11.2) WILD-TYPE 
                           170                            266 
  DEL PEAK 29(15Q11.2) MUTATED DEL PEAK 29(15Q11.2) WILD-TYPE 
                            38                             63 
$`DEL PEAK 29(15Q11.2) MUTATED`
TCGA-A6-2677 TCGA-A6-2681 TCGA-AA-3522 TCGA-AA-3552 TCGA-AA-3556 TCGA-AA-3560 
       24.33        45.60        37.05        13.02        23.01        19.99 
TCGA-AA-3562 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3867 TCGA-AA-3870 
       19.99        19.00        36.00        85.05        24.03        29.98 
TCGA-AA-3939 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AZ-4681 TCGA-CK-5912 
       12.99        50.99        26.01        24.00       106.75        49.08 
TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6310 TCGA-G4-6625 TCGA-4N-A93T TCGA-5M-AAT4 
        5.88        28.21        63.62        91.79         4.80         1.61 
TCGA-5M-AATE TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2683 
       39.45        43.76        43.43        42.28        44.91        16.57 
TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 
       34.65        36.53        32.45        32.91        30.44        29.19 
TCGA-A6-5667 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6780 
       29.16        22.52        25.08        20.61        21.76        20.12 
TCGA-A6-6782 TCGA-A6-A567 TCGA-A6-A56B TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3494 
       20.28        61.84        56.25         5.03         7.04         1.02 
TCGA-AA-3511 TCGA-AA-3532 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
        6.97        29.00        12.99        14.01        33.99        21.01 
TCGA-AA-3553 TCGA-AA-3666 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3685 TCGA-AA-3821 
       24.00         2.01        50.04        47.01        37.05         1.02 
TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3854 
       38.99        36.95        37.02        17.03        10.06        36.03 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3966 TCGA-AA-3968 
        0.99        31.07        17.03        27.02         2.01        21.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3982 TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00Q 
       13.05        34.06        27.02        19.00        34.03        42.02 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01K 
       17.03        14.99        15.02        15.02        32.02        31.00 
TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A02E TCGA-AA-A02W TCGA-AD-6899 TCGA-AD-6901 
       33.04        26.01         2.96        41.00         5.79        22.42 
TCGA-AD-6963 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 
       27.42        16.44         0.46        14.50        16.31         0.95 
TCGA-AY-5543 TCGA-AY-A69D TCGA-AY-A8YK TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 
       33.01        17.85        18.84        65.00        62.79        88.21 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-CA-5256 TCGA-CA-6716 TCGA-CA-6719 
       29.56         5.23         3.19        12.46        12.20        14.30 
TCGA-CK-4948 TCGA-CK-6748 TCGA-CM-4747 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 
      148.01         2.01        25.02        27.02        13.02        29.06 
TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
        5.03        15.02        17.03        14.04        29.03        16.04 
TCGA-CM-6170 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       15.02        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5538 TCGA-D5-6529 TCGA-D5-6531 TCGA-D5-6533 TCGA-D5-6535 
       12.03        54.61        20.19        17.75        25.48        15.12 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6926 TCGA-D5-6932 
       17.13        12.49         7.53        10.13         9.04        11.38 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
      130.65        92.75        13.32        12.59       140.38         7.50 
TCGA-DM-A1HA TCGA-DM-A288 TCGA-DM-A28F TCGA-DM-A28M TCGA-F4-6460 TCGA-F4-6703 
      131.51        14.04        35.97        95.18        31.96        47.87 
TCGA-F4-6704 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
        1.55        43.04        33.67        13.25         0.53        47.41 
TCGA-G4-6295 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6307 TCGA-G4-6315 TCGA-G4-6317 
        8.35        67.30        65.85        55.04        61.91        36.00 
TCGA-G4-6626 TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A6GC TCGA-QG-A5YW TCGA-QL-A97D 
       46.75        10.98        19.33        12.79        29.46        21.90 
TCGA-RU-A8FL TCGA-T9-A92H 
       38.70        11.90 

$`DEL PEAK 29(15Q11.2) WILD-TYPE`
TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3506 TCGA-AA-3516 
       13.94        14.53        24.16         1.02        58.03        13.02 
TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       24.03        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3554 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       17.95         6.05         0.92        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       31.07        24.00         2.01        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 
       39.06        21.37        15.52        25.08        10.88        75.95 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-G4-6298 TCGA-G4-6314 TCGA-G4-6321 TCGA-G4-6586 
      100.01         1.94        23.51        35.93        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6628 TCGA-NH-A8F7 TCGA-3L-AA1B TCGA-4T-AA8H TCGA-5M-AAT6 
       26.17        79.69        17.85        15.62        12.66         9.53 
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2680 TCGA-A6-2684 TCGA-A6-2685 
       43.76        46.65        42.90        35.11        37.05        37.25 
TCGA-A6-2686 TCGA-A6-3809 TCGA-A6-5657 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       37.02        32.75        31.63        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6648 
       22.06        32.71        27.09        24.13         8.38        25.18 
TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 
       24.69        24.39        23.87        19.66        16.24        24.92 
TCGA-A6-A5ZU TCGA-AA-3492 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3514 
        9.63         3.02        37.05        35.01        63.98         1.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3534 
       38.99         1.02         9.07        19.07         0.00        29.00 
TCGA-AA-3538 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       26.01        29.95        20.98        13.94        61.02        78.08 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3675 TCGA-AA-3679 TCGA-AA-3680 
        6.97        54.02        14.01        47.05        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
        5.98         5.03        26.99        10.06        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3845 TCGA-AA-3850 TCGA-AA-3851 
       25.02        17.98        15.95         0.00         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3855 TCGA-AA-3864 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
        0.00        32.05        53.00        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3971 
       24.00        33.01        26.01        20.98        34.03        16.08 
TCGA-AA-3977 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00E 
       25.02         7.96        27.02        13.94        38.04        30.02 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A010 
       18.05        18.05         4.01        27.02         0.99        34.98 
TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       10.98        12.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
        1.02         1.02        37.02        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
        5.03         0.92        22.03        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6965 TCGA-AM-5821 TCGA-AU-6004 
       12.16        83.24        24.53        26.47         0.92        27.09 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A71X TCGA-AZ-4308 
        0.20        21.44        17.82        17.26        19.33       109.28 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 
       58.39         1.41         5.65        32.94         5.13        22.36 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6606 TCGA-CA-5254 TCGA-CA-5255 
       49.41         6.77        12.10        11.74        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 
       12.39        12.59        12.59        12.76        10.06        17.56 
TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        70.16        15.62        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4748 
       82.95       124.27        23.05        20.02        37.02        26.04 
TCGA-CM-4750 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
        8.02        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5863 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
       15.02        15.02        12.00        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-D5-5537 TCGA-D5-5539 
       13.02        14.04        11.01        12.95        45.40        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6536 
       56.09        55.92        20.42        18.25        43.27        17.85 
TCGA-D5-6537 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6923 TCGA-D5-6924 
        4.80        16.14        15.58        12.39        12.43        14.30 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 
        9.44        11.64        13.41        13.35        12.00        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D6 TCGA-DM-A1DB TCGA-DM-A1HB 
      119.70        24.43        38.20        49.91        44.32       135.65 
TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G 
        7.76       139.17        26.47        81.37       119.93        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 
      117.07        98.24         8.61        11.11        35.74        35.74 
TCGA-F4-6570 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6297 
        6.18        34.42        41.42        35.31       133.18        82.39 
TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6320 
       74.56        53.62        44.68        85.48        39.42        26.43 
TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A5IV TCGA-NH-A6GA 
       26.04        13.78        74.79        18.18        19.33         9.93 
TCGA-NH-A6GB TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 
       15.65        16.80        42.77        32.98         8.42        31.30 
TCGA-SS-A7HO TCGA-WS-AB45 
       60.13        70.03 

  DEL PEAK 29(15Q11.2) MUTATED DEL PEAK 29(15Q11.2) WILD-TYPE 
                          0.46                           0.00 
  DEL PEAK 29(15Q11.2) MUTATED DEL PEAK 29(15Q11.2) WILD-TYPE 
                        148.01                         139.17 
  DEL PEAK 29(15Q11.2) MUTATED DEL PEAK 29(15Q11.2) WILD-TYPE 
                         22.47                          22.03 
[1] "0.5 - 148.0 (22.5)" "0.0 - 139.2 (22.0)"
[1] "hr=" "1.1"
D51V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 29(15Q11.2) MUTATED        28        0        8        42         2
  DEL PEAK 29(15Q11.2) WILD-TYPE      46        1       21        90         8
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 29(15Q11.2) MUTATED           0         6          5         23
  DEL PEAK 29(15Q11.2) WILD-TYPE         1        14          3         36
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 29(15Q11.2) MUTATED           20       23        11         2
  DEL PEAK 29(15Q11.2) WILD-TYPE         21       22         6         0
D51V3, multiclass
            clus
vv           DEL PEAK 29(15Q11.2) MUTATED DEL PEAK 29(15Q11.2) WILD-TYPE
  STAGE I                              28                             46
  STAGE IA                              0                              1
  STAGE II                              8                             21
  STAGE IIA                            42                             90
  STAGE IIB                             2                              8
  STAGE IIC                             0                              1
  STAGE III                             6                             14
  STAGE IIIA                            5                              3
  STAGE IIIB                           23                             36
  STAGE IIIC                           20                             21
  STAGE IV                             23                             22
  STAGE IVA                            11                              6
  STAGE IVB                             2                              0
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 29(15Q11.2) MUTATED     5  30 120  21
  DEL PEAK 29(15Q11.2) WILD-TYPE   6  47 185  34
D51V4, multiclass
    clus
vv   DEL PEAK 29(15Q11.2) MUTATED DEL PEAK 29(15Q11.2) WILD-TYPE
  T1                            5                              6
  T2                           30                             47
  T3                          120                            185
  T4                           21                             34
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2
  DEL PEAK 29(15Q11.2) MUTATED    88  49  39
  DEL PEAK 29(15Q11.2) WILD-TYPE 174  56  43
D51V5, multiclass
    clus
vv   DEL PEAK 29(15Q11.2) MUTATED DEL PEAK 29(15Q11.2) WILD-TYPE
  N0                           88                            174
  N1                           49                             56
  N2                           39                             43
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V6, binary
                                cls
clus                               0   1
  DEL PEAK 29(15Q11.2) MUTATED   118  36
  DEL PEAK 29(15Q11.2) WILD-TYPE 210  28
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(15Q11.2) MUTATED    118   36
  DEL PEAK 29(15Q11.2) WILD-TYPE  210   28
   clus
vv  DEL PEAK 29(15Q11.2) MUTATED DEL PEAK 29(15Q11.2) WILD-TYPE
  0                          118                            210
  1                           36                             28
[1] 2 2
[1] FALSE
D51V7, binary
                                cls
clus                               0   1
  DEL PEAK 29(15Q11.2) MUTATED    80  96
  DEL PEAK 29(15Q11.2) WILD-TYPE 133 140
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(15Q11.2) MUTATED     80   96
  DEL PEAK 29(15Q11.2) WILD-TYPE  133  140
        clus
vv       DEL PEAK 29(15Q11.2) MUTATED DEL PEAK 29(15Q11.2) WILD-TYPE
  FEMALE                           80                            133
  MALE                             96                            140
[1] 2 2
[1] FALSE
D51V8, binary
                                cls
clus                               0   1
  DEL PEAK 29(15Q11.2) MUTATED   146   4
  DEL PEAK 29(15Q11.2) WILD-TYPE 224   5
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(15Q11.2) MUTATED    146    4
  DEL PEAK 29(15Q11.2) WILD-TYPE  224    5
     clus
vv    DEL PEAK 29(15Q11.2) MUTATED DEL PEAK 29(15Q11.2) WILD-TYPE
  NO                           146                            224
  YES                            4                              5
[1] 2 2
[1] FALSE
D51V9, binary
                                cls
clus                               0   1
  DEL PEAK 29(15Q11.2) MUTATED   157  16
  DEL PEAK 29(15Q11.2) WILD-TYPE 225  46
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(15Q11.2) MUTATED    157   16
  DEL PEAK 29(15Q11.2) WILD-TYPE  225   46
                               clus
vv                              DEL PEAK 29(15Q11.2) MUTATED
  COLON ADENOCARCINOMA                                   157
  COLON MUCINOUS ADENOCARCINOMA                           16
                               clus
vv                              DEL PEAK 29(15Q11.2) WILD-TYPE
  COLON ADENOCARCINOMA                                     225
  COLON MUCINOUS ADENOCARCINOMA                             46
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 29(15Q11.2) MUTATED   123   1  12   7
  DEL PEAK 29(15Q11.2) WILD-TYPE 200   3  13  18
D51V10, multiclass
    clus
vv   DEL PEAK 29(15Q11.2) MUTATED DEL PEAK 29(15Q11.2) WILD-TYPE
  R0                          123                            200
  R1                            1                              3
  R2                           12                             13
  RX                            7                             18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 29(15Q11.2) MUTATED                                  1     3
  DEL PEAK 29(15Q11.2) WILD-TYPE                                0     8
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 29(15Q11.2) MUTATED                          21    89
  DEL PEAK 29(15Q11.2) WILD-TYPE                        38   123
D51V12, multiclass
                                  clus
vv                                 DEL PEAK 29(15Q11.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       3
  BLACK OR AFRICAN AMERICAN                                  21
  WHITE                                                      89
                                  clus
vv                                 DEL PEAK 29(15Q11.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         8
  BLACK OR AFRICAN AMERICAN                                    38
  WHITE                                                       123
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V13, binary
                                cls
clus                               0   1
  DEL PEAK 29(15Q11.2) MUTATED     2 106
  DEL PEAK 29(15Q11.2) WILD-TYPE   2 163
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(15Q11.2) MUTATED      2  106
  DEL PEAK 29(15Q11.2) WILD-TYPE    2  163
                        clus
vv                       DEL PEAK 29(15Q11.2) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                          106
                        clus
vv                       DEL PEAK 29(15Q11.2) WILD-TYPE
  HISPANIC OR LATINO                                  2
  NOT HISPANIC OR LATINO                            163
[1] 2 2
[1] FALSE

Clustering(52) Variable = DEL PEAK 30(15Q15.2) MUTATION ANALYSIS
D52V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 30(15Q15.2) MUTATED   130  36
  DEL PEAK 30(15Q15.2) WILD-TYPE 205  65
  DEL PEAK 30(15Q15.2) MUTATED DEL PEAK 30(15Q15.2) WILD-TYPE 
                           166                            270 
  DEL PEAK 30(15Q15.2) MUTATED DEL PEAK 30(15Q15.2) WILD-TYPE 
                            36                             65 
$`DEL PEAK 30(15Q15.2) MUTATED`
TCGA-A6-2677 TCGA-A6-2681 TCGA-AA-3522 TCGA-AA-3552 TCGA-AA-3556 TCGA-AA-3560 
       24.33        45.60        37.05        13.02        23.01        19.99 
TCGA-AA-3562 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3867 TCGA-AA-3870 
       19.99        19.00        36.00        85.05        24.03        29.98 
TCGA-AA-3939 TCGA-AA-3972 TCGA-AA-3979 TCGA-AZ-4681 TCGA-CK-5912 TCGA-DM-A285 
       12.99        50.99        24.00       106.75        49.08         5.88 
TCGA-G4-6294 TCGA-G4-6310 TCGA-G4-6625 TCGA-3L-AA1B TCGA-4N-A93T TCGA-5M-AAT4 
       28.21        63.62        91.79        15.62         4.80         1.61 
TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2678 TCGA-A6-2679 
       39.45        43.76        43.76        43.43        42.28        44.91 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5659 
       16.57        34.65        36.53        32.45        32.91        30.44 
TCGA-A6-5660 TCGA-A6-5667 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6650 TCGA-A6-6651 
       29.19        29.16        22.52        25.08        20.61        21.76 
TCGA-A6-6780 TCGA-A6-6782 TCGA-A6-A567 TCGA-A6-A56B TCGA-AA-3488 TCGA-AA-3489 
       20.12        20.28        61.84        56.25         5.03         7.04 
TCGA-AA-3494 TCGA-AA-3511 TCGA-AA-3519 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 
        1.02         6.97         9.07        12.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3666 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3680 
       21.01        24.00         2.01        50.04        47.01        11.01 
TCGA-AA-3685 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3846 TCGA-AA-3848 
       37.05        38.99        36.95        37.02        17.03        10.06 
TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3866 TCGA-AA-3966 
       33.07        36.03         0.99        31.07        17.03         2.01 
TCGA-AA-3968 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3982 TCGA-AA-A00D TCGA-AA-A00F 
       21.99        13.05        34.06        27.02        19.00        34.03 
TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01K 
       42.02        17.03        14.99        15.02        15.02        31.00 
TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A02E TCGA-AA-A02W TCGA-AD-6899 TCGA-AD-6901 
       33.04        26.01         2.96        41.00         5.79        22.42 
TCGA-AD-6963 TCGA-AD-A5EK TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       27.42        16.44        14.50        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4684 TCGA-AZ-5403 
        0.20        17.85        19.33        18.84        65.00        62.79 
TCGA-AZ-5407 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-CA-5256 TCGA-CA-6716 
       88.21        29.56         5.23         3.19        12.46        12.20 
TCGA-CK-4948 TCGA-CK-6748 TCGA-CM-4747 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 
      148.01         2.01        25.02        27.02        13.02        29.06 
TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
        5.03        15.02        17.03        14.04        29.03        16.04 
TCGA-CM-6170 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       15.02        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5538 TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6898 
       12.03        54.61        20.19        25.48        15.12         7.53 
TCGA-D5-6922 TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.13         9.04        13.41        11.38       130.65        92.75 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1HA TCGA-DM-A28F TCGA-DM-A28M 
       13.32        12.59       140.38       131.51        35.97        95.18 
TCGA-F4-6460 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
       31.96        47.87         1.55        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6295 TCGA-G4-6303 TCGA-G4-6307 TCGA-G4-6315 
        0.53        47.41         8.35        65.85        55.04        61.91 
TCGA-G4-6317 TCGA-G4-6322 TCGA-G4-6626 TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A6GC 
       36.00        26.04        46.75        10.98        19.33        12.79 
TCGA-QG-A5YW TCGA-QL-A97D TCGA-RU-A8FL TCGA-T9-A92H 
       29.46        21.90        38.70        11.90 

$`DEL PEAK 30(15Q15.2) WILD-TYPE`
TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3506 TCGA-AA-3516 
       13.94        14.53        24.16         1.02        58.03        13.02 
TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       24.03        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3554 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       17.95         6.05         0.92        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3976 TCGA-AA-3986 TCGA-AA-A00L 
       31.07        24.00         2.01        26.01        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4313 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-G4-6298 TCGA-G4-6314 TCGA-G4-6321 
       75.95       100.01         1.94        23.51        35.93        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 TCGA-NH-A8F7 TCGA-4T-AA8H TCGA-5M-AAT6 
       35.80        26.17        79.69        17.85        12.66         9.53 
TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2680 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 
       46.65        42.90        35.11        37.05        37.25        37.02 
TCGA-A6-3809 TCGA-A6-5657 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       32.75        31.63        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6652 
       32.71        27.09        24.13         8.38        25.18        24.69 
TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A5ZU 
       24.39        23.87        19.66        16.24        24.92         9.63 
TCGA-AA-3492 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3517 
        3.02        37.05        35.01        63.98         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        1.02        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         6.97 
TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3675 TCGA-AA-3679 TCGA-AA-3681 TCGA-AA-3696 
       54.02        14.01        47.05        15.02         5.98         5.03 
TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       26.99        10.06        35.05         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3845 TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3855 
       17.98        15.95         0.00         0.00         0.00        32.05 
TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       53.00        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3977 
       33.01        26.01        20.98        34.03        16.08        25.02 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00J 
        7.96        27.02        13.94        38.04        30.02        18.05 
TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A010 TCGA-AA-A01D 
       18.05         4.01        27.02         0.99        34.98        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       32.02        12.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
        1.02         1.02        37.02        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
        5.03         0.92        22.03        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6965 TCGA-AM-5820 TCGA-AM-5821 
       12.16        83.24        24.53        26.47         0.46         0.92 
TCGA-AU-6004 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AZ-4308 TCGA-AZ-4315 
       27.09        21.44        17.82        17.26       109.28        58.39 
TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-6598 
        1.41         5.65        32.94         5.13        22.36        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6606 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        6.77        12.10        11.74        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.59        12.76        10.06        14.30        17.56 
TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        70.16        15.62        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4748 
       82.95       124.27        23.05        20.02        37.02        26.04 
TCGA-CM-4750 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
        8.02        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5863 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
       15.02        15.02        12.00        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-D5-5537 TCGA-D5-5539 
       13.02        14.04        11.01        12.95        45.40        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6534 
       56.09        55.92        20.42        17.75        18.25        43.27 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6920 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 
       12.39        12.43        14.30         9.44        11.64        13.35 
TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D6 
       12.00        10.26       119.70        24.43        38.20        49.91 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 
        7.50        44.32       135.65         7.76       139.17        14.04 
TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       26.47        81.37       119.93        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6805 
        8.61        11.11        35.74        35.74         6.18        34.42 
TCGA-F4-6806 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6302 
       41.42        35.31       133.18        82.39        74.56        67.30 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6320 TCGA-G4-6323 
       53.62        44.68        85.48        39.42        26.43        13.78 
TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A8F8 
       74.79        18.18        19.33         9.93        15.65        16.80 
TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-SS-A7HO TCGA-WS-AB45 
       42.77        32.98         8.42        31.30        60.13        70.03 

  DEL PEAK 30(15Q15.2) MUTATED DEL PEAK 30(15Q15.2) WILD-TYPE 
                           0.2                            0.0 
  DEL PEAK 30(15Q15.2) MUTATED DEL PEAK 30(15Q15.2) WILD-TYPE 
                        148.01                         139.17 
  DEL PEAK 30(15Q15.2) MUTATED DEL PEAK 30(15Q15.2) WILD-TYPE 
                         22.47                          22.03 
[1] "0.2 - 148.0 (22.5)" "0.0 - 139.2 (22.0)"
[1] "hr=" "1.1"
D52V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 30(15Q15.2) MUTATED        29        0        8        39         2
  DEL PEAK 30(15Q15.2) WILD-TYPE      45        1       21        93         8
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 30(15Q15.2) MUTATED           0         6          4         22
  DEL PEAK 30(15Q15.2) WILD-TYPE         1        14          4         37
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 30(15Q15.2) MUTATED           19       25        10         2
  DEL PEAK 30(15Q15.2) WILD-TYPE         22       20         7         0
D52V3, multiclass
            clus
vv           DEL PEAK 30(15Q15.2) MUTATED DEL PEAK 30(15Q15.2) WILD-TYPE
  STAGE I                              29                             45
  STAGE IA                              0                              1
  STAGE II                              8                             21
  STAGE IIA                            39                             93
  STAGE IIB                             2                              8
  STAGE IIC                             0                              1
  STAGE III                             6                             14
  STAGE IIIA                            4                              4
  STAGE IIIB                           22                             37
  STAGE IIIC                           19                             22
  STAGE IV                             25                             20
  STAGE IVA                            10                              7
  STAGE IVB                             2                              0
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 30(15Q15.2) MUTATED     5  30 116  20
  DEL PEAK 30(15Q15.2) WILD-TYPE   6  47 189  35
D52V4, multiclass
    clus
vv   DEL PEAK 30(15Q15.2) MUTATED DEL PEAK 30(15Q15.2) WILD-TYPE
  T1                            5                              6
  T2                           30                             47
  T3                          116                            189
  T4                           20                             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"
                                vv
clus                              N0  N1  N2
  DEL PEAK 30(15Q15.2) MUTATED    85  50  36
  DEL PEAK 30(15Q15.2) WILD-TYPE 177  55  46
D52V5, multiclass
    clus
vv   DEL PEAK 30(15Q15.2) MUTATED DEL PEAK 30(15Q15.2) WILD-TYPE
  N0                           85                            177
  N1                           50                             55
  N2                           36                             46
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V6, binary
                                cls
clus                               0   1
  DEL PEAK 30(15Q15.2) MUTATED   110  37
  DEL PEAK 30(15Q15.2) WILD-TYPE 218  27
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(15Q15.2) MUTATED    110   37
  DEL PEAK 30(15Q15.2) WILD-TYPE  218   27
   clus
vv  DEL PEAK 30(15Q15.2) MUTATED DEL PEAK 30(15Q15.2) WILD-TYPE
  0                          110                            218
  1                           37                             27
[1] 2 2
[1] FALSE
D52V7, binary
                                cls
clus                               0   1
  DEL PEAK 30(15Q15.2) MUTATED    78  93
  DEL PEAK 30(15Q15.2) WILD-TYPE 135 143
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(15Q15.2) MUTATED     78   93
  DEL PEAK 30(15Q15.2) WILD-TYPE  135  143
        clus
vv       DEL PEAK 30(15Q15.2) MUTATED DEL PEAK 30(15Q15.2) WILD-TYPE
  FEMALE                           78                            135
  MALE                             93                            143
[1] 2 2
[1] FALSE
D52V8, binary
                                cls
clus                               0   1
  DEL PEAK 30(15Q15.2) MUTATED   144   4
  DEL PEAK 30(15Q15.2) WILD-TYPE 226   5
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(15Q15.2) MUTATED    144    4
  DEL PEAK 30(15Q15.2) WILD-TYPE  226    5
     clus
vv    DEL PEAK 30(15Q15.2) MUTATED DEL PEAK 30(15Q15.2) WILD-TYPE
  NO                           144                            226
  YES                            4                              5
[1] 2 2
[1] FALSE
D52V9, binary
                                cls
clus                               0   1
  DEL PEAK 30(15Q15.2) MUTATED   153  15
  DEL PEAK 30(15Q15.2) WILD-TYPE 229  47
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(15Q15.2) MUTATED    153   15
  DEL PEAK 30(15Q15.2) WILD-TYPE  229   47
                               clus
vv                              DEL PEAK 30(15Q15.2) MUTATED
  COLON ADENOCARCINOMA                                   153
  COLON MUCINOUS ADENOCARCINOMA                           15
                               clus
vv                              DEL PEAK 30(15Q15.2) WILD-TYPE
  COLON ADENOCARCINOMA                                     229
  COLON MUCINOUS ADENOCARCINOMA                             47
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 30(15Q15.2) MUTATED   121   1  12   6
  DEL PEAK 30(15Q15.2) WILD-TYPE 202   3  13  19
D52V10, multiclass
    clus
vv   DEL PEAK 30(15Q15.2) MUTATED DEL PEAK 30(15Q15.2) WILD-TYPE
  R0                          121                            202
  R1                            1                              3
  R2                           12                             13
  RX                            6                             19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 30(15Q15.2) MUTATED                                  1     2
  DEL PEAK 30(15Q15.2) WILD-TYPE                                0     9
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 30(15Q15.2) MUTATED                          23    86
  DEL PEAK 30(15Q15.2) WILD-TYPE                        36   126
D52V12, multiclass
                                  clus
vv                                 DEL PEAK 30(15Q15.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                  23
  WHITE                                                      86
                                  clus
vv                                 DEL PEAK 30(15Q15.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         9
  BLACK OR AFRICAN AMERICAN                                    36
  WHITE                                                       126
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V13, binary
                                cls
clus                               0   1
  DEL PEAK 30(15Q15.2) MUTATED     2 104
  DEL PEAK 30(15Q15.2) WILD-TYPE   2 165
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(15Q15.2) MUTATED      2  104
  DEL PEAK 30(15Q15.2) WILD-TYPE    2  165
                        clus
vv                       DEL PEAK 30(15Q15.2) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                          104
                        clus
vv                       DEL PEAK 30(15Q15.2) WILD-TYPE
  HISPANIC OR LATINO                                  2
  NOT HISPANIC OR LATINO                            165
[1] 2 2
[1] FALSE

Clustering(53) Variable = DEL PEAK 31(15Q21.1) MUTATION ANALYSIS
D53V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 31(15Q21.1) MUTATED   129  34
  DEL PEAK 31(15Q21.1) WILD-TYPE 206  67
  DEL PEAK 31(15Q21.1) MUTATED DEL PEAK 31(15Q21.1) WILD-TYPE 
                           163                            273 
  DEL PEAK 31(15Q21.1) MUTATED DEL PEAK 31(15Q21.1) WILD-TYPE 
                            34                             67 
$`DEL PEAK 31(15Q21.1) MUTATED`
TCGA-A6-2677 TCGA-A6-2681 TCGA-AA-3522 TCGA-AA-3552 TCGA-AA-3556 TCGA-AA-3560 
       24.33        45.60        37.05        13.02        23.01        19.99 
TCGA-AA-3562 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3867 TCGA-AA-3870 
       19.99        19.00        36.00        85.05        24.03        29.98 
TCGA-AA-3939 TCGA-AA-3972 TCGA-AA-3979 TCGA-AZ-4681 TCGA-CK-5912 TCGA-DM-A285 
       12.99        50.99        24.00       106.75        49.08         5.88 
TCGA-G4-6310 TCGA-G4-6625 TCGA-4N-A93T TCGA-5M-AAT4 TCGA-5M-AATE TCGA-A6-2671 
       63.62        91.79         4.80         1.61        39.45        43.76 
TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2679 TCGA-A6-2683 TCGA-A6-3807 
       43.76        43.43        42.90        44.91        16.57        34.65 
TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5667 
       36.53        32.45        32.91        30.44        29.19        29.16 
TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6780 TCGA-A6-6782 
       22.52        25.08        20.61        21.76        20.12        20.28 
TCGA-A6-A567 TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3494 TCGA-AA-3511 TCGA-AA-3519 
       61.84         5.03         7.04         1.02         6.97         9.07 
TCGA-AA-3532 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 
       29.00        12.99        14.01        33.99        21.01        24.00 
TCGA-AA-3666 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3680 TCGA-AA-3685 TCGA-AA-3837 
        2.01        50.04        47.01        11.01        37.05        38.99 
TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 
       36.95        37.02         0.00        17.03        10.06        33.07 
TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3866 TCGA-AA-3966 TCGA-AA-3968 
       36.03         0.99        31.07        17.03         2.01        21.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3982 TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       13.05        34.06        27.02        19.00        30.02        34.03 
TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01K 
       42.02        17.03        14.99        15.02        15.02        31.00 
TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A02E TCGA-AA-A02W TCGA-AD-6899 TCGA-AD-6901 
       33.04        26.01         2.96        41.00         5.79        22.42 
TCGA-AD-6963 TCGA-AD-A5EK TCGA-AU-3779 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-A69D 
       27.42        16.44        14.50        33.01         0.20        17.85 
TCGA-AY-A8YK TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6603 TCGA-AZ-6605 
       18.84        65.00        62.79        88.21        29.56         5.23 
TCGA-AZ-6607 TCGA-CA-5256 TCGA-CA-6716 TCGA-CK-4948 TCGA-CK-6748 TCGA-CM-4747 
        3.19        12.46        12.20       148.01         2.01        25.02 
TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-5868 
       27.02        13.02        29.06         5.03        15.02        17.03 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6170 TCGA-CM-6675 TCGA-CM-6676 
       14.04        29.03        16.04        15.02        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5538 TCGA-D5-6529 
       11.08        11.01        10.06        12.03        54.61        20.19 
TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6926 TCGA-D5-6929 
       25.48        15.12         7.53        10.13         9.04        13.41 
TCGA-D5-6932 TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
       11.38       130.65        92.75        13.32        12.59       140.38 
TCGA-DM-A1HA TCGA-DM-A28F TCGA-DM-A28M TCGA-F4-6460 TCGA-F4-6703 TCGA-F4-6704 
      131.51        35.97        95.18        31.96        47.87         1.55 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6295 
       43.04        33.67        13.25         0.53        47.41         8.35 
TCGA-G4-6303 TCGA-G4-6307 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6322 TCGA-G4-6626 
       65.85        55.04        61.91        36.00        26.04        46.75 
TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A6GC TCGA-QG-A5YW TCGA-QL-A97D TCGA-RU-A8FL 
       10.98        19.33        12.79        29.46        21.90        38.70 
TCGA-T9-A92H 
       11.90 

$`DEL PEAK 31(15Q21.1) WILD-TYPE`
TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3506 TCGA-AA-3516 
       13.94        14.53        24.16         1.02        58.03        13.02 
TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       24.03        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3554 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       17.95         6.05         0.92        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3976 TCGA-AA-3986 TCGA-AA-A00L 
       31.07        24.00         2.01        26.01        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4313 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6314 
       75.95       100.01         1.94        28.21        23.51        35.93 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 TCGA-NH-A8F7 TCGA-3L-AA1B 
       22.09        35.80        26.17        79.69        17.85        15.62 
TCGA-4T-AA8H TCGA-5M-AAT6 TCGA-A6-2672 TCGA-A6-2678 TCGA-A6-2680 TCGA-A6-2684 
       12.66         9.53        46.65        42.28        35.11        37.05 
TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3809 TCGA-A6-5657 TCGA-A6-5661 TCGA-A6-5662 
       37.25        37.02        32.75        31.63        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        24.13         8.38 
TCGA-A6-6648 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-A565 
       25.18        24.69        24.39        23.87        19.66        16.24 
TCGA-A6-A566 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3492 TCGA-AA-3495 TCGA-AA-3502 
       24.92        56.25         9.63         3.02        37.05        35.01 
TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3526 TCGA-AA-3529 
       63.98         1.02        38.99         1.02        19.07         0.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       29.00        26.01        29.95        20.98        13.94        61.02 
TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3675 TCGA-AA-3679 
       78.08         6.97        54.02        14.01        47.05        15.02 
TCGA-AA-3681 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
        5.98         5.03        26.99        10.06        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3850 TCGA-AA-3852 
       25.02         1.02        17.98        15.95         0.00         0.00 
TCGA-AA-3855 TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       32.05        53.00        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3971 
       24.00        33.01        26.01        20.98        34.03        16.08 
TCGA-AA-3977 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00J 
       25.02         7.96        27.02        13.94        38.04        18.05 
TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A010 TCGA-AA-A01D 
       18.05         4.01        27.02         0.99        34.98        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       32.02        12.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
        1.02         1.02        37.02        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
        5.03         0.92        22.03        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6965 TCGA-AM-5820 TCGA-AM-5821 
       12.16        83.24        24.53        26.47         0.46         0.92 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L 
       27.09        16.31         0.95        21.44        17.82        17.26 
TCGA-AY-A71X TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 
       19.33       109.28        58.39         1.41         5.65        32.94 
TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6606 
        5.13        22.36        49.41         6.77        12.10        11.74 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6717 
       12.69        12.36        12.39        12.59        12.59        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 
       10.06        14.30        17.56        85.45        70.16        15.62 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 
       51.32        21.99        21.14        82.95       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-5344 TCGA-CM-5348 
       20.02        37.02        26.04         8.02        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-6161 TCGA-CM-6162 
       30.08        32.02        15.02        15.02        15.02        12.00 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6171 TCGA-CM-6172 
       21.99        14.99        12.99        13.02        14.04        11.01 
TCGA-CM-6674 TCGA-D5-5537 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6530 
       12.95        45.40        19.59        56.09        55.92        20.42 
TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       17.75        18.25        43.27        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6923 TCGA-D5-6924 
       12.49        16.14        15.58        12.39        12.43        14.30 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 
        9.44        11.64        13.35        12.00        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D6 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HB 
       24.43        38.20        49.91         7.50        44.32       135.65 
TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E 
        7.76       139.17        14.04        26.47        81.37       119.93 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6461 TCGA-F4-6463 
       60.79       117.07        98.24         8.61        11.11        35.74 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6856 TCGA-G4-6293 
       35.74         6.18        34.42        41.42        35.31       133.18 
TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 
       82.39        74.56        67.30        53.62        44.68        85.48 
TCGA-G4-6311 TCGA-G4-6320 TCGA-G4-6323 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A5IV 
       39.42        26.43        13.78        74.79        18.18        19.33 
TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 
        9.93        15.65        16.80        42.77        32.98         8.42 
TCGA-QG-A5Z2 TCGA-SS-A7HO TCGA-WS-AB45 
       31.30        60.13        70.03 

  DEL PEAK 31(15Q21.1) MUTATED DEL PEAK 31(15Q21.1) WILD-TYPE 
                             0                              0 
  DEL PEAK 31(15Q21.1) MUTATED DEL PEAK 31(15Q21.1) WILD-TYPE 
                        148.01                         139.17 
  DEL PEAK 31(15Q21.1) MUTATED DEL PEAK 31(15Q21.1) WILD-TYPE 
                         23.01                          21.99 
[1] "0.0 - 148.0 (23.0)" "0.0 - 139.2 (22.0)"
[1] "hr=" "1.2"
D53V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 31(15Q21.1) MUTATED        26        0        8        42         3
  DEL PEAK 31(15Q21.1) WILD-TYPE      48        1       21        90         7
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 31(15Q21.1) MUTATED           0         6          4         20
  DEL PEAK 31(15Q21.1) WILD-TYPE         1        14          4         39
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 31(15Q21.1) MUTATED           18       24        10         2
  DEL PEAK 31(15Q21.1) WILD-TYPE         23       21         7         0
D53V3, multiclass
            clus
vv           DEL PEAK 31(15Q21.1) MUTATED DEL PEAK 31(15Q21.1) WILD-TYPE
  STAGE I                              26                             48
  STAGE IA                              0                              1
  STAGE II                              8                             21
  STAGE IIA                            42                             90
  STAGE IIB                             3                              7
  STAGE IIC                             0                              1
  STAGE III                             6                             14
  STAGE IIIA                            4                              4
  STAGE IIIB                           20                             39
  STAGE IIIC                           18                             23
  STAGE IV                             24                             21
  STAGE IVA                            10                              7
  STAGE IVB                             2                              0
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 31(15Q21.1) MUTATED     4  28 115  21
  DEL PEAK 31(15Q21.1) WILD-TYPE   7  49 190  34
D53V4, multiclass
    clus
vv   DEL PEAK 31(15Q21.1) MUTATED DEL PEAK 31(15Q21.1) WILD-TYPE
  T1                            4                              7
  T2                           28                             49
  T3                          115                            190
  T4                           21                             34
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2
  DEL PEAK 31(15Q21.1) MUTATED    86  47  35
  DEL PEAK 31(15Q21.1) WILD-TYPE 176  58  47
D53V5, multiclass
    clus
vv   DEL PEAK 31(15Q21.1) MUTATED DEL PEAK 31(15Q21.1) WILD-TYPE
  N0                           86                            176
  N1                           47                             58
  N2                           35                             47
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V6, binary
                                cls
clus                               0   1
  DEL PEAK 31(15Q21.1) MUTATED   109  36
  DEL PEAK 31(15Q21.1) WILD-TYPE 219  28
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(15Q21.1) MUTATED    109   36
  DEL PEAK 31(15Q21.1) WILD-TYPE  219   28
   clus
vv  DEL PEAK 31(15Q21.1) MUTATED DEL PEAK 31(15Q21.1) WILD-TYPE
  0                          109                            219
  1                           36                             28
[1] 2 2
[1] FALSE
D53V7, binary
                                cls
clus                               0   1
  DEL PEAK 31(15Q21.1) MUTATED    75  93
  DEL PEAK 31(15Q21.1) WILD-TYPE 138 143
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(15Q21.1) MUTATED     75   93
  DEL PEAK 31(15Q21.1) WILD-TYPE  138  143
        clus
vv       DEL PEAK 31(15Q21.1) MUTATED DEL PEAK 31(15Q21.1) WILD-TYPE
  FEMALE                           75                            138
  MALE                             93                            143
[1] 2 2
[1] FALSE
D53V8, binary
                                cls
clus                               0   1
  DEL PEAK 31(15Q21.1) MUTATED   140   4
  DEL PEAK 31(15Q21.1) WILD-TYPE 230   5
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(15Q21.1) MUTATED    140    4
  DEL PEAK 31(15Q21.1) WILD-TYPE  230    5
     clus
vv    DEL PEAK 31(15Q21.1) MUTATED DEL PEAK 31(15Q21.1) WILD-TYPE
  NO                           140                            230
  YES                            4                              5
[1] 2 2
[1] FALSE
D53V9, binary
                                cls
clus                               0   1
  DEL PEAK 31(15Q21.1) MUTATED   151  15
  DEL PEAK 31(15Q21.1) WILD-TYPE 231  47
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(15Q21.1) MUTATED    151   15
  DEL PEAK 31(15Q21.1) WILD-TYPE  231   47
                               clus
vv                              DEL PEAK 31(15Q21.1) MUTATED
  COLON ADENOCARCINOMA                                   151
  COLON MUCINOUS ADENOCARCINOMA                           15
                               clus
vv                              DEL PEAK 31(15Q21.1) WILD-TYPE
  COLON ADENOCARCINOMA                                     231
  COLON MUCINOUS ADENOCARCINOMA                             47
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 31(15Q21.1) MUTATED   119   0  12   6
  DEL PEAK 31(15Q21.1) WILD-TYPE 204   4  13  19
D53V10, multiclass
    clus
vv   DEL PEAK 31(15Q21.1) MUTATED DEL PEAK 31(15Q21.1) WILD-TYPE
  R0                          119                            204
  R1                            0                              4
  R2                           12                             13
  RX                            6                             19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 31(15Q21.1) MUTATED                                  1     2
  DEL PEAK 31(15Q21.1) WILD-TYPE                                0     9
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 31(15Q21.1) MUTATED                          19    84
  DEL PEAK 31(15Q21.1) WILD-TYPE                        40   128
D53V12, multiclass
                                  clus
vv                                 DEL PEAK 31(15Q21.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                  19
  WHITE                                                      84
                                  clus
vv                                 DEL PEAK 31(15Q21.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         9
  BLACK OR AFRICAN AMERICAN                                    40
  WHITE                                                       128
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V13, binary
                                cls
clus                               0   1
  DEL PEAK 31(15Q21.1) MUTATED     2  98
  DEL PEAK 31(15Q21.1) WILD-TYPE   2 171
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(15Q21.1) MUTATED      2   98
  DEL PEAK 31(15Q21.1) WILD-TYPE    2  171
                        clus
vv                       DEL PEAK 31(15Q21.1) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           98
                        clus
vv                       DEL PEAK 31(15Q21.1) WILD-TYPE
  HISPANIC OR LATINO                                  2
  NOT HISPANIC OR LATINO                            171
[1] 2 2
[1] FALSE

Clustering(54) Variable = DEL PEAK 32(15Q22.33) MUTATION ANALYSIS
D54V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 32(15Q22.33) MUTATED   122  34
  DEL PEAK 32(15Q22.33) WILD-TYPE 213  67
  DEL PEAK 32(15Q22.33) MUTATED DEL PEAK 32(15Q22.33) WILD-TYPE 
                            156                             280 
  DEL PEAK 32(15Q22.33) MUTATED DEL PEAK 32(15Q22.33) WILD-TYPE 
                             34                              67 
$`DEL PEAK 32(15Q22.33) MUTATED`
TCGA-A6-2677 TCGA-A6-2681 TCGA-AA-3522 TCGA-AA-3552 TCGA-AA-3556 TCGA-AA-3560 
       24.33        45.60        37.05        13.02        23.01        19.99 
TCGA-AA-3562 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3867 TCGA-AA-3870 
       19.99        19.00        36.00        85.05        24.03        29.98 
TCGA-AA-3939 TCGA-AA-3972 TCGA-AA-3979 TCGA-AZ-4681 TCGA-CK-5912 TCGA-DM-A285 
       12.99        50.99        24.00       106.75        49.08         5.88 
TCGA-G4-6310 TCGA-G4-6625 TCGA-4N-A93T TCGA-5M-AAT4 TCGA-5M-AATE TCGA-A6-2671 
       63.62        91.79         4.80         1.61        39.45        43.76 
TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2679 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3810 
       43.76        43.43        44.91        16.57        34.65        36.53 
TCGA-A6-4107 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5667 TCGA-A6-6138 TCGA-A6-6142 
       32.45        30.44        29.19        29.16        22.52        25.08 
TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6782 TCGA-A6-A567 TCGA-AA-3488 TCGA-AA-3489 
       20.61        21.76        20.28        61.84         5.03         7.04 
TCGA-AA-3494 TCGA-AA-3511 TCGA-AA-3519 TCGA-AA-3532 TCGA-AA-3542 TCGA-AA-3548 
        1.02         6.97         9.07        29.00        12.99        33.99 
TCGA-AA-3549 TCGA-AA-3666 TCGA-AA-3673 TCGA-AA-3685 TCGA-AA-3837 TCGA-AA-3841 
       21.01         2.01        50.04        37.05        38.99        36.95 
TCGA-AA-3842 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3866 
       37.02        17.03        10.06         0.99        31.07        17.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3982 TCGA-AA-A00D 
        2.01        21.99        13.05        34.06        27.02        19.00 
TCGA-AA-A00F TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01C 
       34.03        42.02        17.03        14.99        15.02        15.02 
TCGA-AA-A01K TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A02E TCGA-AA-A02W TCGA-AD-6899 
       31.00        33.04        26.01         2.96        41.00         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AU-3779 TCGA-AY-4070 
       22.42        27.42        16.44         0.46        14.50        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-A69D TCGA-AY-A8YK TCGA-AZ-4684 
        0.95        33.01         0.20        17.85        18.84        65.00 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-CA-5256 
       62.79        88.21        29.56         5.23         3.19        12.46 
TCGA-CA-6716 TCGA-CK-4948 TCGA-CK-6748 TCGA-CM-4747 TCGA-CM-4751 TCGA-CM-4752 
       12.20       148.01         2.01        25.02        27.02        13.02 
TCGA-CM-5341 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6163 TCGA-CM-6164 
       29.06         5.03        15.02        17.03        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6170 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       16.04        15.02        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6538 TCGA-D5-6539 
       12.03        20.19        25.48        15.12        17.13        12.49 
TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A1D0 
        7.53        10.13         9.04        13.41        11.38       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1HA 
       92.75        49.91        13.32        12.59       140.38       131.51 
TCGA-DM-A288 TCGA-DM-A28M TCGA-F4-6460 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6807 
       14.04        95.18        31.96        47.87         1.55        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6295 TCGA-G4-6303 
       33.67        13.25         0.53        47.41         8.35        65.85 
TCGA-G4-6307 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6626 TCGA-NH-A50U TCGA-NH-A50V 
       55.04        61.91        36.00        46.75        10.98        19.33 
TCGA-NH-A6GC TCGA-QG-A5YW TCGA-QG-A5Z1 TCGA-QL-A97D TCGA-RU-A8FL TCGA-T9-A92H 
       12.79        29.46         8.42        21.90        38.70        11.90 

$`DEL PEAK 32(15Q22.33) WILD-TYPE`
TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3506 TCGA-AA-3516 
       13.94        14.53        24.16         1.02        58.03        13.02 
TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       24.03        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3554 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       17.95         6.05         0.92        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3976 TCGA-AA-3986 TCGA-AA-A00L 
       31.07        24.00         2.01        26.01        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4313 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6314 
       75.95       100.01         1.94        28.21        23.51        35.93 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 TCGA-NH-A8F7 TCGA-3L-AA1B 
       22.09        35.80        26.17        79.69        17.85        15.62 
TCGA-4T-AA8H TCGA-5M-AAT6 TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2680 
       12.66         9.53        46.65        42.90        42.28        35.11 
TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3809 TCGA-A6-5656 TCGA-A6-5657 
       37.05        37.25        37.02        32.75        32.91        31.63 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 
       33.53        23.61        22.09        22.06        32.71        27.09 
TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       24.13         8.38        25.18        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A56B TCGA-A6-A5ZU 
       20.12        19.66        16.24        24.92        56.25         9.63 
TCGA-AA-3492 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3517 
        3.02        37.05        35.01        63.98         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3544 
        1.02        19.07         0.00        29.00        26.01        14.01 
TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        61.02        78.08 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 
        6.97        54.02        14.01        47.05        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
       11.01         5.98         5.03        26.99        10.06        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3845 
        0.99        25.02         1.02        17.98        15.95         0.00 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3864 
        0.00        33.07         0.00        36.03        32.05        53.00 
TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3977 TCGA-AA-3989 
       26.01        20.98        34.03        16.08        25.02         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K 
       27.02        13.94        38.04        30.02        18.05        18.05 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A010 TCGA-AA-A01D TCGA-AA-A01F 
        4.01        27.02         0.99        34.98        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       12.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
        1.02        37.02        51.98        39.98         2.01         5.03 
TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        22.03        39.98        18.05        40.96        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6965 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-6197 
       83.24        24.53        26.47         0.92        27.09        21.44 
TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A71X TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 
       17.82        17.26        19.33       109.28        58.39         1.41 
TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-6598 TCGA-AZ-6599 
        5.65        32.94         5.13        22.36        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6606 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
       12.10        11.74        12.69        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 
       12.59        12.76        10.06        14.30        17.56        85.45 
TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       70.16        15.62        51.32        21.99        21.14        82.95 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-4750 
      124.27        23.05        20.02        37.02        26.04         8.02 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 
       22.03        22.98        30.08        32.02        15.02        15.02 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       15.02        12.00        21.99        14.99        12.99        13.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-D5-5537 TCGA-D5-5538 
       14.04        11.01        12.95        13.05        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 
       19.59        56.09        55.92        20.42        17.75        18.25 
TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 
       43.27        17.85         4.80        16.14        15.58        12.39 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 
       12.43        14.30         9.44        11.64        13.35        12.00 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1DA TCGA-DM-A1DB 
       10.26       119.70        24.43        38.20         7.50        44.32 
TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E 
      135.65         7.76       139.17        26.47        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6461 
       35.97        60.79       117.07        98.24         8.61        11.11 
TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6856 
       35.74        35.74         6.18        34.42        41.42        35.31 
TCGA-G4-6293 TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6306 
      133.18        82.39        74.56        67.30        53.62        44.68 
TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6627 
       85.48        39.42        26.43        26.04        13.78        74.79 
TCGA-NH-A50T TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A8F8 TCGA-QG-A5YV 
       18.18        19.33         9.93        15.65        16.80        42.77 
TCGA-QG-A5YX TCGA-QG-A5Z2 TCGA-SS-A7HO TCGA-WS-AB45 
       32.98        31.30        60.13        70.03 

  DEL PEAK 32(15Q22.33) MUTATED DEL PEAK 32(15Q22.33) WILD-TYPE 
                            0.2                             0.0 
  DEL PEAK 32(15Q22.33) MUTATED DEL PEAK 32(15Q22.33) WILD-TYPE 
                         148.01                          139.17 
  DEL PEAK 32(15Q22.33) MUTATED DEL PEAK 32(15Q22.33) WILD-TYPE 
                         21.385                          22.225 
[1] "0.2 - 148.0 (21.4)" "0.0 - 139.2 (22.2)"
[1] "hr=" "1.1"
D54V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 32(15Q22.33) MUTATED        23        0        7        39         2
  DEL PEAK 32(15Q22.33) WILD-TYPE      51        1       22        93         8
                                 vv
clus                              STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 32(15Q22.33) MUTATED           0         5          4         19
  DEL PEAK 32(15Q22.33) WILD-TYPE         1        15          4         40
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 32(15Q22.33) MUTATED           20       23        11         1
  DEL PEAK 32(15Q22.33) WILD-TYPE         21       22         6         1
D54V3, multiclass
            clus
vv           DEL PEAK 32(15Q22.33) MUTATED DEL PEAK 32(15Q22.33) WILD-TYPE
  STAGE I                               23                              51
  STAGE IA                               0                               1
  STAGE II                               7                              22
  STAGE IIA                             39                              93
  STAGE IIB                              2                               8
  STAGE IIC                              0                               1
  STAGE III                              5                              15
  STAGE IIIA                             4                               4
  STAGE IIIB                            19                              40
  STAGE IIIC                            20                              21
  STAGE IV                              23                              22
  STAGE IVA                             11                               6
  STAGE IVB                              1                               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               T1  T2  T3  T4
  DEL PEAK 32(15Q22.33) MUTATED     5  23 113  19
  DEL PEAK 32(15Q22.33) WILD-TYPE   6  54 192  36
D54V4, multiclass
    clus
vv   DEL PEAK 32(15Q22.33) MUTATED DEL PEAK 32(15Q22.33) WILD-TYPE
  T1                             5                               6
  T2                            23                              54
  T3                           113                             192
  T4                            19                              36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               N0  N1  N2
  DEL PEAK 32(15Q22.33) MUTATED    79  44  37
  DEL PEAK 32(15Q22.33) WILD-TYPE 183  61  45
D54V5, multiclass
    clus
vv   DEL PEAK 32(15Q22.33) MUTATED DEL PEAK 32(15Q22.33) WILD-TYPE
  N0                            79                             183
  N1                            44                              61
  N2                            37                              45
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V6, binary
                                 cls
clus                                0   1
  DEL PEAK 32(15Q22.33) MUTATED   102  35
  DEL PEAK 32(15Q22.33) WILD-TYPE 226  29
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 32(15Q22.33) MUTATED    102   35
  DEL PEAK 32(15Q22.33) WILD-TYPE  226   29
   clus
vv  DEL PEAK 32(15Q22.33) MUTATED DEL PEAK 32(15Q22.33) WILD-TYPE
  0                           102                             226
  1                            35                              29
[1] 2 2
[1] FALSE
D54V7, binary
                                 cls
clus                                0   1
  DEL PEAK 32(15Q22.33) MUTATED    72  88
  DEL PEAK 32(15Q22.33) WILD-TYPE 141 148
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 32(15Q22.33) MUTATED     72   88
  DEL PEAK 32(15Q22.33) WILD-TYPE  141  148
        clus
vv       DEL PEAK 32(15Q22.33) MUTATED DEL PEAK 32(15Q22.33) WILD-TYPE
  FEMALE                            72                             141
  MALE                              88                             148
[1] 2 2
[1] FALSE
D54V8, binary
                                 cls
clus                                0   1
  DEL PEAK 32(15Q22.33) MUTATED   132   4
  DEL PEAK 32(15Q22.33) WILD-TYPE 238   5
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 32(15Q22.33) MUTATED    132    4
  DEL PEAK 32(15Q22.33) WILD-TYPE  238    5
     clus
vv    DEL PEAK 32(15Q22.33) MUTATED DEL PEAK 32(15Q22.33) WILD-TYPE
  NO                            132                             238
  YES                             4                               5
[1] 2 2
[1] FALSE
D54V9, binary
                                 cls
clus                                0   1
  DEL PEAK 32(15Q22.33) MUTATED   143  14
  DEL PEAK 32(15Q22.33) WILD-TYPE 239  48
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 32(15Q22.33) MUTATED    143   14
  DEL PEAK 32(15Q22.33) WILD-TYPE  239   48
                               clus
vv                              DEL PEAK 32(15Q22.33) MUTATED
  COLON ADENOCARCINOMA                                    143
  COLON MUCINOUS ADENOCARCINOMA                            14
                               clus
vv                              DEL PEAK 32(15Q22.33) WILD-TYPE
  COLON ADENOCARCINOMA                                      239
  COLON MUCINOUS ADENOCARCINOMA                              48
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 32(15Q22.33) MUTATED   112   1  11   6
  DEL PEAK 32(15Q22.33) WILD-TYPE 211   3  14  19
D54V10, multiclass
    clus
vv   DEL PEAK 32(15Q22.33) MUTATED DEL PEAK 32(15Q22.33) WILD-TYPE
  R0                           112                             211
  R1                             1                               3
  R2                            11                              14
  RX                             6                              19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V11, continuous
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 32(15Q22.33) MUTATED                                  1     2
  DEL PEAK 32(15Q22.33) WILD-TYPE                                0     9
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 32(15Q22.33) MUTATED                          20    84
  DEL PEAK 32(15Q22.33) WILD-TYPE                        39   128
D54V12, multiclass
                                  clus
vv                                 DEL PEAK 32(15Q22.33) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        2
  BLACK OR AFRICAN AMERICAN                                   20
  WHITE                                                       84
                                  clus
vv                                 DEL PEAK 32(15Q22.33) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               0
  ASIAN                                                          9
  BLACK OR AFRICAN AMERICAN                                     39
  WHITE                                                        128
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V13, binary
                                 cls
clus                                0   1
  DEL PEAK 32(15Q22.33) MUTATED     2  99
  DEL PEAK 32(15Q22.33) WILD-TYPE   2 170
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 32(15Q22.33) MUTATED      2   99
  DEL PEAK 32(15Q22.33) WILD-TYPE    2  170
                        clus
vv                       DEL PEAK 32(15Q22.33) MUTATED
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                            99
                        clus
vv                       DEL PEAK 32(15Q22.33) WILD-TYPE
  HISPANIC OR LATINO                                   2
  NOT HISPANIC OR LATINO                             170
[1] 2 2
[1] FALSE

Clustering(55) Variable = DEL PEAK 33(16P13.3) MUTATION ANALYSIS
D55V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 33(16P13.3) MUTATED    35  19
  DEL PEAK 33(16P13.3) WILD-TYPE 300  82
  DEL PEAK 33(16P13.3) MUTATED DEL PEAK 33(16P13.3) WILD-TYPE 
                            54                            382 
  DEL PEAK 33(16P13.3) MUTATED DEL PEAK 33(16P13.3) WILD-TYPE 
                            19                             82 
$`DEL PEAK 33(16P13.3) MUTATED`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-4105 TCGA-AA-3552 TCGA-AA-3860 TCGA-AA-3952 
       24.33        45.60        14.53        13.02        31.07         2.01 
TCGA-G4-6294 TCGA-A6-2676 TCGA-A6-2679 TCGA-A6-3807 TCGA-A6-6651 TCGA-A6-A567 
       28.21        42.90        44.91        34.65        21.76        61.84 
TCGA-AA-3488 TCGA-AA-3664 TCGA-AA-3685 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3930 
        5.03        54.02        37.05        38.99        36.95         2.01 
TCGA-AA-3947 TCGA-AA-3966 TCGA-AA-3982 TCGA-AA-A00F TCGA-AA-A00O TCGA-AA-A02F 
       33.01         2.01        27.02        34.03        27.02        39.98 
TCGA-AA-A02Y TCGA-AD-A5EK TCGA-AM-5820 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-6196 
       39.98        16.44         0.46        14.50        16.31         0.20 
TCGA-AY-A69D TCGA-AZ-4614 TCGA-AZ-6607 TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5348 
       17.85         5.65         3.19        13.02        22.03        22.98 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-6165 TCGA-CM-6169 TCGA-CM-6172 TCGA-CM-6678 
        5.03        15.02        16.04        13.02        11.01        11.01 
TCGA-D5-6529 TCGA-D5-6531 TCGA-DM-A1D6 TCGA-DM-A1D8 TCGA-DM-A1DB TCGA-F4-6459 
       20.19        17.75        49.91        12.59        44.32         8.61 
TCGA-G4-6626 TCGA-NH-A50T TCGA-NH-A50U TCGA-QG-A5YV TCGA-RU-A8FL TCGA-T9-A92H 
       46.75        18.18        10.98        42.77        38.70        11.90 

$`DEL PEAK 33(16P13.3) WILD-TYPE`
TCGA-A6-2682 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3506 TCGA-AA-3516 TCGA-AA-3520 
       13.94        24.16         1.02        58.03        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3972 TCGA-AA-3976 
       24.03        29.98        12.99        24.00        50.99        26.01 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 
       24.00        19.07        38.04        21.99        39.06        21.37 
TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 
       15.52        25.08        10.88        75.95       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6314 
        1.94        49.08         5.88        23.51        63.62        35.93 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-NH-A8F7 
       22.09        35.80        26.17        91.79        79.69        17.85 
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-5M-AATE 
       15.62         4.80        12.66         1.61         9.53        39.45 
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2678 TCGA-A6-2680 
       43.76        46.65        43.76        43.43        42.28        35.11 
TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3809 TCGA-A6-3810 
       16.57        37.05        37.25        37.02        32.75        36.53 
TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 
       32.45        32.91        31.63        30.44        29.19        33.53 
TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 
       23.61        22.09        22.06        32.71        29.16        27.09 
TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 
       22.52        24.13         8.38        25.08        25.18        20.61 
TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       24.69        24.39        23.87        20.12        19.66        20.28 
TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3489 TCGA-AA-3492 
       16.24        24.92        56.25         9.63         7.04         3.02 
TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
        1.02        37.05        35.01        63.98         6.97         1.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       29.00        26.01        12.99        14.01        33.99        21.01 
TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        61.02        78.08 
TCGA-AA-3663 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 
        6.97         2.01        14.01        50.04        47.05        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 
       15.02        11.01         5.98         5.03        26.99        10.06 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 
        0.00        36.03        32.05         0.99        31.07        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3941 TCGA-AA-3949 
       17.03        27.02        18.05        31.00        24.00        26.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       20.98        34.03        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       25.02         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00Q TCGA-AA-A00R 
       30.02        18.05        18.05         4.01        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D 
       17.03        14.99        34.98        15.02        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04         1.02        26.01        37.02 
TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R 
       51.98         2.96         2.01         5.03         0.92        22.03 
TCGA-AA-A02W TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 
       41.00        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AM-5821 TCGA-AU-6004 
        5.79        22.42        27.42        26.47         0.92        27.09 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A71X 
        0.95        33.01        21.44        17.82        17.26        19.33 
TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4616 
       18.84       109.28        58.39         1.41        32.94         5.13 
TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       22.36        65.00        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-CA-5254 TCGA-CA-5255 
       12.10        29.56         5.23        11.74        12.69        12.36 
TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
       12.46        12.39        12.59        12.59        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 
       10.06        14.30        17.56       148.01        85.45        70.16 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 
      124.27        23.05        20.02        37.02        25.02        26.04 
TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-5341 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
        8.02        27.02        29.06        30.08        32.02        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00        14.04        29.03 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6674 
       21.99        14.99        12.99        15.02        14.04        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       13.05        11.08        11.08        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6530 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.42        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1DA 
       38.20       130.65        92.75        13.32       140.38         7.50 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A 
      131.51       135.65         7.76       139.17        14.04        26.47 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-DM-A28M TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 
       95.18        31.96        11.11        35.74        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6295 
       13.25         0.53        47.41        35.31       133.18         8.35 
TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       82.39        74.56        67.30        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 
       55.04        85.48        39.42        61.91        36.00        26.43 
TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6627 TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA 
       26.04        13.78        74.79        19.33        19.33         9.93 
TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F8 TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 
       15.65        12.79        16.80        29.46        32.98         8.42 
TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-SS-A7HO TCGA-WS-AB45 
       31.30        21.90        60.13        70.03 

  DEL PEAK 33(16P13.3) MUTATED DEL PEAK 33(16P13.3) WILD-TYPE 
                           0.2                            0.0 
  DEL PEAK 33(16P13.3) MUTATED DEL PEAK 33(16P13.3) WILD-TYPE 
                         61.84                         148.01 
  DEL PEAK 33(16P13.3) MUTATED DEL PEAK 33(16P13.3) WILD-TYPE 
                        19.185                         22.225 
[1] "0.2 - 61.8 (19.2)"  "0.0 - 148.0 (22.2)"
[1] "hr=" "2.1"
D55V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 33(16P13.3) MUTATED         3        0        3        17         3
  DEL PEAK 33(16P13.3) WILD-TYPE      71        1       26       115         7
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 33(16P13.3) MUTATED           0         0          0          9
  DEL PEAK 33(16P13.3) WILD-TYPE         1        20          8         50
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 33(16P13.3) MUTATED            9        6         5         0
  DEL PEAK 33(16P13.3) WILD-TYPE         32       39        12         2
D55V3, multiclass
            clus
vv           DEL PEAK 33(16P13.3) MUTATED DEL PEAK 33(16P13.3) WILD-TYPE
  STAGE I                               3                             71
  STAGE IA                              0                              1
  STAGE II                              3                             26
  STAGE IIA                            17                            115
  STAGE IIB                             3                              7
  STAGE IIC                             0                              1
  STAGE III                             0                             20
  STAGE IIIA                            0                              8
  STAGE IIIB                            9                             50
  STAGE IIIC                            9                             32
  STAGE IV                              6                             39
  STAGE IVA                             5                             12
  STAGE IVB                             0                              2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 33(16P13.3) MUTATED     0   3  45   8
  DEL PEAK 33(16P13.3) WILD-TYPE  11  74 260  47
D55V4, multiclass
    clus
vv   DEL PEAK 33(16P13.3) MUTATED DEL PEAK 33(16P13.3) WILD-TYPE
  T1                            0                             11
  T2                            3                             74
  T3                           45                            260
  T4                            8                             47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2
  DEL PEAK 33(16P13.3) MUTATED    27  15  14
  DEL PEAK 33(16P13.3) WILD-TYPE 235  90  68
D55V5, multiclass
    clus
vv   DEL PEAK 33(16P13.3) MUTATED DEL PEAK 33(16P13.3) WILD-TYPE
  N0                           27                            235
  N1                           15                             90
  N2                           14                             68
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V6, binary
                                cls
clus                               0   1
  DEL PEAK 33(16P13.3) MUTATED    36  11
  DEL PEAK 33(16P13.3) WILD-TYPE 292  53
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 33(16P13.3) MUTATED     36   11
  DEL PEAK 33(16P13.3) WILD-TYPE  292   53
   clus
vv  DEL PEAK 33(16P13.3) MUTATED DEL PEAK 33(16P13.3) WILD-TYPE
  0                           36                            292
  1                           11                             53
[1] 2 2
[1] FALSE
D55V7, binary
                                cls
clus                               0   1
  DEL PEAK 33(16P13.3) MUTATED    25  31
  DEL PEAK 33(16P13.3) WILD-TYPE 188 205
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 33(16P13.3) MUTATED     25   31
  DEL PEAK 33(16P13.3) WILD-TYPE  188  205
        clus
vv       DEL PEAK 33(16P13.3) MUTATED DEL PEAK 33(16P13.3) WILD-TYPE
  FEMALE                           25                            188
  MALE                             31                            205
[1] 2 2
[1] FALSE
D55V8, binary
                                cls
clus                               0   1
  DEL PEAK 33(16P13.3) MUTATED    46   0
  DEL PEAK 33(16P13.3) WILD-TYPE 324   9
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 33(16P13.3) MUTATED     46    0
  DEL PEAK 33(16P13.3) WILD-TYPE  324    9
     clus
vv    DEL PEAK 33(16P13.3) MUTATED DEL PEAK 33(16P13.3) WILD-TYPE
  NO                            46                            324
  YES                            0                              9
[1] 2 2
[1] FALSE
D55V9, binary
                                cls
clus                               0   1
  DEL PEAK 33(16P13.3) MUTATED    49   7
  DEL PEAK 33(16P13.3) WILD-TYPE 333  55
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 33(16P13.3) MUTATED     49    7
  DEL PEAK 33(16P13.3) WILD-TYPE  333   55
                               clus
vv                              DEL PEAK 33(16P13.3) MUTATED
  COLON ADENOCARCINOMA                                    49
  COLON MUCINOUS ADENOCARCINOMA                            7
                               clus
vv                              DEL PEAK 33(16P13.3) WILD-TYPE
  COLON ADENOCARCINOMA                                     333
  COLON MUCINOUS ADENOCARCINOMA                             55
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 33(16P13.3) MUTATED    42   1   3   1
  DEL PEAK 33(16P13.3) WILD-TYPE 281   3  22  24
D55V10, multiclass
    clus
vv   DEL PEAK 33(16P13.3) MUTATED DEL PEAK 33(16P13.3) WILD-TYPE
  R0                           42                            281
  R1                            1                              3
  R2                            3                             22
  RX                            1                             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 33(16P13.3) MUTATED                                  0     0
  DEL PEAK 33(16P13.3) WILD-TYPE                                1    11
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 33(16P13.3) MUTATED                          11    28
  DEL PEAK 33(16P13.3) WILD-TYPE                        48   184
D55V12, multiclass
                                  clus
vv                                 DEL PEAK 33(16P13.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       0
  BLACK OR AFRICAN AMERICAN                                  11
  WHITE                                                      28
                                  clus
vv                                 DEL PEAK 33(16P13.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        11
  BLACK OR AFRICAN AMERICAN                                    48
  WHITE                                                       184
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V13, binary
                                cls
clus                               0   1
  DEL PEAK 33(16P13.3) MUTATED     1  37
  DEL PEAK 33(16P13.3) WILD-TYPE   3 232
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 33(16P13.3) MUTATED      1   37
  DEL PEAK 33(16P13.3) WILD-TYPE    3  232
                        clus
vv                       DEL PEAK 33(16P13.3) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           37
                        clus
vv                       DEL PEAK 33(16P13.3) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            232
[1] 2 2
[1] FALSE

Clustering(56) Variable = DEL PEAK 34(16Q23.1) MUTATION ANALYSIS
D56V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 34(16Q23.1) MUTATED    42  17
  DEL PEAK 34(16Q23.1) WILD-TYPE 293  84
  DEL PEAK 34(16Q23.1) MUTATED DEL PEAK 34(16Q23.1) WILD-TYPE 
                            59                            377 
  DEL PEAK 34(16Q23.1) MUTATED DEL PEAK 34(16Q23.1) WILD-TYPE 
                            17                             84 
$`DEL PEAK 34(16Q23.1) MUTATED`
TCGA-A6-2681 TCGA-AA-3516 TCGA-AA-3543 TCGA-AA-3672 TCGA-AA-3860 TCGA-5M-AAT4 
       45.60        13.02         0.99         0.92        31.07         1.61 
TCGA-A6-2671 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5665 
       43.76        42.90        42.28        29.19        33.53        22.06 
TCGA-A6-6138 TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-A565 TCGA-AA-3494 TCGA-AA-3511 
       22.52        21.76        24.39        16.24         1.02         6.97 
TCGA-AA-3518 TCGA-AA-3549 TCGA-AA-3685 TCGA-AA-3831 TCGA-AA-3837 TCGA-AA-3854 
        1.02        21.01        37.05        17.98        38.99        36.03 
TCGA-AA-3864 TCGA-AA-3947 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-A00E TCGA-AA-A00J 
       53.00        33.01         2.01        21.99        30.02        18.05 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A02E TCGA-AA-A02R TCGA-AA-A02W TCGA-AD-A5EK 
       38.07         1.02         2.96        22.03        41.00        16.44 
TCGA-AY-A69D TCGA-AZ-4614 TCGA-AZ-4616 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6607 
       17.85         5.65         5.13        49.41        12.10         3.19 
TCGA-CA-5254 TCGA-CA-5797 TCGA-CM-5344 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-6169 
       12.69        12.59        22.03         5.03        15.02        13.02 
TCGA-CM-6678 TCGA-D5-6529 TCGA-D5-6531 TCGA-D5-6535 TCGA-DM-A0XD TCGA-DM-A1DA 
       11.01        20.19        17.75        15.12        24.43         7.50 
TCGA-NH-A50T TCGA-NH-A50U TCGA-QG-A5Z2 TCGA-RU-A8FL TCGA-T9-A92H 
       18.18        10.98        31.30        38.70        11.90 

$`DEL PEAK 34(16Q23.1) WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3506 
       24.33        13.94        14.53        24.16         1.02        58.03 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 
       24.03        37.05        36.03         8.05        19.07        34.03 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 
       21.37        15.52        25.08        10.88        75.95       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6298 
      100.01         1.94        49.08         5.88        28.21        23.51 
TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       63.62        35.93        22.09        35.80        26.17        91.79 
TCGA-G4-6628 TCGA-NH-A8F7 TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT6 
       79.69        17.85        15.62         4.80        12.66         9.53 
TCGA-5M-AATE TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2679 TCGA-A6-2680 
       39.45        46.65        43.76        43.43        44.91        35.11 
TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3809 
       16.57        37.05        37.25        37.02        34.65        32.75 
TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5662 
       36.53        32.45        32.91        31.63        30.44        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6141 
       22.09        32.71        29.16        27.09        24.13         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 
       25.08        25.18        20.61        24.69        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU 
       19.66        20.28        24.92        61.84        56.25         9.63 
TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 
        5.03         7.04         3.02        37.05        35.01        63.98 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
        1.02        38.99         9.07        19.07         0.00        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3553 
       29.00        26.01        12.99        14.01        33.99        24.00 
TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 
       54.02         2.01        14.01        50.04        47.05        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 
       15.02        11.01         5.98         5.03        26.99        10.06 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3833 TCGA-AA-3841 
       35.05         0.99        25.02         1.02        15.95        36.95 
TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3866 TCGA-AA-3869 
        0.00        32.05         0.99        31.07        17.03        27.02 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3955 
       18.05        31.00         2.01        24.00        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3982 
       34.03        16.08        13.05        34.06        25.02        27.02 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00F 
        7.96        27.02        13.94        38.04        19.00        34.03 
TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F 
       14.99        34.98        15.02        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       12.00        31.00        31.00        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
        1.02        26.01        37.02        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        5.03         0.92        39.98        18.05        40.96        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
        0.46         0.92        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A71X 
       33.01         0.20        21.44        17.82        17.26        19.33 
TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4682 
       18.84       109.28        58.39         1.41        32.94        22.36 
TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6603 TCGA-AZ-6605 
       65.00        62.79        88.21         6.77        29.56         5.23 
TCGA-AZ-6606 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6716 
       11.74        12.36        12.46        12.39        12.59        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       70.16        15.62        51.32        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5348 
       26.04         8.02        27.02        13.02        29.06        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       30.08        32.02        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00        14.04        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       12.99        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.08        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.42        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       43.27        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         7.53        12.39        10.13        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       11.38        10.26       119.70        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA 
       49.91        13.32        12.59       140.38        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C 
      135.65         7.76       139.17        14.04        26.47        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M 
      119.93        35.97        60.79       117.07        98.24        95.18 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 
        8.61        31.96        11.11        35.74        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6295 
       13.25         0.53        47.41        35.31       133.18         8.35 
TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       82.39        74.56        67.30        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 
       55.04        85.48        39.42        61.91        36.00        26.43 
TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50V TCGA-NH-A5IV 
       26.04        13.78        46.75        74.79        19.33        19.33 
TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW 
        9.93        15.65        12.79        16.80        42.77        29.46 
TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QL-A97D TCGA-SS-A7HO TCGA-WS-AB45 
       32.98         8.42        21.90        60.13        70.03 

  DEL PEAK 34(16Q23.1) MUTATED DEL PEAK 34(16Q23.1) WILD-TYPE 
                          0.92                           0.00 
  DEL PEAK 34(16Q23.1) MUTATED DEL PEAK 34(16Q23.1) WILD-TYPE 
                         53.00                         148.01 
  DEL PEAK 34(16Q23.1) MUTATED DEL PEAK 34(16Q23.1) WILD-TYPE 
                         18.05                          23.51 
[1] "0.9 - 53.0 (18.1)"  "0.0 - 148.0 (23.5)"
[1] "hr=" "1.9"
D56V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 34(16Q23.1) MUTATED        10        0        5        18         2
  DEL PEAK 34(16Q23.1) WILD-TYPE      64        1       24       114         8
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 34(16Q23.1) MUTATED           0         3          0          8
  DEL PEAK 34(16Q23.1) WILD-TYPE         1        17          8         51
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 34(16Q23.1) MUTATED            3        7         4         0
  DEL PEAK 34(16Q23.1) WILD-TYPE         38       38        13         2
D56V3, multiclass
            clus
vv           DEL PEAK 34(16Q23.1) MUTATED DEL PEAK 34(16Q23.1) WILD-TYPE
  STAGE I                              10                             64
  STAGE IA                              0                              1
  STAGE II                              5                             24
  STAGE IIA                            18                            114
  STAGE IIB                             2                              8
  STAGE IIC                             0                              1
  STAGE III                             3                             17
  STAGE IIIA                            0                              8
  STAGE IIIB                            8                             51
  STAGE IIIC                            3                             38
  STAGE IV                              7                             38
  STAGE IVA                             4                             13
  STAGE IVB                             0                              2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 34(16Q23.1) MUTATED     0  10  41   9
  DEL PEAK 34(16Q23.1) WILD-TYPE  11  67 264  46
D56V4, multiclass
    clus
vv   DEL PEAK 34(16Q23.1) MUTATED DEL PEAK 34(16Q23.1) WILD-TYPE
  T1                            0                             11
  T2                           10                             67
  T3                           41                            264
  T4                            9                             46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2
  DEL PEAK 34(16Q23.1) MUTATED    38  14   8
  DEL PEAK 34(16Q23.1) WILD-TYPE 224  91  74
D56V5, multiclass
    clus
vv   DEL PEAK 34(16Q23.1) MUTATED DEL PEAK 34(16Q23.1) WILD-TYPE
  N0                           38                            224
  N1                           14                             91
  N2                            8                             74
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V6, binary
                                cls
clus                               0   1
  DEL PEAK 34(16Q23.1) MUTATED    41  11
  DEL PEAK 34(16Q23.1) WILD-TYPE 287  53
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 34(16Q23.1) MUTATED     41   11
  DEL PEAK 34(16Q23.1) WILD-TYPE  287   53
   clus
vv  DEL PEAK 34(16Q23.1) MUTATED DEL PEAK 34(16Q23.1) WILD-TYPE
  0                           41                            287
  1                           11                             53
[1] 2 2
[1] FALSE
D56V7, binary
                                cls
clus                               0   1
  DEL PEAK 34(16Q23.1) MUTATED    31  29
  DEL PEAK 34(16Q23.1) WILD-TYPE 182 207
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 34(16Q23.1) MUTATED     31   29
  DEL PEAK 34(16Q23.1) WILD-TYPE  182  207
        clus
vv       DEL PEAK 34(16Q23.1) MUTATED DEL PEAK 34(16Q23.1) WILD-TYPE
  FEMALE                           31                            182
  MALE                             29                            207
[1] 2 2
[1] FALSE
D56V8, binary
                                cls
clus                               0   1
  DEL PEAK 34(16Q23.1) MUTATED    50   1
  DEL PEAK 34(16Q23.1) WILD-TYPE 320   8
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 34(16Q23.1) MUTATED     50    1
  DEL PEAK 34(16Q23.1) WILD-TYPE  320    8
     clus
vv    DEL PEAK 34(16Q23.1) MUTATED DEL PEAK 34(16Q23.1) WILD-TYPE
  NO                            50                            320
  YES                            1                              8
[1] 2 2
[1] FALSE
D56V9, binary
                                cls
clus                               0   1
  DEL PEAK 34(16Q23.1) MUTATED    50  10
  DEL PEAK 34(16Q23.1) WILD-TYPE 332  52
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 34(16Q23.1) MUTATED     50   10
  DEL PEAK 34(16Q23.1) WILD-TYPE  332   52
                               clus
vv                              DEL PEAK 34(16Q23.1) MUTATED
  COLON ADENOCARCINOMA                                    50
  COLON MUCINOUS ADENOCARCINOMA                           10
                               clus
vv                              DEL PEAK 34(16Q23.1) WILD-TYPE
  COLON ADENOCARCINOMA                                     332
  COLON MUCINOUS ADENOCARCINOMA                             52
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 34(16Q23.1) MUTATED    42   0   2   4
  DEL PEAK 34(16Q23.1) WILD-TYPE 281   4  23  21
D56V10, multiclass
    clus
vv   DEL PEAK 34(16Q23.1) MUTATED DEL PEAK 34(16Q23.1) WILD-TYPE
  R0                           42                            281
  R1                            0                              4
  R2                            2                             23
  RX                            4                             21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 34(16Q23.1) MUTATED                                  0     2
  DEL PEAK 34(16Q23.1) WILD-TYPE                                1     9
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 34(16Q23.1) MUTATED                          13    22
  DEL PEAK 34(16Q23.1) WILD-TYPE                        46   190
D56V12, multiclass
                                  clus
vv                                 DEL PEAK 34(16Q23.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                  13
  WHITE                                                      22
                                  clus
vv                                 DEL PEAK 34(16Q23.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         9
  BLACK OR AFRICAN AMERICAN                                    46
  WHITE                                                       190
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V13, binary
                                cls
clus                               0   1
  DEL PEAK 34(16Q23.1) MUTATED     2  34
  DEL PEAK 34(16Q23.1) WILD-TYPE   2 235
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 34(16Q23.1) MUTATED      2   34
  DEL PEAK 34(16Q23.1) WILD-TYPE    2  235
                        clus
vv                       DEL PEAK 34(16Q23.1) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           34
                        clus
vv                       DEL PEAK 34(16Q23.1) WILD-TYPE
  HISPANIC OR LATINO                                  2
  NOT HISPANIC OR LATINO                            235
[1] 2 2
[1] FALSE

Clustering(57) Variable = DEL PEAK 35(17P12) MUTATION ANALYSIS
D57V1, survival
                              sevent
clus2                            0   1
  DEL PEAK 35(17P12) MUTATED   186  59
  DEL PEAK 35(17P12) WILD-TYPE 149  42
  DEL PEAK 35(17P12) MUTATED DEL PEAK 35(17P12) WILD-TYPE 
                         245                          191 
  DEL PEAK 35(17P12) MUTATED DEL PEAK 35(17P12) WILD-TYPE 
                          59                           42 
$`DEL PEAK 35(17P12) MUTATED`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3520 
       24.33        45.60        14.53        24.16         1.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3552 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 
       37.05        36.03        13.02        23.01        19.99        19.99 
TCGA-AA-3662 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3867 TCGA-AA-3870 
        6.05        19.00        36.00        85.05        24.03        29.98 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-A00L TCGA-AA-A00Z 
        2.01        50.99        26.01        24.00        38.04        21.99 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 
       21.37        15.52       106.75         1.94        49.08         5.88 
TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6625 TCGA-NH-A8F7 TCGA-3L-AA1B 
       23.51        63.62        35.93        91.79        17.85        15.62 
TCGA-4N-A93T TCGA-5M-AAT4 TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 
        4.80         1.61        39.45        43.76        43.76        43.43 
TCGA-A6-2678 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-3807 
       42.28        35.11        16.57        37.05        37.25        34.65 
TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5666 
       32.45        32.91        31.63        30.44        29.19        32.71 
TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6648 TCGA-A6-6650 
       29.16        27.09        22.52        24.13        25.18        20.61 
TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6782 TCGA-A6-A567 TCGA-AA-3488 TCGA-AA-3489 
       24.69        23.87        20.28        61.84         5.03         7.04 
TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3519 
        1.02        37.05         6.97         1.02        38.99         9.07 
TCGA-AA-3532 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 
       29.00        12.99        14.01        33.99        21.01        24.00 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       13.94        61.02        78.08         2.01        14.01        50.04 
TCGA-AA-3678 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3811 TCGA-AA-3819 TCGA-AA-3837 
       47.01         5.98        37.05        10.06        25.02        38.99 
TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3855 TCGA-AA-3856 
       36.95        37.02        10.06        33.07        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3941 
       31.07        17.03        27.02        18.05         2.01        24.00 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3975 TCGA-AA-3982 
       20.98        34.03        21.99        16.08        34.06        27.02 
TCGA-AA-3989 TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00U 
        7.96        19.00        34.03        27.02        42.02        17.03 
TCGA-AA-A00W TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01K 
       14.99        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01Z TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H 
        1.02        33.04        37.02         2.96        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02W TCGA-AA-A03J TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
        5.03        41.00        40.96        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AU-3779 TCGA-AY-4070 
       27.42        26.47        16.44         0.46        14.50        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-A69D TCGA-AZ-4308 TCGA-AZ-4323 
        0.95        33.01         0.20        17.85       109.28         1.41 
TCGA-AZ-4614 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5407 TCGA-AZ-6600 
        5.65         5.13        22.36        65.00        88.21        12.10 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5256 TCGA-CA-5797 
       29.56         5.23         3.19        12.69        12.46        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-5914 TCGA-CK-6748 
       12.59        12.20        14.30       148.01        21.99         2.01 
TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       25.02         8.02        27.02        13.02        29.06        22.03 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6164 TCGA-CM-6166 
        5.03        15.02        15.02        17.03        29.03        21.99 
TCGA-CM-6167 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6676 
       14.99        13.02        15.02        11.01        13.05        11.08 
TCGA-CM-6679 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       10.06        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6538 
       17.75        18.25        25.48        43.27        15.12        17.13 
TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       12.49        15.58         7.53        10.13        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
        9.04        13.41        11.38        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA 
       92.75        13.32        12.59       140.38        44.32       131.51 
TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28H 
      139.17        14.04        26.47       119.93        35.97       117.07 
TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6805 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
       31.96        11.11        34.42        43.04        33.67        13.25 
TCGA-G4-6295 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6311 TCGA-G4-6315 
        8.35        65.85        44.68        55.04        39.42        61.91 
TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6626 TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A6GA 
       36.00        26.43        46.75        10.98        19.33         9.93 
TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX 
       15.65        12.79        16.80        42.77        29.46        32.98 
TCGA-QG-A5Z1 TCGA-QL-A97D TCGA-RU-A8FL TCGA-SS-A7HO TCGA-T9-A92H 
        8.42        21.90        38.70        60.13        11.90 

$`DEL PEAK 35(17P12) WILD-TYPE`
TCGA-A6-2682 TCGA-AA-3506 TCGA-AA-3516 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 
       13.94        58.03        13.02         8.05        19.07        34.03 
TCGA-AA-3543 TCGA-AA-3554 TCGA-AA-3672 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
        0.99        17.95         0.92        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3986 TCGA-AA-A024 TCGA-AD-6895 
       31.07        12.99        24.00        19.07        39.06        25.08 
TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-6601 TCGA-G4-6294 TCGA-G4-6321 TCGA-G4-6586 
       10.88        75.95       100.01        28.21        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6628 TCGA-4T-AA8H TCGA-5M-AAT6 TCGA-A6-2672 TCGA-A6-2676 
       26.17        79.69        12.66         9.53        46.65        42.90 
TCGA-A6-2679 TCGA-A6-2686 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5661 TCGA-A6-5662 
       44.91        37.02        32.75        36.53        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6651 TCGA-A6-6653 
       22.09        22.06         8.38        25.08        21.76        24.39 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A56B TCGA-A6-A5ZU 
       20.12        19.66        16.24        24.92        56.25         9.63 
TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3518 TCGA-AA-3526 TCGA-AA-3529 
        3.02        35.01        63.98         1.02        19.07         0.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3663 TCGA-AA-3664 
       29.00        26.01        29.95        20.98         6.97        54.02 
TCGA-AA-3675 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3812 
       47.05        15.02        11.01         5.03        26.99        35.05 
TCGA-AA-3818 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3845 TCGA-AA-3846 
        0.99         1.02        17.98        15.95         0.00        17.03 
TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3864 TCGA-AA-3877 TCGA-AA-3947 
        0.00         0.00        36.03        53.00        31.00        33.01 
TCGA-AA-3949 TCGA-AA-3966 TCGA-AA-3973 TCGA-AA-3977 TCGA-AA-3994 TCGA-AA-A004 
       26.01         2.01        13.05        25.02        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00R 
       38.04        30.02        18.05        18.05         4.01         0.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       34.98        15.02        31.00        38.07         1.02        35.01 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A029 TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y 
        1.02        26.01        51.98         0.92        22.03        39.98 
TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6889 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-6197 
       18.05        12.16        83.24         0.92        27.09        21.44 
TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4315 TCGA-AZ-4615 
       17.82        17.26        19.33        18.84        58.39        32.94 
TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6606 TCGA-CA-5255 TCGA-CA-5796 
       62.79        49.41         6.77        11.74        12.36        12.39 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 
       12.76        10.06        17.56        85.45        70.16        15.62 
TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       51.32        21.14        82.95       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       37.02        26.04        22.98        30.08        32.02        15.02 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6165 TCGA-CM-6168 TCGA-CM-6171 
       15.02        12.00        14.04        16.04        12.99        14.04 
TCGA-CM-6674 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-6529 TCGA-D5-6530 
       12.95        11.08        11.01        12.03        20.19        20.42 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6540 TCGA-D5-6920 TCGA-D5-6927 TCGA-D5-6928 
       17.85         4.80        16.14        12.39         9.44        11.64 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A1D6 TCGA-DM-A1DA 
       13.35        12.00        10.26       119.70        49.91         7.50 
TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A28C TCGA-DM-A28G TCGA-DM-A28K TCGA-DM-A28M 
      135.65         7.76        81.37        60.79        98.24        95.18 
TCGA-F4-6459 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        35.74        35.74         6.18        47.87         1.55 
TCGA-F4-6806 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6297 
       41.42         0.53        47.41        35.31       133.18        82.39 
TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6309 TCGA-G4-6322 TCGA-G4-6323 
       74.56        67.30        53.62        85.48        26.04        13.78 
TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A5IV TCGA-QG-A5Z2 TCGA-WS-AB45 
       74.79        18.18        19.33        31.30        70.03 

  DEL PEAK 35(17P12) MUTATED DEL PEAK 35(17P12) WILD-TYPE 
                         0.2                          0.0 
  DEL PEAK 35(17P12) MUTATED DEL PEAK 35(17P12) WILD-TYPE 
                      148.01                       135.65 
  DEL PEAK 35(17P12) MUTATED DEL PEAK 35(17P12) WILD-TYPE 
                       23.01                        21.14 
[1] "0.2 - 148.0 (23.0)" "0.0 - 135.7 (21.1)"
[1] "hr=" "1.2"
D57V2, continuous
                              vv
clus                           STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 35(17P12) MUTATED        36        0       14        56         2
  DEL PEAK 35(17P12) WILD-TYPE      38        1       15        76         8
                              vv
clus                           STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 35(17P12) MUTATED           1        12          8         35
  DEL PEAK 35(17P12) WILD-TYPE         0         8          0         24
                              vv
clus                           STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 35(17P12) MUTATED           31       34        13         2
  DEL PEAK 35(17P12) WILD-TYPE         10       11         4         0
D57V3, multiclass
            clus
vv           DEL PEAK 35(17P12) MUTATED DEL PEAK 35(17P12) WILD-TYPE
  STAGE I                            36                           38
  STAGE IA                            0                            1
  STAGE II                           14                           15
  STAGE IIA                          56                           76
  STAGE IIB                           2                            8
  STAGE IIC                           1                            0
  STAGE III                          12                            8
  STAGE IIIA                          8                            0
  STAGE IIIB                         35                           24
  STAGE IIIC                         31                           10
  STAGE IV                           34                           11
  STAGE IVA                          13                            4
  STAGE IVB                           2                            0
[1] 13  2
[1] 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 35(17P12) MUTATED     7  40 174  31
  DEL PEAK 35(17P12) WILD-TYPE   4  37 131  24
D57V4, multiclass
    clus
vv   DEL PEAK 35(17P12) MUTATED DEL PEAK 35(17P12) WILD-TYPE
  T1                          7                            4
  T2                         40                           37
  T3                        174                          131
  T4                         31                           24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            N0  N1  N2
  DEL PEAK 35(17P12) MUTATED   122  71  59
  DEL PEAK 35(17P12) WILD-TYPE 140  34  23
D57V5, multiclass
    clus
vv   DEL PEAK 35(17P12) MUTATED DEL PEAK 35(17P12) WILD-TYPE
  N0                        122                          140
  N1                         71                           34
  N2                         59                           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"
D57V6, binary
                              cls
clus                             0   1
  DEL PEAK 35(17P12) MUTATED   173  49
  DEL PEAK 35(17P12) WILD-TYPE 155  15
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 35(17P12) MUTATED    173   49
  DEL PEAK 35(17P12) WILD-TYPE  155   15
   clus
vv  DEL PEAK 35(17P12) MUTATED DEL PEAK 35(17P12) WILD-TYPE
  0                        173                          155
  1                         49                           15
[1] 2 2
[1] FALSE
D57V7, binary
                              cls
clus                             0   1
  DEL PEAK 35(17P12) MUTATED   112 140
  DEL PEAK 35(17P12) WILD-TYPE 101  96
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 35(17P12) MUTATED    112  140
  DEL PEAK 35(17P12) WILD-TYPE  101   96
        clus
vv       DEL PEAK 35(17P12) MUTATED DEL PEAK 35(17P12) WILD-TYPE
  FEMALE                        112                          101
  MALE                          140                           96
[1] 2 2
[1] FALSE
D57V8, binary
                              cls
clus                             0   1
  DEL PEAK 35(17P12) MUTATED   210   5
  DEL PEAK 35(17P12) WILD-TYPE 160   4
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 35(17P12) MUTATED    210    5
  DEL PEAK 35(17P12) WILD-TYPE  160    4
     clus
vv    DEL PEAK 35(17P12) MUTATED DEL PEAK 35(17P12) WILD-TYPE
  NO                         210                          160
  YES                          5                            4
[1] 2 2
[1] FALSE
D57V9, binary
                              cls
clus                             0   1
  DEL PEAK 35(17P12) MUTATED   232  16
  DEL PEAK 35(17P12) WILD-TYPE 150  46
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 35(17P12) MUTATED    232   16
  DEL PEAK 35(17P12) WILD-TYPE  150   46
                               clus
vv                              DEL PEAK 35(17P12) MUTATED
  COLON ADENOCARCINOMA                                 232
  COLON MUCINOUS ADENOCARCINOMA                         16
                               clus
vv                              DEL PEAK 35(17P12) WILD-TYPE
  COLON ADENOCARCINOMA                                   150
  COLON MUCINOUS ADENOCARCINOMA                           46
[1] 2 2
[1] FALSE
                              vv
clus                            R0  R1  R2  RX
  DEL PEAK 35(17P12) MUTATED   177   2  17  10
  DEL PEAK 35(17P12) WILD-TYPE 146   2   8  15
D57V10, multiclass
    clus
vv   DEL PEAK 35(17P12) MUTATED DEL PEAK 35(17P12) WILD-TYPE
  R0                        177                          146
  R1                          2                            2
  R2                         17                            8
  RX                         10                           15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V11, continuous
                              vv
clus                           AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 35(17P12) MUTATED                                  0     6
  DEL PEAK 35(17P12) WILD-TYPE                                1     5
                              vv
clus                           BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 35(17P12) MUTATED                          36   119
  DEL PEAK 35(17P12) WILD-TYPE                        23    93
D57V12, multiclass
                                  clus
vv                                 DEL PEAK 35(17P12) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          0
  ASIAN                                                     6
  BLACK OR AFRICAN AMERICAN                                36
  WHITE                                                   119
                                  clus
vv                                 DEL PEAK 35(17P12) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       5
  BLACK OR AFRICAN AMERICAN                                  23
  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"
D57V13, binary
                              cls
clus                             0   1
  DEL PEAK 35(17P12) MUTATED     3 151
  DEL PEAK 35(17P12) WILD-TYPE   1 118
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 35(17P12) MUTATED      3  151
  DEL PEAK 35(17P12) WILD-TYPE    1  118
                        clus
vv                       DEL PEAK 35(17P12) MUTATED
  HISPANIC OR LATINO                              3
  NOT HISPANIC OR LATINO                        151
                        clus
vv                       DEL PEAK 35(17P12) WILD-TYPE
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                          118
[1] 2 2
[1] FALSE

Clustering(58) Variable = DEL PEAK 36(17Q24.3) MUTATION ANALYSIS
D58V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 36(17Q24.3) MUTATED    47  21
  DEL PEAK 36(17Q24.3) WILD-TYPE 288  80
  DEL PEAK 36(17Q24.3) MUTATED DEL PEAK 36(17Q24.3) WILD-TYPE 
                            68                            368 
  DEL PEAK 36(17Q24.3) MUTATED DEL PEAK 36(17Q24.3) WILD-TYPE 
                            21                             80 
$`DEL PEAK 36(17Q24.3) MUTATED`
TCGA-A6-6649 TCGA-AA-3520 TCGA-AA-3560 TCGA-AA-3662 TCGA-AA-3688 TCGA-AA-3976 
       24.16        24.03        19.99         6.05        19.00        26.01 
TCGA-CK-5912 TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2684 TCGA-A6-4107 TCGA-A6-5657 
       49.08        43.76        43.76        37.05        32.45        31.63 
TCGA-A6-6138 TCGA-A6-6648 TCGA-AA-3542 TCGA-AA-3549 TCGA-AA-3666 TCGA-AA-3673 
       22.52        25.18        12.99        21.01         2.01        50.04 
TCGA-AA-3685 TCGA-AA-3811 TCGA-AA-3842 TCGA-AA-3858 TCGA-AA-3869 TCGA-AA-3941 
       37.05        10.06        37.02        31.07        27.02        24.00 
TCGA-AA-3989 TCGA-AA-A00F TCGA-AA-A00Q TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01T 
        7.96        34.03        42.02        10.98        32.02        33.04 
TCGA-AA-A02E TCGA-AA-A02F TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6965 TCGA-AY-6196 
        2.96        39.98         5.79        22.42        26.47         0.20 
TCGA-AY-A69D TCGA-AY-A8YK TCGA-AZ-6600 TCGA-CA-5797 TCGA-CA-6716 TCGA-CM-4747 
       17.85        18.84        12.10        12.59        12.20        25.02 
TCGA-CM-4751 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-6170 TCGA-D5-5537 TCGA-D5-6534 
       27.02         5.03        15.02        15.02        45.40        43.27 
TCGA-D5-6539 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D8 
       12.49        13.41        11.38        38.20       130.65        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A280 TCGA-DM-A28H TCGA-F4-6460 TCGA-F4-6569 
      140.38        44.32         7.76       117.07        31.96        35.74 
TCGA-F4-6704 TCGA-F4-6809 TCGA-G4-6295 TCGA-NH-A50U TCGA-NH-A6GA TCGA-NH-A6GC 
        1.55        13.25         8.35        10.98         9.93        12.79 
TCGA-QG-A5YV TCGA-QL-A97D 
       42.77        21.90 

$`DEL PEAK 36(17Q24.3) WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-4105 TCGA-AA-3496 TCGA-AA-3506 
       24.33        45.60        13.94        14.53         1.02        58.03 
TCGA-AA-3516 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 
       13.02        37.05        36.03         8.05        19.07        34.03 
TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3562 TCGA-AA-3672 
        0.99        13.02        17.95        23.01        19.99         0.92 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 
       36.00        85.05        19.04        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 
       24.00        19.07        38.04        21.99        39.06        21.37 
TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 
       15.52        25.08        10.88        75.95       106.75       100.01 
TCGA-AZ-6608 TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6314 
        1.94         5.88        28.21        23.51        63.62        35.93 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-NH-A8F7 
       22.09        35.80        26.17        91.79        79.69        17.85 
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-5M-AATE 
       15.62         4.80        12.66         1.61         9.53        39.45 
TCGA-A6-2672 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 
       46.65        43.43        42.90        42.28        44.91        35.11 
TCGA-A6-2683 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-3810 
       16.57        37.25        37.02        34.65        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6141 
       22.06        32.71        29.16        27.09        24.13         8.38 
TCGA-A6-6142 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.08        20.61        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 
       20.12        19.66        20.28        16.24        24.92        61.84 
TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 
       56.25         9.63         5.03         7.04         3.02         1.02 
TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
       37.05        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       26.01        14.01        33.99        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 
       13.94        61.02        78.08         6.97        54.02        14.01 
TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3696 
       47.05        47.01        15.02        11.01         5.98         5.03 
TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       26.99        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       15.95        38.99        36.95         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 
       53.00        17.03        18.05        31.00         2.01        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3994 TCGA-AA-A004 
       13.05        34.06        25.02        27.02        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N 
       38.04        19.00        30.02        18.05        18.05         4.01 
TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       27.02         0.99        17.03        14.99        34.98        15.02 
TCGA-AA-A01C TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       15.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 
       35.01         1.02         1.02        26.01        37.02        51.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03         0.92        22.03        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6963 
       18.05        40.96        12.16        83.24        24.53        27.42 
TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       16.44         0.46         0.92        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A71X 
        0.95        33.01        21.44        17.82        17.26        19.33 
TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 
      109.28        58.39         1.41         5.65        32.94         5.13 
TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       22.36        65.00        62.79        88.21        49.41         6.77 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.46        12.39        12.59        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 
       17.56       148.01        85.45        70.16        15.62        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14        82.95         2.01       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5341 
       20.02        37.02        26.04         8.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 
       22.03        22.98        30.08        32.02        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6171 TCGA-CM-6172 
       21.99        14.99        12.99        13.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       12.03        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6536 
       20.42        17.75        18.25        25.48        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
        4.80        17.13        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A1D4 
       13.35        12.00        10.26       119.70        24.43        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
       49.91        13.32         7.50       131.51       135.65       139.17 
TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
       14.04        26.47        81.37       119.93        35.97        60.79 
TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6570 
       98.24        95.18         8.61        11.11        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6854 
       47.87        34.42        41.42        43.04        33.67         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6302 
       47.41        35.31       133.18        82.39        74.56        67.30 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 
       65.85        53.62        44.68        55.04        85.48        39.42 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6626 
       61.91        36.00        26.43        26.04        13.78        46.75 
TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GB TCGA-NH-A8F8 
       74.79        18.18        19.33        19.33        15.65        16.80 
TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-RU-A8FL TCGA-SS-A7HO 
       29.46        32.98         8.42        31.30        38.70        60.13 
TCGA-T9-A92H TCGA-WS-AB45 
       11.90        70.03 

  DEL PEAK 36(17Q24.3) MUTATED DEL PEAK 36(17Q24.3) WILD-TYPE 
                           0.2                            0.0 
  DEL PEAK 36(17Q24.3) MUTATED DEL PEAK 36(17Q24.3) WILD-TYPE 
                        140.38                         148.01 
  DEL PEAK 36(17Q24.3) MUTATED DEL PEAK 36(17Q24.3) WILD-TYPE 
                         23.26                          22.01 
[1] "0.2 - 140.4 (23.3)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.6"
D58V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 36(17Q24.3) MUTATED        10        0        4        10         0
  DEL PEAK 36(17Q24.3) WILD-TYPE      64        1       25       122        10
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 36(17Q24.3) MUTATED           0         3          2          7
  DEL PEAK 36(17Q24.3) WILD-TYPE         1        17          6         52
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 36(17Q24.3) MUTATED           12       10         7         1
  DEL PEAK 36(17Q24.3) WILD-TYPE         29       35        10         1
D58V3, multiclass
            clus
vv           DEL PEAK 36(17Q24.3) MUTATED DEL PEAK 36(17Q24.3) WILD-TYPE
  STAGE I                              10                             64
  STAGE IA                              0                              1
  STAGE II                              4                             25
  STAGE IIA                            10                            122
  STAGE IIB                             0                             10
  STAGE IIC                             0                              1
  STAGE III                             3                             17
  STAGE IIIA                            2                              6
  STAGE IIIB                            7                             52
  STAGE IIIC                           12                             29
  STAGE IV                             10                             35
  STAGE IVA                             7                             10
  STAGE IVB                             1                              1
[1] 13  2
[1] 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 36(17Q24.3) MUTATED     0  12  45  12
  DEL PEAK 36(17Q24.3) WILD-TYPE  11  65 260  43
D58V4, multiclass
    clus
vv   DEL PEAK 36(17Q24.3) MUTATED DEL PEAK 36(17Q24.3) WILD-TYPE
  T1                            0                             11
  T2                           12                             65
  T3                           45                            260
  T4                           12                             43
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2
  DEL PEAK 36(17Q24.3) MUTATED    27  23  19
  DEL PEAK 36(17Q24.3) WILD-TYPE 235  82  63
D58V5, multiclass
    clus
vv   DEL PEAK 36(17Q24.3) MUTATED DEL PEAK 36(17Q24.3) WILD-TYPE
  N0                           27                            235
  N1                           23                             82
  N2                           19                             63
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V6, binary
                                cls
clus                               0   1
  DEL PEAK 36(17Q24.3) MUTATED    40  18
  DEL PEAK 36(17Q24.3) WILD-TYPE 288  46
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 36(17Q24.3) MUTATED     40   18
  DEL PEAK 36(17Q24.3) WILD-TYPE  288   46
   clus
vv  DEL PEAK 36(17Q24.3) MUTATED DEL PEAK 36(17Q24.3) WILD-TYPE
  0                           40                            288
  1                           18                             46
[1] 2 2
[1] FALSE
D58V7, binary
                                cls
clus                               0   1
  DEL PEAK 36(17Q24.3) MUTATED    29  40
  DEL PEAK 36(17Q24.3) WILD-TYPE 184 196
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 36(17Q24.3) MUTATED     29   40
  DEL PEAK 36(17Q24.3) WILD-TYPE  184  196
        clus
vv       DEL PEAK 36(17Q24.3) MUTATED DEL PEAK 36(17Q24.3) WILD-TYPE
  FEMALE                           29                            184
  MALE                             40                            196
[1] 2 2
[1] FALSE
D58V8, binary
                                cls
clus                               0   1
  DEL PEAK 36(17Q24.3) MUTATED    56   1
  DEL PEAK 36(17Q24.3) WILD-TYPE 314   8
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 36(17Q24.3) MUTATED     56    1
  DEL PEAK 36(17Q24.3) WILD-TYPE  314    8
     clus
vv    DEL PEAK 36(17Q24.3) MUTATED DEL PEAK 36(17Q24.3) WILD-TYPE
  NO                            56                            314
  YES                            1                              8
[1] 2 2
[1] FALSE
D58V9, binary
                                cls
clus                               0   1
  DEL PEAK 36(17Q24.3) MUTATED    59   9
  DEL PEAK 36(17Q24.3) WILD-TYPE 323  53
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 36(17Q24.3) MUTATED     59    9
  DEL PEAK 36(17Q24.3) WILD-TYPE  323   53
                               clus
vv                              DEL PEAK 36(17Q24.3) MUTATED
  COLON ADENOCARCINOMA                                    59
  COLON MUCINOUS ADENOCARCINOMA                            9
                               clus
vv                              DEL PEAK 36(17Q24.3) WILD-TYPE
  COLON ADENOCARCINOMA                                     323
  COLON MUCINOUS ADENOCARCINOMA                             53
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 36(17Q24.3) MUTATED    43   1   6   4
  DEL PEAK 36(17Q24.3) WILD-TYPE 280   3  19  21
D58V10, multiclass
    clus
vv   DEL PEAK 36(17Q24.3) MUTATED DEL PEAK 36(17Q24.3) WILD-TYPE
  R0                           43                            280
  R1                            1                              3
  R2                            6                             19
  RX                            4                             21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 36(17Q24.3) MUTATED                                  1     2
  DEL PEAK 36(17Q24.3) WILD-TYPE                                0     9
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 36(17Q24.3) MUTATED                           9    34
  DEL PEAK 36(17Q24.3) WILD-TYPE                        50   178
D58V12, multiclass
                                  clus
vv                                 DEL PEAK 36(17Q24.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                   9
  WHITE                                                      34
                                  clus
vv                                 DEL PEAK 36(17Q24.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         9
  BLACK OR AFRICAN AMERICAN                                    50
  WHITE                                                       178
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V13, binary
                                cls
clus                               0   1
  DEL PEAK 36(17Q24.3) MUTATED     0  43
  DEL PEAK 36(17Q24.3) WILD-TYPE   4 226
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 36(17Q24.3) MUTATED      0   43
  DEL PEAK 36(17Q24.3) WILD-TYPE    4  226
                        clus
vv                       DEL PEAK 36(17Q24.3) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           43
                        clus
vv                       DEL PEAK 36(17Q24.3) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            226
[1] 2 2
[1] FALSE

Clustering(59) Variable = DEL PEAK 37(18P11.31) MUTATION ANALYSIS
D59V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 37(18P11.31) MUTATED   190  51
  DEL PEAK 37(18P11.31) WILD-TYPE 145  50
  DEL PEAK 37(18P11.31) MUTATED DEL PEAK 37(18P11.31) WILD-TYPE 
                            241                             195 
  DEL PEAK 37(18P11.31) MUTATED DEL PEAK 37(18P11.31) WILD-TYPE 
                             51                              50 
$`DEL PEAK 37(18P11.31) MUTATED`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-4105 TCGA-AA-3496 TCGA-AA-3522 
       24.33        45.60        13.94        14.53         1.02        37.05 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3552 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 
       19.07        34.03        13.02        23.01        19.99        19.99 
TCGA-AA-3662 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3844 TCGA-AA-3860 
        6.05        19.00        36.00        85.05        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 
       24.03        29.98        12.99        50.99        26.01        24.00 
TCGA-AA-A00L TCGA-AA-A00Z TCGA-AD-6548 TCGA-AD-6888 TCGA-AZ-4681 TCGA-AZ-6608 
       38.04        21.99        21.37        15.52       106.75         1.94 
TCGA-CK-5912 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6625 TCGA-NH-A8F7 
       49.08        28.21        23.51        63.62        91.79        17.85 
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AATE TCGA-A6-2671 
       15.62         4.80        12.66         1.61        39.45        43.76 
TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 
       43.76        43.43        42.28        44.91        35.11        16.57 
TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 
       37.05        37.25        34.65        36.53        32.45        32.91 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-5667 
       30.44        29.19        23.61        22.09        32.71        29.16 
TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6651 
       27.09        24.13        25.08        25.18        20.61        21.76 
TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6782 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU 
       24.69        23.87        20.28        61.84        56.25         9.63 
TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3511 TCGA-AA-3517 
        5.03         7.04         1.02        37.05         6.97        38.99 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3532 TCGA-AA-3538 TCGA-AA-3544 TCGA-AA-3548 
        9.07        19.07        29.00        26.01        14.01        33.99 
TCGA-AA-3553 TCGA-AA-3561 TCGA-AA-3660 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       24.00        13.94        78.08         2.01        14.01        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3685 TCGA-AA-3819 TCGA-AA-3837 TCGA-AA-3841 
       47.01        15.02        37.05        25.02        38.99        36.95 
TCGA-AA-3842 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3856 TCGA-AA-3858 
       37.02        17.03        10.06        33.07         0.99        31.07 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3941 TCGA-AA-3955 TCGA-AA-3956 
       17.03        27.02        18.05        24.00        20.98        34.03 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3982 TCGA-AA-3989 
       21.99        16.08        13.05        34.06        27.02         7.96 
TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00W 
       13.94        19.00        34.03        27.02        42.02        14.99 
TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01K TCGA-AA-A01T TCGA-AA-A01X 
       15.02        15.02        32.02        31.00        33.04        26.01 
TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02W TCGA-AA-A03J 
        2.96        39.98         2.01         5.03        41.00        40.96 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK 
       24.53         5.79        22.42        27.42        26.47        16.44 
TCGA-AU-3779 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A8YK 
       14.50         0.95        33.01        17.26        17.85        18.84 
TCGA-AZ-4308 TCGA-AZ-4614 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 
      109.28         5.65         5.13        22.36        65.00        62.79 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-CA-5256 TCGA-CA-5797 TCGA-CA-6715 
       12.10        29.56         5.23        12.46        12.59        12.59 
TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-5914 TCGA-CK-6748 TCGA-CM-4747 TCGA-CM-4748 
       12.20        14.30        21.99         2.01        25.02        26.04 
TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5862 
        8.02        13.02        29.06        22.03        30.08         5.03 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        17.03        14.04        29.03        16.04        21.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       13.02        15.02        11.01        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       12.03        45.40        54.61        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6539 
       18.25        25.48        15.12        17.85        17.13        12.49 
TCGA-D5-6898 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6932 
        7.53        12.43        14.30         9.04        13.41        11.38 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
       24.43        38.20       130.65        13.32        12.59       140.38 
TCGA-DM-A1DB TCGA-DM-A282 TCGA-DM-A28A TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28H 
       44.32       139.17        26.47       119.93        35.97       117.07 
TCGA-DM-A28M TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       95.18        31.96        35.74         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6295 
       43.04        33.67        13.25         0.53        47.41         8.35 
TCGA-G4-6297 TCGA-G4-6303 TCGA-G4-6307 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6626 
       82.39        65.85        55.04        61.91        36.00        46.75 
TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A6GC TCGA-NH-A8F8 
       74.79        18.18        10.98        19.33        12.79        16.80 
TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QL-A97D TCGA-RU-A8FL TCGA-SS-A7HO 
       42.77        32.98         8.42        21.90        38.70        60.13 
TCGA-T9-A92H 
       11.90 

$`DEL PEAK 37(18P11.31) WILD-TYPE`
TCGA-A6-6649 TCGA-AA-3506 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3525 
       24.16        58.03        13.02        24.03        36.03         8.05 
TCGA-AA-3543 TCGA-AA-3554 TCGA-AA-3672 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3950 
        0.99        17.95         0.92        19.04        19.04        24.00 
TCGA-AA-3952 TCGA-AA-3986 TCGA-AA-A024 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 
        2.01        19.07        39.06        25.08        10.88        75.95 
TCGA-AZ-6601 TCGA-DM-A285 TCGA-G4-6314 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
      100.01         5.88        35.93        22.09        35.80        26.17 
TCGA-G4-6628 TCGA-5M-AAT6 TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2686 TCGA-A6-3809 
       79.69         9.53        46.65        42.90        37.02        32.75 
TCGA-A6-5657 TCGA-A6-5661 TCGA-A6-5665 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6653 
       31.63        33.53        22.06        22.52         8.38        24.39 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 TCGA-AA-3492 TCGA-AA-3502 
       20.12        19.66        16.24        24.92         3.02        35.01 
TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3518 TCGA-AA-3529 TCGA-AA-3534 TCGA-AA-3542 
       63.98         1.02         1.02         0.00        29.00        12.99 
TCGA-AA-3549 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3664 
       21.01        29.95        20.98        61.02         6.97        54.02 
TCGA-AA-3675 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 
       47.05        11.01         5.98         5.03        26.99        10.06 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3845 
       35.05         0.99         1.02        17.98        15.95         0.00 
TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3864 TCGA-AA-3877 
        0.00         0.00        36.03        32.05        53.00        31.00 
TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-3994 
        2.01        33.01        26.01         2.01        25.02        27.02 
TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00R 
       38.04        30.02        18.05        18.05         4.01         0.99 
TCGA-AA-A00U TCGA-AA-A010 TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P 
       17.03        34.98        10.98        12.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A029 
        1.02        35.01         1.02         1.02        37.02        51.98 
TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6889 
        0.92        22.03        39.98        18.05        12.16        83.24 
TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-6196 TCGA-AY-6197 
        0.46         0.92        27.09        16.31         0.20        21.44 
TCGA-AY-6386 TCGA-AY-A71X TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-5407 
       17.82        19.33        58.39         1.41        32.94        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 
       49.41         6.77        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.39        12.76        10.06        17.56       148.01        85.45 
TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 
       70.16        15.62        51.32        21.14        82.95       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4751 TCGA-CM-5348 TCGA-CM-5860 
       23.05        20.02        37.02        27.02        22.98        32.02 
TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6167 TCGA-CM-6168 
       15.02        15.02        15.02        12.00        14.99        12.99 
TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-D5-5539 TCGA-D5-6530 
       14.04        12.95        13.05        11.08        19.59        20.42 
TCGA-D5-6531 TCGA-D5-6534 TCGA-D5-6537 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 
       17.75        43.27         4.80        16.14        15.58        12.39 
TCGA-D5-6922 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 
       10.13         9.44        11.64        13.35        12.00        10.26 
TCGA-DM-A0X9 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A1HB 
      119.70        92.75        49.91         7.50       131.51       135.65 
TCGA-DM-A280 TCGA-DM-A288 TCGA-DM-A28C TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6459 
        7.76        14.04        81.37        60.79        98.24         8.61 
TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6856 TCGA-G4-6293 
       11.11        35.74         6.18        47.87        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6311 
       74.56        67.30        53.62        44.68        85.48        39.42 
TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB 
       26.43        26.04        13.78        19.33         9.93        15.65 
TCGA-QG-A5YW TCGA-QG-A5Z2 TCGA-WS-AB45 
       29.46        31.30        70.03 

  DEL PEAK 37(18P11.31) MUTATED DEL PEAK 37(18P11.31) WILD-TYPE 
                           0.53                            0.00 
  DEL PEAK 37(18P11.31) MUTATED DEL PEAK 37(18P11.31) WILD-TYPE 
                         140.38                          148.01 
  DEL PEAK 37(18P11.31) MUTATED DEL PEAK 37(18P11.31) WILD-TYPE 
                          23.87                           20.12 
[1] "0.5 - 140.4 (23.9)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.2"
D59V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 37(18P11.31) MUTATED        37        0       11        66         3
  DEL PEAK 37(18P11.31) WILD-TYPE      37        1       18        66         7
                                 vv
clus                              STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 37(18P11.31) MUTATED           1         7          6         36
  DEL PEAK 37(18P11.31) WILD-TYPE         0        13          2         23
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 37(18P11.31) MUTATED           22       34        16         1
  DEL PEAK 37(18P11.31) WILD-TYPE         19       11         1         1
D59V3, multiclass
            clus
vv           DEL PEAK 37(18P11.31) MUTATED DEL PEAK 37(18P11.31) WILD-TYPE
  STAGE I                               37                              37
  STAGE IA                               0                               1
  STAGE II                              11                              18
  STAGE IIA                             66                              66
  STAGE IIB                              3                               7
  STAGE IIC                              1                               0
  STAGE III                              7                              13
  STAGE IIIA                             6                               2
  STAGE IIIB                            36                              23
  STAGE IIIC                            22                              19
  STAGE IV                              34                              11
  STAGE IVA                             16                               1
  STAGE IVB                              1                               1
[1] 13  2
[1] 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 37(18P11.31) MUTATED     7  41 168  31
  DEL PEAK 37(18P11.31) WILD-TYPE   4  36 137  24
D59V4, multiclass
    clus
vv   DEL PEAK 37(18P11.31) MUTATED DEL PEAK 37(18P11.31) WILD-TYPE
  T1                             7                               4
  T2                            41                              36
  T3                           168                             137
  T4                            31                              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               N0  N1  N2
  DEL PEAK 37(18P11.31) MUTATED   130  70  47
  DEL PEAK 37(18P11.31) WILD-TYPE 132  35  35
D59V5, multiclass
    clus
vv   DEL PEAK 37(18P11.31) MUTATED DEL PEAK 37(18P11.31) WILD-TYPE
  N0                           130                             132
  N1                            70                              35
  N2                            47                              35
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V6, binary
                                 cls
clus                                0   1
  DEL PEAK 37(18P11.31) MUTATED   165  51
  DEL PEAK 37(18P11.31) WILD-TYPE 163  13
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 37(18P11.31) MUTATED    165   51
  DEL PEAK 37(18P11.31) WILD-TYPE  163   13
   clus
vv  DEL PEAK 37(18P11.31) MUTATED DEL PEAK 37(18P11.31) WILD-TYPE
  0                           165                             163
  1                            51                              13
[1] 2 2
[1] FALSE
D59V7, binary
                                 cls
clus                                0   1
  DEL PEAK 37(18P11.31) MUTATED   113 134
  DEL PEAK 37(18P11.31) WILD-TYPE 100 102
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 37(18P11.31) MUTATED    113  134
  DEL PEAK 37(18P11.31) WILD-TYPE  100  102
        clus
vv       DEL PEAK 37(18P11.31) MUTATED DEL PEAK 37(18P11.31) WILD-TYPE
  FEMALE                           113                             100
  MALE                             134                             102
[1] 2 2
[1] FALSE
D59V8, binary
                                 cls
clus                                0   1
  DEL PEAK 37(18P11.31) MUTATED   212   5
  DEL PEAK 37(18P11.31) WILD-TYPE 158   4
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 37(18P11.31) MUTATED    212    5
  DEL PEAK 37(18P11.31) WILD-TYPE  158    4
     clus
vv    DEL PEAK 37(18P11.31) MUTATED DEL PEAK 37(18P11.31) WILD-TYPE
  NO                            212                             158
  YES                             5                               4
[1] 2 2
[1] FALSE
D59V9, binary
                                 cls
clus                                0   1
  DEL PEAK 37(18P11.31) MUTATED   233  10
  DEL PEAK 37(18P11.31) WILD-TYPE 149  52
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 37(18P11.31) MUTATED    233   10
  DEL PEAK 37(18P11.31) WILD-TYPE  149   52
                               clus
vv                              DEL PEAK 37(18P11.31) MUTATED
  COLON ADENOCARCINOMA                                    233
  COLON MUCINOUS ADENOCARCINOMA                            10
                               clus
vv                              DEL PEAK 37(18P11.31) WILD-TYPE
  COLON ADENOCARCINOMA                                      149
  COLON MUCINOUS ADENOCARCINOMA                              52
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 37(18P11.31) MUTATED   174   1  18  11
  DEL PEAK 37(18P11.31) WILD-TYPE 149   3   7  14
D59V10, multiclass
    clus
vv   DEL PEAK 37(18P11.31) MUTATED DEL PEAK 37(18P11.31) WILD-TYPE
  R0                           174                             149
  R1                             1                               3
  R2                            18                               7
  RX                            11                              14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V11, continuous
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 37(18P11.31) MUTATED                                  1     5
  DEL PEAK 37(18P11.31) WILD-TYPE                                0     6
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 37(18P11.31) MUTATED                          36   118
  DEL PEAK 37(18P11.31) WILD-TYPE                        23    94
D59V12, multiclass
                                  clus
vv                                 DEL PEAK 37(18P11.31) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        5
  BLACK OR AFRICAN AMERICAN                                   36
  WHITE                                                      118
                                  clus
vv                                 DEL PEAK 37(18P11.31) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               0
  ASIAN                                                          6
  BLACK OR AFRICAN AMERICAN                                     23
  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"
D59V13, binary
                                 cls
clus                                0   1
  DEL PEAK 37(18P11.31) MUTATED     3 149
  DEL PEAK 37(18P11.31) WILD-TYPE   1 120
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 37(18P11.31) MUTATED      3  149
  DEL PEAK 37(18P11.31) WILD-TYPE    1  120
                        clus
vv                       DEL PEAK 37(18P11.31) MUTATED
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           149
                        clus
vv                       DEL PEAK 37(18P11.31) WILD-TYPE
  HISPANIC OR LATINO                                   1
  NOT HISPANIC OR LATINO                             120
[1] 2 2
[1] FALSE

Clustering(60) Variable = DEL PEAK 38(18Q12.2) MUTATION ANALYSIS
D60V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 38(18Q12.2) MUTATED   206  60
  DEL PEAK 38(18Q12.2) WILD-TYPE 129  41
  DEL PEAK 38(18Q12.2) MUTATED DEL PEAK 38(18Q12.2) WILD-TYPE 
                           266                            170 
  DEL PEAK 38(18Q12.2) MUTATED DEL PEAK 38(18Q12.2) WILD-TYPE 
                            60                             41 
$`DEL PEAK 38(18Q12.2) MUTATED`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-4105 TCGA-AA-3496 TCGA-AA-3520 
       24.33        45.60        13.94        14.53         1.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3552 TCGA-AA-3556 
       37.05        36.03        19.07        34.03        13.02        23.01 
TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 
       19.99        19.99         6.05        19.00        36.00        85.05 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 
       14.93        31.07        24.03        29.98        12.99         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-A00Z TCGA-AD-6888 TCGA-AD-6964 
       50.99        26.01        24.00        21.99        15.52        10.88 
TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6298 
      106.75         1.94        49.08         5.88        28.21        23.51 
TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6625 TCGA-NH-A8F7 TCGA-3L-AA1B TCGA-4N-A93T 
       63.62        35.93        91.79        17.85        15.62         4.80 
TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 
       12.66         1.61        39.45        43.76        43.76        43.43 
TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 
       42.28        44.91        35.11        16.57        37.05        37.25 
TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 
       37.02        34.65        36.53        32.45        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 
       30.44        29.19        23.61        32.71        29.16        27.09 
TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6654 
       22.52        24.13        25.18        20.61        21.76        23.87 
TCGA-A6-6782 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 
       20.28        61.84        56.25         9.63         5.03         7.04 
TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3511 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3526 
        1.02        37.05         6.97        38.99         9.07        19.07 
TCGA-AA-3532 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       29.00        26.01        12.99        14.01        33.99        21.01 
TCGA-AA-3553 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3666 TCGA-AA-3667 
       24.00        13.94        61.02        78.08         2.01        14.01 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3819 
       50.04        47.01        15.02         5.98        37.05        25.02 
TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 
       38.99        36.95        37.02        17.03        10.06        33.07 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3941 
        0.99        31.07        17.03        27.02        18.05        24.00 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       20.98        34.03        21.99        16.08        13.05        34.06 
TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00Q 
       27.02         7.96        19.00        34.03        18.05        42.02 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        15.02        15.02        10.98        32.02 
TCGA-AA-A01K TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A02E 
       31.00         1.02        33.04        26.01        37.02         2.96 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A03J 
       39.98         2.01         5.03         0.92        41.00        40.96 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK 
       24.53         5.79        22.42        27.42        26.47        16.44 
TCGA-AM-5820 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-5543 TCGA-AY-A54L TCGA-AY-A69D 
        0.46        14.50        16.31        33.01        17.26        17.85 
TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 
       18.84       109.28         5.13        22.36        65.00        62.79 
TCGA-AZ-5407 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-CA-5254 TCGA-CA-5256 
       88.21        12.10        29.56         5.23        12.69        12.46 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-5914 
       12.59        12.59        12.20        14.30       148.01        21.99 
TCGA-CK-6748 TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 
        2.01        25.02         8.02        27.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6163 
       22.03        30.08         5.03        15.02        17.03        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 
       29.03        16.04        21.99        13.02        15.02        11.01 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 
       25.48        17.85        17.13        12.49        15.58         7.53 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6932 
       10.13        12.43        14.30         9.04        13.41        11.38 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 
       12.59       140.38         7.50        44.32       131.51       139.17 
TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28E TCGA-DM-A28H TCGA-DM-A28M TCGA-F4-6459 
       14.04        26.47       119.93       117.07        95.18         8.61 
TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6569 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       31.96        11.11        35.74         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6295 TCGA-G4-6297 
       43.04        13.25         0.53        47.41         8.35        82.39 
TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6317 
       65.85        44.68        55.04        39.42        61.91        36.00 
TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A6GC 
       46.75        74.79        18.18        10.98        19.33        12.79 
TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QL-A97D TCGA-RU-A8FL 
       16.80        42.77        32.98         8.42        21.90        38.70 
TCGA-SS-A7HO TCGA-T9-A92H 
       60.13        11.90 

$`DEL PEAK 38(18Q12.2) WILD-TYPE`
TCGA-A6-6649 TCGA-AA-3506 TCGA-AA-3516 TCGA-AA-3525 TCGA-AA-3543 TCGA-AA-3554 
       24.16        58.03        13.02         8.05         0.99        17.95 
TCGA-AA-3672 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3950 TCGA-AA-3986 TCGA-AA-A00L 
        0.92        19.04        19.04        24.00        19.07        38.04 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6895 TCGA-AZ-4313 TCGA-AZ-6601 TCGA-G4-6321 
       39.06        21.37        25.08        75.95       100.01        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 TCGA-5M-AAT6 TCGA-A6-2672 TCGA-A6-2676 
       35.80        26.17        79.69         9.53        46.65        42.90 
TCGA-A6-3809 TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6141 TCGA-A6-6142 
       32.75        33.53        22.09        22.06         8.38        25.08 
TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 
       24.69        24.39        20.12        19.66        16.24        24.92 
TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3518 TCGA-AA-3529 
        3.02        35.01        63.98         1.02         1.02         0.00 
TCGA-AA-3534 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3675 
       29.00        29.95        20.98         6.97        54.02        47.05 
TCGA-AA-3680 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
       11.01         5.03        26.99        10.06        35.05         0.99 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3845 TCGA-AA-3850 TCGA-AA-3852 
        1.02        17.98        15.95         0.00         0.00         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3864 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 
       36.03        32.05        53.00        31.00         2.01        33.01 
TCGA-AA-3949 TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       26.01         2.01        25.02        27.02        13.94        38.04 
TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A010 
       30.02        18.05         4.01        27.02         0.99        34.98 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01V 
       12.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A029 TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6889 
       51.98        22.03        39.98        18.05        12.16        83.24 
TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
        0.92        27.09         0.95         0.20        21.44        17.82 
TCGA-AY-A71X TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-6598 
       19.33        58.39         1.41         5.65        32.94        49.41 
TCGA-AZ-6599 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6717 
        6.77        11.74         3.19        12.36        12.39        12.76 
TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 
       10.06        17.56        85.45        70.16        15.62        51.32 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       21.14        82.95       124.27        23.05        20.02        37.02 
TCGA-CM-4748 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-6161 
       26.04        22.98        32.02        15.02        15.02        15.02 
TCGA-CM-6162 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 
       12.00        14.99        12.99        14.04        12.95        13.05 
TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6540 
       20.42        17.75        43.27        15.12         4.80        16.14 
TCGA-D5-6920 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 
       12.39         9.44        11.64        13.35        12.00        10.26 
TCGA-DM-A0X9 TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A28C TCGA-DM-A28F TCGA-DM-A28G 
      119.70       135.65         7.76        81.37        35.97        60.79 
TCGA-DM-A28K TCGA-F4-6463 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6808 TCGA-F4-6856 
       98.24        35.74         6.18        47.87        33.67        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6309 TCGA-G4-6320 
      133.18        74.56        67.30        53.62        85.48        26.43 
TCGA-G4-6322 TCGA-G4-6323 TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-QG-A5YW 
       26.04        13.78        19.33         9.93        15.65        29.46 
TCGA-QG-A5Z2 TCGA-WS-AB45 
       31.30        70.03 

  DEL PEAK 38(18Q12.2) MUTATED DEL PEAK 38(18Q12.2) WILD-TYPE 
                          0.46                           0.00 
  DEL PEAK 38(18Q12.2) MUTATED DEL PEAK 38(18Q12.2) WILD-TYPE 
                        148.01                         135.65 
  DEL PEAK 38(18Q12.2) MUTATED DEL PEAK 38(18Q12.2) WILD-TYPE 
                        22.470                         21.405 
[1] "0.5 - 148.0 (22.5)" "0.0 - 135.7 (21.4)"
[1] "hr=" "1.1"
D60V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 38(18Q12.2) MUTATED        38        0       16        70         3
  DEL PEAK 38(18Q12.2) WILD-TYPE      36        1       13        62         7
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 38(18Q12.2) MUTATED           1        11          8         37
  DEL PEAK 38(18Q12.2) WILD-TYPE         0         9          0         22
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 38(18Q12.2) MUTATED           28       36        14         1
  DEL PEAK 38(18Q12.2) WILD-TYPE         13        9         3         1
D60V3, multiclass
            clus
vv           DEL PEAK 38(18Q12.2) MUTATED DEL PEAK 38(18Q12.2) WILD-TYPE
  STAGE I                              38                             36
  STAGE IA                              0                              1
  STAGE II                             16                             13
  STAGE IIA                            70                             62
  STAGE IIB                             3                              7
  STAGE IIC                             1                              0
  STAGE III                            11                              9
  STAGE IIIA                            8                              0
  STAGE IIIB                           37                             22
  STAGE IIIC                           28                             13
  STAGE IV                             36                              9
  STAGE IVA                            14                              3
  STAGE IVB                             1                              1
[1] 13  2
[1] 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 38(18Q12.2) MUTATED     6  44 191  31
  DEL PEAK 38(18Q12.2) WILD-TYPE   5  33 114  24
D60V4, multiclass
    clus
vv   DEL PEAK 38(18Q12.2) MUTATED DEL PEAK 38(18Q12.2) WILD-TYPE
  T1                            6                              5
  T2                           44                             33
  T3                          191                            114
  T4                           31                             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2
  DEL PEAK 38(18Q12.2) MUTATED   140  74  58
  DEL PEAK 38(18Q12.2) WILD-TYPE 122  31  24
D60V5, multiclass
    clus
vv   DEL PEAK 38(18Q12.2) MUTATED DEL PEAK 38(18Q12.2) WILD-TYPE
  N0                          140                            122
  N1                           74                             31
  N2                           58                             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"
D60V6, binary
                                cls
clus                               0   1
  DEL PEAK 38(18Q12.2) MUTATED   191  51
  DEL PEAK 38(18Q12.2) WILD-TYPE 137  13
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 38(18Q12.2) MUTATED    191   51
  DEL PEAK 38(18Q12.2) WILD-TYPE  137   13
   clus
vv  DEL PEAK 38(18Q12.2) MUTATED DEL PEAK 38(18Q12.2) WILD-TYPE
  0                          191                            137
  1                           51                             13
[1] 2 2
[1] FALSE
D60V7, binary
                                cls
clus                               0   1
  DEL PEAK 38(18Q12.2) MUTATED   121 151
  DEL PEAK 38(18Q12.2) WILD-TYPE  92  85
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 38(18Q12.2) MUTATED    121  151
  DEL PEAK 38(18Q12.2) WILD-TYPE   92   85
        clus
vv       DEL PEAK 38(18Q12.2) MUTATED DEL PEAK 38(18Q12.2) WILD-TYPE
  FEMALE                          121                             92
  MALE                            151                             85
[1] 2 2
[1] FALSE
D60V8, binary
                                cls
clus                               0   1
  DEL PEAK 38(18Q12.2) MUTATED   226   6
  DEL PEAK 38(18Q12.2) WILD-TYPE 144   3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 38(18Q12.2) MUTATED    226    6
  DEL PEAK 38(18Q12.2) WILD-TYPE  144    3
     clus
vv    DEL PEAK 38(18Q12.2) MUTATED DEL PEAK 38(18Q12.2) WILD-TYPE
  NO                           226                            144
  YES                            6                              3
[1] 2 2
[1] FALSE
D60V9, binary
                                cls
clus                               0   1
  DEL PEAK 38(18Q12.2) MUTATED   255  14
  DEL PEAK 38(18Q12.2) WILD-TYPE 127  48
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 38(18Q12.2) MUTATED    255   14
  DEL PEAK 38(18Q12.2) WILD-TYPE  127   48
                               clus
vv                              DEL PEAK 38(18Q12.2) MUTATED
  COLON ADENOCARCINOMA                                   255
  COLON MUCINOUS ADENOCARCINOMA                           14
                               clus
vv                              DEL PEAK 38(18Q12.2) WILD-TYPE
  COLON ADENOCARCINOMA                                     127
  COLON MUCINOUS ADENOCARCINOMA                             48
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 38(18Q12.2) MUTATED   193   2  18  11
  DEL PEAK 38(18Q12.2) WILD-TYPE 130   2   7  14
D60V10, multiclass
    clus
vv   DEL PEAK 38(18Q12.2) MUTATED DEL PEAK 38(18Q12.2) WILD-TYPE
  R0                          193                            130
  R1                            2                              2
  R2                           18                              7
  RX                           11                             14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 38(18Q12.2) MUTATED                                  1     6
  DEL PEAK 38(18Q12.2) WILD-TYPE                                0     5
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 38(18Q12.2) MUTATED                          36   132
  DEL PEAK 38(18Q12.2) WILD-TYPE                        23    80
D60V12, multiclass
                                  clus
vv                                 DEL PEAK 38(18Q12.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       6
  BLACK OR AFRICAN AMERICAN                                  36
  WHITE                                                     132
                                  clus
vv                                 DEL PEAK 38(18Q12.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         5
  BLACK OR AFRICAN AMERICAN                                    23
  WHITE                                                        80
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V13, binary
                                cls
clus                               0   1
  DEL PEAK 38(18Q12.2) MUTATED     3 164
  DEL PEAK 38(18Q12.2) WILD-TYPE   1 105
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 38(18Q12.2) MUTATED      3  164
  DEL PEAK 38(18Q12.2) WILD-TYPE    1  105
                        clus
vv                       DEL PEAK 38(18Q12.2) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                          164
                        clus
vv                       DEL PEAK 38(18Q12.2) WILD-TYPE
  HISPANIC OR LATINO                                  1
  NOT HISPANIC OR LATINO                            105
[1] 2 2
[1] FALSE

Clustering(61) Variable = DEL PEAK 39(18Q21.2) MUTATION ANALYSIS
D61V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 39(18Q21.2) MUTATED   216  64
  DEL PEAK 39(18Q21.2) WILD-TYPE 119  37
  DEL PEAK 39(18Q21.2) MUTATED DEL PEAK 39(18Q21.2) WILD-TYPE 
                           280                            156 
  DEL PEAK 39(18Q21.2) MUTATED DEL PEAK 39(18Q21.2) WILD-TYPE 
                            64                             37 
$`DEL PEAK 39(18Q21.2) MUTATED`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-4105 TCGA-AA-3496 TCGA-AA-3520 
       24.33        45.60        13.94        14.53         1.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3552 TCGA-AA-3556 
       37.05        36.03        19.07        34.03        13.02        23.01 
TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 
       19.99        19.99         6.05        19.00        36.00        85.05 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 
       14.93        31.07        24.03        29.98        12.99         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-A00Z TCGA-AD-6888 TCGA-AZ-4681 
       50.99        26.01        24.00        21.99        15.52       106.75 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6310 
        1.94        49.08         5.88        28.21        23.51        63.62 
TCGA-G4-6314 TCGA-G4-6625 TCGA-NH-A8F7 TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H 
       35.93        91.79        17.85        15.62         4.80        12.66 
TCGA-5M-AAT4 TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2678 
        1.61        39.45        43.76        43.76        43.43        42.28 
TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 
       44.91        35.11        16.57        37.05        37.25        37.02 
TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       34.65        36.53        32.45        32.91        31.63        30.44 
TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 
       29.19        23.61        22.09        32.71        29.16        27.09 
TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6653 
       22.52        24.13        25.18        20.61        21.76        24.39 
TCGA-A6-6654 TCGA-A6-6782 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 
       23.87        20.28        61.84        56.25         9.63         5.03 
TCGA-AA-3489 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3511 TCGA-AA-3517 TCGA-AA-3519 
        7.04         1.02        37.05         6.97        38.99         9.07 
TCGA-AA-3526 TCGA-AA-3532 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 
       19.07        29.00        26.01        12.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 
       21.01        24.00        13.94        61.02        78.08        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3681 
        2.01        14.01        50.04        47.01        15.02         5.98 
TCGA-AA-3685 TCGA-AA-3819 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3846 
       37.05        25.02        38.99        36.95        37.02        17.03 
TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3866 TCGA-AA-3869 
       10.06        33.07         0.99        31.07        17.03        27.02 
TCGA-AA-3875 TCGA-AA-3941 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 
       18.05        24.00        20.98        34.03        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-A00D TCGA-AA-A00F 
       13.05        34.06        27.02         7.96        19.00        34.03 
TCGA-AA-A00K TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01C 
       18.05        42.02        17.03        14.99        15.02        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01K TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01X 
       10.98        32.02        31.00         1.02        33.04        26.01 
TCGA-AA-A01Z TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O 
       37.02         2.96        39.98         2.01         5.03         0.92 
TCGA-AA-A02W TCGA-AA-A03J TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       41.00        40.96        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-5543 
       26.47        16.44         0.46        14.50        16.31        33.01 
TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4614 
       17.82        17.26        17.85        18.84       109.28         5.65 
TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6600 
        5.13        22.36        65.00        62.79        88.21        12.10 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5256 
       29.56         5.23        11.74         3.19        12.69        12.46 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-5914 
       12.59        12.59        12.20        14.30       148.01        21.99 
TCGA-CK-6748 TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 
        2.01        25.02         8.02        27.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6163 
       22.03        30.08         5.03        15.02        17.03        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 
       29.03        16.04        21.99        13.02        15.02        11.01 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6539 
       17.75        18.25        25.48        17.85        17.13        12.49 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
       15.58         7.53        10.13        12.43        14.30         9.04 
TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       13.41        11.38        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28E TCGA-DM-A28F 
      131.51       139.17        14.04        26.47       119.93        35.97 
TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 
      117.07        98.24        95.18         8.61        31.96        11.11 
TCGA-F4-6569 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.74         1.55        34.42        41.42        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6299 
       13.25         0.53        47.41         8.35        82.39        74.56 
TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6317 
       65.85        44.68        55.04        39.42        61.91        36.00 
TCGA-G4-6322 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V 
       26.04        46.75        74.79        18.18        10.98        19.33 
TCGA-NH-A6GA TCGA-NH-A6GC TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 
        9.93        12.79        16.80        42.77        32.98         8.42 
TCGA-QL-A97D TCGA-RU-A8FL TCGA-SS-A7HO TCGA-T9-A92H 
       21.90        38.70        60.13        11.90 

$`DEL PEAK 39(18Q21.2) WILD-TYPE`
TCGA-A6-6649 TCGA-AA-3506 TCGA-AA-3516 TCGA-AA-3525 TCGA-AA-3543 TCGA-AA-3554 
       24.16        58.03        13.02         8.05         0.99        17.95 
TCGA-AA-3672 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3950 TCGA-AA-3986 TCGA-AA-A00L 
        0.92        19.04        19.04        24.00        19.07        38.04 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-6601 
       39.06        21.37        25.08        10.88        75.95       100.01 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 TCGA-5M-AAT6 TCGA-A6-2672 
       22.09        35.80        26.17        79.69         9.53        46.65 
TCGA-A6-2676 TCGA-A6-3809 TCGA-A6-5661 TCGA-A6-5665 TCGA-A6-6141 TCGA-A6-6142 
       42.90        32.75        33.53        22.06         8.38        25.08 
TCGA-A6-6652 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 TCGA-AA-3492 
       24.69        20.12        19.66        16.24        24.92         3.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3518 TCGA-AA-3529 TCGA-AA-3534 
       35.01        63.98         1.02         1.02         0.00        29.00 
TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3663 TCGA-AA-3675 TCGA-AA-3680 TCGA-AA-3696 
       29.95        20.98         6.97        47.05        11.01         5.03 
TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3821 TCGA-AA-3831 
       26.99        10.06        35.05         0.99         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3845 TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       15.95         0.00         0.00         0.00        36.03        32.05 
TCGA-AA-3864 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3966 
       53.00        31.00         2.01        33.01        26.01         2.01 
TCGA-AA-3977 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00J 
       25.02        27.02        13.94        38.04        30.02        18.05 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A010 TCGA-AA-A01G TCGA-AA-A01I 
        4.01        27.02         0.99        34.98        12.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01V TCGA-AA-A029 TCGA-AA-A02R 
       38.07         1.02        35.01         1.02        51.98        22.03 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6889 TCGA-AM-5821 TCGA-AU-6004 
       39.98        18.05        12.16        83.24         0.92        27.09 
TCGA-AY-4071 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-A71X TCGA-AZ-4315 TCGA-AZ-4323 
        0.95         0.20        21.44        19.33        58.39         1.41 
TCGA-AZ-4615 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6717 
       32.94        49.41         6.77        12.36        12.39        12.76 
TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 
       10.06        17.56        85.45        70.16        15.62        51.32 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       21.14        82.95       124.27        23.05        20.02        37.02 
TCGA-CM-4748 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-6161 
       26.04        22.98        32.02        15.02        15.02        15.02 
TCGA-CM-6162 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6171 TCGA-CM-6674 TCGA-D5-6530 
       12.00        14.99        12.99        14.04        12.95        20.42 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6540 TCGA-D5-6920 TCGA-D5-6927 
       43.27        15.12         4.80        16.14        12.39         9.44 
TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A1HB 
       11.64        13.35        12.00        10.26       119.70       135.65 
TCGA-DM-A280 TCGA-DM-A28C TCGA-DM-A28G TCGA-F4-6463 TCGA-F4-6570 TCGA-F4-6703 
        7.76        81.37        60.79        35.74         6.18        47.87 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6309 TCGA-G4-6320 
       35.31       133.18        67.30        53.62        85.48        26.43 
TCGA-G4-6323 TCGA-NH-A5IV TCGA-NH-A6GB TCGA-QG-A5YW TCGA-QG-A5Z2 TCGA-WS-AB45 
       13.78        19.33        15.65        29.46        31.30        70.03 

  DEL PEAK 39(18Q21.2) MUTATED DEL PEAK 39(18Q21.2) WILD-TYPE 
                          0.46                           0.00 
  DEL PEAK 39(18Q21.2) MUTATED DEL PEAK 39(18Q21.2) WILD-TYPE 
                        148.01                         135.65 
  DEL PEAK 39(18Q21.2) MUTATED DEL PEAK 39(18Q21.2) WILD-TYPE 
                        22.470                         21.255 
[1] "0.5 - 148.0 (22.5)" "0.0 - 135.7 (21.3)"
[1] "hr=" "1.1"
D61V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 39(18Q21.2) MUTATED        40        0       17        72         3
  DEL PEAK 39(18Q21.2) WILD-TYPE      34        1       12        60         7
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 39(18Q21.2) MUTATED           1        11          8         40
  DEL PEAK 39(18Q21.2) WILD-TYPE         0         9          0         19
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 39(18Q21.2) MUTATED           31       38        15         2
  DEL PEAK 39(18Q21.2) WILD-TYPE         10        7         2         0
D61V3, multiclass
            clus
vv           DEL PEAK 39(18Q21.2) MUTATED DEL PEAK 39(18Q21.2) WILD-TYPE
  STAGE I                              40                             34
  STAGE IA                              0                              1
  STAGE II                             17                             12
  STAGE IIA                            72                             60
  STAGE IIB                             3                              7
  STAGE IIC                             1                              0
  STAGE III                            11                              9
  STAGE IIIA                            8                              0
  STAGE IIIB                           40                             19
  STAGE IIIC                           31                             10
  STAGE IV                             38                              7
  STAGE IVA                            15                              2
  STAGE IVB                             2                              0
[1] 13  2
[1] 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 39(18Q21.2) MUTATED     7  45 199  35
  DEL PEAK 39(18Q21.2) WILD-TYPE   4  32 106  20
D61V4, multiclass
    clus
vv   DEL PEAK 39(18Q21.2) MUTATED DEL PEAK 39(18Q21.2) WILD-TYPE
  T1                            7                              4
  T2                           45                             32
  T3                          199                            106
  T4                           35                             20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2
  DEL PEAK 39(18Q21.2) MUTATED   145  78  63
  DEL PEAK 39(18Q21.2) WILD-TYPE 117  27  19
D61V5, multiclass
    clus
vv   DEL PEAK 39(18Q21.2) MUTATED DEL PEAK 39(18Q21.2) WILD-TYPE
  N0                          145                            117
  N1                           78                             27
  N2                           63                             19
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V6, binary
                                cls
clus                               0   1
  DEL PEAK 39(18Q21.2) MUTATED   199  55
  DEL PEAK 39(18Q21.2) WILD-TYPE 129   9
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 39(18Q21.2) MUTATED    199   55
  DEL PEAK 39(18Q21.2) WILD-TYPE  129    9
   clus
vv  DEL PEAK 39(18Q21.2) MUTATED DEL PEAK 39(18Q21.2) WILD-TYPE
  0                          199                            129
  1                           55                              9
[1] 2 2
[1] FALSE
D61V7, binary
                                cls
clus                               0   1
  DEL PEAK 39(18Q21.2) MUTATED   125 161
  DEL PEAK 39(18Q21.2) WILD-TYPE  88  75
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 39(18Q21.2) MUTATED    125  161
  DEL PEAK 39(18Q21.2) WILD-TYPE   88   75
        clus
vv       DEL PEAK 39(18Q21.2) MUTATED DEL PEAK 39(18Q21.2) WILD-TYPE
  FEMALE                          125                             88
  MALE                            161                             75
[1] 2 2
[1] FALSE
D61V8, binary
                                cls
clus                               0   1
  DEL PEAK 39(18Q21.2) MUTATED   238   6
  DEL PEAK 39(18Q21.2) WILD-TYPE 132   3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 39(18Q21.2) MUTATED    238    6
  DEL PEAK 39(18Q21.2) WILD-TYPE  132    3
     clus
vv    DEL PEAK 39(18Q21.2) MUTATED DEL PEAK 39(18Q21.2) WILD-TYPE
  NO                           238                            132
  YES                            6                              3
[1] 2 2
[1] FALSE
D61V9, binary
                                cls
clus                               0   1
  DEL PEAK 39(18Q21.2) MUTATED   267  16
  DEL PEAK 39(18Q21.2) WILD-TYPE 115  46
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 39(18Q21.2) MUTATED    267   16
  DEL PEAK 39(18Q21.2) WILD-TYPE  115   46
                               clus
vv                              DEL PEAK 39(18Q21.2) MUTATED
  COLON ADENOCARCINOMA                                   267
  COLON MUCINOUS ADENOCARCINOMA                           16
                               clus
vv                              DEL PEAK 39(18Q21.2) WILD-TYPE
  COLON ADENOCARCINOMA                                     115
  COLON MUCINOUS ADENOCARCINOMA                             46
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 39(18Q21.2) MUTATED   202   2  18  11
  DEL PEAK 39(18Q21.2) WILD-TYPE 121   2   7  14
D61V10, multiclass
    clus
vv   DEL PEAK 39(18Q21.2) MUTATED DEL PEAK 39(18Q21.2) WILD-TYPE
  R0                          202                            121
  R1                            2                              2
  R2                           18                              7
  RX                           11                             14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 39(18Q21.2) MUTATED                                  1     6
  DEL PEAK 39(18Q21.2) WILD-TYPE                                0     5
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 39(18Q21.2) MUTATED                          40   141
  DEL PEAK 39(18Q21.2) WILD-TYPE                        19    71
D61V12, multiclass
                                  clus
vv                                 DEL PEAK 39(18Q21.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       6
  BLACK OR AFRICAN AMERICAN                                  40
  WHITE                                                     141
                                  clus
vv                                 DEL PEAK 39(18Q21.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         5
  BLACK OR AFRICAN AMERICAN                                    19
  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"
D61V13, binary
                                cls
clus                               0   1
  DEL PEAK 39(18Q21.2) MUTATED     3 177
  DEL PEAK 39(18Q21.2) WILD-TYPE   1  92
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 39(18Q21.2) MUTATED      3  177
  DEL PEAK 39(18Q21.2) WILD-TYPE    1   92
                        clus
vv                       DEL PEAK 39(18Q21.2) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                          177
                        clus
vv                       DEL PEAK 39(18Q21.2) WILD-TYPE
  HISPANIC OR LATINO                                  1
  NOT HISPANIC OR LATINO                             92
[1] 2 2
[1] FALSE

Clustering(62) Variable = DEL PEAK 40(18Q22.1) MUTATION ANALYSIS
D62V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 40(18Q22.1) MUTATED   215  64
  DEL PEAK 40(18Q22.1) WILD-TYPE 120  37
  DEL PEAK 40(18Q22.1) MUTATED DEL PEAK 40(18Q22.1) WILD-TYPE 
                           279                            157 
  DEL PEAK 40(18Q22.1) MUTATED DEL PEAK 40(18Q22.1) WILD-TYPE 
                            64                             37 
$`DEL PEAK 40(18Q22.1) MUTATED`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-4105 TCGA-AA-3496 TCGA-AA-3520 
       24.33        45.60        13.94        14.53         1.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3552 TCGA-AA-3556 
       37.05        36.03        19.07        34.03        13.02        23.01 
TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 
       19.99        19.99         6.05        19.00        36.00        85.05 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 
       14.93        31.07        24.03        29.98        12.99         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-A00Z TCGA-AD-6888 TCGA-AZ-4681 
       50.99        26.01        24.00        21.99        15.52       106.75 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6310 
        1.94        49.08         5.88        28.21        23.51        63.62 
TCGA-G4-6314 TCGA-G4-6625 TCGA-NH-A8F7 TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H 
       35.93        91.79        17.85        15.62         4.80        12.66 
TCGA-5M-AAT4 TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2678 
        1.61        39.45        43.76        43.76        43.43        42.28 
TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 
       44.91        35.11        16.57        37.05        37.25        37.02 
TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       34.65        36.53        32.45        32.91        31.63        30.44 
TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 
       29.19        23.61        22.09        32.71        29.16        27.09 
TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6653 
       22.52        24.13        25.18        20.61        21.76        24.39 
TCGA-A6-6654 TCGA-A6-6782 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 
       23.87        20.28        61.84        56.25         9.63         5.03 
TCGA-AA-3489 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3511 TCGA-AA-3517 TCGA-AA-3519 
        7.04         1.02        37.05         6.97        38.99         9.07 
TCGA-AA-3526 TCGA-AA-3532 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 
       19.07        29.00        26.01        12.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 
       21.01        24.00        13.94        61.02        78.08        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3681 
        2.01        14.01        50.04        47.01        15.02         5.98 
TCGA-AA-3685 TCGA-AA-3819 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3846 
       37.05        25.02        38.99        36.95        37.02        17.03 
TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3866 
       10.06        33.07         0.99        31.07        53.00        17.03 
TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3941 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 
       27.02        18.05        24.00        20.98        34.03        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-A004 
       16.08        13.05        34.06        27.02         7.96        13.94 
TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 
       19.00        34.03        42.02        17.03        14.99        15.02 
TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01K TCGA-AA-A01S TCGA-AA-A01T 
       15.02        10.98        32.02        31.00         1.02        33.04 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       26.01        37.02         2.96        39.98         2.01         5.03 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A03J TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
        0.92        41.00        40.96        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AU-3779 TCGA-AY-4070 
       27.42        26.47        16.44         0.46        14.50        16.31 
TCGA-AY-5543 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4614 
       33.01        17.26        17.85        18.84       109.28         5.65 
TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6600 
        5.13        22.36        65.00        62.79        88.21        12.10 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5256 
       29.56         5.23        11.74         3.19        12.69        12.46 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-5914 TCGA-CK-6748 
       12.59        12.59        12.20        14.30        21.99         2.01 
TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       25.02         8.02        27.02        13.02        29.06        22.03 
TCGA-CM-5349 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6163 TCGA-CM-6164 
       30.08         5.03        15.02        17.03        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6675 
       16.04        21.99        13.02        15.02        11.01        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6531 
       54.61        19.59        56.09        55.92        20.19        17.75 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6539 
       18.25        25.48        15.12        17.85        17.13        12.49 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
       15.58         7.53        10.13        12.43        14.30         9.04 
TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       13.41        11.38        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28E TCGA-DM-A28F 
      131.51       139.17        14.04        26.47       119.93        35.97 
TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 
      117.07        98.24        95.18         8.61        31.96        11.11 
TCGA-F4-6569 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.74         1.55        34.42        41.42        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6299 
       13.25         0.53        47.41         8.35        82.39        74.56 
TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6317 
       65.85        44.68        55.04        39.42        61.91        36.00 
TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A6GA 
       46.75        74.79        18.18        10.98        19.33         9.93 
TCGA-NH-A6GC TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QL-A97D 
       12.79        16.80        42.77        32.98         8.42        21.90 
TCGA-RU-A8FL TCGA-SS-A7HO TCGA-T9-A92H 
       38.70        60.13        11.90 

$`DEL PEAK 40(18Q22.1) WILD-TYPE`
TCGA-A6-6649 TCGA-AA-3506 TCGA-AA-3516 TCGA-AA-3525 TCGA-AA-3543 TCGA-AA-3554 
       24.16        58.03        13.02         8.05         0.99        17.95 
TCGA-AA-3672 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3950 TCGA-AA-3986 TCGA-AA-A00L 
        0.92        19.04        19.04        24.00        19.07        38.04 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-6601 
       39.06        21.37        25.08        10.88        75.95       100.01 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 TCGA-5M-AAT6 TCGA-A6-2672 
       22.09        35.80        26.17        79.69         9.53        46.65 
TCGA-A6-2676 TCGA-A6-3809 TCGA-A6-5661 TCGA-A6-5665 TCGA-A6-6141 TCGA-A6-6142 
       42.90        32.75        33.53        22.06         8.38        25.08 
TCGA-A6-6652 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 TCGA-AA-3492 
       24.69        20.12        19.66        16.24        24.92         3.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3518 TCGA-AA-3529 TCGA-AA-3534 
       35.01        63.98         1.02         1.02         0.00        29.00 
TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3663 TCGA-AA-3675 TCGA-AA-3680 TCGA-AA-3696 
       29.95        20.98         6.97        47.05        11.01         5.03 
TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3821 TCGA-AA-3831 
       26.99        10.06        35.05         0.99         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3845 TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       15.95         0.00         0.00         0.00        36.03        32.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3966 TCGA-AA-3977 
       31.00         2.01        33.01        26.01         2.01        25.02 
TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N 
       27.02        38.04        30.02        18.05        18.05         4.01 
TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A010 TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P 
       27.02         0.99        34.98        12.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01V TCGA-AA-A029 TCGA-AA-A02R TCGA-AA-A02Y 
        1.02        35.01         1.02        51.98        22.03        39.98 
TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6889 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4071 
       18.05        12.16        83.24         0.92        27.09         0.95 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A71X TCGA-AZ-4315 TCGA-AZ-4323 
        0.20        21.44        17.82        19.33        58.39         1.41 
TCGA-AZ-4615 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6717 
       32.94        49.41         6.77        12.36        12.39        12.76 
TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 
       10.06        17.56       148.01        85.45        70.16        15.62 
TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       51.32        21.14        82.95       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 
       37.02        26.04        22.98        32.02        15.02        15.02 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6171 TCGA-CM-6674 
       15.02        12.00        14.99        12.99        14.04        12.95 
TCGA-D5-6530 TCGA-D5-6534 TCGA-D5-6537 TCGA-D5-6540 TCGA-D5-6920 TCGA-D5-6927 
       20.42        43.27         4.80        16.14        12.39         9.44 
TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A1HB 
       11.64        13.35        12.00        10.26       119.70       135.65 
TCGA-DM-A280 TCGA-DM-A28C TCGA-DM-A28G TCGA-F4-6463 TCGA-F4-6570 TCGA-F4-6703 
        7.76        81.37        60.79        35.74         6.18        47.87 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6309 TCGA-G4-6320 
       35.31       133.18        67.30        53.62        85.48        26.43 
TCGA-G4-6322 TCGA-G4-6323 TCGA-NH-A5IV TCGA-NH-A6GB TCGA-QG-A5YW TCGA-QG-A5Z2 
       26.04        13.78        19.33        15.65        29.46        31.30 
TCGA-WS-AB45 
       70.03 

  DEL PEAK 40(18Q22.1) MUTATED DEL PEAK 40(18Q22.1) WILD-TYPE 
                          0.46                           0.00 
  DEL PEAK 40(18Q22.1) MUTATED DEL PEAK 40(18Q22.1) WILD-TYPE 
                        140.38                         148.01 
  DEL PEAK 40(18Q22.1) MUTATED DEL PEAK 40(18Q22.1) WILD-TYPE 
                         22.42                          21.37 
[1] "0.5 - 140.4 (22.4)" "0.0 - 148.0 (21.4)"
[1] "hr=" "1"  
D62V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 40(18Q22.1) MUTATED        40        0       18        72         3
  DEL PEAK 40(18Q22.1) WILD-TYPE      34        1       11        60         7
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 40(18Q22.1) MUTATED           1        10          8         39
  DEL PEAK 40(18Q22.1) WILD-TYPE         0        10          0         20
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 40(18Q22.1) MUTATED           31       38        15         2
  DEL PEAK 40(18Q22.1) WILD-TYPE         10        7         2         0
D62V3, multiclass
            clus
vv           DEL PEAK 40(18Q22.1) MUTATED DEL PEAK 40(18Q22.1) WILD-TYPE
  STAGE I                              40                             34
  STAGE IA                              0                              1
  STAGE II                             18                             11
  STAGE IIA                            72                             60
  STAGE IIB                             3                              7
  STAGE IIC                             1                              0
  STAGE III                            10                             10
  STAGE IIIA                            8                              0
  STAGE IIIB                           39                             20
  STAGE IIIC                           31                             10
  STAGE IV                             38                              7
  STAGE IVA                            15                              2
  STAGE IVB                             2                              0
[1] 13  2
[1] 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 40(18Q22.1) MUTATED     7  45 198  35
  DEL PEAK 40(18Q22.1) WILD-TYPE   4  32 107  20
D62V4, multiclass
    clus
vv   DEL PEAK 40(18Q22.1) MUTATED DEL PEAK 40(18Q22.1) WILD-TYPE
  T1                            7                              4
  T2                           45                             32
  T3                          198                            107
  T4                           35                             20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2
  DEL PEAK 40(18Q22.1) MUTATED   146  76  63
  DEL PEAK 40(18Q22.1) WILD-TYPE 116  29  19
D62V5, multiclass
    clus
vv   DEL PEAK 40(18Q22.1) MUTATED DEL PEAK 40(18Q22.1) WILD-TYPE
  N0                          146                            116
  N1                           76                             29
  N2                           63                             19
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V6, binary
                                cls
clus                               0   1
  DEL PEAK 40(18Q22.1) MUTATED   198  55
  DEL PEAK 40(18Q22.1) WILD-TYPE 130   9
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 40(18Q22.1) MUTATED    198   55
  DEL PEAK 40(18Q22.1) WILD-TYPE  130    9
   clus
vv  DEL PEAK 40(18Q22.1) MUTATED DEL PEAK 40(18Q22.1) WILD-TYPE
  0                          198                            130
  1                           55                              9
[1] 2 2
[1] FALSE
D62V7, binary
                                cls
clus                               0   1
  DEL PEAK 40(18Q22.1) MUTATED   124 161
  DEL PEAK 40(18Q22.1) WILD-TYPE  89  75
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 40(18Q22.1) MUTATED    124  161
  DEL PEAK 40(18Q22.1) WILD-TYPE   89   75
        clus
vv       DEL PEAK 40(18Q22.1) MUTATED DEL PEAK 40(18Q22.1) WILD-TYPE
  FEMALE                          124                             89
  MALE                            161                             75
[1] 2 2
[1] FALSE
D62V8, binary
                                cls
clus                               0   1
  DEL PEAK 40(18Q22.1) MUTATED   238   6
  DEL PEAK 40(18Q22.1) WILD-TYPE 132   3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 40(18Q22.1) MUTATED    238    6
  DEL PEAK 40(18Q22.1) WILD-TYPE  132    3
     clus
vv    DEL PEAK 40(18Q22.1) MUTATED DEL PEAK 40(18Q22.1) WILD-TYPE
  NO                           238                            132
  YES                            6                              3
[1] 2 2
[1] FALSE
D62V9, binary
                                cls
clus                               0   1
  DEL PEAK 40(18Q22.1) MUTATED   267  15
  DEL PEAK 40(18Q22.1) WILD-TYPE 115  47
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 40(18Q22.1) MUTATED    267   15
  DEL PEAK 40(18Q22.1) WILD-TYPE  115   47
                               clus
vv                              DEL PEAK 40(18Q22.1) MUTATED
  COLON ADENOCARCINOMA                                   267
  COLON MUCINOUS ADENOCARCINOMA                           15
                               clus
vv                              DEL PEAK 40(18Q22.1) WILD-TYPE
  COLON ADENOCARCINOMA                                     115
  COLON MUCINOUS ADENOCARCINOMA                             47
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 40(18Q22.1) MUTATED   200   2  18  12
  DEL PEAK 40(18Q22.1) WILD-TYPE 123   2   7  13
D62V10, multiclass
    clus
vv   DEL PEAK 40(18Q22.1) MUTATED DEL PEAK 40(18Q22.1) WILD-TYPE
  R0                          200                            123
  R1                            2                              2
  R2                           18                              7
  RX                           12                             13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 40(18Q22.1) MUTATED                                  1     6
  DEL PEAK 40(18Q22.1) WILD-TYPE                                0     5
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 40(18Q22.1) MUTATED                          39   140
  DEL PEAK 40(18Q22.1) WILD-TYPE                        20    72
D62V12, multiclass
                                  clus
vv                                 DEL PEAK 40(18Q22.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       6
  BLACK OR AFRICAN AMERICAN                                  39
  WHITE                                                     140
                                  clus
vv                                 DEL PEAK 40(18Q22.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         5
  BLACK OR AFRICAN AMERICAN                                    20
  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"
D62V13, binary
                                cls
clus                               0   1
  DEL PEAK 40(18Q22.1) MUTATED     3 175
  DEL PEAK 40(18Q22.1) WILD-TYPE   1  94
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 40(18Q22.1) MUTATED      3  175
  DEL PEAK 40(18Q22.1) WILD-TYPE    1   94
                        clus
vv                       DEL PEAK 40(18Q22.1) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                          175
                        clus
vv                       DEL PEAK 40(18Q22.1) WILD-TYPE
  HISPANIC OR LATINO                                  1
  NOT HISPANIC OR LATINO                             94
[1] 2 2
[1] FALSE

Clustering(63) Variable = DEL PEAK 41(19P13.3) MUTATION ANALYSIS
D63V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 41(19P13.3) MUTATED    45  17
  DEL PEAK 41(19P13.3) WILD-TYPE 290  84
  DEL PEAK 41(19P13.3) MUTATED DEL PEAK 41(19P13.3) WILD-TYPE 
                            62                            374 
  DEL PEAK 41(19P13.3) MUTATED DEL PEAK 41(19P13.3) WILD-TYPE 
                            17                             84 
$`DEL PEAK 41(19P13.3) MUTATED`
TCGA-AA-3506 TCGA-AA-3552 TCGA-AA-3556 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3692 
       58.03        13.02        23.01        19.99         6.05        36.00 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3979 TCGA-CK-5912 
       31.07        24.03         2.01        50.99        24.00        49.08 
TCGA-4N-A93T TCGA-A6-3807 TCGA-A6-6142 TCGA-A6-6651 TCGA-A6-A567 TCGA-AA-3519 
        4.80        34.65        25.08        21.76        61.84         9.07 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3666 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3850 
       26.01        12.99         2.01        36.95        37.02         0.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3941 TCGA-AA-A00O TCGA-AA-A01D TCGA-AA-A01G 
       17.03        27.02        24.00        27.02        10.98        12.00 
TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A02F TCGA-AA-A02W TCGA-AD-6901 TCGA-AD-6965 
       33.04        26.01        39.98        41.00        22.42        26.47 
TCGA-AY-4070 TCGA-AY-6196 TCGA-AZ-4616 TCGA-AZ-4684 TCGA-CA-5797 TCGA-CK-4948 
       16.31         0.20         5.13        65.00        12.59       148.01 
TCGA-CM-6169 TCGA-CM-6675 TCGA-CM-6679 TCGA-D5-5537 TCGA-D5-6529 TCGA-D5-6533 
       13.02        13.05        10.06        45.40        20.19        25.48 
TCGA-D5-6537 TCGA-D5-6541 TCGA-D5-6922 TCGA-DM-A0X9 TCGA-DM-A1DB TCGA-DM-A1HA 
        4.80        15.58        10.13       119.70        44.32       131.51 
TCGA-F4-6461 TCGA-F4-6808 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6317 TCGA-NH-A50U 
       11.11        33.67         8.35        82.39        36.00        10.98 
TCGA-RU-A8FL TCGA-SS-A7HO 
       38.70        60.13 

$`DEL PEAK 41(19P13.3) WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 
       24.33        45.60        13.94        14.53        24.16         1.02 
TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 
       13.02        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3554 TCGA-AA-3560 TCGA-AA-3672 TCGA-AA-3688 
       34.03         0.99        17.95        19.99         0.92        19.00 
TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3870 TCGA-AA-3939 
       85.05        19.04        19.04        14.93        29.98        12.99 
TCGA-AA-3950 TCGA-AA-3976 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       24.00        26.01        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 
       21.37        15.52        25.08        10.88        75.95       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6310 
      100.01         1.94         5.88        28.21        23.51        63.62 
TCGA-G4-6314 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 
       35.93        22.09        35.80        26.17        91.79        79.69 
TCGA-NH-A8F7 TCGA-3L-AA1B TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-5M-AATE 
       17.85        15.62        12.66         1.61         9.53        39.45 
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2678 
       43.76        46.65        43.76        43.43        42.90        42.28 
TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 
       44.91        35.11        16.57        37.05        37.25        37.02 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       32.75        36.53        32.45        32.91        31.63        30.44 
TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 
       29.19        33.53        23.61        22.09        22.06        32.71 
TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6648 
       29.16        27.09        22.52        24.13         8.38        25.18 
TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       20.61        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 
       20.28        16.24        24.92        56.25         9.63         5.03 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 
        7.04         3.02         1.02        37.05        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3526 TCGA-AA-3529 
        6.97         1.02        38.99         1.02        19.07         0.00 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 
       29.00        29.00        14.01        33.99        21.01        24.00 
TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         6.97 
TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 
       54.02        14.01        50.04        47.05        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        26.99        10.06 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3852 
       38.99         0.00        17.03        10.06        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3875 
       36.03        32.05         0.99        31.07        53.00        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
       31.00         2.01        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       27.02         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00Q 
       30.02        34.03        18.05        18.05         4.01        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C 
        0.99        17.03        14.99        34.98        15.02        15.02 
TCGA-AA-A01F TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       32.02        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02H 
        1.02         1.02        37.02        51.98         2.96         2.01 
TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
        5.03         0.92        22.03        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-A5EK 
       12.16        83.24        24.53         5.79        27.42        16.44 
TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-5543 
        0.46         0.92        14.50        27.09         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK 
       21.44        17.82        17.26        17.85        19.33        18.84 
TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4682 
      109.28        58.39         1.41         5.65        32.94        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 
       62.79        88.21        49.41         6.77        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 
        5.23        11.74         3.19        12.69        12.36        12.46 
TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.39        12.59        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 
       17.56        85.45        70.16        15.62        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 
       37.02        25.02        26.04         8.02        27.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6676 TCGA-CM-6677 
       15.02        14.04        11.01        12.95        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       11.01        12.03        54.61        19.59        56.09        55.92 
TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.42        17.75        18.25        43.27        15.12        17.85 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6923 
       17.13        12.49        16.14         7.53        12.39        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       12.00        11.38        10.26        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C 
      135.65         7.76       139.17        14.04        26.47        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M 
      119.93        35.97        60.79       117.07        98.24        95.18 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
        8.61        31.96        35.74        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 
        1.55        34.42        41.42        43.04        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 
       47.41        35.31       133.18        74.56        67.30        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        39.42        61.91 
TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T 
       26.43        26.04        13.78        46.75        74.79        18.18 
TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F8 
       19.33        19.33         9.93        15.65        12.79        16.80 
TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D 
       42.77        29.46        32.98         8.42        31.30        21.90 
TCGA-T9-A92H TCGA-WS-AB45 
       11.90        70.03 

  DEL PEAK 41(19P13.3) MUTATED DEL PEAK 41(19P13.3) WILD-TYPE 
                             0                              0 
  DEL PEAK 41(19P13.3) MUTATED DEL PEAK 41(19P13.3) WILD-TYPE 
                        148.01                         140.38 
  DEL PEAK 41(19P13.3) MUTATED DEL PEAK 41(19P13.3) WILD-TYPE 
                        24.015                         21.990 
[1] "0.0 - 148.0 (24.0)" "0.0 - 140.4 (22.0)"
[1] "hr=" "1.2"
D63V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 41(19P13.3) MUTATED         8        0        1        11         1
  DEL PEAK 41(19P13.3) WILD-TYPE      66        1       28       121         9
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 41(19P13.3) MUTATED           0         5          2          5
  DEL PEAK 41(19P13.3) WILD-TYPE         1        15          6         54
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 41(19P13.3) MUTATED           13       10         4         1
  DEL PEAK 41(19P13.3) WILD-TYPE         28       35        13         1
D63V3, multiclass
            clus
vv           DEL PEAK 41(19P13.3) MUTATED DEL PEAK 41(19P13.3) WILD-TYPE
  STAGE I                               8                             66
  STAGE IA                              0                              1
  STAGE II                              1                             28
  STAGE IIA                            11                            121
  STAGE IIB                             1                              9
  STAGE IIC                             0                              1
  STAGE III                             5                             15
  STAGE IIIA                            2                              6
  STAGE IIIB                            5                             54
  STAGE IIIC                           13                             28
  STAGE IV                             10                             35
  STAGE IVA                             4                             13
  STAGE IVB                             1                              1
[1] 13  2
[1] 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 41(19P13.3) MUTATED     1   9  43  10
  DEL PEAK 41(19P13.3) WILD-TYPE  10  68 262  45
D63V4, multiclass
    clus
vv   DEL PEAK 41(19P13.3) MUTATED DEL PEAK 41(19P13.3) WILD-TYPE
  T1                            1                             10
  T2                            9                             68
  T3                           43                            262
  T4                           10                             45
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2
  DEL PEAK 41(19P13.3) MUTATED    23  16  24
  DEL PEAK 41(19P13.3) WILD-TYPE 239  89  58
D63V5, multiclass
    clus
vv   DEL PEAK 41(19P13.3) MUTATED DEL PEAK 41(19P13.3) WILD-TYPE
  N0                           23                            239
  N1                           16                             89
  N2                           24                             58
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V6, binary
                                cls
clus                               0   1
  DEL PEAK 41(19P13.3) MUTATED    40  15
  DEL PEAK 41(19P13.3) WILD-TYPE 288  49
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 41(19P13.3) MUTATED     40   15
  DEL PEAK 41(19P13.3) WILD-TYPE  288   49
   clus
vv  DEL PEAK 41(19P13.3) MUTATED DEL PEAK 41(19P13.3) WILD-TYPE
  0                           40                            288
  1                           15                             49
[1] 2 2
[1] FALSE
D63V7, binary
                                cls
clus                               0   1
  DEL PEAK 41(19P13.3) MUTATED    26  37
  DEL PEAK 41(19P13.3) WILD-TYPE 187 199
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 41(19P13.3) MUTATED     26   37
  DEL PEAK 41(19P13.3) WILD-TYPE  187  199
        clus
vv       DEL PEAK 41(19P13.3) MUTATED DEL PEAK 41(19P13.3) WILD-TYPE
  FEMALE                           26                            187
  MALE                             37                            199
[1] 2 2
[1] FALSE
D63V8, binary
                                cls
clus                               0   1
  DEL PEAK 41(19P13.3) MUTATED    54   1
  DEL PEAK 41(19P13.3) WILD-TYPE 316   8
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 41(19P13.3) MUTATED     54    1
  DEL PEAK 41(19P13.3) WILD-TYPE  316    8
     clus
vv    DEL PEAK 41(19P13.3) MUTATED DEL PEAK 41(19P13.3) WILD-TYPE
  NO                            54                            316
  YES                            1                              8
[1] 2 2
[1] FALSE
D63V9, binary
                                cls
clus                               0   1
  DEL PEAK 41(19P13.3) MUTATED    57   5
  DEL PEAK 41(19P13.3) WILD-TYPE 325  57
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 41(19P13.3) MUTATED     57    5
  DEL PEAK 41(19P13.3) WILD-TYPE  325   57
                               clus
vv                              DEL PEAK 41(19P13.3) MUTATED
  COLON ADENOCARCINOMA                                    57
  COLON MUCINOUS ADENOCARCINOMA                            5
                               clus
vv                              DEL PEAK 41(19P13.3) WILD-TYPE
  COLON ADENOCARCINOMA                                     325
  COLON MUCINOUS ADENOCARCINOMA                             57
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 41(19P13.3) MUTATED    41   2   7   3
  DEL PEAK 41(19P13.3) WILD-TYPE 282   2  18  22
D63V10, multiclass
    clus
vv   DEL PEAK 41(19P13.3) MUTATED DEL PEAK 41(19P13.3) WILD-TYPE
  R0                           41                            282
  R1                            2                              2
  R2                            7                             18
  RX                            3                             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 41(19P13.3) MUTATED                                  0     1
  DEL PEAK 41(19P13.3) WILD-TYPE                                1    10
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 41(19P13.3) MUTATED                           8    25
  DEL PEAK 41(19P13.3) WILD-TYPE                        51   187
D63V12, multiclass
                                  clus
vv                                 DEL PEAK 41(19P13.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       1
  BLACK OR AFRICAN AMERICAN                                   8
  WHITE                                                      25
                                  clus
vv                                 DEL PEAK 41(19P13.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        10
  BLACK OR AFRICAN AMERICAN                                    51
  WHITE                                                       187
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V13, binary
                                cls
clus                               0   1
  DEL PEAK 41(19P13.3) MUTATED     0  32
  DEL PEAK 41(19P13.3) WILD-TYPE   4 237
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 41(19P13.3) MUTATED      0   32
  DEL PEAK 41(19P13.3) WILD-TYPE    4  237
                        clus
vv                       DEL PEAK 41(19P13.3) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           32
                        clus
vv                       DEL PEAK 41(19P13.3) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            237
[1] 2 2
[1] FALSE

Clustering(64) Variable = DEL PEAK 42(20P12.1) MUTATION ANALYSIS
D64V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 42(20P12.1) MUTATED    69  16
  DEL PEAK 42(20P12.1) WILD-TYPE 266  85
  DEL PEAK 42(20P12.1) MUTATED DEL PEAK 42(20P12.1) WILD-TYPE 
                            85                            351 
  DEL PEAK 42(20P12.1) MUTATED DEL PEAK 42(20P12.1) WILD-TYPE 
                            16                             85 
$`DEL PEAK 42(20P12.1) MUTATED`
TCGA-A6-2677 TCGA-A6-4105 TCGA-AA-3496 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3697 
       24.33        14.53         1.02        34.03         0.99        85.05 
TCGA-AA-3867 TCGA-AA-3952 TCGA-AZ-6608 TCGA-G4-6298 TCGA-A6-5660 TCGA-A6-5662 
       24.03         2.01         1.94        23.51        29.19        23.61 
TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6140 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6651 
       32.71        29.16        24.13        25.18        20.61        21.76 
TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3553 TCGA-AA-3561 
       38.99         9.07        26.01        12.99        24.00        13.94 
TCGA-AA-3660 TCGA-AA-3681 TCGA-AA-3819 TCGA-AA-3841 TCGA-AA-3855 TCGA-AA-3955 
       78.08         5.98        25.02        36.95        32.05        20.98 
TCGA-AA-3966 TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00Q TCGA-AA-A01F TCGA-AA-A01K 
        2.01        19.00        34.03        42.02        32.02        31.00 
TCGA-AA-A01Q TCGA-AA-A01Z TCGA-AA-A02F TCGA-AA-A03J TCGA-AD-6965 TCGA-AY-5543 
        1.02        37.02        39.98        40.96        26.47        33.01 
TCGA-AZ-4308 TCGA-AZ-5403 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-CK-4948 TCGA-CK-5914 
      109.28        62.79         5.23        11.74       148.01        21.99 
TCGA-CK-6748 TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-6164 TCGA-CM-6168 TCGA-CM-6169 
        2.01        22.03        30.08        29.03        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6676 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6533 TCGA-D5-6534 
       15.02        11.08        56.09        55.92        25.48        43.27 
TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A0X9 TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       13.41        11.38       119.70        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1HA TCGA-DM-A28A TCGA-DM-A28E TCGA-F4-6806 
       49.91        13.32       131.51        26.47       119.93        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-G4-6295 TCGA-G4-6315 
       43.04        33.67        13.25         0.53         8.35        61.91 
TCGA-G4-6320 TCGA-NH-A50V TCGA-NH-A8F8 TCGA-QG-A5Z1 TCGA-RU-A8FL TCGA-SS-A7HO 
       26.43        19.33        16.80         8.42        38.70        60.13 
TCGA-T9-A92H 
       11.90 

$`DEL PEAK 42(20P12.1) WILD-TYPE`
TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-6649 TCGA-AA-3506 TCGA-AA-3516 TCGA-AA-3520 
       45.60        13.94        24.16        58.03        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3552 TCGA-AA-3554 
       37.05        36.03         8.05        19.07        13.02        17.95 
TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 
       23.01        19.99        19.99         6.05         0.92        19.00 
TCGA-AA-3692 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3870 
       36.00        19.04        19.04        14.93        31.07        29.98 
TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 
       12.99        24.00        50.99        26.01        24.00        19.07 
TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 
       38.04        21.99        39.06        21.37        15.52        25.08 
TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-CK-5912 TCGA-DM-A285 
       10.88        75.95       106.75       100.01        49.08         5.88 
TCGA-G4-6294 TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       28.21        63.62        35.93        22.09        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-NH-A8F7 TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H 
       91.79        79.69        17.85        15.62         4.80        12.66 
TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
        1.61         9.53        39.45        43.76        46.65        43.76 
TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 
       43.43        42.90        42.28        44.91        35.11        16.57 
TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-3810 
       37.05        37.25        37.02        34.65        32.75        36.53 
TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5664 
       32.45        32.91        31.63        30.44        33.53        22.09 
TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6652 
       22.06        27.09        22.52         8.38        25.08        24.69 
TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 
       24.39        23.87        20.12        19.66        20.28        16.24 
TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 
       24.92        61.84        56.25         9.63         5.03         7.04 
TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
        3.02         1.02        37.05        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3518 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         1.02        19.07         0.00        29.00        29.00 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3655 
       14.01        33.99        21.01        29.95        20.98        61.02 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3675 
        6.97        54.02         2.01        14.01        50.04        47.05 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3710 
       47.01        15.02        11.01        37.05         5.03        26.99 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       10.06        35.05         0.99         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       38.99        37.02         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 
       33.07         0.00        36.03         0.99        31.07        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 
       33.01        26.01        34.03        21.99        16.08        13.05 
TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       34.06        25.02        27.02         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O 
       38.04        30.02        18.05        18.05         4.01        27.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C 
        0.99        17.03        14.99        34.98        15.02        15.02 
TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01R TCGA-AA-A01S 
       10.98        12.00        31.00        38.07        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02H 
       33.04         1.02        26.01        51.98         2.96         2.01 
TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03         0.92        22.03        41.00        39.98        18.05 
TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       16.44         0.46         0.92        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D 
        0.95         0.20        21.44        17.82        17.26        17.85 
TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 
       19.33        18.84        58.39         1.41         5.65        32.94 
TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
        5.13        22.36        65.00        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 
       12.10        29.56         3.19        12.69        12.36        12.46 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 
       14.30        17.56        85.45        70.16        15.62        51.32 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       21.14        82.95       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 
       25.02        26.04         8.02        27.02        13.02        29.06 
TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       22.98        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6165 TCGA-CM-6166 
       17.03        15.02        12.00        14.04        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6677 
       14.99        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        54.61        19.59 
TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6535 TCGA-D5-6536 
       20.19        20.42        17.75        18.25        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0XD TCGA-DM-A1D8 
       11.64        13.35        12.00        10.26        24.43        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 
      140.38         7.50        44.32       135.65         7.76       139.17 
TCGA-DM-A288 TCGA-DM-A28C TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       14.04        81.37        35.97        60.79       117.07        98.24 
TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 
       95.18         8.61        31.96        11.11        35.74        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6855 TCGA-F4-6856 
        6.18        47.87         1.55        34.42        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 
      133.18        82.39        74.56        67.30        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6317 TCGA-G4-6322 
       44.68        55.04        85.48        39.42        36.00        26.04 
TCGA-G4-6323 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A5IV 
       13.78        46.75        74.79        18.18        10.98        19.33 
TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX 
        9.93        15.65        12.79        42.77        29.46        32.98 
TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-WS-AB45 
       31.30        21.90        70.03 

  DEL PEAK 42(20P12.1) MUTATED DEL PEAK 42(20P12.1) WILD-TYPE 
                          0.53                           0.00 
  DEL PEAK 42(20P12.1) MUTATED DEL PEAK 42(20P12.1) WILD-TYPE 
                        148.01                         140.38 
  DEL PEAK 42(20P12.1) MUTATED DEL PEAK 42(20P12.1) WILD-TYPE 
                         25.48                          21.01 
[1] "0.5 - 148.0 (25.5)" "0.0 - 140.4 (21.0)"
[1] "hr=" "1.5"
D64V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 42(20P12.1) MUTATED        10        0        7        24         1
  DEL PEAK 42(20P12.1) WILD-TYPE      64        1       22       108         9
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 42(20P12.1) MUTATED           1         4          1         14
  DEL PEAK 42(20P12.1) WILD-TYPE         0        16          7         45
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 42(20P12.1) MUTATED           11        8         4         0
  DEL PEAK 42(20P12.1) WILD-TYPE         30       37        13         2
D64V3, multiclass
            clus
vv           DEL PEAK 42(20P12.1) MUTATED DEL PEAK 42(20P12.1) WILD-TYPE
  STAGE I                              10                             64
  STAGE IA                              0                              1
  STAGE II                              7                             22
  STAGE IIA                            24                            108
  STAGE IIB                             1                              9
  STAGE IIC                             1                              0
  STAGE III                             4                             16
  STAGE IIIA                            1                              7
  STAGE IIIB                           14                             45
  STAGE IIIC                           11                             30
  STAGE IV                              8                             37
  STAGE IVA                             4                             13
  STAGE IVB                             0                              2
[1] 13  2
[1] 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 42(20P12.1) MUTATED     1  11  64  10
  DEL PEAK 42(20P12.1) WILD-TYPE  10  66 241  45
D64V4, multiclass
    clus
vv   DEL PEAK 42(20P12.1) MUTATED DEL PEAK 42(20P12.1) WILD-TYPE
  T1                            1                             10
  T2                           11                             66
  T3                           64                            241
  T4                           10                             45
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2
  DEL PEAK 42(20P12.1) MUTATED    45  23  18
  DEL PEAK 42(20P12.1) WILD-TYPE 217  82  64
D64V5, multiclass
    clus
vv   DEL PEAK 42(20P12.1) MUTATED DEL PEAK 42(20P12.1) WILD-TYPE
  N0                           45                            217
  N1                           23                             82
  N2                           18                             64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V6, binary
                                cls
clus                               0   1
  DEL PEAK 42(20P12.1) MUTATED    66  12
  DEL PEAK 42(20P12.1) WILD-TYPE 262  52
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 42(20P12.1) MUTATED     66   12
  DEL PEAK 42(20P12.1) WILD-TYPE  262   52
   clus
vv  DEL PEAK 42(20P12.1) MUTATED DEL PEAK 42(20P12.1) WILD-TYPE
  0                           66                            262
  1                           12                             52
[1] 2 2
[1] FALSE
D64V7, binary
                                cls
clus                               0   1
  DEL PEAK 42(20P12.1) MUTATED    42  44
  DEL PEAK 42(20P12.1) WILD-TYPE 171 192
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 42(20P12.1) MUTATED     42   44
  DEL PEAK 42(20P12.1) WILD-TYPE  171  192
        clus
vv       DEL PEAK 42(20P12.1) MUTATED DEL PEAK 42(20P12.1) WILD-TYPE
  FEMALE                           42                            171
  MALE                             44                            192
[1] 2 2
[1] FALSE
D64V8, binary
                                cls
clus                               0   1
  DEL PEAK 42(20P12.1) MUTATED    71   0
  DEL PEAK 42(20P12.1) WILD-TYPE 299   9
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 42(20P12.1) MUTATED     71    0
  DEL PEAK 42(20P12.1) WILD-TYPE  299    9
     clus
vv    DEL PEAK 42(20P12.1) MUTATED DEL PEAK 42(20P12.1) WILD-TYPE
  NO                            71                            299
  YES                            0                              9
[1] 2 2
[1] FALSE
D64V9, binary
                                cls
clus                               0   1
  DEL PEAK 42(20P12.1) MUTATED    79   5
  DEL PEAK 42(20P12.1) WILD-TYPE 303  57
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 42(20P12.1) MUTATED     79    5
  DEL PEAK 42(20P12.1) WILD-TYPE  303   57
                               clus
vv                              DEL PEAK 42(20P12.1) MUTATED
  COLON ADENOCARCINOMA                                    79
  COLON MUCINOUS ADENOCARCINOMA                            5
                               clus
vv                              DEL PEAK 42(20P12.1) WILD-TYPE
  COLON ADENOCARCINOMA                                     303
  COLON MUCINOUS ADENOCARCINOMA                             57
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 42(20P12.1) MUTATED    57   1   3   2
  DEL PEAK 42(20P12.1) WILD-TYPE 266   3  22  23
D64V10, multiclass
    clus
vv   DEL PEAK 42(20P12.1) MUTATED DEL PEAK 42(20P12.1) WILD-TYPE
  R0                           57                            266
  R1                            1                              3
  R2                            3                             22
  RX                            2                             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 42(20P12.1) MUTATED                                  0     0
  DEL PEAK 42(20P12.1) WILD-TYPE                                1    11
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 42(20P12.1) MUTATED                          12    45
  DEL PEAK 42(20P12.1) WILD-TYPE                        47   167
D64V12, multiclass
                                  clus
vv                                 DEL PEAK 42(20P12.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       0
  BLACK OR AFRICAN AMERICAN                                  12
  WHITE                                                      45
                                  clus
vv                                 DEL PEAK 42(20P12.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        11
  BLACK OR AFRICAN AMERICAN                                    47
  WHITE                                                       167
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V13, binary
                                cls
clus                               0   1
  DEL PEAK 42(20P12.1) MUTATED     1  56
  DEL PEAK 42(20P12.1) WILD-TYPE   3 213
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 42(20P12.1) MUTATED      1   56
  DEL PEAK 42(20P12.1) WILD-TYPE    3  213
                        clus
vv                       DEL PEAK 42(20P12.1) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           56
                        clus
vv                       DEL PEAK 42(20P12.1) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            213
[1] 2 2
[1] FALSE

Clustering(65) Variable = DEL PEAK 43(21Q11.2) MUTATION ANALYSIS
D65V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 43(21Q11.2) MUTATED   103  31
  DEL PEAK 43(21Q11.2) WILD-TYPE 232  70
  DEL PEAK 43(21Q11.2) MUTATED DEL PEAK 43(21Q11.2) WILD-TYPE 
                           134                            302 
  DEL PEAK 43(21Q11.2) MUTATED DEL PEAK 43(21Q11.2) WILD-TYPE 
                            31                             70 
$`DEL PEAK 43(21Q11.2) MUTATED`
TCGA-A6-4105 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3552 TCGA-AA-3556 TCGA-AA-3560 
       14.53        19.07        34.03        13.02        23.01        19.99 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-A00L 
       19.00        36.00        14.93        31.07        24.03        38.04 
TCGA-AA-A00Z TCGA-CK-5912 TCGA-G4-6314 TCGA-G4-6625 TCGA-NH-A8F7 TCGA-5M-AAT4 
       21.99        49.08        35.93        91.79        17.85         1.61 
TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2678 TCGA-A6-2684 TCGA-A6-5659 
       39.45        43.76        43.76        42.28        37.05        30.44 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5667 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6653 
       22.09        22.06        29.16        20.61        21.76        24.39 
TCGA-A6-6654 TCGA-A6-6782 TCGA-A6-A567 TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3511 
       23.87        20.28        61.84         9.63         5.03         6.97 
TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3538 TCGA-AA-3544 TCGA-AA-3660 
       38.99         9.07        19.07        26.01        14.01        78.08 
TCGA-AA-3685 TCGA-AA-3811 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3848 TCGA-AA-3856 
       37.05        10.06        38.99        37.02        10.06         0.99 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3941 TCGA-AA-3955 TCGA-AA-3966 
       17.03        27.02        18.05        24.00        20.98         2.01 
TCGA-AA-3968 TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A01C 
       21.99         7.96        13.94        27.02        42.02        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01K TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       10.98        32.02        31.00        51.98        39.98         2.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AD-6890 TCGA-AD-6901 TCGA-AD-6965 TCGA-AD-A5EK 
        0.92        41.00        24.53        22.42        26.47        16.44 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-A69D TCGA-AY-A71X TCGA-AZ-4616 
       14.50        16.31         0.95        17.85        19.33         5.13 
TCGA-AZ-4684 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-CA-5254 
       65.00        12.10        29.56         5.23         3.19        12.69 
TCGA-CA-5256 TCGA-CA-5797 TCGA-CA-6716 TCGA-CK-5914 TCGA-CK-6748 TCGA-CM-4744 
       12.46        12.59        12.20        21.99         2.01        20.02 
TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5860 TCGA-CM-5862 
        8.02        27.02        13.02        22.03        32.02         5.03 
TCGA-CM-5864 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6170 TCGA-CM-6677 TCGA-CM-6678 
       15.02        14.04        29.03        15.02        11.08        11.01 
TCGA-D5-5537 TCGA-D5-6531 TCGA-D5-6533 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       45.40        17.75        25.48        10.13        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D9 
        9.04        13.41        11.38        49.91        13.32       140.38 
TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A28A TCGA-F4-6460 TCGA-F4-6703 TCGA-F4-6704 
        7.50       131.51        26.47        31.96        47.87         1.55 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6295 
       41.42        43.04        33.67         0.53        47.41         8.35 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6626 TCGA-NH-A50T TCGA-NH-A6GA 
       61.91        36.00        26.43        46.75        18.18         9.93 
TCGA-QG-A5YV TCGA-SS-A7HO 
       42.77        60.13 

$`DEL PEAK 43(21Q11.2) WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3506 
       24.33        45.60        13.94        24.16         1.02        58.03 
TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3543 
       13.02        24.03        37.05        36.03         8.05         0.99 
TCGA-AA-3554 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3697 TCGA-AA-3713 
       17.95        19.99         6.05         0.92        85.05        19.04 
TCGA-AA-3715 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       19.04        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 
       26.01        24.00        19.07        39.06        21.37        15.52 
TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 
       25.08        10.88        75.95       106.75       100.01         1.94 
TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        5.88        28.21        23.51        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6628 TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT6 
       26.17        79.69        15.62         4.80        12.66         9.53 
TCGA-A6-2672 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 
       46.65        43.43        42.90        44.91        35.11        16.57 
TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4107 
       37.25        37.02        34.65        32.75        36.53        32.45 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5666 
       32.91        31.63        29.19        33.53        23.61        32.71 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       27.09        22.52        24.13         8.38        25.08        25.18 
TCGA-A6-6652 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A56B 
       24.69        20.12        19.66        16.24        24.92        56.25 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 
        7.04         3.02         1.02        37.05        35.01        63.98 
TCGA-AA-3514 TCGA-AA-3518 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3542 
        1.02         1.02         0.00        29.00        29.00        12.99 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       61.02         6.97        54.02         2.01        14.01        50.04 
TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3696 
       47.05        47.01        15.02        11.01         5.98         5.03 
TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       26.99        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3841 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3850 TCGA-AA-3851 
       15.95        36.95         0.00        17.03         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3877 
        0.00        36.03        32.05        31.07        53.00        31.00 
TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3973 
        2.01        33.01        26.01        34.03        16.08        13.05 
TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00D 
       34.06        25.02        27.02        27.02        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00R 
       30.02        34.03        18.05        18.05         4.01         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01G TCGA-AA-A01I 
       17.03        14.99        34.98        15.02        12.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A02E TCGA-AA-A02J TCGA-AA-A02R TCGA-AA-A02Y 
       26.01        37.02         2.96         5.03        22.03        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6899 TCGA-AD-6963 
       18.05        40.96        12.16        83.24         5.79        27.42 
TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
        0.46         0.92        27.09        33.01         0.20        21.44 
TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 
       17.82        17.26        18.84       109.28        58.39         1.41 
TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.65        32.94        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6606 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6717 
        6.77        11.74        12.36        12.39        12.59        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 
       10.06        14.30        17.56       148.01        85.45        70.16 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 
       15.62        51.32        21.14        82.95       124.27        23.05 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5349 
       37.02        25.02        26.04        29.06        22.98        30.08 
TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6165 
       15.02        15.02        17.03        15.02        12.00        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6171 TCGA-CM-6172 
       21.99        14.99        12.99        13.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5538 
       12.95        13.05        11.08        10.06        12.03        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6532 
       19.59        56.09        55.92        20.19        20.42        18.25 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6927 TCGA-D5-6928 
       16.14        15.58         7.53        12.39         9.44        11.64 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       13.35        12.00        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D8 TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A280 
      130.65        92.75        12.59        44.32       135.65         7.76 
TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17        14.04        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6461 TCGA-F4-6463 
      117.07        98.24        95.18         8.61        11.11        35.74 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6805 TCGA-F4-6809 TCGA-F4-6856 TCGA-G4-6293 
       35.74         6.18        34.42        13.25        35.31       133.18 
TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       82.39        74.56        67.30        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6627 
       55.04        85.48        39.42        26.04        13.78        74.79 
TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F8 
       10.98        19.33        19.33        15.65        12.79        16.80 
TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-RU-A8FL 
       29.46        32.98         8.42        31.30        21.90        38.70 
TCGA-T9-A92H TCGA-WS-AB45 
       11.90        70.03 

  DEL PEAK 43(21Q11.2) MUTATED DEL PEAK 43(21Q11.2) WILD-TYPE 
                          0.53                           0.00 
  DEL PEAK 43(21Q11.2) MUTATED DEL PEAK 43(21Q11.2) WILD-TYPE 
                        140.38                         148.01 
  DEL PEAK 43(21Q11.2) MUTATED DEL PEAK 43(21Q11.2) WILD-TYPE 
                         21.37                          23.28 
[1] "0.5 - 140.4 (21.4)" "0.0 - 148.0 (23.3)"
[1] "hr=" "1.2"
D65V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 43(21Q11.2) MUTATED        23        0        8        37         2
  DEL PEAK 43(21Q11.2) WILD-TYPE      51        1       21        95         8
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 43(21Q11.2) MUTATED           0         4          4         15
  DEL PEAK 43(21Q11.2) WILD-TYPE         1        16          4         44
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 43(21Q11.2) MUTATED           18       21         4         0
  DEL PEAK 43(21Q11.2) WILD-TYPE         23       24        13         2
D65V3, multiclass
            clus
vv           DEL PEAK 43(21Q11.2) MUTATED DEL PEAK 43(21Q11.2) WILD-TYPE
  STAGE I                              23                             51
  STAGE IA                              0                              1
  STAGE II                              8                             21
  STAGE IIA                            37                             95
  STAGE IIB                             2                              8
  STAGE IIC                             0                              1
  STAGE III                             4                             16
  STAGE IIIA                            4                              4
  STAGE IIIB                           15                             44
  STAGE IIIC                           18                             23
  STAGE IV                             21                             24
  STAGE IVA                             4                             13
  STAGE IVB                             0                              2
[1] 13  2
[1] 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 43(21Q11.2) MUTATED     6  23  93  18
  DEL PEAK 43(21Q11.2) WILD-TYPE   5  54 212  37
D65V4, multiclass
    clus
vv   DEL PEAK 43(21Q11.2) MUTATED DEL PEAK 43(21Q11.2) WILD-TYPE
  T1                            6                              5
  T2                           23                             54
  T3                           93                            212
  T4                           18                             37
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2
  DEL PEAK 43(21Q11.2) MUTATED    73  32  35
  DEL PEAK 43(21Q11.2) WILD-TYPE 189  73  47
D65V5, multiclass
    clus
vv   DEL PEAK 43(21Q11.2) MUTATED DEL PEAK 43(21Q11.2) WILD-TYPE
  N0                           73                            189
  N1                           32                             73
  N2                           35                             47
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V6, binary
                                cls
clus                               0   1
  DEL PEAK 43(21Q11.2) MUTATED    95  25
  DEL PEAK 43(21Q11.2) WILD-TYPE 233  39
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 43(21Q11.2) MUTATED     95   25
  DEL PEAK 43(21Q11.2) WILD-TYPE  233   39
   clus
vv  DEL PEAK 43(21Q11.2) MUTATED DEL PEAK 43(21Q11.2) WILD-TYPE
  0                           95                            233
  1                           25                             39
[1] 2 2
[1] FALSE
D65V7, binary
                                cls
clus                               0   1
  DEL PEAK 43(21Q11.2) MUTATED    65  75
  DEL PEAK 43(21Q11.2) WILD-TYPE 148 161
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 43(21Q11.2) MUTATED     65   75
  DEL PEAK 43(21Q11.2) WILD-TYPE  148  161
        clus
vv       DEL PEAK 43(21Q11.2) MUTATED DEL PEAK 43(21Q11.2) WILD-TYPE
  FEMALE                           65                            148
  MALE                             75                            161
[1] 2 2
[1] FALSE
D65V8, binary
                                cls
clus                               0   1
  DEL PEAK 43(21Q11.2) MUTATED   117   4
  DEL PEAK 43(21Q11.2) WILD-TYPE 253   5
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 43(21Q11.2) MUTATED    117    4
  DEL PEAK 43(21Q11.2) WILD-TYPE  253    5
     clus
vv    DEL PEAK 43(21Q11.2) MUTATED DEL PEAK 43(21Q11.2) WILD-TYPE
  NO                           117                            253
  YES                            4                              5
[1] 2 2
[1] FALSE
D65V9, binary
                                cls
clus                               0   1
  DEL PEAK 43(21Q11.2) MUTATED   129   8
  DEL PEAK 43(21Q11.2) WILD-TYPE 253  54
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 43(21Q11.2) MUTATED    129    8
  DEL PEAK 43(21Q11.2) WILD-TYPE  253   54
                               clus
vv                              DEL PEAK 43(21Q11.2) MUTATED
  COLON ADENOCARCINOMA                                   129
  COLON MUCINOUS ADENOCARCINOMA                            8
                               clus
vv                              DEL PEAK 43(21Q11.2) WILD-TYPE
  COLON ADENOCARCINOMA                                     253
  COLON MUCINOUS ADENOCARCINOMA                             54
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 43(21Q11.2) MUTATED    97   2  10   7
  DEL PEAK 43(21Q11.2) WILD-TYPE 226   2  15  18
D65V10, multiclass
    clus
vv   DEL PEAK 43(21Q11.2) MUTATED DEL PEAK 43(21Q11.2) WILD-TYPE
  R0                           97                            226
  R1                            2                              2
  R2                           10                             15
  RX                            7                             18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 43(21Q11.2) MUTATED                                  1     4
  DEL PEAK 43(21Q11.2) WILD-TYPE                                0     7
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 43(21Q11.2) MUTATED                          18    66
  DEL PEAK 43(21Q11.2) WILD-TYPE                        41   146
D65V12, multiclass
                                  clus
vv                                 DEL PEAK 43(21Q11.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       4
  BLACK OR AFRICAN AMERICAN                                  18
  WHITE                                                      66
                                  clus
vv                                 DEL PEAK 43(21Q11.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         7
  BLACK OR AFRICAN AMERICAN                                    41
  WHITE                                                       146
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V13, binary
                                cls
clus                               0   1
  DEL PEAK 43(21Q11.2) MUTATED     3  82
  DEL PEAK 43(21Q11.2) WILD-TYPE   1 187
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 43(21Q11.2) MUTATED      3   82
  DEL PEAK 43(21Q11.2) WILD-TYPE    1  187
                        clus
vv                       DEL PEAK 43(21Q11.2) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           82
                        clus
vv                       DEL PEAK 43(21Q11.2) WILD-TYPE
  HISPANIC OR LATINO                                  1
  NOT HISPANIC OR LATINO                            187
[1] 2 2
[1] FALSE

Clustering(66) Variable = DEL PEAK 44(22Q13.32) MUTATION ANALYSIS
D66V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 44(22Q13.32) MUTATED   116  39
  DEL PEAK 44(22Q13.32) WILD-TYPE 219  62
  DEL PEAK 44(22Q13.32) MUTATED DEL PEAK 44(22Q13.32) WILD-TYPE 
                            155                             281 
  DEL PEAK 44(22Q13.32) MUTATED DEL PEAK 44(22Q13.32) WILD-TYPE 
                             39                              62 
$`DEL PEAK 44(22Q13.32) MUTATED`
TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-4105 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3552 
       45.60        13.94        14.53        24.03        37.05        13.02 
TCGA-AA-3560 TCGA-AA-3662 TCGA-AA-3697 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 
       19.99         6.05        85.05        31.07        24.03        29.98 
TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-A00Z TCGA-AZ-6608 
       12.99         2.01        50.99        26.01        21.99         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6625 TCGA-4N-A93T TCGA-5M-AAT4 
       49.08         5.88        63.62        91.79         4.80         1.61 
TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 
       39.45        43.76        42.28        44.91        35.11        16.57 
TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 
       34.65        36.53        31.63        30.44        29.19        23.61 
TCGA-A6-6138 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6654 TCGA-A6-A567 TCGA-A6-A56B 
       22.52        20.61        21.76        23.87        61.84        56.25 
TCGA-A6-A5ZU TCGA-AA-3511 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3532 TCGA-AA-3538 
        9.63         6.97        38.99         9.07        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3561 TCGA-AA-3666 TCGA-AA-3673 
       12.99        33.99        21.01        13.94         2.01        50.04 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3811 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 
        5.98        37.05        10.06        38.99        36.95        37.02 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       17.03        10.06        33.07        32.05         0.99        31.07 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3966 TCGA-AA-3968 
       17.03        27.02        18.05         2.01         2.01        21.99 
TCGA-AA-3973 TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00F TCGA-AA-A00O TCGA-AA-A00Q 
       13.05         7.96        13.94        34.03        27.02        42.02 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A01C TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A01Z 
       17.03        14.99        15.02        33.04        26.01        37.02 
TCGA-AA-A02F TCGA-AA-A02W TCGA-AA-A03J TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6965 
       39.98        41.00        40.96         5.79        22.42        26.47 
TCGA-AD-A5EK TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-A69D 
       16.44        14.50        16.31        33.01         0.20        17.85 
TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4616 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 
        1.41         5.65         5.13        12.10        29.56         5.23 
TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-6748 
        3.19        12.69        12.36        12.20        14.30         2.01 
TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-5341 TCGA-CM-5349 TCGA-CM-5862 TCGA-CM-5863 
       25.02         8.02        29.06        30.08         5.03        15.02 
TCGA-CM-6170 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-D5-5537 TCGA-D5-5540 
       15.02        11.08        11.01        10.06        45.40        56.09 
TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6539 
       20.19        25.48        43.27        15.12        17.85        12.49 
TCGA-D5-6898 TCGA-D5-6923 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A1D0 TCGA-DM-A1D7 
        7.53        12.43        13.41        11.38       130.65        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A28A TCGA-F4-6460 
       12.59       140.38        44.32       131.51        26.47        31.96 
TCGA-F4-6704 TCGA-F4-6807 TCGA-F4-6809 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6309 
        1.55        43.04        13.25         8.35        82.39        85.48 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6626 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V 
       61.91        36.00        46.75        18.18        10.98        19.33 
TCGA-NH-A6GA TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QL-A97D TCGA-RU-A8FL 
        9.93        42.77        29.46        21.90        38.70 

$`DEL PEAK 44(22Q13.32) WILD-TYPE`
TCGA-A6-2677 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3506 TCGA-AA-3516 TCGA-AA-3524 
       24.33        24.16         1.02        58.03        13.02        36.03 
TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3554 TCGA-AA-3556 
        8.05        19.07        34.03         0.99        17.95        23.01 
TCGA-AA-3562 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3713 TCGA-AA-3715 
       19.99         0.92        19.00        36.00        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3950 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A024 
       14.93        24.00        24.00        19.07        38.04        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 
       21.37        15.52        25.08        10.88        75.95       106.75 
TCGA-AZ-6601 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6314 TCGA-G4-6321 TCGA-G4-6586 
      100.01        28.21        23.51        35.93        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6628 TCGA-NH-A8F7 TCGA-3L-AA1B TCGA-4T-AA8H TCGA-5M-AAT6 
       26.17        79.69        17.85        15.62        12.66         9.53 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2684 TCGA-A6-2685 
       46.65        43.76        43.43        42.90        37.05        37.25 
TCGA-A6-2686 TCGA-A6-3809 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5661 TCGA-A6-5664 
       37.02        32.75        32.45        32.91        33.53        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6141 
       22.06        32.71        29.16        27.09        24.13         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 
       25.08        25.18        24.69        24.39        20.12        19.66 
TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 
       20.28        16.24        24.92         5.03         7.04         3.02 
TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3518 
        1.02        37.05        35.01        63.98         1.02         1.02 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3534 TCGA-AA-3544 TCGA-AA-3553 TCGA-AA-3555 
       19.07         0.00        29.00        14.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 
       20.98        61.02        78.08         6.97        54.02        14.01 
TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3696 TCGA-AA-3710 
       47.05        47.01        15.02        11.01         5.03        26.99 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3845 TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3864 TCGA-AA-3877 
        0.00         0.00         0.00        36.03        53.00        31.00 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3971 
       24.00        33.01        26.01        20.98        34.03        16.08 
TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00D 
       34.06        25.02        27.02        27.02        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00R TCGA-AA-A010 
       30.02        18.05        18.05         4.01         0.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A029 
       38.07         1.02        35.01         1.02         1.02        51.98 
TCGA-AA-A02E TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y 
        2.96         2.01         5.03         0.92        22.03        39.98 
TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6963 TCGA-AM-5820 
       18.05        12.16        83.24        24.53        27.42         0.46 
TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L 
        0.92        27.09         0.95        21.44        17.82        17.26 
TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4615 TCGA-AZ-4682 
       19.33        18.84       109.28        58.39        32.94        22.36 
TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6606 
       65.00        62.79        88.21        49.41         6.77        11.74 
TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 
       12.46        12.39        12.59        12.59        12.76        10.06 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 
       17.56       148.01        85.45        70.16        15.62        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.99        21.14        82.95       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5348 
       37.02        26.04        27.02        13.02        22.03        22.98 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
       32.02        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       13.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6680 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6530 TCGA-D5-6531 
       12.03        54.61        19.59        55.92        20.42        17.75 
TCGA-D5-6532 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 
       18.25         4.80        17.13        16.14        15.58        12.39 
TCGA-D5-6922 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 
       10.13        14.30         9.04         9.44        11.64        13.35 
TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D4 
       12.00        10.26       119.70        24.43        38.20        92.75 
TCGA-DM-A1D6 TCGA-DM-A1DA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 
       49.91         7.50       135.65         7.76       139.17        14.04 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 
       95.18         8.61        11.11        35.74        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6808 TCGA-F4-6854 TCGA-F4-6855 
       47.87        34.42        41.42        33.67         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 
       35.31       133.18        74.56        67.30        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6311 TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 
       44.68        55.04        39.42        26.43        26.04        13.78 
TCGA-G4-6627 TCGA-NH-A5IV TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F8 TCGA-QG-A5YX 
       74.79        19.33        15.65        12.79        16.80        32.98 
TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-SS-A7HO TCGA-T9-A92H TCGA-WS-AB45 
        8.42        31.30        60.13        11.90        70.03 

  DEL PEAK 44(22Q13.32) MUTATED DEL PEAK 44(22Q13.32) WILD-TYPE 
                            0.2                             0.0 
  DEL PEAK 44(22Q13.32) MUTATED DEL PEAK 44(22Q13.32) WILD-TYPE 
                         140.38                          148.01 
  DEL PEAK 44(22Q13.32) MUTATED DEL PEAK 44(22Q13.32) WILD-TYPE 
                          21.90                           22.09 
[1] "0.2 - 140.4 (21.9)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.3"
D66V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 44(22Q13.32) MUTATED        19        0        8        40         1
  DEL PEAK 44(22Q13.32) WILD-TYPE      55        1       21        92         9
                                 vv
clus                              STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 44(22Q13.32) MUTATED           0         6          6         18
  DEL PEAK 44(22Q13.32) WILD-TYPE         1        14          2         41
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 44(22Q13.32) MUTATED           22       25         8         0
  DEL PEAK 44(22Q13.32) WILD-TYPE         19       20         9         2
D66V3, multiclass
            clus
vv           DEL PEAK 44(22Q13.32) MUTATED DEL PEAK 44(22Q13.32) WILD-TYPE
  STAGE I                               19                              55
  STAGE IA                               0                               1
  STAGE II                               8                              21
  STAGE IIA                             40                              92
  STAGE IIB                              1                               9
  STAGE IIC                              0                               1
  STAGE III                              6                              14
  STAGE IIIA                             6                               2
  STAGE IIIB                            18                              41
  STAGE IIIC                            22                              19
  STAGE IV                              25                              20
  STAGE IVA                              8                               9
  STAGE IVB                              0                               2
[1] 13  2
[1] 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 44(22Q13.32) MUTATED     3  24 109  22
  DEL PEAK 44(22Q13.32) WILD-TYPE   8  53 196  33
D66V4, multiclass
    clus
vv   DEL PEAK 44(22Q13.32) MUTATED DEL PEAK 44(22Q13.32) WILD-TYPE
  T1                             3                               8
  T2                            24                              53
  T3                           109                             196
  T4                            22                              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"
                                 vv
clus                               N0  N1  N2
  DEL PEAK 44(22Q13.32) MUTATED    73  45  40
  DEL PEAK 44(22Q13.32) WILD-TYPE 189  60  42
D66V5, multiclass
    clus
vv   DEL PEAK 44(22Q13.32) MUTATED DEL PEAK 44(22Q13.32) WILD-TYPE
  N0                            73                             189
  N1                            45                              60
  N2                            40                              42
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V6, binary
                                 cls
clus                                0   1
  DEL PEAK 44(22Q13.32) MUTATED   105  33
  DEL PEAK 44(22Q13.32) WILD-TYPE 223  31
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 44(22Q13.32) MUTATED    105   33
  DEL PEAK 44(22Q13.32) WILD-TYPE  223   31
   clus
vv  DEL PEAK 44(22Q13.32) MUTATED DEL PEAK 44(22Q13.32) WILD-TYPE
  0                           105                             223
  1                            33                              31
[1] 2 2
[1] FALSE
D66V7, binary
                                 cls
clus                                0   1
  DEL PEAK 44(22Q13.32) MUTATED    72  86
  DEL PEAK 44(22Q13.32) WILD-TYPE 141 150
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 44(22Q13.32) MUTATED     72   86
  DEL PEAK 44(22Q13.32) WILD-TYPE  141  150
        clus
vv       DEL PEAK 44(22Q13.32) MUTATED DEL PEAK 44(22Q13.32) WILD-TYPE
  FEMALE                            72                             141
  MALE                              86                             150
[1] 2 2
[1] FALSE
D66V8, binary
                                 cls
clus                                0   1
  DEL PEAK 44(22Q13.32) MUTATED   137   3
  DEL PEAK 44(22Q13.32) WILD-TYPE 233   6
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 44(22Q13.32) MUTATED    137    3
  DEL PEAK 44(22Q13.32) WILD-TYPE  233    6
     clus
vv    DEL PEAK 44(22Q13.32) MUTATED DEL PEAK 44(22Q13.32) WILD-TYPE
  NO                            137                             233
  YES                             3                               6
[1] 2 2
[1] FALSE
D66V9, binary
                                 cls
clus                                0   1
  DEL PEAK 44(22Q13.32) MUTATED   146  11
  DEL PEAK 44(22Q13.32) WILD-TYPE 236  51
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 44(22Q13.32) MUTATED    146   11
  DEL PEAK 44(22Q13.32) WILD-TYPE  236   51
                               clus
vv                              DEL PEAK 44(22Q13.32) MUTATED
  COLON ADENOCARCINOMA                                    146
  COLON MUCINOUS ADENOCARCINOMA                            11
                               clus
vv                              DEL PEAK 44(22Q13.32) WILD-TYPE
  COLON ADENOCARCINOMA                                      236
  COLON MUCINOUS ADENOCARCINOMA                              51
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 44(22Q13.32) MUTATED   107   2  10  11
  DEL PEAK 44(22Q13.32) WILD-TYPE 216   2  15  14
D66V10, multiclass
    clus
vv   DEL PEAK 44(22Q13.32) MUTATED DEL PEAK 44(22Q13.32) WILD-TYPE
  R0                           107                             216
  R1                             2                               2
  R2                            10                              15
  RX                            11                              14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V11, continuous
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 44(22Q13.32) MUTATED                                  1     4
  DEL PEAK 44(22Q13.32) WILD-TYPE                                0     7
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 44(22Q13.32) MUTATED                          24    69
  DEL PEAK 44(22Q13.32) WILD-TYPE                        35   143
D66V12, multiclass
                                  clus
vv                                 DEL PEAK 44(22Q13.32) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        4
  BLACK OR AFRICAN AMERICAN                                   24
  WHITE                                                       69
                                  clus
vv                                 DEL PEAK 44(22Q13.32) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               0
  ASIAN                                                          7
  BLACK OR AFRICAN AMERICAN                                     35
  WHITE                                                        143
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V13, binary
                                 cls
clus                                0   1
  DEL PEAK 44(22Q13.32) MUTATED     2  92
  DEL PEAK 44(22Q13.32) WILD-TYPE   2 177
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 44(22Q13.32) MUTATED      2   92
  DEL PEAK 44(22Q13.32) WILD-TYPE    2  177
                        clus
vv                       DEL PEAK 44(22Q13.32) MUTATED
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                            92
                        clus
vv                       DEL PEAK 44(22Q13.32) WILD-TYPE
  HISPANIC OR LATINO                                   2
  NOT HISPANIC OR LATINO                             177
[1] 2 2
[1] FALSE
