[1] "ofn"        "-oTSKCM-TM"
[1] "opt"       "-OPMUTSIG"
[1] "tl" ""  
[1] "dx" ""  
[1] "opt"    "MUTSIG"
[1] "dx" ""  
[1] "cfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/SKCM-TM/22507034/SKCM-TM.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/SKCM-TM/22533834/transformed.cor.cli.txt"

nPatients in clinical file=368, in cluster file=367, common to both=367
[1]  54 367
[1] "AMP PEAK  1(1P12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  1(1P12) MUTATED AMP PEAK  1(1P12) WILD-TYPE 
                        121                         246 
  AMP PEAK  1(1P12) MUTATED AMP PEAK  1(1P12) WILD-TYPE 
                        121                         246 
[1] "AMP PEAK  2(1Q21.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                          203                           164 
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                          203                           164 
[1] "AMP PEAK  3(1Q44) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  3(1Q44) MUTATED AMP PEAK  3(1Q44) WILD-TYPE 
                        201                         166 
  AMP PEAK  3(1Q44) MUTATED AMP PEAK  3(1Q44) WILD-TYPE 
                        201                         166 
[1] "AMP PEAK  4(3P13) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  4(3P13) MUTATED AMP PEAK  4(3P13) WILD-TYPE 
                        103                         264 
  AMP PEAK  4(3P13) MUTATED AMP PEAK  4(3P13) WILD-TYPE 
                        103                         264 
[1] "AMP PEAK  5(4Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE 
                         65                         302 
  AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE 
                         65                         302 
[1] "AMP PEAK  6(5P15.33) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  6(5P15.33) MUTATED AMP PEAK  6(5P15.33) WILD-TYPE 
                           110                            257 
  AMP PEAK  6(5P15.33) MUTATED AMP PEAK  6(5P15.33) WILD-TYPE 
                           110                            257 
[1] "AMP PEAK  7(5Q35.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  7(5Q35.3) MUTATED AMP PEAK  7(5Q35.3) WILD-TYPE 
                           59                           308 
  AMP PEAK  7(5Q35.3) MUTATED AMP PEAK  7(5Q35.3) WILD-TYPE 
                           59                           308 
[1] "AMP PEAK  8(6P24.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  8(6P24.3) MUTATED AMP PEAK  8(6P24.3) WILD-TYPE 
                          211                           156 
  AMP PEAK  8(6P24.3) MUTATED AMP PEAK  8(6P24.3) WILD-TYPE 
                          211                           156 
[1] "AMP PEAK  9(6Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  9(6Q12) MUTATED AMP PEAK  9(6Q12) WILD-TYPE 
                         81                         286 
  AMP PEAK  9(6Q12) MUTATED AMP PEAK  9(6Q12) WILD-TYPE 
                         81                         286 
[1] "AMP PEAK 10(7P22.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 10(7P22.1) MUTATED AMP PEAK 10(7P22.1) WILD-TYPE 
                          209                           158 
  AMP PEAK 10(7P22.1) MUTATED AMP PEAK 10(7P22.1) WILD-TYPE 
                          209                           158 
[1] "AMP PEAK 11(7Q34) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 11(7Q34) MUTATED AMP PEAK 11(7Q34) WILD-TYPE 
                        225                         142 
  AMP PEAK 11(7Q34) MUTATED AMP PEAK 11(7Q34) WILD-TYPE 
                        225                         142 
[1] "AMP PEAK 12(8Q24.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 12(8Q24.21) MUTATED AMP PEAK 12(8Q24.21) WILD-TYPE 
                           192                            175 
  AMP PEAK 12(8Q24.21) MUTATED AMP PEAK 12(8Q24.21) WILD-TYPE 
                           192                            175 
[1] "AMP PEAK 13(11Q13.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 13(11Q13.3) MUTATED AMP PEAK 13(11Q13.3) WILD-TYPE 
                            69                            298 
  AMP PEAK 13(11Q13.3) MUTATED AMP PEAK 13(11Q13.3) WILD-TYPE 
                            69                            298 
[1] "AMP PEAK 14(12Q14.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 14(12Q14.1) MUTATED AMP PEAK 14(12Q14.1) WILD-TYPE 
                            58                            309 
  AMP PEAK 14(12Q14.1) MUTATED AMP PEAK 14(12Q14.1) WILD-TYPE 
                            58                            309 
[1] "AMP PEAK 15(12Q15) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 15(12Q15) MUTATED AMP PEAK 15(12Q15) WILD-TYPE 
                          59                          308 
  AMP PEAK 15(12Q15) MUTATED AMP PEAK 15(12Q15) WILD-TYPE 
                          59                          308 
[1] "AMP PEAK 16(13Q31.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 16(13Q31.3) MUTATED AMP PEAK 16(13Q31.3) WILD-TYPE 
                           104                            263 
  AMP PEAK 16(13Q31.3) MUTATED AMP PEAK 16(13Q31.3) WILD-TYPE 
                           104                            263 
[1] "AMP PEAK 17(15Q26.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 17(15Q26.2) MUTATED AMP PEAK 17(15Q26.2) WILD-TYPE 
                           120                            247 
  AMP PEAK 17(15Q26.2) MUTATED AMP PEAK 17(15Q26.2) WILD-TYPE 
                           120                            247 
[1] "AMP PEAK 18(17Q25.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 18(17Q25.3) MUTATED AMP PEAK 18(17Q25.3) WILD-TYPE 
                           122                            245 
  AMP PEAK 18(17Q25.3) MUTATED AMP PEAK 18(17Q25.3) WILD-TYPE 
                           122                            245 
[1] "AMP PEAK 19(20Q13.33) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 19(20Q13.33) MUTATED AMP PEAK 19(20Q13.33) WILD-TYPE 
                            188                             179 
  AMP PEAK 19(20Q13.33) MUTATED AMP PEAK 19(20Q13.33) WILD-TYPE 
                            188                             179 
[1] "AMP PEAK 20(22Q13.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 20(22Q13.2) MUTATED AMP PEAK 20(22Q13.2) WILD-TYPE 
                           152                            215 
  AMP PEAK 20(22Q13.2) MUTATED AMP PEAK 20(22Q13.2) WILD-TYPE 
                           152                            215 
[1] "DEL PEAK  1(1P36.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                            81                            286 
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                            81                            286 
[1] "DEL PEAK  2(1P22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  2(1P22.1) MUTATED DEL PEAK  2(1P22.1) WILD-TYPE 
                           97                           270 
  DEL PEAK  2(1P22.1) MUTATED DEL PEAK  2(1P22.1) WILD-TYPE 
                           97                           270 
[1] "DEL PEAK  3(2Q37.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE 
                           93                           274 
  DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE 
                           93                           274 
[1] "DEL PEAK  4(3P25.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  4(3P25.1) MUTATED DEL PEAK  4(3P25.1) WILD-TYPE 
                           71                           296 
  DEL PEAK  4(3P25.1) MUTATED DEL PEAK  4(3P25.1) WILD-TYPE 
                           71                           296 
[1] "DEL PEAK  5(3Q13.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  5(3Q13.31) MUTATED DEL PEAK  5(3Q13.31) WILD-TYPE 
                            62                            305 
  DEL PEAK  5(3Q13.31) MUTATED DEL PEAK  5(3Q13.31) WILD-TYPE 
                            62                            305 
[1] "DEL PEAK  6(4P16.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  6(4P16.3) MUTATED DEL PEAK  6(4P16.3) WILD-TYPE 
                           91                           276 
  DEL PEAK  6(4P16.3) MUTATED DEL PEAK  6(4P16.3) WILD-TYPE 
                           91                           276 
[1] "DEL PEAK  7(4Q34.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  7(4Q34.3) MUTATED DEL PEAK  7(4Q34.3) WILD-TYPE 
                          110                           257 
  DEL PEAK  7(4Q34.3) MUTATED DEL PEAK  7(4Q34.3) WILD-TYPE 
                          110                           257 
[1] "DEL PEAK  8(5P15.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  8(5P15.31) MUTATED DEL PEAK  8(5P15.31) WILD-TYPE 
                            79                            288 
  DEL PEAK  8(5P15.31) MUTATED DEL PEAK  8(5P15.31) WILD-TYPE 
                            79                            288 
[1] "DEL PEAK  9(5Q12.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE 
                           97                           270 
  DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE 
                           97                           270 
[1] "DEL PEAK 10(5Q31.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 10(5Q31.3) MUTATED DEL PEAK 10(5Q31.3) WILD-TYPE 
                          131                           236 
  DEL PEAK 10(5Q31.3) MUTATED DEL PEAK 10(5Q31.3) WILD-TYPE 
                          131                           236 
[1] "DEL PEAK 11(6Q21) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 11(6Q21) MUTATED DEL PEAK 11(6Q21) WILD-TYPE 
                        214                         153 
  DEL PEAK 11(6Q21) MUTATED DEL PEAK 11(6Q21) WILD-TYPE 
                        214                         153 
[1] "DEL PEAK 12(6Q26) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 12(6Q26) MUTATED DEL PEAK 12(6Q26) WILD-TYPE 
                        221                         146 
  DEL PEAK 12(6Q26) MUTATED DEL PEAK 12(6Q26) WILD-TYPE 
                        221                         146 
[1] "DEL PEAK 13(8P23.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 13(8P23.3) MUTATED DEL PEAK 13(8P23.3) WILD-TYPE 
                           89                           278 
  DEL PEAK 13(8P23.3) MUTATED DEL PEAK 13(8P23.3) WILD-TYPE 
                           89                           278 
[1] "DEL PEAK 14(9P23) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 14(9P23) MUTATED DEL PEAK 14(9P23) WILD-TYPE 
                        249                         118 
  DEL PEAK 14(9P23) MUTATED DEL PEAK 14(9P23) WILD-TYPE 
                        249                         118 
[1] "DEL PEAK 15(9P21.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 15(9P21.3) MUTATED DEL PEAK 15(9P21.3) WILD-TYPE 
                          278                            89 
  DEL PEAK 15(9P21.3) MUTATED DEL PEAK 15(9P21.3) WILD-TYPE 
                          278                            89 
[1] "DEL PEAK 16(10P15.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 16(10P15.3) MUTATED DEL PEAK 16(10P15.3) WILD-TYPE 
                           199                            168 
  DEL PEAK 16(10P15.3) MUTATED DEL PEAK 16(10P15.3) WILD-TYPE 
                           199                            168 
[1] "DEL PEAK 17(10Q21.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 17(10Q21.1) MUTATED DEL PEAK 17(10Q21.1) WILD-TYPE 
                           217                            150 
  DEL PEAK 17(10Q21.1) MUTATED DEL PEAK 17(10Q21.1) WILD-TYPE 
                           217                            150 
[1] "DEL PEAK 18(10Q23.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 18(10Q23.31) MUTATED DEL PEAK 18(10Q23.31) WILD-TYPE 
                            230                             137 
  DEL PEAK 18(10Q23.31) MUTATED DEL PEAK 18(10Q23.31) WILD-TYPE 
                            230                             137 
[1] "DEL PEAK 19(10Q26.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 19(10Q26.3) MUTATED DEL PEAK 19(10Q26.3) WILD-TYPE 
                           236                            131 
  DEL PEAK 19(10Q26.3) MUTATED DEL PEAK 19(10Q26.3) WILD-TYPE 
                           236                            131 
[1] "DEL PEAK 20(11P15.5) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 20(11P15.5) MUTATED DEL PEAK 20(11P15.5) WILD-TYPE 
                           114                            253 
  DEL PEAK 20(11P15.5) MUTATED DEL PEAK 20(11P15.5) WILD-TYPE 
                           114                            253 
[1] "DEL PEAK 21(11Q23.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 21(11Q23.3) MUTATED DEL PEAK 21(11Q23.3) WILD-TYPE 
                           204                            163 
  DEL PEAK 21(11Q23.3) MUTATED DEL PEAK 21(11Q23.3) WILD-TYPE 
                           204                            163 
[1] "DEL PEAK 22(12Q23.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 22(12Q23.3) MUTATED DEL PEAK 22(12Q23.3) WILD-TYPE 
                            92                            275 
  DEL PEAK 22(12Q23.3) MUTATED DEL PEAK 22(12Q23.3) WILD-TYPE 
                            92                            275 
[1] "DEL PEAK 23(13Q34) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 23(13Q34) MUTATED DEL PEAK 23(13Q34) WILD-TYPE 
                          85                          282 
  DEL PEAK 23(13Q34) MUTATED DEL PEAK 23(13Q34) WILD-TYPE 
                          85                          282 
[1] "DEL PEAK 24(14Q23.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 24(14Q23.3) MUTATED DEL PEAK 24(14Q23.3) WILD-TYPE 
                           120                            247 
  DEL PEAK 24(14Q23.3) MUTATED DEL PEAK 24(14Q23.3) WILD-TYPE 
                           120                            247 
[1] "DEL PEAK 25(14Q32.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 25(14Q32.31) MUTATED DEL PEAK 25(14Q32.31) WILD-TYPE 
                            117                             250 
  DEL PEAK 25(14Q32.31) MUTATED DEL PEAK 25(14Q32.31) WILD-TYPE 
                            117                             250 
[1] "DEL PEAK 26(15Q13.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 26(15Q13.3) MUTATED DEL PEAK 26(15Q13.3) WILD-TYPE 
                            84                            283 
  DEL PEAK 26(15Q13.3) MUTATED DEL PEAK 26(15Q13.3) WILD-TYPE 
                            84                            283 
[1] "DEL PEAK 27(15Q21.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 27(15Q21.1) MUTATED DEL PEAK 27(15Q21.1) WILD-TYPE 
                            91                            276 
  DEL PEAK 27(15Q21.1) MUTATED DEL PEAK 27(15Q21.1) WILD-TYPE 
                            91                            276 
[1] "DEL PEAK 28(16P13.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 28(16P13.3) MUTATED DEL PEAK 28(16P13.3) WILD-TYPE 
                            62                            305 
  DEL PEAK 28(16P13.3) MUTATED DEL PEAK 28(16P13.3) WILD-TYPE 
                            62                            305 
[1] "DEL PEAK 29(16Q12.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 29(16Q12.1) MUTATED DEL PEAK 29(16Q12.1) WILD-TYPE 
                           117                            250 
  DEL PEAK 29(16Q12.1) MUTATED DEL PEAK 29(16Q12.1) WILD-TYPE 
                           117                            250 
[1] "DEL PEAK 30(16Q23.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 30(16Q23.1) MUTATED DEL PEAK 30(16Q23.1) WILD-TYPE 
                           120                            247 
  DEL PEAK 30(16Q23.1) MUTATED DEL PEAK 30(16Q23.1) WILD-TYPE 
                           120                            247 
[1] "DEL PEAK 31(16Q24.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 31(16Q24.3) MUTATED DEL PEAK 31(16Q24.3) WILD-TYPE 
                           133                            234 
  DEL PEAK 31(16Q24.3) MUTATED DEL PEAK 31(16Q24.3) WILD-TYPE 
                           133                            234 
[1] "DEL PEAK 32(17P13.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 32(17P13.3) MUTATED DEL PEAK 32(17P13.3) WILD-TYPE 
                           134                            233 
  DEL PEAK 32(17P13.3) MUTATED DEL PEAK 32(17P13.3) WILD-TYPE 
                           134                            233 
[1] "DEL PEAK 33(19P13.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 33(19P13.3) MUTATED DEL PEAK 33(19P13.3) WILD-TYPE 
                           104                            263 
  DEL PEAK 33(19P13.3) MUTATED DEL PEAK 33(19P13.3) WILD-TYPE 
                           104                            263 
[1] "DEL PEAK 34(XP21.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 34(XP21.1) MUTATED DEL PEAK 34(XP21.1) WILD-TYPE 
                           86                           281 
  DEL PEAK 34(XP21.1) MUTATED DEL PEAK 34(XP21.1) WILD-TYPE 
                           86                           281 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                      
 [2] "VITAL_STATUS"                        
 [3] "DAYS_TO_DEATH"                       
 [4] "DAYS_TO_LAST_FOLLOWUP"               
 [5] "DAYS_TO_SUBMITTED_SPECIMEN_DX"       
 [6] "PATHOLOGIC_STAGE"                    
 [7] "PATHOLOGY_T_STAGE"                   
 [8] "PATHOLOGY_N_STAGE"                   
 [9] "PATHOLOGY_M_STAGE"                   
[10] "MELANOMA_ULCERATION"                 
[11] "MELANOMA_PRIMARY_KNOWN"              
[12] "BRESLOW_THICKNESS"                   
[13] "GENDER"                              
[14] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"
[15] "RADIATION_THERAPY"                   
[16] "RACE"                                
[17] "ETHNICITY"                           

Input Data has 17 rows and 367 columns.

[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=68,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=190,	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=164,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'DAYS_TO_SUBMITTED_SPECIMEN_DX':	nDistinctValues=287,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 6:'PATHOLOGIC_STAGE':	nDistinctValues=14,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY_T_STAGE':	nDistinctValues=15,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY_N_STAGE':	nDistinctValues=10,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY_M_STAGE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'MELANOMA_ULCERATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'MELANOMA_PRIMARY_KNOWN':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'BRESLOW_THICKNESS':	nDistinctValues=109,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 13:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=31,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 15:'RADIATION_THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "TIME_FROM_SPECIMEN_DX_TO_DEATH_OR_LAST_FUP"
[2] "VITAL_STATUS"                              
[3] "DAYS_TO_DEATH_OR_LAST_FUP"                 
[4] "VITAL_STATUS"                              
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "TIME_FROM_SPECIMEN_DX_TO_DEATH_OR_LAST_FUP"
[2] "VITAL_STATUS"                              
[3] "DAYS_TO_DEATH_OR_LAST_FUP"                 
[4] "VITAL_STATUS"                              
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "TIME_FROM_SPECIMEN_DX_TO_DEATH_OR_LAST_FUP"
[2] "VITAL_STATUS"                              
[3] "DAYS_TO_DEATH_OR_LAST_FUP"                 
[4] "VITAL_STATUS"                              
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "TIME_FROM_SPECIMEN_DX_TO_DEATH_OR_LAST_FUP"
[2] "VITAL_STATUS"                              
[3] "DAYS_TO_DEATH_OR_LAST_FUP"                 
[4] "VITAL_STATUS"                              
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "TIME_FROM_SPECIMEN_DX_TO_DEATH_OR_LAST_FUP"
[2] "VITAL_STATUS"                              
[3] "DAYS_TO_DEATH_OR_LAST_FUP"                 
[4] "VITAL_STATUS"                              
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "TIME_FROM_SPECIMEN_DX_TO_DEATH_OR_LAST_FUP"
[2] "VITAL_STATUS"                              
[3] "DAYS_TO_DEATH_OR_LAST_FUP"                 
[4] "VITAL_STATUS"                              
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "TIME_FROM_SPECIMEN_DX_TO_DEATH_OR_LAST_FUP"
[2] "VITAL_STATUS"                              
[3] "DAYS_TO_DEATH_OR_LAST_FUP"                 
[4] "VITAL_STATUS"                              
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "TIME_FROM_SPECIMEN_DX_TO_DEATH_OR_LAST_FUP"
[2] "VITAL_STATUS"                              
[3] "DAYS_TO_DEATH_OR_LAST_FUP"                 
[4] "VITAL_STATUS"                              
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "TIME_FROM_SPECIMEN_DX_TO_DEATH_OR_LAST_FUP"
[2] "VITAL_STATUS"                              
[3] "DAYS_TO_DEATH_OR_LAST_FUP"                 
[4] "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 367 columns, 2 survival variables, and 12 non-survival variables.
[1] "* survival variables: "
[1] "TIME_FROM_SPECIMEN_DX_TO_DEATH_OR_LAST_FUP"
[2] "VITAL_STATUS"                              
[3] "DAYS_TO_DEATH_OR_LAST_FUP"                 
[4] "VITAL_STATUS"                              
[1] "* non-survival variables: "
 [1] "YEARS_TO_BIRTH"         "PATHOLOGIC_STAGE"       "PATHOLOGY_T_STAGE"     
 [4] "PATHOLOGY_N_STAGE"      "PATHOLOGY_M_STAGE"      "MELANOMA_ULCERATION"   
 [7] "MELANOMA_PRIMARY_KNOWN" "BRESLOW_THICKNESS"      "GENDER"                
[10] "RADIATION_THERAPY"      "RACE"                   "ETHNICITY"             
YEARS_TO_BIRTH, nv=68, binary=FALSE, numeric=TRUE
PATHOLOGIC_STAGE, nv=14, binary=FALSE, numeric=FALSE
PATHOLOGY_T_STAGE, nv=5, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
T0 T1 T2 T3 T4 
23 41 73 81 67 
[1] "table(vv)"
vv
T0+T1    T2    T3    T4 
   64    73    81    67 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
T0 T1 T2 T3 T4 
23 41 73 81 67 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


T0+T1    T2    T3    T4 
   64    73    81    67 
PATHOLOGY_N_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2  N3 
177  65  39  45 
[1] "table(vv)"
vv
 N0  N1  N2  N3 
177  65  39  45 
$ClinVariableName
[1] "PATHOLOGY_N_STAGE"

$Table
vv
 N0  N1  N2  N3 
177  65  39  45 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 N0  N1  N2  N3 
177  65  39  45 
PATHOLOGY_M_STAGE, nv=2, binary=FALSE, numeric=TRUE
MELANOMA_ULCERATION, nv=2, binary=FALSE, numeric=FALSE
MELANOMA_PRIMARY_KNOWN, nv=2, binary=FALSE, numeric=FALSE
BRESLOW_THICKNESS, nv=109, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
RADIATION_THERAPY, nv=2, binary=FALSE, numeric=FALSE
RACE, nv=3, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = AMP PEAK  1(1P12) MUTATION ANALYSIS
D1V1, survival
                             sevent
clus2                          0  1
  AMP PEAK  1(1P12) MUTATED   40 39
  AMP PEAK  1(1P12) WILD-TYPE 88 85
  AMP PEAK  1(1P12) MUTATED AMP PEAK  1(1P12) WILD-TYPE 
                         79                         173 
  AMP PEAK  1(1P12) MUTATED AMP PEAK  1(1P12) WILD-TYPE 
                         39                          85 
$`AMP PEAK  1(1P12) MUTATED`
TCGA-D3-A8GI TCGA-EE-A180 TCGA-EE-A2MR TCGA-FR-A729 TCGA-WE-AAA3 TCGA-3N-A9WD 
       13.41        31.96       134.40       216.43         7.40        12.99 
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A2J6 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JL 
        8.42        15.72        25.64        15.75        86.30       171.58 
TCGA-D3-A2JO TCGA-D3-A3C6 TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A51E TCGA-D3-A51R 
       66.08        58.06         9.34        90.21       173.85        62.70 
TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GJ TCGA-D3-A8GM TCGA-D3-A8GR TCGA-D9-A1X3 
       78.21        23.61       179.97        70.62        36.53        10.78 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6EC TCGA-DA-A95V TCGA-EB-A5UN TCGA-EB-A6L9 
       15.02        16.90        69.21        72.10        52.41        18.21 
TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G 
       20.38        26.24        76.14        12.99         0.26        44.28 
TCGA-EE-A29M TCGA-EE-A29W TCGA-EE-A2GB TCGA-EE-A2GJ TCGA-EE-A2GL TCGA-EE-A2GP 
       47.74       185.19        26.14        68.65        32.48         0.76 
TCGA-EE-A2GR TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MM TCGA-EE-A2MU TCGA-EE-A3AB 
        0.20       171.85        63.25       145.45        53.26       122.73 
TCGA-EE-A3AD TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-ER-A199 TCGA-ER-A19D TCGA-ER-A19G 
        4.41        67.89        45.90         7.82        11.47       184.60 
TCGA-ER-A19L TCGA-ER-A2ND TCGA-ER-A3ET TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A 
       99.06         4.70        68.52        32.05         4.50       174.21 
TCGA-FR-A69P TCGA-FR-A7UA TCGA-FS-A1ZQ TCGA-FS-A1ZU TCGA-GF-A4EO TCGA-GN-A264 
        4.14         5.65       130.95         4.47        18.25       117.93 
TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-W3-A825 TCGA-W3-A828 
       17.06         7.59       120.53        34.49         1.97       120.07 
TCGA-W3-AA1W TCGA-WE-A8K1 TCGA-WE-A8ZQ TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 
      185.13        47.54        62.89        48.39         1.94        37.32 
TCGA-YG-AA3O 
       28.21 

$`AMP PEAK  1(1P12) WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A20H TCGA-EE-A2GD 
        9.76        62.07        38.76        33.24       166.75       269.03 
TCGA-EE-A2GO TCGA-EE-A3JD TCGA-ER-A193 TCGA-FW-A3R5 TCGA-WE-A8K5 TCGA-3N-A9WC 
       52.90        27.35        19.04        36.95        52.73        60.46 
TCGA-BF-AAP0 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       14.83        31.89       110.93        49.35       133.25        19.04 
TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JB TCGA-D3-A2JG 
       76.41        62.60        45.99        62.86       168.00       107.61 
TCGA-D3-A2JH TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE 
       36.30        64.83        43.53       140.98        40.01        59.70 
TCGA-D3-A3CF TCGA-D3-A3MU TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51T 
       24.53        23.67        30.67       144.46        31.76        11.34 
TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D3-A8GK TCGA-D3-A8GL 
       42.05        45.70       177.86       124.08       120.00        69.53 
TCGA-D3-A8GP TCGA-D9-A4Z6 TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 
      135.12        18.44        22.85        76.34       138.67        68.68 
TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 
      150.61       110.53        60.10        64.83        58.85        30.44 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-DA-A95W TCGA-DA-A95X TCGA-DA-A95Y TCGA-DA-A95Z 
      225.11         8.71         0.76        65.03        14.14        12.30 
TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A182 TCGA-EE-A20C 
        3.91        16.41        13.15        24.89         0.00        75.55 
TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29H TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T 
       79.20        75.22        47.41        27.16        61.12       346.49 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GK 
      115.43        30.02        77.98        12.95       201.60        10.62 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 
       18.35        93.63        71.31        81.99       103.13        15.25 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MK TCGA-EE-A2ML 
        5.75        23.77       209.79        94.19        89.26       104.78 
TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AE 
      227.01       143.93        23.51       124.31        64.04        54.51 
TCGA-EE-A3AF TCGA-EE-A3J4 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI 
        6.28       111.85         3.35       168.85        19.86       135.98 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19H 
       34.45        10.49         4.54        53.29        39.81       150.12 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W 
       59.84        42.51       120.76        49.71        47.18       146.63 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES 
       73.05        22.36        16.87        10.19        28.67       173.29 
TCGA-ER-A3EV TCGA-ER-A42L TCGA-FR-A7U8 TCGA-FR-A8YC TCGA-FS-A1YW TCGA-FS-A1YY 
       15.48        74.47        26.20        10.06       171.78        49.74 
TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE 
      195.98         8.35        27.62       312.07        32.78        43.92 
TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZW 
        7.82        36.33        78.61       136.27        35.28        23.21 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 
        5.29         3.06        30.90        66.67       173.19        13.28 
TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 
       80.68        55.59        11.54        19.30         9.90         1.91 
TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A268 TCGA-GN-A4U8 TCGA-GN-A8LK TCGA-GN-A9SD 
       53.29        96.92        42.48        46.92        43.23        59.41 
TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 TCGA-W3-A824 
       85.05       297.01         7.23         0.20         0.33       174.12 
TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1V TCGA-W3-AA21 TCGA-WE-A8ZM TCGA-WE-A8ZN 
       44.05        79.99         8.09        92.84        65.42        12.69 
TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-AAA4 TCGA-XV-AB01 TCGA-Z2-AA3S 
       21.90        10.95        24.99         6.61        91.23 

  AMP PEAK  1(1P12) MUTATED AMP PEAK  1(1P12) WILD-TYPE 
                        0.2                         0.0 
  AMP PEAK  1(1P12) MUTATED AMP PEAK  1(1P12) WILD-TYPE 
                     216.43                      346.49 
  AMP PEAK  1(1P12) MUTATED AMP PEAK  1(1P12) WILD-TYPE 
                      37.32                       47.41 
[1] "0.2 - 216.4 (37.3)" "0.0 - 346.5 (47.4)"
[1] "hr=" "1.2"
D1V2, survival
                             sevent
clus2                           0   1
  AMP PEAK  1(1P12) MUTATED    53  65
  AMP PEAK  1(1P12) WILD-TYPE 113 127
  AMP PEAK  1(1P12) MUTATED AMP PEAK  1(1P12) WILD-TYPE 
                        118                         240 
  AMP PEAK  1(1P12) MUTATED AMP PEAK  1(1P12) WILD-TYPE 
                         65                         127 
$`AMP PEAK  1(1P12) MUTATED`
TCGA-D3-A3ML TCGA-D3-A8GI TCGA-EE-A180 TCGA-EE-A29L TCGA-EE-A2MR TCGA-FR-A729 
       13.87        58.52        94.98         2.60       134.40       220.80 
TCGA-QB-AA9O TCGA-WE-AAA3 TCGA-3N-A9WB TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q3 
       18.05        21.40        17.03        12.99        16.57        16.67 
TCGA-D3-A2J6 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JL TCGA-D3-A2JO 
       43.43       115.53        86.76        11.87       171.58        66.08 
TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A51E TCGA-D3-A51R 
      130.72        58.06         9.34       103.59       174.84        63.81 
TCGA-D3-A5GO TCGA-D3-A5GS TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GJ TCGA-D3-A8GM 
      137.92        18.18        79.59        23.61       241.38       107.15 
TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 
       29.06       129.63        18.12        15.39        22.29         9.90 
TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A3F3 TCGA-DA-A95V TCGA-EB-A44R TCGA-EB-A5UL 
       25.18        77.56        10.49        72.10        10.36        29.29 
TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B 
       58.92        36.46        33.73        26.89         4.96       133.81 
TCGA-EE-A20I TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29M 
       13.55        78.97        13.97        63.78        72.07        56.84 
TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2GB TCGA-EE-A2GI TCGA-EE-A2GJ 
       25.87       195.02        17.92        59.28        48.72       107.38 
TCGA-EE-A2GL TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2MD TCGA-EE-A2MI TCGA-EE-A2MJ 
       79.66        13.91        42.77        47.28       204.66        96.23 
TCGA-EE-A2MM TCGA-EE-A2MQ TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AG 
      167.90        43.23        53.26       122.73        28.77        41.59 
TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-ER-A199 TCGA-ER-A19D TCGA-ER-A19E 
      172.18        64.08        53.19         9.17        12.59        13.02 
TCGA-ER-A19G TCGA-ER-A19L TCGA-ER-A19T TCGA-ER-A2ND TCGA-ER-A3ET TCGA-ER-A3PL 
      302.07       131.51         8.88        23.34        93.01        33.21 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FS-A1YX 
       92.98       174.21        15.72        18.77        38.27        48.59 
TCGA-FS-A1ZH TCGA-FS-A1ZK TCGA-FS-A1ZQ TCGA-FS-A1ZU TCGA-FS-A4F2 TCGA-FS-A4F5 
       32.75        23.93       133.55        26.56        50.14        28.73 
TCGA-FW-A3I3 TCGA-GF-A4EO TCGA-GF-A6C9 TCGA-GN-A264 TCGA-GN-A266 TCGA-GN-A267 
       17.46        19.43        15.78       117.93        10.13        64.44 
TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-HR-A2OG TCGA-HR-A2OH TCGA-W3-A825 
       32.48       121.91        39.35         0.23        65.88        63.02 
TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1W TCGA-WE-A8K1 TCGA-WE-A8ZQ TCGA-WE-A8ZY 
      121.08         4.01       219.16        49.05        63.22        49.51 
TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-YD-A9TA TCGA-YG-AA3O 
       12.16        40.41        49.18        37.94 

$`AMP PEAK  1(1P12) WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A184 
       27.65        62.07        46.32        68.25        54.02        68.15 
TCGA-EE-A20H TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A3JD TCGA-ER-A193 TCGA-ER-A198 
      168.26       340.14       126.81        27.35        31.40        50.76 
TCGA-FS-A1ZF TCGA-FW-A3R5 TCGA-WE-A8K5 TCGA-3N-A9WC TCGA-BF-AAP0 TCGA-D3-A1Q4 
       15.45        36.95        61.15        66.48        14.93       112.04 
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA 
      112.57        71.80       133.25        28.08        31.59        90.90 
TCGA-D3-A1QB TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JG 
       95.74       103.10        65.49        23.77       168.00       113.52 
TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3C7 TCGA-D3-A3CB 
       42.08        12.10        66.48        59.57        46.98       166.52 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51F 
       86.93        60.23        24.53        39.75        45.30        55.73 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51T TCGA-D3-A5GL 
       56.35       145.12        32.94        22.62        26.89       125.79 
TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GE TCGA-D3-A8GK 
      135.75       178.32       125.19        30.84        26.43       170.20 
TCGA-D3-A8GL TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GS TCGA-D3-A8GV TCGA-D9-A148 
       89.13       161.00       152.75       117.17       167.70       151.53 
TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A4Z6 TCGA-D9-A6EG TCGA-DA-A1HV 
       54.67         3.65         7.10        18.44        22.95        76.57 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 
       36.03       144.89        20.38       222.51       176.55        35.93 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
      135.02        88.87        53.92        65.92        40.60        68.09 
TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-DA-A95W TCGA-DA-A95X TCGA-DA-A95Y 
       33.93       225.96        43.36        37.35        73.94        14.14 
TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5VV TCGA-EE-A17X TCGA-EE-A17Y 
       13.02        13.87        20.35         7.04        29.82        27.22 
TCGA-EE-A17Z TCGA-EE-A182 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29A TCGA-EE-A29B 
        8.65        14.70       151.27        91.56        63.35        85.08 
TCGA-EE-A29H TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
       64.64        18.61        56.42        66.74        14.47        61.28 
TCGA-EE-A29T TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
      369.93        46.82       115.96        59.64        39.29        86.14 
TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GK TCGA-EE-A2GM TCGA-EE-A2GN 
       67.43       173.79       220.24        54.74        75.48       102.12 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 
       81.21        44.88        94.82        21.67       129.27        28.83 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH 
       19.76        61.51       103.27       268.73       103.20        16.96 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT 
      180.39       216.66        47.54       248.65       162.48        71.21 
TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J4 
      124.31        64.04        54.51        13.81       138.81       127.20 
TCGA-EE-A3J5 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
       36.95        34.32       201.80        51.35       134.33       152.81 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19F 
       35.44        13.94        77.75        98.40        48.89        26.37 
TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
      152.35         6.44        61.05        44.09       162.08        50.89 
TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF 
       49.48       148.18       105.07        43.82        20.15        28.83 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3EV TCGA-ER-A42K TCGA-ER-A42L 
       48.99        41.56       247.04        46.98        12.95       149.03 
TCGA-FR-A7U8 TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YY 
       27.85        34.82        36.26       104.42       216.92       228.59 
TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB 
      202.65        20.91        28.08         7.79        27.72        48.85 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM 
      357.37        53.52        46.45         9.70        47.38       101.26 
TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A1ZY 
       74.73        11.41       148.80        53.16        49.48        27.09 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB 
       27.02        77.82        66.67       174.84        34.03        26.73 
TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
       54.41        80.68        55.59        13.51        19.30         9.90 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A268 TCGA-GN-A26D TCGA-GN-A4U7 
        2.04       139.89        96.92        62.79        48.00        10.42 
TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL TCGA-GN-A9SD TCGA-LH-A9QB 
       48.89        22.13        50.10        21.37        59.41       368.78 
TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 
      297.90         7.23         0.20         0.33         0.69       228.16 
TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1V TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K6 
       69.07       111.09        42.08       105.04        24.03        17.95 
TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-AAA4 
      101.33        58.98        70.52        11.80        35.80        24.99 
TCGA-XV-AB01 TCGA-YD-A89C TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       13.25         6.90        14.43        27.58        96.99        15.98 

  AMP PEAK  1(1P12) MUTATED AMP PEAK  1(1P12) WILD-TYPE 
                       0.23                        0.20 
  AMP PEAK  1(1P12) MUTATED AMP PEAK  1(1P12) WILD-TYPE 
                     302.07                      369.93 
  AMP PEAK  1(1P12) MUTATED AMP PEAK  1(1P12) WILD-TYPE 
                     45.355                      54.705 
[1] "0.2 - 302.1 (45.4)" "0.2 - 369.9 (54.7)"
[1] "hr=" "1.3"
D1V3, continuous
                             vv
clus                          I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB
  AMP PEAK  1(1P12) MUTATED          5       4       5        6       11
  AMP PEAK  1(1P12) WILD-TYPE        8       3      24       12       17
                             vv
clus                          STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  AMP PEAK  1(1P12) MUTATED         12         5         4         5        11
  AMP PEAK  1(1P12) WILD-TYPE       14         9        15        10        28
                             vv
clus                          STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  AMP PEAK  1(1P12) MUTATED           10          8         21        6
  AMP PEAK  1(1P12) WILD-TYPE          5         27         33       15
D1V4, multiclass
            clus
vv           AMP PEAK  1(1P12) MUTATED AMP PEAK  1(1P12) WILD-TYPE
  I/II NOS                           5                           8
  STAGE 0                            4                           3
  STAGE I                            5                          24
  STAGE IA                           6                          12
  STAGE IB                          11                          17
  STAGE II                          12                          14
  STAGE IIA                          5                           9
  STAGE IIB                          4                          15
  STAGE IIC                          5                          10
  STAGE III                         11                          28
  STAGE IIIA                        10                           5
  STAGE IIIB                         8                          27
  STAGE IIIC                        21                          33
  STAGE IV                           6                          15
[1] 14  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          T0+T1 T2 T3 T4
  AMP PEAK  1(1P12) MUTATED      17 23 31 24
  AMP PEAK  1(1P12) WILD-TYPE    47 50 50 43
D1V5, multiclass
       clus
vv      AMP PEAK  1(1P12) MUTATED AMP PEAK  1(1P12) WILD-TYPE
  T0+T1                        17                          47
  T2                           23                          50
  T3                           31                          50
  T4                           24                          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  N3
  AMP PEAK  1(1P12) MUTATED    59  19  14  18
  AMP PEAK  1(1P12) WILD-TYPE 118  46  25  27
D1V6, multiclass
    clus
vv   AMP PEAK  1(1P12) MUTATED AMP PEAK  1(1P12) WILD-TYPE
  N0                        59                         118
  N1                        19                          46
  N2                        14                          25
  N3                        18                          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"
D1V7, binary
                             cls
clus                            0   1
  AMP PEAK  1(1P12) MUTATED   105   6
  AMP PEAK  1(1P12) WILD-TYPE 214  16
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  1(1P12) MUTATED    105    6
  AMP PEAK  1(1P12) WILD-TYPE  214   16
   clus
vv  AMP PEAK  1(1P12) MUTATED AMP PEAK  1(1P12) WILD-TYPE
  0                       105                         214
  1                         6                          16
[1] 2 2
[1] FALSE
D1V8, binary
                             cls
clus                           0  1
  AMP PEAK  1(1P12) MUTATED   48 29
  AMP PEAK  1(1P12) WILD-TYPE 86 61
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  1(1P12) MUTATED     48   29
  AMP PEAK  1(1P12) WILD-TYPE   86   61
     clus
vv    AMP PEAK  1(1P12) MUTATED AMP PEAK  1(1P12) WILD-TYPE
  NO                         48                          86
  YES                        29                          61
[1] 2 2
[1] FALSE
D1V9, binary
                             cls
clus                            0   1
  AMP PEAK  1(1P12) MUTATED    14 107
  AMP PEAK  1(1P12) WILD-TYPE  33 213
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  1(1P12) MUTATED     14  107
  AMP PEAK  1(1P12) WILD-TYPE   33  213
     clus
vv    AMP PEAK  1(1P12) MUTATED AMP PEAK  1(1P12) WILD-TYPE
  NO                         14                          33
  YES                       107                         213
[1] 2 2
[1] FALSE
D1V10, continuous
D1V11, binary
                             cls
clus                            0   1
  AMP PEAK  1(1P12) MUTATED    43  78
  AMP PEAK  1(1P12) WILD-TYPE  95 151
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  1(1P12) MUTATED     43   78
  AMP PEAK  1(1P12) WILD-TYPE   95  151
        clus
vv       AMP PEAK  1(1P12) MUTATED AMP PEAK  1(1P12) WILD-TYPE
  FEMALE                        43                          95
  MALE                          78                         151
[1] 2 2
[1] FALSE
D1V12, binary
                             cls
clus                            0   1
  AMP PEAK  1(1P12) MUTATED    98  23
  AMP PEAK  1(1P12) WILD-TYPE 221  24
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  1(1P12) MUTATED     98   23
  AMP PEAK  1(1P12) WILD-TYPE  221   24
     clus
vv    AMP PEAK  1(1P12) MUTATED AMP PEAK  1(1P12) WILD-TYPE
  NO                         98                         221
  YES                        23                          24
[1] 2 2
[1] FALSE
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  1(1P12) MUTATED       2                         0   115
  AMP PEAK  1(1P12) WILD-TYPE     3                         1   238
D1V13, multiclass
                           clus
vv                          AMP PEAK  1(1P12) MUTATED
  ASIAN                                             2
  BLACK OR AFRICAN AMERICAN                         0
  WHITE                                           115
                           clus
vv                          AMP PEAK  1(1P12) WILD-TYPE
  ASIAN                                               3
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                             238
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V14, binary
                             cls
clus                            0   1
  AMP PEAK  1(1P12) MUTATED     3 116
  AMP PEAK  1(1P12) WILD-TYPE   4 236
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  1(1P12) MUTATED      3  116
  AMP PEAK  1(1P12) WILD-TYPE    4  236
                        clus
vv                       AMP PEAK  1(1P12) MUTATED AMP PEAK  1(1P12) WILD-TYPE
  HISPANIC OR LATINO                             3                           4
  NOT HISPANIC OR LATINO                       116                         236
[1] 2 2
[1] FALSE

Clustering(2) Variable = AMP PEAK  2(1Q21.3) MUTATION ANALYSIS
D2V1, survival
                               sevent
clus2                            0  1
  AMP PEAK  2(1Q21.3) MUTATED   71 69
  AMP PEAK  2(1Q21.3) WILD-TYPE 57 55
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                          140                           112 
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                           69                            55 
$`AMP PEAK  2(1Q21.3) MUTATED`
TCGA-D3-A2JE TCGA-D3-A8GI TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GD TCGA-EE-A2GO 
        9.76        13.41        31.96       166.75       269.03        52.90 
TCGA-EE-A2MR TCGA-FR-A729 TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-3N-A9WC TCGA-3N-A9WD 
      134.40       216.43        52.73         7.40        60.46        12.99 
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QB TCGA-D3-A2J8 
        8.42        15.72       133.25        19.04        62.60        62.86 
TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A3C6 TCGA-D3-A3CE 
       15.75        86.30       171.58        64.83        58.06        59.70 
TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51K TCGA-D3-A51R 
        9.34        90.21        23.67       173.85        31.76        62.70 
TCGA-D3-A5GN TCGA-D3-A5GU TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GJ TCGA-D3-A8GK 
       45.70       124.08        78.21        23.61       179.97       120.00 
TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GP TCGA-D3-A8GR TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       69.53        70.62       135.12        36.53        15.02        16.90 
TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1I1 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA 
       69.21        22.85        68.68       110.53        60.10        64.83 
TCGA-DA-A1IC TCGA-DA-A3F5 TCGA-DA-A95V TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A5UN 
       58.85       225.11        72.10        14.14        12.30        52.41 
TCGA-EB-A6L9 TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A29B 
       18.21        24.89        20.38         0.00        26.24        75.22 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29M TCGA-EE-A29T TCGA-EE-A29W 
       12.99         0.26        44.28        47.74       346.49       185.19 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH 
      115.43        30.02        77.98        26.14        12.95       201.60 
TCGA-EE-A2GJ TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GS TCGA-EE-A2GU 
       68.65        32.48        18.35        93.63        71.31        81.99 
TCGA-EE-A2M7 TCGA-EE-A2MJ TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB 
       15.25        63.25       143.93        23.51        53.26       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-EE-A3JH TCGA-ER-A197 
       64.04         4.41        67.89        45.90        19.86        10.49 
TCGA-ER-A199 TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19Q TCGA-ER-A2ND 
        7.82        11.47       184.60       150.12        49.71         4.70 
TCGA-ER-A2NG TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       28.67        15.48        32.05         4.50       174.21         4.14 
TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FS-A1YW TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1ZC 
        5.65        10.06       171.78       195.98         8.35       312.07 
TCGA-FS-A1ZD TCGA-FS-A1ZQ TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A1ZZ 
       32.78       130.95        35.28         4.47         5.29         3.06 
TCGA-FS-A4F0 TCGA-FS-A4FD TCGA-GF-A6C8 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A4U3 
       30.90        80.68         1.91        17.06         7.59       120.53 
TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-GN-A8LK TCGA-GN-A9SD TCGA-LH-A9QB TCGA-QB-A6FS 
       34.49        46.92        43.23        59.41        85.05         7.23 
TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1W TCGA-W3-AA21 
        1.97       120.07        44.05        79.99       185.13        92.84 
TCGA-WE-A8K1 TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZY TCGA-WE-AAA0 TCGA-WE-AAA4 
       47.54        21.90        62.89        48.39        37.32        24.99 
TCGA-XV-AB01 TCGA-YG-AA3O 
        6.61        28.21 

$`AMP PEAK  2(1Q21.3) WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A3JD TCGA-ER-A193 TCGA-FW-A3R5 
       62.07        38.76        33.24        27.35        19.04        36.95 
TCGA-BF-AAP0 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1QA TCGA-D3-A2J6 
       14.83        31.89       110.93        49.35        76.41        25.64 
TCGA-D3-A2J7 TCGA-D3-A2JB TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JO TCGA-D3-A2JP 
       45.99       168.00       107.61        36.30        66.08        43.53 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51T 
      140.98        40.01        24.53        30.67       144.46        11.34 
TCGA-D3-A5GL TCGA-D3-A5GR TCGA-D9-A1X3 TCGA-D9-A4Z6 TCGA-DA-A1HV TCGA-DA-A1HY 
       42.05       177.86        10.78        18.44        76.34       138.67 
TCGA-DA-A1I2 TCGA-DA-A3F2 TCGA-DA-A3F8 TCGA-DA-A95W TCGA-DA-A95X TCGA-EB-A44Q 
      150.61        30.44         8.71         0.76        65.03         3.91 
TCGA-EB-A5KH TCGA-EE-A17X TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29H 
       16.41        13.15        75.55        79.20        76.14        47.41 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A2GK TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2M6 
       27.16        61.12        10.62         0.76         0.20       103.13 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MK 
        5.75        23.77       209.79        94.19       171.85        89.26 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A3AA TCGA-EE-A3AE TCGA-EE-A3AF 
      104.78       145.45       227.01       124.31        54.51         6.28 
TCGA-EE-A3J4 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A19A 
      111.85         3.35       168.85       135.98        34.45         4.54 
TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P 
       53.29        39.81        99.06        59.84        42.51       120.76 
TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF 
       47.18       146.63        73.05        22.36        16.87        10.19 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A42L TCGA-FR-A7U8 TCGA-FS-A1YY TCGA-FS-A1Z4 
      173.29        68.52        74.47        26.20        49.74        27.62 
TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZS TCGA-FS-A1ZW 
       43.92         7.82        36.33        78.61       136.27        23.21 
TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
       66.67       173.19        13.28        55.59        11.54        19.30 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A268 
        9.90        18.25        53.29       117.93        96.92        42.48 
TCGA-OD-A75X TCGA-RP-A690 TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-AA1V TCGA-WE-A8ZM 
      297.01         0.20         0.33       174.12         8.09        65.42 
TCGA-WE-A8ZN TCGA-WE-A8ZT TCGA-WE-AA9Y TCGA-Z2-AA3S 
       12.69        10.95         1.94        91.23 

  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                          0.0                           0.2 
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                       346.49                        297.01 
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                       47.230                        44.955 
[1] "0.0 - 346.5 (47.2)" "0.2 - 297.0 (45.0)"
[1] "hr=" "1"  
D2V2, survival
                               sevent
clus2                             0   1
  AMP PEAK  2(1Q21.3) MUTATED    90 109
  AMP PEAK  2(1Q21.3) WILD-TYPE  76  83
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                          199                           159 
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                          109                            83 
$`AMP PEAK  2(1Q21.3) MUTATED`
TCGA-D3-A2JE TCGA-D3-A3ML TCGA-D3-A8GI TCGA-EB-A5SH TCGA-EE-A180 TCGA-EE-A184 
       27.65        13.87        58.52        54.02        94.98        68.15 
TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR TCGA-FR-A729 
      168.26         2.60       340.14       126.81       134.40       220.80 
TCGA-FS-A1ZF TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD 
       15.45        61.15        21.40        17.03        66.48        12.99 
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QB TCGA-D3-A2J8 
       16.57        16.67       133.25        28.08        95.74        65.49 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JL TCGA-D3-A2JN 
       23.77       115.53        86.76        11.87       171.58        66.48 
TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU 
      130.72        58.06        60.23         9.34       103.59        39.75 
TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A5GO 
       45.30       174.84        32.94        63.81       135.75       137.92 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GJ TCGA-D3-A8GK 
       18.18       125.19        79.59        23.61       241.38       170.20 
TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D9-A1JW 
       89.13       107.15       152.75        29.06       129.63         3.65 
TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC 
        7.10        15.39        22.29         9.90        25.18        77.56 
TCGA-D9-A6EG TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 
       22.95        20.38       222.51        35.93       135.02        88.87 
TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A95V TCGA-DA-A95Y 
       65.92        68.09        10.49       225.96        72.10        14.14 
TCGA-DA-A95Z TCGA-EB-A44R TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17Y 
       13.02        10.36        29.29        58.92        36.46        27.22 
TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B 
        8.65        33.73        14.70        26.89         4.96       133.81 
TCGA-EE-A20I TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29M 
       13.55        85.08        13.97        63.78        72.07        56.84 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A2 
       14.47        61.28       369.93       195.02       115.96        59.64 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       86.14        59.28       173.79       220.24        48.72       107.38 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M7 
       79.66        75.48       102.12        81.21        94.82        28.83 
TCGA-EE-A2MJ TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU 
       96.23        47.54        43.23       162.48        71.21        53.26 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J5 
      122.73        64.04        28.77        41.59       172.18        36.95 
TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-EE-A3JH TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19D 
       64.08        53.19       134.33        13.94         9.17        12.59 
TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19Q TCGA-ER-A19T 
       13.02        26.37       302.07       152.35        50.89         8.88 
TCGA-ER-A2ND TCGA-ER-A2NG TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN 
       23.34        48.99        46.98        33.21        12.95        92.98 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD 
      174.21        15.72        18.77        38.27        34.82        36.26 
TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1ZA TCGA-FS-A1ZC 
      216.92        48.59       202.65        20.91        27.72       357.37 
TCGA-FS-A1ZD TCGA-FS-A1ZH TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZT 
       53.52        32.75        23.93        74.73       133.55        53.16 
TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F5 TCGA-FS-A4FD 
       26.56        27.09        27.02        77.82        28.73        80.68 
TCGA-FW-A3I3 TCGA-GF-A6C8 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A26D 
       17.46         2.04        10.13        64.44        32.48        48.00 
TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK 
      121.91        39.35        10.42        48.89        22.13        50.10 
TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OG TCGA-HR-A2OH TCGA-LH-A9QB TCGA-QB-A6FS 
       21.37        59.41         0.23        65.88       368.78         7.23 
TCGA-RP-A694 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1Q TCGA-W3-AA1R 
        0.69        63.02       121.08         4.01        69.07       111.09 
TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZX 
      219.16       105.04        49.05        70.52        63.22        35.80 
TCGA-WE-A8ZY TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-XV-AB01 TCGA-YD-A89C TCGA-YD-A9TA 
       49.51        40.41        24.99        13.25         6.90        49.18 
TCGA-YG-AA3O 
       37.94 

$`AMP PEAK  2(1Q21.3) WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A3JD TCGA-ER-A193 TCGA-ER-A198 
       62.07        46.32        68.25        27.35        31.40        50.76 
TCGA-FW-A3R5 TCGA-QB-AA9O TCGA-BF-AAP0 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 
       36.95        18.05        14.93       112.04       112.57        71.80 
TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2JB TCGA-D3-A2JG 
       31.59        90.90        43.43       103.10       168.00       113.52 
TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C7 TCGA-D3-A3CB 
       42.08        12.10        66.08        59.57        46.98       166.52 
TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51N 
       86.93        24.53        55.73        56.35       145.12        22.62 
TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GR TCGA-D3-A8GB TCGA-D3-A8GE TCGA-D3-A8GN 
       26.89       125.79       178.32        30.84        26.43       161.00 
TCGA-D3-A8GS TCGA-D3-A8GV TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1X3 TCGA-D9-A4Z6 
      117.17       167.70       151.53        54.67        18.12        18.44 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A1I8 TCGA-DA-A1IB 
       76.57        36.03       144.89       176.55        53.92        40.60 
TCGA-DA-A3F2 TCGA-DA-A3F8 TCGA-DA-A95W TCGA-DA-A95X TCGA-EB-A44Q TCGA-EB-A5KH 
       33.93        43.36        37.35        73.94        13.87        20.35 
TCGA-EB-A5VV TCGA-EE-A17X TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29A TCGA-EE-A29C 
        7.04        29.82       151.27        91.56        63.35        78.97 
TCGA-EE-A29H TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29V TCGA-EE-A29X 
       64.64        18.61        56.42        66.74        25.87        17.92 
TCGA-EE-A2A0 TCGA-EE-A2A5 TCGA-EE-A2GC TCGA-EE-A2GK TCGA-EE-A2GP TCGA-EE-A2GR 
       46.82        39.29        67.43        54.74        13.91        42.77 
TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD 
       44.88        21.67       129.27        19.76        61.51        47.28 
TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK 
      103.27       268.73       103.20        16.96       204.66       180.39 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A3AA TCGA-EE-A3AE TCGA-EE-A3AF 
      216.66       167.90       248.65       124.31        54.51        13.81 
TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JE TCGA-EE-A3JI 
      138.81       127.20        34.32       201.80        51.35       152.81 
TCGA-ER-A195 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19J TCGA-ER-A19L 
       35.44        77.75        98.40        48.89         6.44       131.51 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 
       61.05        44.09       162.08        49.48       148.18       105.07 
TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
       43.82        20.15        28.83        41.56       247.04        93.01 
TCGA-ER-A42L TCGA-FR-A7U8 TCGA-FR-A8YE TCGA-FS-A1YY TCGA-FS-A1Z4 TCGA-FS-A1Z7 
      149.03        27.85       104.42       228.59        28.08         7.79 
TCGA-FS-A1ZB TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZR 
       48.85        46.45         9.70        47.38       101.26        11.41 
TCGA-FS-A1ZS TCGA-FS-A1ZW TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 
      148.80        49.48        50.14        66.67       174.84        34.03 
TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
       26.73        54.41        55.59        13.51        19.30         9.90 
TCGA-GF-A4EO TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A268 
       19.43        15.78       139.89       117.93        96.92        62.79 
TCGA-OD-A75X TCGA-RP-A690 TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-AA1V TCGA-WE-A8JZ 
      297.90         0.20         0.33       228.16        42.08        24.03 
TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZT TCGA-WE-AA9Y TCGA-YG-AA3P 
       17.95       101.33        58.98        11.80        12.16        14.43 
TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       27.58        96.99        15.98 

  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                         0.23                          0.20 
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                       369.93                        297.90 
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                        50.89                         53.92 
[1] "0.2 - 369.9 (50.9)" "0.2 - 297.9 (53.9)"
[1] "hr=" "1.1"
D2V3, continuous
                               vv
clus                            I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB
  AMP PEAK  2(1Q21.3) MUTATED          5       4      11       11       19
  AMP PEAK  2(1Q21.3) WILD-TYPE        8       3      18        7        9
                               vv
clus                            STAGE II STAGE IIA STAGE IIB STAGE IIC
  AMP PEAK  2(1Q21.3) MUTATED         16        10        10        10
  AMP PEAK  2(1Q21.3) WILD-TYPE       10         4         9         5
                               vv
clus                            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  AMP PEAK  2(1Q21.3) MUTATED          22         11         17         29
  AMP PEAK  2(1Q21.3) WILD-TYPE        17          4         18         25
                               vv
clus                            STAGE IV
  AMP PEAK  2(1Q21.3) MUTATED         14
  AMP PEAK  2(1Q21.3) WILD-TYPE        7
D2V4, multiclass
            clus
vv           AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  I/II NOS                             5                             8
  STAGE 0                              4                             3
  STAGE I                             11                            18
  STAGE IA                            11                             7
  STAGE IB                            19                             9
  STAGE II                            16                            10
  STAGE IIA                           10                             4
  STAGE IIB                           10                             9
  STAGE IIC                           10                             5
  STAGE III                           22                            17
  STAGE IIIA                          11                             4
  STAGE IIIB                          17                            18
  STAGE IIIC                          29                            25
  STAGE IV                            14                             7
[1] 14  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3 T4
  AMP PEAK  2(1Q21.3) MUTATED      37 42 47 39
  AMP PEAK  2(1Q21.3) WILD-TYPE    27 31 34 28
D2V5, multiclass
       clus
vv      AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  T0+T1                          37                            27
  T2                             42                            31
  T3                             47                            34
  T4                             39                            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 N3
  AMP PEAK  2(1Q21.3) MUTATED   99 31 25 26
  AMP PEAK  2(1Q21.3) WILD-TYPE 78 34 14 19
D2V6, multiclass
    clus
vv   AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  N0                          99                            78
  N1                          31                            34
  N2                          25                            14
  N3                          26                            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"
D2V7, binary
                               cls
clus                              0   1
  AMP PEAK  2(1Q21.3) MUTATED   178  14
  AMP PEAK  2(1Q21.3) WILD-TYPE 141   8
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q21.3) MUTATED    178   14
  AMP PEAK  2(1Q21.3) WILD-TYPE  141    8
   clus
vv  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  0                         178                           141
  1                          14                             8
[1] 2 2
[1] FALSE
D2V8, binary
                               cls
clus                             0  1
  AMP PEAK  2(1Q21.3) MUTATED   80 52
  AMP PEAK  2(1Q21.3) WILD-TYPE 54 38
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q21.3) MUTATED     80   52
  AMP PEAK  2(1Q21.3) WILD-TYPE   54   38
     clus
vv    AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  NO                           80                            54
  YES                          52                            38
[1] 2 2
[1] FALSE
D2V9, binary
                               cls
clus                              0   1
  AMP PEAK  2(1Q21.3) MUTATED    24 179
  AMP PEAK  2(1Q21.3) WILD-TYPE  23 141
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q21.3) MUTATED     24  179
  AMP PEAK  2(1Q21.3) WILD-TYPE   23  141
     clus
vv    AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  NO                           24                            23
  YES                         179                           141
[1] 2 2
[1] FALSE
D2V10, continuous
D2V11, binary
                               cls
clus                              0   1
  AMP PEAK  2(1Q21.3) MUTATED    78 125
  AMP PEAK  2(1Q21.3) WILD-TYPE  60 104
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q21.3) MUTATED     78  125
  AMP PEAK  2(1Q21.3) WILD-TYPE   60  104
        clus
vv       AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  FEMALE                          78                            60
  MALE                           125                           104
[1] 2 2
[1] FALSE
D2V12, binary
                               cls
clus                              0   1
  AMP PEAK  2(1Q21.3) MUTATED   175  28
  AMP PEAK  2(1Q21.3) WILD-TYPE 144  19
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q21.3) MUTATED    175   28
  AMP PEAK  2(1Q21.3) WILD-TYPE  144   19
     clus
vv    AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  NO                          175                           144
  YES                          28                            19
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  2(1Q21.3) MUTATED       3                         0   195
  AMP PEAK  2(1Q21.3) WILD-TYPE     2                         1   158
D2V13, multiclass
                           clus
vv                          AMP PEAK  2(1Q21.3) MUTATED
  ASIAN                                               3
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                             195
                           clus
vv                          AMP PEAK  2(1Q21.3) WILD-TYPE
  ASIAN                                                 2
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                               158
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V14, binary
                               cls
clus                              0   1
  AMP PEAK  2(1Q21.3) MUTATED     5 195
  AMP PEAK  2(1Q21.3) WILD-TYPE   2 157
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q21.3) MUTATED      5  195
  AMP PEAK  2(1Q21.3) WILD-TYPE    2  157
                        clus
vv                       AMP PEAK  2(1Q21.3) MUTATED
  HISPANIC OR LATINO                               5
  NOT HISPANIC OR LATINO                         195
                        clus
vv                       AMP PEAK  2(1Q21.3) WILD-TYPE
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                           157
[1] 2 2
[1] FALSE

Clustering(3) Variable = AMP PEAK  3(1Q44) MUTATION ANALYSIS
D3V1, survival
                             sevent
clus2                          0  1
  AMP PEAK  3(1Q44) MUTATED   72 70
  AMP PEAK  3(1Q44) WILD-TYPE 56 54
  AMP PEAK  3(1Q44) MUTATED AMP PEAK  3(1Q44) WILD-TYPE 
                        142                         110 
  AMP PEAK  3(1Q44) MUTATED AMP PEAK  3(1Q44) WILD-TYPE 
                         70                          54 
$`AMP PEAK  3(1Q44) MUTATED`
TCGA-D3-A2JE TCGA-D3-A8GI TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GD TCGA-EE-A2GO 
        9.76        13.41        31.96       166.75       269.03        52.90 
TCGA-EE-A2MR TCGA-FR-A729 TCGA-WE-AAA3 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q7 
      134.40       216.43         7.40         8.42        15.72       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1QB TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JL 
       19.04        62.60        62.86        15.75        86.30       171.58 
TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3MO TCGA-D3-A3MR 
       64.83        66.08        58.06        59.70         9.34        90.21 
TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A5GL TCGA-D3-A5GN 
       23.67       173.85        31.76        62.70        42.05        45.70 
TCGA-D3-A5GU TCGA-D3-A8GD TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM 
      124.08        23.61       179.97       120.00        69.53        70.62 
TCGA-D3-A8GP TCGA-D3-A8GR TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6EC TCGA-D9-A6EG 
      135.12        36.53        15.02        16.90        69.21        22.85 
TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC 
      138.67        68.68       110.53        60.10        64.83        58.85 
TCGA-DA-A3F5 TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17Y 
      225.11        14.14        12.30        52.41        18.21        24.89 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G 
       20.38         0.00        75.22        12.99         0.26        44.28 
TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A2 
       47.74        27.16       346.49       185.19       115.43        30.02 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GM 
       77.98        26.14        12.95       201.60        68.65        18.35 
TCGA-EE-A2GN TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M7 TCGA-EE-A2MF TCGA-EE-A2MJ 
       93.63        71.31        81.99        15.25       209.79        63.25 
TCGA-EE-A2ML TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB 
      104.78       227.01       143.93        23.51        53.26       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-EE-A3JH TCGA-ER-A197 
       64.04         4.41        67.89        45.90        19.86        10.49 
TCGA-ER-A199 TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19P 
        7.82        39.81        11.47       184.60       150.12       120.76 
TCGA-ER-A19Q TCGA-ER-A2ND TCGA-ER-A2NF TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       49.71         4.70        10.19       173.29        68.52        15.48 
TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A8YC 
       32.05        74.47         4.50       174.21         4.14        10.06 
TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1ZC TCGA-FS-A1ZJ TCGA-FS-A1ZQ TCGA-FS-A1ZT 
      195.98         8.35       312.07        36.33       130.95        35.28 
TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4FD TCGA-GN-A267 
        4.47         5.29         3.06        30.90        80.68        17.06 
TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-GN-A8LK TCGA-GN-A9SD 
        7.59       120.53        34.49        46.92        43.23        59.41 
TCGA-LH-A9QB TCGA-QB-A6FS TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1Q TCGA-W3-AA1R 
       85.05         7.23         1.97       120.07        44.05        79.99 
TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZY 
      185.13        92.84        47.54        21.90        62.89        48.39 
TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-XV-AB01 TCGA-YG-AA3O 
       37.32        24.99         6.61        28.21 

$`AMP PEAK  3(1Q44) WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A3JD TCGA-ER-A193 TCGA-FW-A3R5 
       62.07        38.76        33.24        27.35        19.04        36.95 
TCGA-WE-A8K5 TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
       52.73        60.46        12.99        14.83        31.89       110.93 
TCGA-D3-A1Q6 TCGA-D3-A1QA TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2JB TCGA-D3-A2JG 
       49.35        76.41        25.64        45.99       168.00       107.61 
TCGA-D3-A2JH TCGA-D3-A2JP TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A51F 
       36.30        43.53       140.98        40.01        24.53        30.67 
TCGA-D3-A51J TCGA-D3-A51T TCGA-D3-A5GR TCGA-D3-A8GC TCGA-D9-A1X3 TCGA-D9-A4Z6 
      144.46        11.34       177.86        78.21        10.78        18.44 
TCGA-DA-A1HV TCGA-DA-A1I2 TCGA-DA-A3F2 TCGA-DA-A3F8 TCGA-DA-A95V TCGA-DA-A95W 
       76.34       150.61        30.44         8.71        72.10         0.76 
TCGA-DA-A95X TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EE-A17X TCGA-EE-A183 TCGA-EE-A20C 
       65.03         3.91        16.41        13.15        26.24        75.55 
TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29H TCGA-EE-A29Q TCGA-EE-A2GK TCGA-EE-A2GL 
       79.20        76.14        47.41        61.12        10.62        32.48 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2M6 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MG 
        0.76         0.20       103.13         5.75        23.77        94.19 
TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A3AA TCGA-EE-A3AE TCGA-EE-A3AF 
      171.85        89.26       145.45       124.31        54.51         6.28 
TCGA-EE-A3J4 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A19A 
      111.85         3.35       168.85       135.98        34.45         4.54 
TCGA-ER-A19B TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19S TCGA-ER-A19W 
       53.29        99.06        59.84        42.51        47.18       146.63 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NG TCGA-FR-A7U8 TCGA-FR-A7UA 
       73.05        22.36        16.87        28.67        26.20         5.65 
TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z4 TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG 
      171.78        49.74        27.62        32.78        43.92         7.82 
TCGA-FS-A1ZM TCGA-FS-A1ZS TCGA-FS-A1ZW TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 
       78.61       136.27        23.21        66.67       173.19        13.28 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
       55.59        11.54        19.30         9.90        18.25         1.91 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A268 TCGA-OD-A75X TCGA-RP-A690 
       53.29       117.93        96.92        42.48       297.01         0.20 
TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-AA1V TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZT 
        0.33       174.12         8.09        65.42        12.69        10.95 
TCGA-WE-AA9Y TCGA-Z2-AA3S 
        1.94        91.23 

  AMP PEAK  3(1Q44) MUTATED AMP PEAK  3(1Q44) WILD-TYPE 
                        0.0                         0.2 
  AMP PEAK  3(1Q44) MUTATED AMP PEAK  3(1Q44) WILD-TYPE 
                     346.49                      297.01 
  AMP PEAK  3(1Q44) MUTATED AMP PEAK  3(1Q44) WILD-TYPE 
                     49.050                      42.495 
[1] "0.0 - 346.5 (49.0)" "0.2 - 297.0 (42.5)"
[1] "hr=" "1.2"
D3V2, survival
                             sevent
clus2                           0   1
  AMP PEAK  3(1Q44) MUTATED    92 105
  AMP PEAK  3(1Q44) WILD-TYPE  74  87
  AMP PEAK  3(1Q44) MUTATED AMP PEAK  3(1Q44) WILD-TYPE 
                        197                         161 
  AMP PEAK  3(1Q44) MUTATED AMP PEAK  3(1Q44) WILD-TYPE 
                        105                          87 
$`AMP PEAK  3(1Q44) MUTATED`
TCGA-D3-A2JE TCGA-D3-A3ML TCGA-D3-A8GI TCGA-EB-A5SH TCGA-EE-A180 TCGA-EE-A184 
       27.65        13.87        58.52        54.02        94.98        68.15 
TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR TCGA-FR-A729 
      168.26         2.60       340.14       126.81       134.40       220.80 
TCGA-FS-A1ZF TCGA-QB-AA9O TCGA-WE-AAA3 TCGA-3N-A9WB TCGA-D3-A1Q1 TCGA-D3-A1Q3 
       15.45        18.05        21.40        17.03        16.57        16.67 
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QB TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA 
      133.25        28.08        95.74        65.49        23.77       115.53 
TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A3BZ 
       86.76        11.87       171.58        66.48        66.08       130.72 
TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CE TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU 
       58.06        46.98        60.23         9.34       103.59        39.75 
TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A5GL TCGA-D3-A5GN 
       45.30       174.84        32.94        63.81       125.79       135.75 
TCGA-D3-A5GO TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GD TCGA-D3-A8GJ TCGA-D3-A8GK 
      137.92        18.18       125.19        23.61       241.38       170.20 
TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D9-A1JW 
       89.13       107.15       152.75        29.06       129.63         3.65 
TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC 
        7.10        15.39        22.29         9.90        25.18        77.56 
TCGA-D9-A6EG TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I4 TCGA-DA-A1I5 
       22.95       144.89        20.38       222.51        35.93       135.02 
TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A95Y 
       88.87        65.92        68.09        10.49       225.96        14.14 
TCGA-DA-A95Z TCGA-EB-A44R TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17Y 
       13.02        10.36        29.29        58.92        36.46        27.22 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20I TCGA-EE-A29B 
       33.73        14.70         4.96       133.81        13.55        85.08 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29R 
       13.97        63.78        72.07        56.84        56.42        14.47 
TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB 
      369.93       195.02       115.96        59.64        86.14        59.28 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GM TCGA-EE-A2GN 
      173.79       220.24        48.72       107.38        75.48       102.12 
TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M7 TCGA-EE-A2MF TCGA-EE-A2MJ TCGA-EE-A2ML 
       81.21        94.82        28.83       268.73        96.23       216.66 
TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU 
       47.54       248.65        43.23       162.48        71.21        53.26 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 
      122.73        64.04        28.77        41.59       138.81       172.18 
TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-EE-A3JH TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19C 
       64.08        53.19       134.33        13.94         9.17        48.89 
TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19P TCGA-ER-A19Q 
       12.59        26.37       302.07       152.35       162.08        50.89 
TCGA-ER-A2ND TCGA-ER-A2NF TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       23.34        28.83        41.56       247.04        93.01        46.98 
TCGA-ER-A3PL TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       33.21        12.95       149.03        92.98       174.21        15.72 
TCGA-FR-A8YC TCGA-FS-A1YX TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1ZC TCGA-FS-A1ZH 
       34.82        48.59       202.65        20.91       357.37        32.75 
TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZT TCGA-FS-A1ZU 
       47.38        23.93        74.73       133.55        53.16        26.56 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F5 TCGA-FS-A4FC TCGA-FS-A4FD 
       27.09        27.02        77.82        28.73        54.41        80.68 
TCGA-FW-A3I3 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U3 
       17.46        10.13        64.44        32.48        48.00       121.91 
TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A9SD 
       39.35        10.42        48.89        22.13        50.10        59.41 
TCGA-HR-A2OG TCGA-HR-A2OH TCGA-LH-A9QB TCGA-QB-A6FS TCGA-RP-A694 TCGA-W3-A825 
        0.23        65.88       368.78         7.23         0.69        63.02 
TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1W TCGA-W3-AA21 
      121.08         4.01        69.07       111.09       219.16       105.04 
TCGA-WE-A8K1 TCGA-WE-A8K6 TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZX TCGA-WE-A8ZY 
       49.05        17.95        70.52        63.22        35.80        49.51 
TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-XV-AB01 TCGA-YD-A89C TCGA-YG-AA3O 
       40.41        24.99        13.25         6.90        37.94 

$`AMP PEAK  3(1Q44) WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A3JD TCGA-ER-A193 TCGA-ER-A198 
       62.07        46.32        68.25        27.35        31.40        50.76 
TCGA-FW-A3R5 TCGA-WE-A8K5 TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q4 
       36.95        61.15        66.48        12.99        14.93       112.04 
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A2J6 TCGA-D3-A2J7 
      112.57        71.80        31.59        90.90        43.43       103.10 
TCGA-D3-A2JB TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JP TCGA-D3-A3CB 
      168.00       113.52        42.08        12.10        59.57       166.52 
TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51N 
       86.93        24.53        55.73        56.35       145.12        22.62 
TCGA-D3-A51T TCGA-D3-A5GR TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GE TCGA-D3-A8GN 
       26.89       178.32        30.84        79.59        26.43       161.00 
TCGA-D3-A8GS TCGA-D3-A8GV TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1X3 TCGA-D9-A4Z6 
      117.17       167.70       151.53        54.67        18.12        18.44 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I2 TCGA-DA-A1I8 TCGA-DA-A1IB TCGA-DA-A3F2 
       76.57        36.03       176.55        53.92        40.60        33.93 
TCGA-DA-A3F8 TCGA-DA-A95V TCGA-DA-A95W TCGA-DA-A95X TCGA-EB-A44Q TCGA-EB-A5KH 
       43.36        72.10        37.35        73.94        13.87        20.35 
TCGA-EB-A5VV TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A20F 
        7.04        29.82         8.65        26.89       151.27        91.56 
TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29H TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29S 
       63.35        78.97        64.64        18.61        66.74        61.28 
TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A5 TCGA-EE-A2GC TCGA-EE-A2GK 
       25.87        17.92        46.82        39.29        67.43        54.74 
TCGA-EE-A2GL TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2M6 
       79.66        13.91        42.77        44.88        21.67       129.27 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH 
       19.76        61.51        47.28       103.27       103.20        16.96 
TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A3AA TCGA-EE-A3AE TCGA-EE-A3AF 
      204.66       180.39       167.90       124.31        54.51        13.81 
TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JE TCGA-EE-A3JI 
      127.20        36.95        34.32       201.80        51.35       152.81 
TCGA-ER-A195 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19E TCGA-ER-A19J TCGA-ER-A19L 
       35.44        77.75        98.40        13.02         6.44       131.51 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 
       61.05        44.09        49.48         8.88       148.18       105.07 
TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NG TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA 
       43.82        20.15        48.99        27.85        18.77        38.27 
TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z4 TCGA-FS-A1Z7 
       36.26       104.42       216.92       228.59        28.08         7.79 
TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZM 
       27.72        48.85        53.52        46.45         9.70       101.26 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZW TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F8 
       11.41       148.80        49.48        50.14        66.67       174.84 
TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
       34.03        26.73        55.59        13.51        19.30         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
       19.43         2.04        15.78       139.89       117.93        96.92 
TCGA-GN-A268 TCGA-GN-A8LL TCGA-OD-A75X TCGA-RP-A690 TCGA-RP-A693 TCGA-W3-A824 
       62.79        21.37       297.90         0.20         0.33       228.16 
TCGA-W3-AA1V TCGA-WE-A8JZ TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZT TCGA-WE-AA9Y 
       42.08        24.03       101.33        58.98        11.80        12.16 
TCGA-YD-A9TA TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       49.18        14.43        27.58        96.99        15.98 

  AMP PEAK  3(1Q44) MUTATED AMP PEAK  3(1Q44) WILD-TYPE 
                       0.23                        0.20 
  AMP PEAK  3(1Q44) MUTATED AMP PEAK  3(1Q44) WILD-TYPE 
                     369.93                      297.90 
  AMP PEAK  3(1Q44) MUTATED AMP PEAK  3(1Q44) WILD-TYPE 
                      56.42                       49.18 
[1] "0.2 - 369.9 (56.4)" "0.2 - 297.9 (49.2)"
[1] "hr=" "1.2"
D3V3, continuous
                             vv
clus                          I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB
  AMP PEAK  3(1Q44) MUTATED          5       3      15       11       17
  AMP PEAK  3(1Q44) WILD-TYPE        8       4      14        7       11
                             vv
clus                          STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  AMP PEAK  3(1Q44) MUTATED         19         7         8         8        23
  AMP PEAK  3(1Q44) WILD-TYPE        7         7        11         7        16
                             vv
clus                          STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  AMP PEAK  3(1Q44) MUTATED           11         18         29       12
  AMP PEAK  3(1Q44) WILD-TYPE          4         17         25        9
D3V4, multiclass
            clus
vv           AMP PEAK  3(1Q44) MUTATED AMP PEAK  3(1Q44) WILD-TYPE
  I/II NOS                           5                           8
  STAGE 0                            3                           4
  STAGE I                           15                          14
  STAGE IA                          11                           7
  STAGE IB                          17                          11
  STAGE II                          19                           7
  STAGE IIA                          7                           7
  STAGE IIB                          8                          11
  STAGE IIC                          8                           7
  STAGE III                         23                          16
  STAGE IIIA                        11                           4
  STAGE IIIB                        18                          17
  STAGE IIIC                        29                          25
  STAGE IV                          12                           9
[1] 14  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          T0+T1 T2 T3 T4
  AMP PEAK  3(1Q44) MUTATED      37 42 49 33
  AMP PEAK  3(1Q44) WILD-TYPE    27 31 32 34
D3V5, multiclass
       clus
vv      AMP PEAK  3(1Q44) MUTATED AMP PEAK  3(1Q44) WILD-TYPE
  T0+T1                        37                          27
  T2                           42                          31
  T3                           49                          32
  T4                           33                          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 N3
  AMP PEAK  3(1Q44) MUTATED   99 33 24 25
  AMP PEAK  3(1Q44) WILD-TYPE 78 32 15 20
D3V6, multiclass
    clus
vv   AMP PEAK  3(1Q44) MUTATED AMP PEAK  3(1Q44) WILD-TYPE
  N0                        99                          78
  N1                        33                          32
  N2                        24                          15
  N3                        25                          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"
D3V7, binary
                             cls
clus                            0   1
  AMP PEAK  3(1Q44) MUTATED   179  12
  AMP PEAK  3(1Q44) WILD-TYPE 140  10
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  3(1Q44) MUTATED    179   12
  AMP PEAK  3(1Q44) WILD-TYPE  140   10
   clus
vv  AMP PEAK  3(1Q44) MUTATED AMP PEAK  3(1Q44) WILD-TYPE
  0                       179                         140
  1                        12                          10
[1] 2 2
[1] FALSE
D3V8, binary
                             cls
clus                           0  1
  AMP PEAK  3(1Q44) MUTATED   78 47
  AMP PEAK  3(1Q44) WILD-TYPE 56 43
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  3(1Q44) MUTATED     78   47
  AMP PEAK  3(1Q44) WILD-TYPE   56   43
     clus
vv    AMP PEAK  3(1Q44) MUTATED AMP PEAK  3(1Q44) WILD-TYPE
  NO                         78                          56
  YES                        47                          43
[1] 2 2
[1] FALSE
D3V9, binary
                             cls
clus                            0   1
  AMP PEAK  3(1Q44) MUTATED    25 176
  AMP PEAK  3(1Q44) WILD-TYPE  22 144
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  3(1Q44) MUTATED     25  176
  AMP PEAK  3(1Q44) WILD-TYPE   22  144
     clus
vv    AMP PEAK  3(1Q44) MUTATED AMP PEAK  3(1Q44) WILD-TYPE
  NO                         25                          22
  YES                       176                         144
[1] 2 2
[1] FALSE
D3V10, continuous
D3V11, binary
                             cls
clus                            0   1
  AMP PEAK  3(1Q44) MUTATED    77 124
  AMP PEAK  3(1Q44) WILD-TYPE  61 105
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  3(1Q44) MUTATED     77  124
  AMP PEAK  3(1Q44) WILD-TYPE   61  105
        clus
vv       AMP PEAK  3(1Q44) MUTATED AMP PEAK  3(1Q44) WILD-TYPE
  FEMALE                        77                          61
  MALE                         124                         105
[1] 2 2
[1] FALSE
D3V12, binary
                             cls
clus                            0   1
  AMP PEAK  3(1Q44) MUTATED   173  28
  AMP PEAK  3(1Q44) WILD-TYPE 146  19
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  3(1Q44) MUTATED    173   28
  AMP PEAK  3(1Q44) WILD-TYPE  146   19
     clus
vv    AMP PEAK  3(1Q44) MUTATED AMP PEAK  3(1Q44) WILD-TYPE
  NO                        173                         146
  YES                        28                          19
[1] 2 2
[1] FALSE
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  3(1Q44) MUTATED       3                         0   193
  AMP PEAK  3(1Q44) WILD-TYPE     2                         1   160
D3V13, multiclass
                           clus
vv                          AMP PEAK  3(1Q44) MUTATED
  ASIAN                                             3
  BLACK OR AFRICAN AMERICAN                         0
  WHITE                                           193
                           clus
vv                          AMP PEAK  3(1Q44) WILD-TYPE
  ASIAN                                               2
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                             160
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V14, binary
                             cls
clus                            0   1
  AMP PEAK  3(1Q44) MUTATED     5 193
  AMP PEAK  3(1Q44) WILD-TYPE   2 159
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  3(1Q44) MUTATED      5  193
  AMP PEAK  3(1Q44) WILD-TYPE    2  159
                        clus
vv                       AMP PEAK  3(1Q44) MUTATED AMP PEAK  3(1Q44) WILD-TYPE
  HISPANIC OR LATINO                             5                           2
  NOT HISPANIC OR LATINO                       193                         159
[1] 2 2
[1] FALSE

Clustering(4) Variable = AMP PEAK  4(3P13) MUTATION ANALYSIS
D4V1, survival
                             sevent
clus2                          0  1
  AMP PEAK  4(3P13) MUTATED   45 26
  AMP PEAK  4(3P13) WILD-TYPE 83 98
  AMP PEAK  4(3P13) MUTATED AMP PEAK  4(3P13) WILD-TYPE 
                         71                         181 
  AMP PEAK  4(3P13) MUTATED AMP PEAK  4(3P13) WILD-TYPE 
                         26                          98 
$`AMP PEAK  4(3P13) MUTATED`
TCGA-D3-A2JF TCGA-D3-A8GI TCGA-EB-A5SG TCGA-EE-A180 TCGA-FR-A729 TCGA-WE-A8K5 
       62.07        13.41        33.24        31.96       216.43        52.73 
TCGA-WE-AAA3 TCGA-BF-AAP0 TCGA-D3-A1QA TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JC 
        7.40        14.83        76.41        62.86        15.75        86.30 
TCGA-D3-A2JG TCGA-D3-A2JL TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3MR 
      107.61       171.58       140.98        40.01        59.70        90.21 
TCGA-D3-A51E TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A8GD TCGA-D3-A8GM 
      173.85        42.05        45.70       177.86        23.61        70.62 
TCGA-D3-A8GR TCGA-D9-A6EC TCGA-DA-A1I5 TCGA-DA-A1IA TCGA-DA-A3F5 TCGA-DA-A3F8 
       36.53        69.21       110.53        64.83       225.11         8.71 
TCGA-DA-A95V TCGA-EB-A44Q TCGA-EB-A6L9 TCGA-EE-A20F TCGA-EE-A29H TCGA-EE-A29M 
       72.10         3.91        18.21        79.20        47.41        47.74 
TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2GH TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2M6 
      346.49       185.19       201.60        93.63         0.76       103.13 
TCGA-EE-A2MP TCGA-EE-A2MU TCGA-EE-A3AE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A197 
      227.01        53.26        54.51        19.86       135.98        10.49 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19S TCGA-ER-A2NG 
      184.60       150.12        99.06        59.84        47.18        28.67 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A44A TCGA-FR-A7UA 
       68.52        15.48        32.05        74.47       174.21         5.65 
TCGA-FS-A1Z0 TCGA-FS-A4FD TCGA-GF-A4EO TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A268 
      195.98        80.68        18.25       117.93        96.92        42.48 
TCGA-W3-AA1R TCGA-W3-AA1W TCGA-WE-A8K1 TCGA-WE-A8ZY TCGA-Z2-AA3S 
       79.99       185.13        47.54        48.39        91.23 

$`AMP PEAK  4(3P13) WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A3C8 TCGA-EE-A20H TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR 
        9.76        38.76       166.75       269.03        52.90       134.40 
TCGA-EE-A3JD TCGA-ER-A193 TCGA-FW-A3R5 TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 
       27.35        19.04        36.95        60.46        12.99         8.42 
TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       15.72        31.89       110.93        49.35       133.25        19.04 
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2JB TCGA-D3-A2JH TCGA-D3-A2JN 
       62.60        25.64        45.99       168.00        36.30        64.83 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MU 
       66.08        43.53        58.06        24.53         9.34        23.67 
TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GU 
       30.67       144.46        31.76        62.70        11.34       124.08 
TCGA-D3-A8GC TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GP TCGA-D9-A1X3 
       78.21       179.97       120.00        69.53       135.12        10.78 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY 
       15.02        16.90        18.44        22.85        76.34       138.67 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I7 TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A95W 
       68.68       150.61        60.10        58.85        30.44         0.76 
TCGA-DA-A95X TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EE-A17X 
       65.03        14.14        12.30        16.41        52.41        13.15 
TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A29B 
       24.89        20.38         0.00        26.24        75.55        75.22 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29P TCGA-EE-A29Q 
       76.14        12.99         0.26        44.28        27.16        61.12 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GJ 
      115.43        30.02        77.98        26.14        12.95        68.65 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU 
       10.62        32.48        18.35         0.20        71.31        81.99 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI 
       15.25         5.75        23.77       209.79        94.19       171.85 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MS TCGA-EE-A2MT 
       63.25        89.26       104.78       145.45       143.93        23.51 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3J3 
      124.31       122.73        64.04         4.41         6.28        67.89 
TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-ER-A195 TCGA-ER-A199 
      111.85        45.90         3.35       168.85        34.45         7.82 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19N TCGA-ER-A19P 
        4.54        53.29        39.81        11.47        42.51       120.76 
TCGA-ER-A19Q TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
       49.71       146.63        73.05        22.36         4.70        16.87 
TCGA-ER-A2NF TCGA-ER-A3ES TCGA-FR-A3YN TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A8YC 
       10.19       173.29         4.50         4.14        26.20        10.06 
TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD 
      171.78        49.74         8.35        27.62       312.07        32.78 
TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS 
       43.92         7.82        36.33        78.61       130.95       136.27 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 
       35.28         4.47        23.21         5.29         3.06        30.90 
TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
       66.67       173.19        13.28        55.59        11.54        19.30 
TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A4U3 
        9.90         1.91        53.29        17.06         7.59       120.53 
TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-GN-A8LK TCGA-GN-A9SD TCGA-LH-A9QB TCGA-OD-A75X 
       34.49        46.92        43.23        59.41        85.05       297.01 
TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 
        7.23         0.20         0.33       174.12         1.97       120.07 
TCGA-W3-AA1Q TCGA-W3-AA1V TCGA-W3-AA21 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO 
       44.05         8.09        92.84        65.42        12.69        21.90 
TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-XV-AB01 
       62.89        10.95         1.94        37.32        24.99         6.61 
TCGA-YG-AA3O 
       28.21 

  AMP PEAK  4(3P13) MUTATED AMP PEAK  4(3P13) WILD-TYPE 
                       0.76                        0.00 
  AMP PEAK  4(3P13) MUTATED AMP PEAK  4(3P13) WILD-TYPE 
                     346.49                      312.07 
  AMP PEAK  4(3P13) MUTATED AMP PEAK  4(3P13) WILD-TYPE 
                      64.83                       36.33 
[1] "0.8 - 346.5 (64.8)" "0.0 - 312.1 (36.3)"
[1] "hr=" "2.2"
D4V2, survival
                             sevent
clus2                           0   1
  AMP PEAK  4(3P13) MUTATED    57  44
  AMP PEAK  4(3P13) WILD-TYPE 109 148
  AMP PEAK  4(3P13) MUTATED AMP PEAK  4(3P13) WILD-TYPE 
                        101                         257 
  AMP PEAK  4(3P13) MUTATED AMP PEAK  4(3P13) WILD-TYPE 
                         44                         148 
$`AMP PEAK  4(3P13) MUTATED`
TCGA-D3-A2JF TCGA-D3-A8GI TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A180 TCGA-EE-A184 
       62.07        58.52        68.25        54.02        94.98        68.15 
TCGA-EE-A29L TCGA-FR-A729 TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-BF-AAP0 TCGA-D3-A1Q9 
        2.60       220.80        61.15        21.40        14.93        31.59 
TCGA-D3-A1QA TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG 
       90.90        65.49       115.53        86.76        11.87       113.52 
TCGA-D3-A2JL TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3MR TCGA-D3-A3MV 
      171.58       166.52        86.93        60.23       103.59        45.30 
TCGA-D3-A51E TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A8GD TCGA-D3-A8GM 
      174.84       125.79       135.75       178.32        23.61       107.15 
TCGA-D3-A8GN TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-DA-A1HW 
      161.00        29.06       129.63         9.90        77.56        36.03 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1IA TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-DA-A95V 
       35.93       135.02        65.92       225.96        43.36        72.10 
TCGA-EB-A44Q TCGA-EB-A5UL TCGA-EB-A6L9 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A29H 
       13.87        29.29        36.46       133.81        91.56        64.64 
TCGA-EE-A29M TCGA-EE-A29R TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2GH TCGA-EE-A2GI 
       56.84        14.47       369.93       195.02       220.24        48.72 
TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2MP TCGA-EE-A2MU 
      102.12        13.91        21.67       129.27       248.65        53.26 
TCGA-EE-A3AE TCGA-EE-A3J5 TCGA-EE-A3JA TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A197 
       54.51        36.95        53.19       134.33       152.81        13.94 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19S TCGA-ER-A2NG 
      302.07       152.35       131.51        61.05        49.48        48.99 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A44A TCGA-FR-A7UA 
       93.01        46.98        33.21       149.03       174.21        38.27 
TCGA-FR-A8YD TCGA-FS-A1Z0 TCGA-FS-A1ZA TCGA-FS-A1ZK TCGA-FS-A4F2 TCGA-FS-A4FD 
       36.26       202.65        27.72        23.93        50.14        80.68 
TCGA-GF-A4EO TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A268 TCGA-GN-A8LL 
       19.43       117.93        96.92        10.13        62.79        21.37 
TCGA-HR-A2OG TCGA-HR-A2OH TCGA-W3-AA1O TCGA-W3-AA1R TCGA-W3-AA1W TCGA-WE-A8JZ 
        0.23        65.88         4.01       111.09       219.16        24.03 
TCGA-WE-A8K1 TCGA-WE-A8K6 TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-Z2-AA3S 
       49.05        17.95        35.80        49.51        96.99 

$`AMP PEAK  4(3P13) WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EE-A20H TCGA-EE-A2GD TCGA-EE-A2GO 
       27.65        46.32        13.87       168.26       340.14       126.81 
TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-ER-A198 TCGA-FS-A1ZF TCGA-FW-A3R5 
      134.40        27.35        31.40        50.76        15.45        36.95 
TCGA-QB-AA9O TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q3 
       18.05        17.03        66.48        12.99        16.57        16.67 
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QB 
      112.04       112.57        71.80       133.25        28.08        95.74 
TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JH TCGA-D3-A2JK 
       43.43       103.10        23.77       168.00        42.08        12.10 
TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 
       66.48        66.08        59.57       130.72        58.06        46.98 
TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MU TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
       24.53         9.34        39.75        55.73        56.35       145.12 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GO TCGA-D3-A5GS 
       32.94        22.62        63.81        26.89       137.92        18.18 
TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GK 
      125.19        30.84        79.59        26.43       241.38       170.20 
TCGA-D3-A8GL TCGA-D3-A8GP TCGA-D3-A8GS TCGA-D3-A8GV TCGA-D9-A148 TCGA-D9-A149 
       89.13       152.75       117.17       167.70       151.53        54.67 
TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 
        3.65         7.10        18.12        15.39        22.29        18.44 
TCGA-D9-A6EA TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 
       25.18        22.95        76.57       144.89        20.38       222.51 
TCGA-DA-A1I2 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
      176.55        88.87        53.92        40.60        68.09        33.93 
TCGA-DA-A3F3 TCGA-DA-A95W TCGA-DA-A95X TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44R 
       10.49        37.35        73.94        14.14        13.02        10.36 
TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
       20.35        58.92         7.04        29.82        27.22         8.65 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20I 
       33.73        14.70        26.89         4.96       151.27        13.55 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G 
       63.35        85.08        78.97        13.97        63.78        72.07 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29X 
       18.61        56.42        66.74        61.28        25.87        17.92 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
       46.82       115.96        59.64        39.29        86.14        59.28 
TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
       67.43       173.79       107.38        54.74        79.66        75.48 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M7 TCGA-EE-A2M8 
       42.77        81.21        44.88        94.82        28.83        19.76 
TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH 
       61.51        47.28       103.27       268.73       103.20        16.96 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN 
      204.66        96.23       180.39       216.66       167.90        47.54 
TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC 
       43.23       162.48        71.21       124.31       122.73        64.04 
TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 
       28.77        13.81        41.59       138.81       172.18       127.20 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JE TCGA-ER-A195 TCGA-ER-A199 
       64.08        34.32       201.80        51.35        35.44         9.17 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F 
       77.75        98.40        48.89        12.59        13.02        26.37 
TCGA-ER-A19J TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19T TCGA-ER-A19W 
        6.44        44.09       162.08        50.89         8.88       148.18 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NH 
      105.07        43.82        23.34        20.15        28.83        41.56 
TCGA-ER-A3ES TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A7U9 
      247.04        12.95        92.98        15.72        27.85        18.77 
TCGA-FR-A8YC TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z3 
       34.82       104.42       216.92        48.59       228.59        20.91 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE 
       28.08         7.79        48.85       357.37        53.52        46.45 
TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ 
        9.70        32.75        47.38       101.26        74.73       133.55 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
       11.41       148.80        53.16        26.56        49.48        27.09 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 
       27.02        77.82        66.67        28.73       174.84        34.03 
TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
       26.73        54.41        17.46        55.59        13.51        19.30 
TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A267 TCGA-GN-A26A 
        9.90         2.04        15.78       139.89        64.44        32.48 
TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A4U9 
       48.00       121.91        39.35        10.42        48.89        22.13 
TCGA-GN-A8LK TCGA-GN-A9SD TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 
       50.10        59.41       368.78       297.90         7.23         0.20 
TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1Q 
        0.33         0.69       228.16        63.02       121.08        69.07 
TCGA-W3-AA1V TCGA-W3-AA21 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ 
       42.08       105.04       101.33        58.98        70.52        63.22 
TCGA-WE-A8ZT TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-XV-AB01 TCGA-YD-A89C 
       11.80        12.16        40.41        24.99        13.25         6.90 
TCGA-YD-A9TA TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3V 
       49.18        37.94        14.43        27.58        15.98 

  AMP PEAK  4(3P13) MUTATED AMP PEAK  4(3P13) WILD-TYPE 
                       0.23                        0.20 
  AMP PEAK  4(3P13) MUTATED AMP PEAK  4(3P13) WILD-TYPE 
                     369.93                      368.78 
  AMP PEAK  4(3P13) MUTATED AMP PEAK  4(3P13) WILD-TYPE 
                      62.79                       48.00 
[1] "0.2 - 369.9 (62.8)" "0.2 - 368.8 (48.0)"
[1] "hr=" "1.7"
D4V3, continuous
                             vv
clus                          I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB
  AMP PEAK  4(3P13) MUTATED          6       2       9        8        9
  AMP PEAK  4(3P13) WILD-TYPE        7       5      20       10       19
                             vv
clus                          STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  AMP PEAK  4(3P13) MUTATED          7         2         2         5        10
  AMP PEAK  4(3P13) WILD-TYPE       19        12        17        10        29
                             vv
clus                          STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  AMP PEAK  4(3P13) MUTATED            5         12         12        4
  AMP PEAK  4(3P13) WILD-TYPE         10         23         42       17
D4V4, multiclass
            clus
vv           AMP PEAK  4(3P13) MUTATED AMP PEAK  4(3P13) WILD-TYPE
  I/II NOS                           6                           7
  STAGE 0                            2                           5
  STAGE I                            9                          20
  STAGE IA                           8                          10
  STAGE IB                           9                          19
  STAGE II                           7                          19
  STAGE IIA                          2                          12
  STAGE IIB                          2                          17
  STAGE IIC                          5                          10
  STAGE III                         10                          29
  STAGE IIIA                         5                          10
  STAGE IIIB                        12                          23
  STAGE IIIC                        12                          42
  STAGE IV                           4                          17
[1] 14  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          T0+T1 T2 T3 T4
  AMP PEAK  4(3P13) MUTATED      20 23 18 21
  AMP PEAK  4(3P13) WILD-TYPE    44 50 63 46
D4V5, multiclass
       clus
vv      AMP PEAK  4(3P13) MUTATED AMP PEAK  4(3P13) WILD-TYPE
  T0+T1                        20                          44
  T2                           23                          50
  T3                           18                          63
  T4                           21                          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  N3
  AMP PEAK  4(3P13) MUTATED    55  19   9   9
  AMP PEAK  4(3P13) WILD-TYPE 122  46  30  36
D4V6, multiclass
    clus
vv   AMP PEAK  4(3P13) MUTATED AMP PEAK  4(3P13) WILD-TYPE
  N0                        55                         122
  N1                        19                          46
  N2                         9                          30
  N3                         9                          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"
D4V7, binary
                             cls
clus                            0   1
  AMP PEAK  4(3P13) MUTATED    91   4
  AMP PEAK  4(3P13) WILD-TYPE 228  18
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  4(3P13) MUTATED     91    4
  AMP PEAK  4(3P13) WILD-TYPE  228   18
   clus
vv  AMP PEAK  4(3P13) MUTATED AMP PEAK  4(3P13) WILD-TYPE
  0                        91                         228
  1                         4                          18
[1] 2 2
[1] FALSE
D4V8, binary
                             cls
clus                           0  1
  AMP PEAK  4(3P13) MUTATED   39 26
  AMP PEAK  4(3P13) WILD-TYPE 95 64
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  4(3P13) MUTATED     39   26
  AMP PEAK  4(3P13) WILD-TYPE   95   64
     clus
vv    AMP PEAK  4(3P13) MUTATED AMP PEAK  4(3P13) WILD-TYPE
  NO                         39                          95
  YES                        26                          64
[1] 2 2
[1] FALSE
D4V9, binary
                             cls
clus                            0   1
  AMP PEAK  4(3P13) MUTATED    10  93
  AMP PEAK  4(3P13) WILD-TYPE  37 227
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  4(3P13) MUTATED     10   93
  AMP PEAK  4(3P13) WILD-TYPE   37  227
     clus
vv    AMP PEAK  4(3P13) MUTATED AMP PEAK  4(3P13) WILD-TYPE
  NO                         10                          37
  YES                        93                         227
[1] 2 2
[1] FALSE
D4V10, continuous
D4V11, binary
                             cls
clus                            0   1
  AMP PEAK  4(3P13) MUTATED    47  56
  AMP PEAK  4(3P13) WILD-TYPE  91 173
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  4(3P13) MUTATED     47   56
  AMP PEAK  4(3P13) WILD-TYPE   91  173
        clus
vv       AMP PEAK  4(3P13) MUTATED AMP PEAK  4(3P13) WILD-TYPE
  FEMALE                        47                          91
  MALE                          56                         173
[1] 2 2
[1] FALSE
D4V12, binary
                             cls
clus                            0   1
  AMP PEAK  4(3P13) MUTATED    86  17
  AMP PEAK  4(3P13) WILD-TYPE 233  30
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  4(3P13) MUTATED     86   17
  AMP PEAK  4(3P13) WILD-TYPE  233   30
     clus
vv    AMP PEAK  4(3P13) MUTATED AMP PEAK  4(3P13) WILD-TYPE
  NO                         86                         233
  YES                        17                          30
[1] 2 2
[1] FALSE
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  4(3P13) MUTATED       2                         0    98
  AMP PEAK  4(3P13) WILD-TYPE     3                         1   255
D4V13, multiclass
                           clus
vv                          AMP PEAK  4(3P13) MUTATED
  ASIAN                                             2
  BLACK OR AFRICAN AMERICAN                         0
  WHITE                                            98
                           clus
vv                          AMP PEAK  4(3P13) WILD-TYPE
  ASIAN                                               3
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                             255
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V14, binary
                             cls
clus                            0   1
  AMP PEAK  4(3P13) MUTATED     0 100
  AMP PEAK  4(3P13) WILD-TYPE   7 252
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  4(3P13) MUTATED      0  100
  AMP PEAK  4(3P13) WILD-TYPE    7  252
                        clus
vv                       AMP PEAK  4(3P13) MUTATED AMP PEAK  4(3P13) WILD-TYPE
  HISPANIC OR LATINO                             0                           7
  NOT HISPANIC OR LATINO                       100                         252
[1] 2 2
[1] FALSE

Clustering(5) Variable = AMP PEAK  5(4Q12) MUTATION ANALYSIS
D5V1, survival
                             sevent
clus2                           0   1
  AMP PEAK  5(4Q12) MUTATED    21  29
  AMP PEAK  5(4Q12) WILD-TYPE 107  95
  AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE 
                         50                         202 
  AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE 
                         29                          95 
$`AMP PEAK  5(4Q12) MUTATED`
TCGA-D3-A2JE TCGA-EE-A2MR TCGA-D3-A1Q3 TCGA-D3-A1Q8 TCGA-D3-A3C6 TCGA-D3-A3CE 
        9.76       134.40        15.72        19.04        58.06        59.70 
TCGA-D3-A3MU TCGA-D3-A51K TCGA-D3-A5GU TCGA-D3-A8GP TCGA-D9-A3Z3 TCGA-DA-A1HV 
       23.67        31.76       124.08       135.12        16.90        76.34 
TCGA-DA-A1I1 TCGA-DA-A3F5 TCGA-DA-A95V TCGA-EB-A5KH TCGA-EE-A181 TCGA-EE-A20F 
       68.68       225.11        72.10        16.41        20.38        79.20 
TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29P TCGA-EE-A2GB TCGA-EE-A2GP TCGA-EE-A2MJ 
       12.99        44.28        27.16        26.14         0.76        63.25 
TCGA-EE-A2MP TCGA-EE-A3AA TCGA-EE-A3AD TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-EE-A3JB 
      227.01       124.31         4.41        67.89        45.90       168.85 
TCGA-EE-A3JI TCGA-ER-A197 TCGA-ER-A19B TCGA-ER-A2ND TCGA-ER-A3ET TCGA-ER-A3EV 
      135.98        10.49        53.29         4.70        68.52        15.48 
TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A8YC TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ 
       32.05         4.50        10.06        36.33        78.61       130.95 
TCGA-FS-A1ZU TCGA-GF-A4EO TCGA-GN-A264 TCGA-GN-A268 TCGA-GN-A8LK TCGA-GN-A9SD 
        4.47        18.25       117.93        42.48        43.23        59.41 
TCGA-W3-AA1V TCGA-WE-A8ZQ 
        8.09        62.89 

$`AMP PEAK  5(4Q12) WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A8GI TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A20H 
       62.07        38.76        13.41        33.24        31.96       166.75 
TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A3JD TCGA-ER-A193 TCGA-FR-A729 TCGA-FW-A3R5 
      269.03        52.90        27.35        19.04       216.43        36.95 
TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 
       52.73         7.40        60.46        12.99        14.83         8.42 
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1QA TCGA-D3-A1QB 
       31.89       110.93        49.35       133.25        76.41        62.60 
TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC 
       25.64        45.99        62.86        15.75       168.00        86.30 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP 
      107.61        36.30       171.58        64.83        66.08        43.53 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A51E 
      140.98        40.01        24.53         9.34        90.21       173.85 
TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN 
       30.67       144.46        62.70        11.34        42.05        45.70 
TCGA-D3-A5GR TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL 
      177.86        78.21        23.61       179.97       120.00        69.53 
TCGA-D3-A8GM TCGA-D3-A8GR TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A4Z6 TCGA-D9-A6EC 
       70.62        36.53        10.78        15.02        18.44        69.21 
TCGA-D9-A6EG TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA 
       22.85       138.67       150.61       110.53        60.10        64.83 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F8 TCGA-DA-A95W TCGA-DA-A95X TCGA-DA-A95Y 
       58.85        30.44         8.71         0.76        65.03        14.14 
TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
       12.30         3.91        52.41        18.21        13.15        24.89 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E 
        0.00        26.24        75.55        75.22        76.14         0.26 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 
       47.41        47.74        61.12       346.49       185.19       115.43 
TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK 
       30.02        77.98        12.95       201.60        68.65        10.62 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU 
       32.48        18.35        93.63         0.20        71.31        81.99 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MG 
      103.13        15.25         5.75        23.77       209.79        94.19 
TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MS TCGA-EE-A2MT 
      171.85        89.26       104.78       145.45       143.93        23.51 
TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J4 
       53.26       122.73        64.04        54.51         6.28       111.85 
TCGA-EE-A3J8 TCGA-EE-A3JH TCGA-ER-A195 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19C 
        3.35        19.86        34.45         7.82         4.54        39.81 
TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
       11.47       184.60       150.12        99.06        59.84        42.51 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
      120.76        49.71        47.18       146.63        73.05        22.36 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A42L TCGA-FR-A44A 
       16.87        10.19        28.67       173.29        74.47       174.21 
TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 
        4.14        26.20         5.65       171.78        49.74       195.98 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG 
        8.35        27.62       312.07        32.78        43.92         7.82 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 
      136.27        35.28        23.21         5.29         3.06        30.90 
TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV 
       66.67       173.19        13.28        80.68        55.59        11.54 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A267 
       19.30         9.90         1.91        53.29        96.92        17.06 
TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-LH-A9QB TCGA-OD-A75X 
        7.59       120.53        34.49        46.92        85.05       297.01 
TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 
        7.23         0.20         0.33       174.12         1.97       120.07 
TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8ZM 
       44.05        79.99       185.13        92.84        47.54        65.42 
TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 
       12.69        21.90        10.95        48.39         1.94        37.32 
TCGA-WE-AAA4 TCGA-XV-AB01 TCGA-YG-AA3O TCGA-Z2-AA3S 
       24.99         6.61        28.21        91.23 

  AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE 
                       0.76                        0.00 
  AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE 
                     227.01                      346.49 
  AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE 
                     43.755                      47.295 
[1] "0.8 - 227.0 (43.8)" "0.0 - 346.5 (47.3)"
[1] "hr=" "1.4"
D5V2, survival
                             sevent
clus2                           0   1
  AMP PEAK  5(4Q12) MUTATED    24  39
  AMP PEAK  5(4Q12) WILD-TYPE 142 153
  AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE 
                         63                         295 
  AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE 
                         39                         153 
$`AMP PEAK  5(4Q12) MUTATED`
TCGA-D3-A2JE TCGA-EB-A5SH TCGA-EE-A184 TCGA-EE-A2MR TCGA-D3-A1Q3 TCGA-D3-A1Q8 
       27.65        54.02        68.15       134.40        16.67        28.08 
TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3MU TCGA-D3-A51K TCGA-D3-A5GU TCGA-D3-A8GB 
       58.06        60.23        39.75        32.94       125.19        30.84 
TCGA-D3-A8GP TCGA-D3-A8GS TCGA-D9-A3Z3 TCGA-D9-A6EA TCGA-DA-A1HV TCGA-DA-A1HW 
      152.75       117.17        22.29        25.18        76.57        36.03 
TCGA-DA-A1I1 TCGA-DA-A1IB TCGA-DA-A3F5 TCGA-DA-A95V TCGA-EB-A5KH TCGA-EE-A181 
      222.51        40.60       225.96        72.10        20.35        33.73 
TCGA-EE-A20F TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29P TCGA-EE-A2GB TCGA-EE-A2GI 
       91.56        13.97        72.07        56.42        59.28        48.72 
TCGA-EE-A2GP TCGA-EE-A2MJ TCGA-EE-A2MP TCGA-EE-A3AA TCGA-EE-A3AD TCGA-EE-A3J3 
       13.91        96.23       248.65       124.31        28.77       172.18 
TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JI TCGA-ER-A197 TCGA-ER-A19B 
       64.08        53.19       201.80       152.81        13.94        98.40 
TCGA-ER-A2ND TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A8YC 
       23.34        93.01        46.98        33.21        92.98        34.82 
TCGA-FS-A1YX TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZU 
       48.59        47.38        23.93       101.26       133.55        26.56 
TCGA-FS-A4F5 TCGA-GF-A4EO TCGA-GN-A264 TCGA-GN-A268 TCGA-GN-A26D TCGA-GN-A8LK 
       28.73        19.43       117.93        62.79        48.00        50.10 
TCGA-GN-A9SD TCGA-W3-AA1V TCGA-WE-A8ZQ 
       59.41        42.08        63.22 

$`AMP PEAK  5(4Q12) WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-D3-A8GI TCGA-EB-A5SG TCGA-EE-A180 
       62.07        46.32        13.87        58.52        68.25        94.98 
TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A3JD TCGA-ER-A193 
      168.26         2.60       340.14       126.81        27.35        31.40 
TCGA-ER-A198 TCGA-FR-A729 TCGA-FS-A1ZF TCGA-FW-A3R5 TCGA-QB-AA9O TCGA-WE-A8K5 
       50.76       220.80        15.45        36.95        18.05        61.15 
TCGA-WE-AAA3 TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 
       21.40        17.03        66.48        12.99        14.93        16.57 
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A1QA 
      112.04       112.57        71.80       133.25        31.59        90.90 
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA 
       95.74        43.43       103.10        65.49        23.77       115.53 
TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK 
      168.00        86.76        11.87       113.52        42.08        12.10 
TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C7 
      171.58        66.48        66.08        59.57       130.72        46.98 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MV 
      166.52        86.93        24.53         9.34       103.59        45.30 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51N TCGA-D3-A51R 
      174.84        55.73        56.35       145.12        22.62        63.81 
TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       26.89       125.79       135.75       137.92       178.32        18.18 
TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL 
       79.59        23.61        26.43       241.38       170.20        89.13 
TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GV TCGA-D9-A148 
      107.15       161.00        29.06       129.63       167.70       151.53 
TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A4Z6 
       54.67         3.65         7.10        18.12        15.39        18.44 
TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 
        9.90        77.56        22.95       144.89        20.38       176.55 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IC 
       35.93       135.02        88.87        53.92        65.92        68.09 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-DA-A95W TCGA-DA-A95X TCGA-DA-A95Y 
       33.93        10.49        43.36        37.35        73.94        14.14 
TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV 
       13.02        13.87        10.36        29.29        58.92         7.04 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A182 TCGA-EE-A183 
       36.46        29.82        27.22         8.65        14.70        26.89 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
        4.96       133.81       151.27        13.55        63.35        85.08 
TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29Q 
       78.97        63.78        64.64        56.84        18.61        66.74 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X 
       14.47        61.28       369.93        25.87       195.02        17.92 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GC 
       46.82       115.96        59.64        39.29        86.14        67.43 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
      173.79       220.24       107.38        54.74        79.66        75.48 
TCGA-EE-A2GN TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 
      102.12        42.77        81.21        44.88        94.82        21.67 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME 
      129.27        28.83        19.76        61.51        47.28       103.27 
TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML 
      268.73       103.20        16.96       204.66       180.39       216.66 
TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU 
      167.90        47.54        43.23       162.48        71.21        53.26 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH 
      122.73        64.04        54.51        13.81        41.59       138.81 
TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J8 TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A195 
      127.20        36.95        34.32        51.35       134.33        35.44 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F 
        9.17        77.75        48.89        12.59        13.02        26.37 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
      302.07       152.35         6.44       131.51        61.05        44.09 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 
      162.08        50.89        49.48         8.88       148.18       105.07 
TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES 
       43.82        20.15        28.83        48.99        41.56       247.04 
TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A7U9 
       12.95       149.03       174.21        15.72        27.85        18.77 
TCGA-FR-A7UA TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 
       38.27        36.26       104.42       216.92       228.59       202.65 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC 
       20.91        28.08         7.79        27.72        48.85       357.37 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZP TCGA-FS-A1ZR 
       53.52        46.45         9.70        32.75        74.73        11.41 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 
      148.80        53.16        49.48        27.09        27.02        77.82 
TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC 
       50.14        66.67       174.84        34.03        26.73        54.41 
TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
       80.68        17.46        55.59        13.51        19.30         9.90 
TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
        2.04        15.78       139.89        96.92        10.13        64.44 
TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A4U9 
       32.48       121.91        39.35        10.42        48.89        22.13 
TCGA-GN-A8LL TCGA-HR-A2OG TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS 
       21.37         0.23        65.88       368.78       297.90         7.23 
TCGA-RP-A690 TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 
        0.20         0.33         0.69       228.16        63.02       121.08 
TCGA-W3-AA1O TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8JZ 
        4.01        69.07       111.09       219.16       105.04        24.03 
TCGA-WE-A8K1 TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT 
       49.05        17.95       101.33        58.98        70.52        11.80 
TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-XV-AB01 
       35.80        49.51        12.16        40.41        24.99        13.25 
TCGA-YD-A89C TCGA-YD-A9TA TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S 
        6.90        49.18        37.94        14.43        27.58        96.99 
TCGA-Z2-AA3V 
       15.98 

  AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE 
                      13.91                        0.20 
  AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE 
                     248.65                      369.93 
  AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE 
                      54.02                       50.89 
[1] "13.9 - 248.7 (54.0)" "0.2 - 369.9 (50.9)" 
[1] "hr=" "1.2"
D5V3, continuous
                             vv
clus                          I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB
  AMP PEAK  5(4Q12) MUTATED          2       0       9        2        8
  AMP PEAK  5(4Q12) WILD-TYPE       11       7      20       16       20
                             vv
clus                          STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  AMP PEAK  5(4Q12) MUTATED          3         1         2         5        11
  AMP PEAK  5(4Q12) WILD-TYPE       23        13        17        10        28
                             vv
clus                          STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  AMP PEAK  5(4Q12) MUTATED            3          8          6        2
  AMP PEAK  5(4Q12) WILD-TYPE         12         27         48       19
D5V4, multiclass
            clus
vv           AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE
  I/II NOS                           2                          11
  STAGE 0                            0                           7
  STAGE I                            9                          20
  STAGE IA                           2                          16
  STAGE IB                           8                          20
  STAGE II                           3                          23
  STAGE IIA                          1                          13
  STAGE IIB                          2                          17
  STAGE IIC                          5                          10
  STAGE III                         11                          28
  STAGE IIIA                         3                          12
  STAGE IIIB                         8                          27
  STAGE IIIC                         6                          48
  STAGE IV                           2                          19
[1] 14  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          T0+T1 T2 T3 T4
  AMP PEAK  5(4Q12) MUTATED      17 17 11 14
  AMP PEAK  5(4Q12) WILD-TYPE    47 56 70 53
D5V5, multiclass
       clus
vv      AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE
  T0+T1                        17                          47
  T2                           17                          56
  T3                           11                          70
  T4                           14                          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  N3
  AMP PEAK  5(4Q12) MUTATED    35  12   9   5
  AMP PEAK  5(4Q12) WILD-TYPE 142  53  30  40
D5V6, multiclass
    clus
vv   AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE
  N0                        35                         142
  N1                        12                          53
  N2                         9                          30
  N3                         5                          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"
D5V7, binary
                             cls
clus                            0   1
  AMP PEAK  5(4Q12) MUTATED    58   2
  AMP PEAK  5(4Q12) WILD-TYPE 261  20
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  5(4Q12) MUTATED     58    2
  AMP PEAK  5(4Q12) WILD-TYPE  261   20
   clus
vv  AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE
  0                        58                         261
  1                         2                          20
[1] 2 2
[1] FALSE
D5V8, binary
                             cls
clus                            0   1
  AMP PEAK  5(4Q12) MUTATED    26  14
  AMP PEAK  5(4Q12) WILD-TYPE 108  76
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  5(4Q12) MUTATED     26   14
  AMP PEAK  5(4Q12) WILD-TYPE  108   76
     clus
vv    AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE
  NO                         26                         108
  YES                        14                          76
[1] 2 2
[1] FALSE
D5V9, binary
                             cls
clus                            0   1
  AMP PEAK  5(4Q12) MUTATED     7  58
  AMP PEAK  5(4Q12) WILD-TYPE  40 262
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  5(4Q12) MUTATED      7   58
  AMP PEAK  5(4Q12) WILD-TYPE   40  262
     clus
vv    AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE
  NO                          7                          40
  YES                        58                         262
[1] 2 2
[1] FALSE
D5V10, continuous
D5V11, binary
                             cls
clus                            0   1
  AMP PEAK  5(4Q12) MUTATED    26  39
  AMP PEAK  5(4Q12) WILD-TYPE 112 190
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  5(4Q12) MUTATED     26   39
  AMP PEAK  5(4Q12) WILD-TYPE  112  190
        clus
vv       AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE
  FEMALE                        26                         112
  MALE                          39                         190
[1] 2 2
[1] FALSE
D5V12, binary
                             cls
clus                            0   1
  AMP PEAK  5(4Q12) MUTATED    56   9
  AMP PEAK  5(4Q12) WILD-TYPE 263  38
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  5(4Q12) MUTATED     56    9
  AMP PEAK  5(4Q12) WILD-TYPE  263   38
     clus
vv    AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE
  NO                         56                         263
  YES                         9                          38
[1] 2 2
[1] FALSE
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  5(4Q12) MUTATED       1                         0    63
  AMP PEAK  5(4Q12) WILD-TYPE     4                         1   290
D5V13, multiclass
                           clus
vv                          AMP PEAK  5(4Q12) MUTATED
  ASIAN                                             1
  BLACK OR AFRICAN AMERICAN                         0
  WHITE                                            63
                           clus
vv                          AMP PEAK  5(4Q12) WILD-TYPE
  ASIAN                                               4
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                             290
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V14, binary
                             cls
clus                            0   1
  AMP PEAK  5(4Q12) MUTATED     2  63
  AMP PEAK  5(4Q12) WILD-TYPE   5 289
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  5(4Q12) MUTATED      2   63
  AMP PEAK  5(4Q12) WILD-TYPE    5  289
                        clus
vv                       AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE
  HISPANIC OR LATINO                             2                           5
  NOT HISPANIC OR LATINO                        63                         289
[1] 2 2
[1] FALSE

Clustering(6) Variable = AMP PEAK  6(5P15.33) MUTATION ANALYSIS
D6V1, survival
                                sevent
clus2                             0  1
  AMP PEAK  6(5P15.33) MUTATED   38 36
  AMP PEAK  6(5P15.33) WILD-TYPE 90 88
  AMP PEAK  6(5P15.33) MUTATED AMP PEAK  6(5P15.33) WILD-TYPE 
                            74                            178 
  AMP PEAK  6(5P15.33) MUTATED AMP PEAK  6(5P15.33) WILD-TYPE 
                            36                             88 
$`AMP PEAK  6(5P15.33) MUTATED`
TCGA-D3-A2JF TCGA-D3-A8GI TCGA-EE-A180 TCGA-EE-A20H TCGA-D3-A1Q3 TCGA-D3-A2JC 
       62.07        13.41        31.96       166.75        15.72        86.30 
TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3CF 
       64.83        66.08        43.53        58.06        40.01        24.53 
TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51K TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GU 
       23.67       173.85        31.76        45.70       177.86       124.08 
TCGA-D3-A8GM TCGA-D9-A1X3 TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1I2 TCGA-DA-A3F5 
       70.62        10.78        69.21        76.34       150.61       225.11 
TCGA-DA-A95V TCGA-DA-A95X TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EE-A181 TCGA-EE-A29D 
       72.10        65.03         3.91        16.41        20.38        12.99 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29M TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2GM 
        0.26        44.28        47.74       346.49       185.19        18.35 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A3AA TCGA-EE-A3AB 
      103.13        15.25       227.01       143.93       124.31       122.73 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3J3 TCGA-EE-A3JI TCGA-ER-A197 TCGA-ER-A19B 
        4.41        54.51        67.89       135.98        10.49        53.29 
TCGA-ER-A19C TCGA-ER-A19G TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
       39.81       184.60        59.84        42.51       120.76        49.71 
TCGA-ER-A2ND TCGA-ER-A2NF TCGA-ER-A3PL TCGA-FR-A44A TCGA-FR-A8YC TCGA-FS-A1ZE 
        4.70        10.19        32.05       174.21        10.06        43.92 
TCGA-FS-A1ZG TCGA-FS-A1ZQ TCGA-FS-A1ZY TCGA-FS-A4F4 TCGA-FW-A3TU TCGA-GF-A4EO 
        7.82       130.95         5.29        66.67        55.59        18.25 
TCGA-GN-A264 TCGA-GN-A265 TCGA-RP-A690 TCGA-W3-AA1V TCGA-W3-AA1W TCGA-WE-A8ZM 
      117.93        96.92         0.20         8.09       185.13        65.42 
TCGA-WE-A8ZQ TCGA-XV-AB01 
       62.89         6.61 

$`AMP PEAK  6(5P15.33) WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR 
        9.76        38.76        33.24       269.03        52.90       134.40 
TCGA-EE-A3JD TCGA-ER-A193 TCGA-FR-A729 TCGA-FW-A3R5 TCGA-WE-A8K5 TCGA-WE-AAA3 
       27.35        19.04       216.43        36.95        52.73         7.40 
TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
       60.46        12.99        14.83         8.42        31.89       110.93 
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 
       49.35       133.25        19.04        76.41        62.60        25.64 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JG TCGA-D3-A2JH 
       45.99        62.86        15.75       168.00       107.61        36.30 
TCGA-D3-A2JL TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A51F 
      171.58       140.98        59.70         9.34        90.21        30.67 
TCGA-D3-A51J TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A8GC TCGA-D3-A8GD 
      144.46        62.70        11.34        42.05        78.21        23.61 
TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GP TCGA-D3-A8GR TCGA-D9-A3Z1 
      179.97       120.00        69.53       135.12        36.53        15.02 
TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6EG TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I5 
       16.90        18.44        22.85       138.67        68.68       110.53 
TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F8 TCGA-DA-A95W 
       60.10        64.83        58.85        30.44         8.71         0.76 
TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
       14.14        12.30        52.41        18.21        13.15        24.89 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29C 
        0.00        26.24        75.55        79.20        75.22        76.14 
TCGA-EE-A29H TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 
       47.41        27.16        61.12       115.43        30.02        77.98 
TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       26.14        12.95       201.60        68.65        10.62        32.48 
TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M8 
       93.63         0.76         0.20        71.31        81.99         5.75 
TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
       23.77       209.79        94.19       171.85        63.25        89.26 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AC TCGA-EE-A3AF 
      104.78       145.45        23.51        53.26        64.04         6.28 
TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH TCGA-ER-A195 
      111.85        45.90         3.35       168.85        19.86        34.45 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19D TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19S 
        7.82         4.54        11.47       150.12        99.06        47.18 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A3ES 
      146.63        73.05        22.36        16.87        28.67       173.29 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A69P TCGA-FR-A7U8 
       68.52        15.48        74.47         4.50         4.14        26.20 
TCGA-FR-A7UA TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 
        5.65       171.78        49.74       195.98         8.35        27.62 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZS TCGA-FS-A1ZT 
      312.07        32.78        36.33        78.61       136.27        35.28 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F8 TCGA-FS-A4F9 
        4.47        23.21         3.06        30.90       173.19        13.28 
TCGA-FS-A4FD TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GN-A262 
       80.68        11.54        19.30         9.90         1.91        53.29 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 
       17.06        42.48         7.59       120.53        34.49        46.92 
TCGA-GN-A8LK TCGA-GN-A9SD TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A693 
       43.23        59.41        85.05       297.01         7.23         0.33 
TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA21 
      174.12         1.97       120.07        44.05        79.99        92.84 
TCGA-WE-A8K1 TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y 
       47.54        12.69        21.90        10.95        48.39         1.94 
TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-Z2-AA3S 
       37.32        24.99        28.21        91.23 

  AMP PEAK  6(5P15.33) MUTATED AMP PEAK  6(5P15.33) WILD-TYPE 
                           0.2                            0.0 
  AMP PEAK  6(5P15.33) MUTATED AMP PEAK  6(5P15.33) WILD-TYPE 
                        346.49                         312.07 
  AMP PEAK  6(5P15.33) MUTATED AMP PEAK  6(5P15.33) WILD-TYPE 
                        55.050                         42.855 
[1] "0.2 - 346.5 (55.0)" "0.0 - 312.1 (42.9)"
[1] "hr=" "1.2"
D6V2, survival
                                sevent
clus2                              0   1
  AMP PEAK  6(5P15.33) MUTATED    51  56
  AMP PEAK  6(5P15.33) WILD-TYPE 115 136
  AMP PEAK  6(5P15.33) MUTATED AMP PEAK  6(5P15.33) WILD-TYPE 
                           107                            251 
  AMP PEAK  6(5P15.33) MUTATED AMP PEAK  6(5P15.33) WILD-TYPE 
                            56                            136 
$`AMP PEAK  6(5P15.33) MUTATED`
TCGA-D3-A2JF TCGA-D3-A8GI TCGA-EE-A180 TCGA-EE-A184 TCGA-EE-A20H TCGA-QB-AA9O 
       62.07        58.52        94.98        68.15       168.26        18.05 
TCGA-3N-A9WB TCGA-D3-A1Q3 TCGA-D3-A1Q9 TCGA-D3-A2JC TCGA-D3-A2JK TCGA-D3-A2JN 
       17.03        16.67        31.59        86.76        12.10        66.48 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3MU 
       66.08        59.57        58.06        86.93        24.53        39.75 
TCGA-D3-A51E TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR 
      174.84        32.94        22.62       135.75       137.92       178.32 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GM TCGA-D9-A148 TCGA-D9-A1JW TCGA-D9-A1X3 
       18.18       125.19       107.15       151.53         3.65        18.12 
TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1I2 TCGA-DA-A3F3 
        9.90        25.18        77.56        76.57       176.55        10.49 
TCGA-DA-A3F5 TCGA-DA-A95V TCGA-DA-A95X TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH 
      225.96        72.10        73.94        13.87        10.36        20.35 
TCGA-EE-A181 TCGA-EE-A20B TCGA-EE-A20I TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G 
       33.73       133.81        13.55        13.97        63.78        72.07 
TCGA-EE-A29M TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A0 TCGA-EE-A2GM TCGA-EE-A2M6 
       56.84       369.93       195.02        46.82        75.48       129.27 
TCGA-EE-A2M7 TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AD 
       28.83       248.65       162.48       124.31       122.73        28.77 
TCGA-EE-A3AE TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3JA TCGA-EE-A3JI 
       54.51        41.59       138.81       172.18        53.19       152.81 
TCGA-ER-A197 TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19G TCGA-ER-A19M TCGA-ER-A19N 
       13.94        98.40        48.89       302.07        61.05        44.09 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19T TCGA-ER-A2ND TCGA-ER-A2NF TCGA-ER-A2NH 
      162.08        50.89         8.88        23.34        28.83        41.56 
TCGA-ER-A3PL TCGA-FR-A44A TCGA-FR-A7U9 TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FS-A1YX 
       33.21       174.21        18.77        34.82        36.26        48.59 
TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZK TCGA-FS-A1ZQ TCGA-FS-A1ZY TCGA-FS-A4F4 
       46.45         9.70        23.93       133.55        27.09        66.67 
TCGA-FS-A4F5 TCGA-FW-A3TU TCGA-GF-A4EO TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A26D 
       28.73        55.59        19.43       117.93        96.92        48.00 
TCGA-GN-A4U9 TCGA-RP-A690 TCGA-W3-AA1O TCGA-W3-AA1V TCGA-W3-AA1W TCGA-WE-A8ZM 
       22.13         0.20         4.01        42.08       219.16       101.33 
TCGA-WE-A8ZQ TCGA-XV-AB01 TCGA-YD-A9TA TCGA-YG-AA3P TCGA-Z2-A8RT 
       63.22        13.25        49.18        14.43        27.58 

$`AMP PEAK  6(5P15.33) WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A29L 
       27.65        46.32        13.87        68.25        54.02         2.60 
TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-ER-A198 
      340.14       126.81       134.40        27.35        31.40        50.76 
TCGA-FR-A729 TCGA-FS-A1ZF TCGA-FW-A3R5 TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-3N-A9WC 
      220.80        15.45        36.95        61.15        21.40        66.48 
TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 
       12.99        14.93        16.57       112.04       112.57        71.80 
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
      133.25        28.08        90.90        95.74        43.43       103.10 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JD TCGA-D3-A2JG 
       65.49        23.77       115.53       168.00        11.87       113.52 
TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CE 
       42.08       171.58       130.72        46.98       166.52        60.23 
TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MV TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
        9.34       103.59        45.30        55.73        56.35       145.12 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GD 
       63.81        26.89       125.79        30.84        79.59        23.61 
TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GN TCGA-D3-A8GP 
       26.43       241.38       170.20        89.13       161.00       152.75 
TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D3-A8GV TCGA-D9-A149 TCGA-D9-A1JX 
       29.06       129.63       117.17       167.70        54.67         7.10 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6EG TCGA-DA-A1HW TCGA-DA-A1HY 
       15.39        22.29        18.44        22.95        36.03       144.89 
TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
       20.38       222.51        35.93       135.02        88.87        53.92 
TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F8 TCGA-DA-A95W 
       65.92        40.60        68.09        33.93        43.36        37.35 
TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 
       14.14        13.02        29.29        58.92         7.04        36.46 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 
       29.82        27.22         8.65        14.70        26.89         4.96 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29H 
      151.27        91.56        63.35        85.08        78.97        64.64 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V 
       18.61        56.42        66.74        14.47        61.28        25.87 
TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
       17.92       115.96        59.64        39.29        86.14        59.28 
TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
       67.43       173.79       220.24        48.72       107.38        54.74 
TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT 
       79.66       102.12        13.91        42.77        81.21        44.88 
TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME 
       94.82        21.67        19.76        61.51        47.28       103.27 
TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
      268.73       103.20        16.96       204.66        96.23       180.39 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MT TCGA-EE-A2MU 
      216.66       167.90        47.54        43.23        71.21        53.26 
TCGA-EE-A3AC TCGA-EE-A3AF TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 
       64.04        13.81       127.20        36.95        64.08        34.32 
TCGA-EE-A3JB TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A195 TCGA-ER-A199 TCGA-ER-A19A 
      201.80        51.35       134.33        35.44         9.17        77.75 
TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L 
       12.59        13.02        26.37       152.35         6.44       131.51 
TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NG 
       49.48       148.18       105.07        43.82        20.15        48.99 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A3YN 
      247.04        93.01        46.98        12.95       149.03        92.98 
TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YY 
       15.72        27.85        38.27       104.42       216.92       228.59 
TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB 
      202.65        20.91        28.08         7.79        27.72        48.85 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZP 
      357.37        53.52        32.75        47.38       101.26        74.73 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZZ 
       11.41       148.80        53.16        26.56        49.48        27.02 
TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC 
       77.82        50.14       174.84        34.03        26.73        54.41 
TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 
       80.68        17.46        13.51        19.30         9.90         2.04 
TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
       15.78       139.89        10.13        64.44        62.79        32.48 
TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A8LK TCGA-GN-A8LL 
      121.91        39.35        10.42        48.89        50.10        21.37 
TCGA-GN-A9SD TCGA-HR-A2OG TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS 
       59.41         0.23        65.88       368.78       297.90         7.23 
TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1Q 
        0.33         0.69       228.16        63.02       121.08        69.07 
TCGA-W3-AA1R TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K6 TCGA-WE-A8ZN 
      111.09       105.04        24.03        49.05        17.95        58.98 
TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 
       70.52        11.80        35.80        49.51        12.16        40.41 
TCGA-WE-AAA4 TCGA-YD-A89C TCGA-YG-AA3O TCGA-Z2-AA3S TCGA-Z2-AA3V 
       24.99         6.90        37.94        96.99        15.98 

  AMP PEAK  6(5P15.33) MUTATED AMP PEAK  6(5P15.33) WILD-TYPE 
                          0.20                           0.23 
  AMP PEAK  6(5P15.33) MUTATED AMP PEAK  6(5P15.33) WILD-TYPE 
                        369.93                         368.78 
  AMP PEAK  6(5P15.33) MUTATED AMP PEAK  6(5P15.33) WILD-TYPE 
                         53.19                          51.35 
[1] "0.2 - 369.9 (53.2)" "0.2 - 368.8 (51.4)"
[1] "hr=" "1.1"
D6V3, continuous
                                vv
clus                             I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB
  AMP PEAK  6(5P15.33) MUTATED          3       2       8        4        9
  AMP PEAK  6(5P15.33) WILD-TYPE       10       5      21       14       19
                                vv
clus                             STAGE II STAGE IIA STAGE IIB STAGE IIC
  AMP PEAK  6(5P15.33) MUTATED         12         2         5         7
  AMP PEAK  6(5P15.33) WILD-TYPE       14        12        14         8
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  AMP PEAK  6(5P15.33) MUTATED          11          4         10         14
  AMP PEAK  6(5P15.33) WILD-TYPE        28         11         25         40
                                vv
clus                             STAGE IV
  AMP PEAK  6(5P15.33) MUTATED          5
  AMP PEAK  6(5P15.33) WILD-TYPE       16
D6V4, multiclass
            clus
vv           AMP PEAK  6(5P15.33) MUTATED AMP PEAK  6(5P15.33) WILD-TYPE
  I/II NOS                              3                             10
  STAGE 0                               2                              5
  STAGE I                               8                             21
  STAGE IA                              4                             14
  STAGE IB                              9                             19
  STAGE II                             12                             14
  STAGE IIA                             2                             12
  STAGE IIB                             5                             14
  STAGE IIC                             7                              8
  STAGE III                            11                             28
  STAGE IIIA                            4                             11
  STAGE IIIB                           10                             25
  STAGE IIIC                           14                             40
  STAGE IV                              5                             16
[1] 14  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  AMP PEAK  6(5P15.33) MUTATED      24 16 26 21
  AMP PEAK  6(5P15.33) WILD-TYPE    40 57 55 46
D6V5, multiclass
       clus
vv      AMP PEAK  6(5P15.33) MUTATED AMP PEAK  6(5P15.33) WILD-TYPE
  T0+T1                           24                             40
  T2                              16                             57
  T3                              26                             55
  T4                              21                             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  N3
  AMP PEAK  6(5P15.33) MUTATED    56  12  17  15
  AMP PEAK  6(5P15.33) WILD-TYPE 121  53  22  30
D6V6, multiclass
    clus
vv   AMP PEAK  6(5P15.33) MUTATED AMP PEAK  6(5P15.33) WILD-TYPE
  N0                           56                            121
  N1                           12                             53
  N2                           17                             22
  N3                           15                             30
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V7, binary
                                cls
clus                               0   1
  AMP PEAK  6(5P15.33) MUTATED    95   6
  AMP PEAK  6(5P15.33) WILD-TYPE 224  16
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  6(5P15.33) MUTATED     95    6
  AMP PEAK  6(5P15.33) WILD-TYPE  224   16
   clus
vv  AMP PEAK  6(5P15.33) MUTATED AMP PEAK  6(5P15.33) WILD-TYPE
  0                           95                            224
  1                            6                             16
[1] 2 2
[1] FALSE
D6V8, binary
                                cls
clus                              0  1
  AMP PEAK  6(5P15.33) MUTATED   40 27
  AMP PEAK  6(5P15.33) WILD-TYPE 94 63
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  6(5P15.33) MUTATED     40   27
  AMP PEAK  6(5P15.33) WILD-TYPE   94   63
     clus
vv    AMP PEAK  6(5P15.33) MUTATED AMP PEAK  6(5P15.33) WILD-TYPE
  NO                            40                             94
  YES                           27                             63
[1] 2 2
[1] FALSE
D6V9, binary
                                cls
clus                               0   1
  AMP PEAK  6(5P15.33) MUTATED    16  94
  AMP PEAK  6(5P15.33) WILD-TYPE  31 226
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  6(5P15.33) MUTATED     16   94
  AMP PEAK  6(5P15.33) WILD-TYPE   31  226
     clus
vv    AMP PEAK  6(5P15.33) MUTATED AMP PEAK  6(5P15.33) WILD-TYPE
  NO                            16                             31
  YES                           94                            226
[1] 2 2
[1] FALSE
D6V10, continuous
D6V11, binary
                                cls
clus                               0   1
  AMP PEAK  6(5P15.33) MUTATED    41  69
  AMP PEAK  6(5P15.33) WILD-TYPE  97 160
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  6(5P15.33) MUTATED     41   69
  AMP PEAK  6(5P15.33) WILD-TYPE   97  160
        clus
vv       AMP PEAK  6(5P15.33) MUTATED AMP PEAK  6(5P15.33) WILD-TYPE
  FEMALE                           41                             97
  MALE                             69                            160
[1] 2 2
[1] FALSE
D6V12, binary
                                cls
clus                               0   1
  AMP PEAK  6(5P15.33) MUTATED    94  15
  AMP PEAK  6(5P15.33) WILD-TYPE 225  32
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  6(5P15.33) MUTATED     94   15
  AMP PEAK  6(5P15.33) WILD-TYPE  225   32
     clus
vv    AMP PEAK  6(5P15.33) MUTATED AMP PEAK  6(5P15.33) WILD-TYPE
  NO                            94                            225
  YES                           15                             32
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  6(5P15.33) MUTATED       3                         0   105
  AMP PEAK  6(5P15.33) WILD-TYPE     2                         1   248
D6V13, multiclass
                           clus
vv                          AMP PEAK  6(5P15.33) MUTATED
  ASIAN                                                3
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                              105
                           clus
vv                          AMP PEAK  6(5P15.33) WILD-TYPE
  ASIAN                                                  2
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                248
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V14, binary
                                cls
clus                               0   1
  AMP PEAK  6(5P15.33) MUTATED     3 106
  AMP PEAK  6(5P15.33) WILD-TYPE   4 246
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  6(5P15.33) MUTATED      3  106
  AMP PEAK  6(5P15.33) WILD-TYPE    4  246
                        clus
vv                       AMP PEAK  6(5P15.33) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                          106
                        clus
vv                       AMP PEAK  6(5P15.33) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            246
[1] 2 2
[1] FALSE

Clustering(7) Variable = AMP PEAK  7(5Q35.3) MUTATION ANALYSIS
D7V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  7(5Q35.3) MUTATED    19  20
  AMP PEAK  7(5Q35.3) WILD-TYPE 109 104
  AMP PEAK  7(5Q35.3) MUTATED AMP PEAK  7(5Q35.3) WILD-TYPE 
                           39                           213 
  AMP PEAK  7(5Q35.3) MUTATED AMP PEAK  7(5Q35.3) WILD-TYPE 
                           20                           104 
$`AMP PEAK  7(5Q35.3) MUTATED`
TCGA-D3-A2JF TCGA-EE-A180 TCGA-EE-A20H TCGA-D3-A1Q3 TCGA-D3-A2JN TCGA-D3-A2JP 
       62.07        31.96       166.75        15.72        64.83        43.53 
TCGA-D3-A3CF TCGA-D3-A3MU TCGA-D3-A51K TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D3-A8GC 
       24.53        23.67        31.76       177.86       124.08        78.21 
TCGA-DA-A1IA TCGA-DA-A95V TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EE-A182 TCGA-EE-A29H 
       64.83        72.10        12.30         3.91         0.00        47.41 
TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2GJ TCGA-EE-A2M7 TCGA-EE-A2MS TCGA-EE-A2MT 
      346.49       185.19        68.65        15.25       143.93        23.51 
TCGA-EE-A3AA TCGA-EE-A3J3 TCGA-EE-A3JI TCGA-ER-A19C TCGA-ER-A19P TCGA-ER-A2ND 
      124.31        67.89       135.98        39.81       120.76         4.70 
TCGA-ER-A3ET TCGA-ER-A3PL TCGA-FR-A8YC TCGA-FS-A1ZD TCGA-FS-A1ZJ TCGA-FW-A3TU 
       68.52        32.05        10.06        32.78        36.33        55.59 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-WE-A8ZQ 
       18.25         1.91        62.89 

$`AMP PEAK  7(5Q35.3) WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A3C8 TCGA-D3-A8GI TCGA-EB-A5SG TCGA-EE-A2GD TCGA-EE-A2GO 
        9.76        38.76        13.41        33.24       269.03        52.90 
TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-FR-A729 TCGA-FW-A3R5 TCGA-WE-A8K5 
      134.40        27.35        19.04       216.43        36.95        52.73 
TCGA-WE-AAA3 TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q4 
        7.40        60.46        12.99        14.83         8.42        31.89 
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB 
      110.93        49.35       133.25        19.04        76.41        62.60 
TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC 
       25.64        45.99        62.86        15.75       168.00        86.30 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JO TCGA-D3-A3C6 TCGA-D3-A3CB 
      107.61        36.30       171.58        66.08        58.06       140.98 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A51E TCGA-D3-A51F 
       40.01        59.70         9.34        90.21       173.85        30.67 
TCGA-D3-A51J TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A8GD 
      144.46        62.70        11.34        42.05        45.70        23.61 
TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GP TCGA-D3-A8GR 
      179.97       120.00        69.53        70.62       135.12        36.53 
TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6EC TCGA-D9-A6EG 
       10.78        15.02        16.90        18.44        69.21        22.85 
TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 
       76.34       138.67        68.68       150.61       110.53        60.10 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-DA-A95W TCGA-DA-A95X 
       58.85        30.44       225.11         8.71         0.76        65.03 
TCGA-DA-A95Y TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
       14.14        16.41        52.41        18.21        13.15        24.89 
TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29C 
       20.38        26.24        75.55        79.20        75.22        76.14 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q 
       12.99         0.26        44.28        47.74        27.16        61.12 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH 
      115.43        30.02        77.98        26.14        12.95       201.60 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR 
       10.62        32.48        18.35        93.63         0.76         0.20 
TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MF 
       71.31        81.99       103.13         5.75        23.77       209.79 
TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
       94.19       171.85        63.25        89.26       104.78       145.45 
TCGA-EE-A2MP TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
      227.01        53.26       122.73        64.04         4.41        54.51 
TCGA-EE-A3AF TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH 
        6.28       111.85        45.90         3.35       168.85        19.86 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19D 
       34.45        10.49         7.82         4.54        53.29        11.47 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19Q 
      184.60       150.12        99.06        59.84        42.51        49.71 
TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF 
       47.18       146.63        73.05        22.36        16.87        10.19 
TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3EV TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A 
       28.67       173.29        15.48        74.47         4.50       174.21 
TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 
        4.14        26.20         5.65       171.78        49.74       195.98 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZM 
        8.35        27.62       312.07        43.92         7.82        78.61 
TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
      130.95       136.27        35.28         4.47        23.21         5.29 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FD 
        3.06        30.90        66.67       173.19        13.28        80.68 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
       11.54        19.30         9.90        53.29       117.93        96.92 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 
       17.06        42.48         7.59       120.53        34.49        46.92 
TCGA-GN-A8LK TCGA-GN-A9SD TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 
       43.23        59.41        85.05       297.01         7.23         0.20 
TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1Q TCGA-W3-AA1R 
        0.33       174.12         1.97       120.07        44.05        79.99 
TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8ZM TCGA-WE-A8ZN 
        8.09       185.13        92.84        47.54        65.42        12.69 
TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 
       21.90        10.95        48.39         1.94        37.32        24.99 
TCGA-XV-AB01 TCGA-YG-AA3O TCGA-Z2-AA3S 
        6.61        28.21        91.23 

  AMP PEAK  7(5Q35.3) MUTATED AMP PEAK  7(5Q35.3) WILD-TYPE 
                          0.0                           0.2 
  AMP PEAK  7(5Q35.3) MUTATED AMP PEAK  7(5Q35.3) WILD-TYPE 
                       346.49                        312.07 
  AMP PEAK  7(5Q35.3) MUTATED AMP PEAK  7(5Q35.3) WILD-TYPE 
                        47.41                         45.99 
[1] "0.0 - 346.5 (47.4)" "0.2 - 312.1 (46.0)"
[1] "hr=" "1"  
D7V2, survival
                               sevent
clus2                             0   1
  AMP PEAK  7(5Q35.3) MUTATED    28  29
  AMP PEAK  7(5Q35.3) WILD-TYPE 138 163
  AMP PEAK  7(5Q35.3) MUTATED AMP PEAK  7(5Q35.3) WILD-TYPE 
                           57                           301 
  AMP PEAK  7(5Q35.3) MUTATED AMP PEAK  7(5Q35.3) WILD-TYPE 
                           29                           163 
$`AMP PEAK  7(5Q35.3) MUTATED`
TCGA-D3-A2JF TCGA-EE-A180 TCGA-EE-A20H TCGA-3N-A9WB TCGA-D3-A1Q3 TCGA-D3-A2JN 
       62.07        94.98       168.26        17.03        16.67        66.48 
TCGA-D3-A2JP TCGA-D3-A3CF TCGA-D3-A3MU TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A5GR 
       59.57        24.53        39.75        32.94        22.62       178.32 
TCGA-D3-A5GU TCGA-D3-A8GC TCGA-D9-A148 TCGA-D9-A1JW TCGA-D9-A6E9 TCGA-D9-A6EA 
      125.19        79.59       151.53         3.65         9.90        25.18 
TCGA-DA-A1IA TCGA-DA-A95V TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EE-A182 TCGA-EE-A29H 
       65.92        72.10        13.02        13.87        14.70        64.64 
TCGA-EE-A29R TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2GJ TCGA-EE-A2M7 TCGA-EE-A2MS 
       14.47       369.93       195.02       107.38        28.83       162.48 
TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3J3 TCGA-EE-A3JA TCGA-EE-A3JI TCGA-ER-A19C 
       71.21       124.31       172.18        53.19       152.81        48.89 
TCGA-ER-A19F TCGA-ER-A19P TCGA-ER-A19T TCGA-ER-A2ND TCGA-ER-A3ET TCGA-ER-A3PL 
       26.37       162.08         8.88        23.34        93.01        33.21 
TCGA-FR-A7U9 TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FS-A1YX TCGA-FS-A1ZD TCGA-FS-A1ZJ 
       18.77        34.82        36.26        48.59        53.52        47.38 
TCGA-FS-A1ZK TCGA-FS-A4F5 TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-GF-A4EO TCGA-GF-A6C8 
       23.93        28.73        17.46        55.59        19.43         2.04 
TCGA-GN-A4U9 TCGA-WE-A8ZQ TCGA-YG-AA3P 
       22.13        63.22        14.43 

$`AMP PEAK  7(5Q35.3) WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-D3-A8GI TCGA-EB-A5SG TCGA-EB-A5SH 
       27.65        46.32        13.87        58.52        68.25        54.02 
TCGA-EE-A184 TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD 
       68.15         2.60       340.14       126.81       134.40        27.35 
TCGA-ER-A193 TCGA-ER-A198 TCGA-FR-A729 TCGA-FS-A1ZF TCGA-FW-A3R5 TCGA-QB-AA9O 
       31.40        50.76       220.80        15.45        36.95        18.05 
TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 
       61.15        21.40        66.48        12.99        14.93        16.57 
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 
      112.04       112.57        71.80       133.25        28.08        31.59 
TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 
       90.90        95.74        43.43       103.10        65.49        23.77 
TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH 
      115.53       168.00        86.76        11.87       113.52        42.08 
TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JO TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 
       12.10       171.58        66.08       130.72        58.06        46.98 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MV 
      166.52        86.93        60.23         9.34       103.59        45.30 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51R TCGA-D3-A51T 
      174.84        55.73        56.35       145.12        63.81        26.89 
TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GS TCGA-D3-A8GB TCGA-D3-A8GD 
      125.79       135.75       137.92        18.18        30.84        23.61 
TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GN 
       26.43       241.38       170.20        89.13       107.15       161.00 
TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D3-A8GV TCGA-D9-A149 
      152.75        29.06       129.63       117.17       167.70        54.67 
TCGA-D9-A1JX TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6EC 
        7.10        18.12        15.39        22.29        18.44        77.56 
TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 
       22.95        76.57        36.03       144.89        20.38       222.51 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IB 
      176.55        35.93       135.02        88.87        53.92        40.60 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-DA-A95W 
       68.09        33.93        10.49       225.96        43.36        37.35 
TCGA-DA-A95X TCGA-DA-A95Y TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5UL TCGA-EB-A5UN 
       73.94        14.14        10.36        20.35        29.29        58.92 
TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A181 
        7.04        36.46        29.82        27.22         8.65        33.73 
TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I 
       26.89         4.96       133.81       151.27        91.56        13.55 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G 
       63.35        85.08        78.97        13.97        63.78        72.07 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29V 
       56.84        18.61        56.42        66.74        61.28        25.87 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
       17.92        46.82       115.96        59.64        39.29        86.14 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GK 
       59.28        67.43       173.79       220.24        48.72        54.74 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
       79.66        75.48       102.12        13.91        42.77        81.21 
TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M8 TCGA-EE-A2MC 
       44.88        94.82        21.67       129.27        19.76        61.51 
TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
       47.28       103.27       268.73       103.20        16.96       204.66 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP 
       96.23       180.39       216.66       167.90        47.54       248.65 
TCGA-EE-A2MQ TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
       43.23        53.26       122.73        64.04        28.77        54.51 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 
       13.81        41.59       138.81       127.20        36.95        64.08 
TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A195 TCGA-ER-A197 
       34.32       201.80        51.35       134.33        35.44        13.94 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19G 
        9.17        77.75        98.40        12.59        13.02       302.07 
TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19Q 
      152.35         6.44       131.51        61.05        44.09        50.89 
TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF 
       49.48       148.18       105.07        43.82        20.15        28.83 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3EV TCGA-ER-A42K TCGA-ER-A42L 
       48.99        41.56       247.04        46.98        12.95       149.03 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FR-A8YE 
       92.98       174.21        15.72        27.85        38.27       104.42 
TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 
      216.92       228.59       202.65        20.91        28.08         7.79 
TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZH 
       27.72        48.85       357.37        46.45         9.70        32.75 
TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT 
      101.26        74.73       133.55        11.41       148.80        53.16 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 
       26.56        49.48        27.09        27.02        77.82        50.14 
TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD 
       66.67       174.84        34.03        26.73        54.41        80.68 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 
       13.51        19.30         9.90        15.78       139.89       117.93 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
       96.92        10.13        64.44        62.79        32.48        48.00 
TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A8LK TCGA-GN-A8LL 
      121.91        39.35        10.42        48.89        50.10        21.37 
TCGA-GN-A9SD TCGA-HR-A2OG TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS 
       59.41         0.23        65.88       368.78       297.90         7.23 
TCGA-RP-A690 TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 
        0.20         0.33         0.69       228.16        63.02       121.08 
TCGA-W3-AA1O TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 
        4.01        69.07       111.09        42.08       219.16       105.04 
TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO 
       24.03        49.05        17.95       101.33        58.98        70.52 
TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 
       11.80        35.80        49.51        12.16        40.41        24.99 
TCGA-XV-AB01 TCGA-YD-A89C TCGA-YD-A9TA TCGA-YG-AA3O TCGA-Z2-A8RT TCGA-Z2-AA3S 
       13.25         6.90        49.18        37.94        27.58        96.99 
TCGA-Z2-AA3V 
       15.98 

  AMP PEAK  7(5Q35.3) MUTATED AMP PEAK  7(5Q35.3) WILD-TYPE 
                         2.04                          0.20 
  AMP PEAK  7(5Q35.3) MUTATED AMP PEAK  7(5Q35.3) WILD-TYPE 
                       369.93                        368.78 
  AMP PEAK  7(5Q35.3) MUTATED AMP PEAK  7(5Q35.3) WILD-TYPE 
                        47.38                         53.92 
[1] "2.0 - 369.9 (47.4)" "0.2 - 368.8 (53.9)"
[1] "hr=" "1.1"
D7V3, continuous
                               vv
clus                            I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB
  AMP PEAK  7(5Q35.3) MUTATED          2       1       5        4        5
  AMP PEAK  7(5Q35.3) WILD-TYPE       11       6      24       14       23
                               vv
clus                            STAGE II STAGE IIA STAGE IIB STAGE IIC
  AMP PEAK  7(5Q35.3) MUTATED          3         2         3         3
  AMP PEAK  7(5Q35.3) WILD-TYPE       23        12        16        12
                               vv
clus                            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  AMP PEAK  7(5Q35.3) MUTATED           4          3          2         11
  AMP PEAK  7(5Q35.3) WILD-TYPE        35         12         33         43
                               vv
clus                            STAGE IV
  AMP PEAK  7(5Q35.3) MUTATED          5
  AMP PEAK  7(5Q35.3) WILD-TYPE       16
D7V4, multiclass
            clus
vv           AMP PEAK  7(5Q35.3) MUTATED AMP PEAK  7(5Q35.3) WILD-TYPE
  I/II NOS                             2                            11
  STAGE 0                              1                             6
  STAGE I                              5                            24
  STAGE IA                             4                            14
  STAGE IB                             5                            23
  STAGE II                             3                            23
  STAGE IIA                            2                            12
  STAGE IIB                            3                            16
  STAGE IIC                            3                            12
  STAGE III                            4                            35
  STAGE IIIA                           3                            12
  STAGE IIIB                           2                            33
  STAGE IIIC                          11                            43
  STAGE IV                             5                            16
[1] 14  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3 T4
  AMP PEAK  7(5Q35.3) MUTATED      13 13 11 10
  AMP PEAK  7(5Q35.3) WILD-TYPE    51 60 70 57
D7V5, multiclass
       clus
vv      AMP PEAK  7(5Q35.3) MUTATED AMP PEAK  7(5Q35.3) WILD-TYPE
  T0+T1                          13                            51
  T2                             13                            60
  T3                             11                            70
  T4                             10                            57
[1] 4 2
[1] 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  N3
  AMP PEAK  7(5Q35.3) MUTATED    31   7   4  12
  AMP PEAK  7(5Q35.3) WILD-TYPE 146  58  35  33
D7V6, multiclass
    clus
vv   AMP PEAK  7(5Q35.3) MUTATED AMP PEAK  7(5Q35.3) WILD-TYPE
  N0                          31                           146
  N1                           7                            58
  N2                           4                            35
  N3                          12                            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"
D7V7, binary
                               cls
clus                              0   1
  AMP PEAK  7(5Q35.3) MUTATED    51   6
  AMP PEAK  7(5Q35.3) WILD-TYPE 268  16
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  7(5Q35.3) MUTATED     51    6
  AMP PEAK  7(5Q35.3) WILD-TYPE  268   16
   clus
vv  AMP PEAK  7(5Q35.3) MUTATED AMP PEAK  7(5Q35.3) WILD-TYPE
  0                          51                           268
  1                           6                            16
[1] 2 2
[1] FALSE
D7V8, binary
                               cls
clus                              0   1
  AMP PEAK  7(5Q35.3) MUTATED    24  13
  AMP PEAK  7(5Q35.3) WILD-TYPE 110  77
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  7(5Q35.3) MUTATED     24   13
  AMP PEAK  7(5Q35.3) WILD-TYPE  110   77
     clus
vv    AMP PEAK  7(5Q35.3) MUTATED AMP PEAK  7(5Q35.3) WILD-TYPE
  NO                           24                           110
  YES                          13                            77
[1] 2 2
[1] FALSE
D7V9, binary
                               cls
clus                              0   1
  AMP PEAK  7(5Q35.3) MUTATED     8  51
  AMP PEAK  7(5Q35.3) WILD-TYPE  39 269
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  7(5Q35.3) MUTATED      8   51
  AMP PEAK  7(5Q35.3) WILD-TYPE   39  269
     clus
vv    AMP PEAK  7(5Q35.3) MUTATED AMP PEAK  7(5Q35.3) WILD-TYPE
  NO                            8                            39
  YES                          51                           269
[1] 2 2
[1] FALSE
D7V10, continuous
D7V11, binary
                               cls
clus                              0   1
  AMP PEAK  7(5Q35.3) MUTATED    26  33
  AMP PEAK  7(5Q35.3) WILD-TYPE 112 196
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  7(5Q35.3) MUTATED     26   33
  AMP PEAK  7(5Q35.3) WILD-TYPE  112  196
        clus
vv       AMP PEAK  7(5Q35.3) MUTATED AMP PEAK  7(5Q35.3) WILD-TYPE
  FEMALE                          26                           112
  MALE                            33                           196
[1] 2 2
[1] FALSE
D7V12, binary
                               cls
clus                              0   1
  AMP PEAK  7(5Q35.3) MUTATED    50   9
  AMP PEAK  7(5Q35.3) WILD-TYPE 269  38
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  7(5Q35.3) MUTATED     50    9
  AMP PEAK  7(5Q35.3) WILD-TYPE  269   38
     clus
vv    AMP PEAK  7(5Q35.3) MUTATED AMP PEAK  7(5Q35.3) WILD-TYPE
  NO                           50                           269
  YES                           9                            38
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  7(5Q35.3) MUTATED       1                         0    56
  AMP PEAK  7(5Q35.3) WILD-TYPE     4                         1   297
D7V13, multiclass
                           clus
vv                          AMP PEAK  7(5Q35.3) MUTATED
  ASIAN                                               1
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                              56
                           clus
vv                          AMP PEAK  7(5Q35.3) WILD-TYPE
  ASIAN                                                 4
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                               297
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V14, binary
                               cls
clus                              0   1
  AMP PEAK  7(5Q35.3) MUTATED     3  56
  AMP PEAK  7(5Q35.3) WILD-TYPE   4 296
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  7(5Q35.3) MUTATED      3   56
  AMP PEAK  7(5Q35.3) WILD-TYPE    4  296
                        clus
vv                       AMP PEAK  7(5Q35.3) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                          56
                        clus
vv                       AMP PEAK  7(5Q35.3) WILD-TYPE
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           296
[1] 2 2
[1] FALSE

Clustering(8) Variable = AMP PEAK  8(6P24.3) MUTATION ANALYSIS
D8V1, survival
                               sevent
clus2                            0  1
  AMP PEAK  8(6P24.3) MUTATED   63 82
  AMP PEAK  8(6P24.3) WILD-TYPE 65 42
  AMP PEAK  8(6P24.3) MUTATED AMP PEAK  8(6P24.3) WILD-TYPE 
                          145                           107 
  AMP PEAK  8(6P24.3) MUTATED AMP PEAK  8(6P24.3) WILD-TYPE 
                           82                            42 
$`AMP PEAK  8(6P24.3) MUTATED`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GD 
        9.76        62.07        33.24        31.96       166.75       269.03 
TCGA-FR-A729 TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-3N-A9WC TCGA-D3-A1Q1 TCGA-D3-A1Q3 
      216.43        52.73         7.40        60.46         8.42        15.72 
TCGA-D3-A1Q7 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J8 TCGA-D3-A2JB TCGA-D3-A2JG 
      133.25        76.41        62.60        62.86       168.00       107.61 
TCGA-D3-A2JO TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E 
       66.08        58.06        40.01        90.21        23.67       173.85 
TCGA-D3-A51K TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GU TCGA-D3-A8GD TCGA-D3-A8GJ 
       31.76        11.34        45.70       124.08        23.61       179.97 
TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GP TCGA-D9-A1X3 TCGA-D9-A4Z6 TCGA-D9-A6EC 
      120.00        69.53       135.12        10.78        18.44        69.21 
TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1IA TCGA-DA-A1IC 
       22.85        76.34        68.68       150.61        64.83        58.85 
TCGA-DA-A95V TCGA-DA-A95X TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5KH 
       72.10        65.03        14.14        12.30         3.91        16.41 
TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29G 
       24.89        20.38        26.24        75.22        12.99        44.28 
TCGA-EE-A29P TCGA-EE-A2GB TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GL TCGA-EE-A2GN 
       27.16        26.14       201.60        68.65        32.48        93.63 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 
        0.76         0.20        71.31        81.99       103.13        15.25 
TCGA-EE-A2MF TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MP 
      209.79       171.85        63.25        89.26       145.45       227.01 
TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3J3 
      143.93        53.26       124.31         4.41         6.28        67.89 
TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JI TCGA-ER-A197 
      111.85        45.90         3.35       168.85       135.98        10.49 
TCGA-ER-A199 TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P 
        7.82        39.81        11.47        59.84        42.51       120.76 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A2NC TCGA-ER-A2NF TCGA-ER-A3ES 
       49.71        47.18       146.63        22.36        10.19       173.29 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A8YC 
       68.52        15.48        32.05         4.14        26.20        10.06 
TCGA-FS-A1YW TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZE 
      171.78       195.98         8.35        27.62       312.07        43.92 
TCGA-FS-A1ZG TCGA-FS-A1ZM TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
        7.82        78.61        35.28         4.47        23.21         5.29 
TCGA-FS-A1ZZ TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-GF-A4EO 
        3.06       173.19        13.28        80.68        55.59        18.25 
TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U4 TCGA-GN-A8LK 
      117.93        17.06        42.48         7.59        34.49        43.23 
TCGA-GN-A9SD TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 
       59.41        85.05       297.01         7.23         0.20         0.33 
TCGA-W3-A825 TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1V TCGA-W3-AA21 TCGA-WE-A8ZM 
        1.97        44.05        79.99         8.09        92.84        65.42 
TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-XV-AB01 
       21.90        62.89        10.95        37.32        24.99         6.61 
TCGA-YG-AA3O 
       28.21 

$`AMP PEAK  8(6P24.3) WILD-TYPE`
TCGA-D3-A3C8 TCGA-D3-A8GI TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 
       38.76        13.41        52.90       134.40        27.35        19.04 
TCGA-FW-A3R5 TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 
       36.95        12.99        14.83        31.89       110.93        49.35 
TCGA-D3-A1Q8 TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JH 
       19.04        25.64        45.99        15.75        86.30        36.30 
TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3CF 
      171.58        64.83        43.53       140.98        59.70        24.53 
TCGA-D3-A3MO TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51R TCGA-D3-A5GL TCGA-D3-A5GR 
        9.34        30.67       144.46        62.70        42.05       177.86 
TCGA-D3-A8GC TCGA-D3-A8GM TCGA-D3-A8GR TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-DA-A1HY 
       78.21        70.62        36.53        15.02        16.90       138.67 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-DA-A95W 
      110.53        60.10        30.44       225.11         8.71         0.76 
TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A182 TCGA-EE-A20C TCGA-EE-A20F 
       52.41        18.21        13.15         0.00        75.55        79.20 
TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29Q TCGA-EE-A29T 
       76.14         0.26        47.41        47.74        61.12       346.49 
TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GE TCGA-EE-A2GK 
      185.19       115.43        30.02        77.98        12.95        10.62 
TCGA-EE-A2GM TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MG TCGA-EE-A2ML TCGA-EE-A2MT 
       18.35         5.75        23.77        94.19       104.78        23.51 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3JH TCGA-ER-A195 TCGA-ER-A19A 
      122.73        64.04        54.51        19.86        34.45         4.54 
TCGA-ER-A19B TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A1A1 TCGA-ER-A2ND 
       53.29       184.60       150.12        99.06        73.05         4.70 
TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A7UA 
       16.87        28.67        74.47         4.50       174.21         5.65 
TCGA-FS-A1YY TCGA-FS-A1ZD TCGA-FS-A1ZJ TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A4F0 
       49.74        32.78        36.33       130.95       136.27        30.90 
TCGA-FS-A4F4 TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GN-A262 
       66.67        11.54        19.30         9.90         1.91        53.29 
TCGA-GN-A265 TCGA-GN-A4U3 TCGA-GN-A4U8 TCGA-W3-A824 TCGA-W3-A828 TCGA-W3-AA1W 
       96.92       120.53        46.92       174.12       120.07       185.13 
TCGA-WE-A8K1 TCGA-WE-A8ZN TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-Z2-AA3S 
       47.54        12.69        48.39         1.94        91.23 

  AMP PEAK  8(6P24.3) MUTATED AMP PEAK  8(6P24.3) WILD-TYPE 
                          0.2                           0.0 
  AMP PEAK  8(6P24.3) MUTATED AMP PEAK  8(6P24.3) WILD-TYPE 
                       312.07                        346.49 
  AMP PEAK  8(6P24.3) MUTATED AMP PEAK  8(6P24.3) WILD-TYPE 
                        45.70                         47.41 
[1] "0.2 - 312.1 (45.7)" "0.0 - 346.5 (47.4)"
[1] "hr=" "1.4"
D8V2, survival
                               sevent
clus2                             0   1
  AMP PEAK  8(6P24.3) MUTATED    83 123
  AMP PEAK  8(6P24.3) WILD-TYPE  83  69
  AMP PEAK  8(6P24.3) MUTATED AMP PEAK  8(6P24.3) WILD-TYPE 
                          206                           152 
  AMP PEAK  8(6P24.3) MUTATED AMP PEAK  8(6P24.3) WILD-TYPE 
                          123                            69 
$`AMP PEAK  8(6P24.3) MUTATED`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A3ML TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A180 
       27.65        62.07        13.87        68.25        54.02        94.98 
TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD TCGA-FR-A729 TCGA-QB-AA9O 
       68.15       168.26         2.60       340.14       220.80        18.05 
TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-3N-A9WC TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q7 
       61.15        21.40        66.48        16.57        16.67       133.25 
TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JB 
       31.59        90.90        95.74        65.49        23.77       168.00 
TCGA-D3-A2JG TCGA-D3-A2JO TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3MR TCGA-D3-A3MU 
      113.52        66.08        58.06        86.93       103.59        39.75 
TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51K TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO 
       45.30       174.84        32.94        26.89       135.75       137.92 
TCGA-D3-A5GU TCGA-D3-A8GD TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GN 
      125.19        23.61       241.38       170.20        89.13       161.00 
TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1X3 
      152.75        29.06       151.53        54.67         3.65        18.12 
TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1I0 
       18.44         9.90        77.56        22.95        76.57        20.38 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F3 
      222.51       176.55        35.93        65.92        68.09        10.49 
TCGA-DA-A95V TCGA-DA-A95X TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5KH 
       72.10        73.94        14.14        13.02        13.87        20.35 
TCGA-EB-A5UL TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A185 
       29.29        27.22         8.65        33.73        26.89         4.96 
TCGA-EE-A20B TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29P 
      133.81        63.35        85.08        13.97        72.07        56.42 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A5 TCGA-EE-A2GB 
       14.47        61.28        25.87        17.92        39.29        59.28 
TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR 
      220.24       107.38        79.66       102.12        13.91        42.77 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MD 
       81.21        44.88        94.82       129.27        28.83        47.28 
TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2MM 
      103.27       268.73       204.66        96.23       180.39       167.90 
TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA 
       47.54       248.65        43.23       162.48        53.26       124.31 
TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 
       28.77        13.81        41.59       172.18       127.20        36.95 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JI TCGA-ER-A197 
       64.08        34.32        53.19       201.80       152.81        13.94 
TCGA-ER-A199 TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19J 
        9.17        48.89        12.59        13.02        26.37         6.44 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T 
       61.05        44.09       162.08        50.89        49.48         8.88 
TCGA-ER-A19W TCGA-ER-A2NC TCGA-ER-A2NF TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
      148.18        43.82        28.83       247.04        93.01        46.98 
TCGA-ER-A3PL TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FS-A1YW 
       33.21        15.72        27.85        34.82        36.26       216.92 
TCGA-FS-A1YX TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZA TCGA-FS-A1ZC 
       48.59       202.65        20.91        28.08        27.72       357.37 
TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP 
       46.45         9.70        32.75        23.93       101.26        74.73 
TCGA-FS-A1ZR TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ 
       11.41        53.16        26.56        49.48        27.09        27.02 
TCGA-FS-A4F2 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3I3 
       50.14        28.73       174.84        34.03        80.68        17.46 
TCGA-FW-A3TU TCGA-GF-A4EO TCGA-GF-A6C9 TCGA-GN-A264 TCGA-GN-A266 TCGA-GN-A267 
       55.59        19.43        15.78       117.93        10.13        64.44 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U4 TCGA-GN-A4U9 TCGA-GN-A8LK 
       62.79        32.48        48.00        39.35        22.13        50.10 
TCGA-GN-A8LL TCGA-GN-A9SD TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 
       21.37        59.41       368.78       297.90         7.23         0.20 
TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A825 TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1V 
        0.33         0.69        63.02        69.07       111.09        42.08 
TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZO TCGA-WE-A8ZQ 
      105.04        24.03        17.95       101.33        70.52        63.22 
TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-XV-AB01 TCGA-YD-A89C 
       11.80        35.80        40.41        24.99        13.25         6.90 
TCGA-YG-AA3O TCGA-YG-AA3P 
       37.94        14.43 

$`AMP PEAK  8(6P24.3) WILD-TYPE`
TCGA-D3-A3C8 TCGA-D3-A8GI TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 
       46.32        58.52       126.81       134.40        27.35        31.40 
TCGA-ER-A198 TCGA-FS-A1ZF TCGA-FW-A3R5 TCGA-3N-A9WB TCGA-3N-A9WD TCGA-BF-AAP0 
       50.76        15.45        36.95        17.03        12.99        14.93 
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q8 TCGA-D3-A2J6 TCGA-D3-A2J7 
      112.04       112.57        71.80        28.08        43.43       103.10 
TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL 
      115.53        86.76        11.87        42.08        12.10       171.58 
TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CE 
       66.48        59.57       130.72        46.98       166.52        60.23 
TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51N 
       24.53         9.34        55.73        56.35       145.12        22.62 
TCGA-D3-A51R TCGA-D3-A5GL TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A8GB TCGA-D3-A8GC 
       63.81       125.79       178.32        18.18        30.84        79.59 
TCGA-D3-A8GE TCGA-D3-A8GM TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D3-A8GV TCGA-D9-A1JX 
       26.43       107.15       129.63       117.17       167.70         7.10 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6EA TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I5 
       15.39        22.29        25.18        36.03       144.89       135.02 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 
       88.87        53.92        40.60        33.93       225.96        43.36 
TCGA-DA-A95W TCGA-EB-A44R TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X 
       37.35        10.36        58.92         7.04        36.46        29.82 
TCGA-EE-A182 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29C TCGA-EE-A29E 
       14.70       151.27        91.56        13.55        78.97        63.78 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W 
       64.64        56.84        18.61        66.74       369.93       195.02 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GC TCGA-EE-A2GE 
       46.82       115.96        59.64        86.14        67.43       173.79 
TCGA-EE-A2GI TCGA-EE-A2GK TCGA-EE-A2GM TCGA-EE-A2M5 TCGA-EE-A2M8 TCGA-EE-A2MC 
       48.72        54.74        75.48        21.67        19.76        61.51 
TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2ML TCGA-EE-A2MT TCGA-EE-A3AB TCGA-EE-A3AC 
      103.20        16.96       216.66        71.21       122.73        64.04 
TCGA-EE-A3AE TCGA-EE-A3AH TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A195 TCGA-ER-A19A 
       54.51       138.81        51.35       134.33        35.44        77.75 
TCGA-ER-A19B TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A1A1 TCGA-ER-A2ND 
       98.40       302.07       152.35       131.51       105.07        23.34 
TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A3YN 
       20.15        48.99        41.56        12.95       149.03        92.98 
TCGA-FR-A44A TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YE TCGA-FS-A1YY TCGA-FS-A1Z7 
      174.21        18.77        38.27       104.42       228.59         7.79 
TCGA-FS-A1ZB TCGA-FS-A1ZD TCGA-FS-A1ZJ TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A4F0 
       48.85        53.52        47.38       133.55       148.80        77.82 
TCGA-FS-A4F4 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
       66.67        26.73        54.41        13.51        19.30         9.90 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A4U3 TCGA-GN-A4U7 TCGA-GN-A4U8 
        2.04       139.89        96.92       121.91        10.42        48.89 
TCGA-HR-A2OG TCGA-HR-A2OH TCGA-W3-A824 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1W 
        0.23        65.88       228.16       121.08         4.01       219.16 
TCGA-WE-A8K1 TCGA-WE-A8ZN TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-YD-A9TA TCGA-Z2-A8RT 
       49.05        58.98        49.51        12.16        49.18        27.58 
TCGA-Z2-AA3S TCGA-Z2-AA3V 
       96.99        15.98 

  AMP PEAK  8(6P24.3) MUTATED AMP PEAK  8(6P24.3) WILD-TYPE 
                         0.20                          0.23 
  AMP PEAK  8(6P24.3) MUTATED AMP PEAK  8(6P24.3) WILD-TYPE 
                       368.78                        369.93 
  AMP PEAK  8(6P24.3) MUTATED AMP PEAK  8(6P24.3) WILD-TYPE 
                       48.295                        56.595 
[1] "0.2 - 368.8 (48.3)" "0.2 - 369.9 (56.6)"
[1] "hr=" "1.4"
D8V3, continuous
                               vv
clus                            I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB
  AMP PEAK  8(6P24.3) MUTATED          4       3      17        8       19
  AMP PEAK  8(6P24.3) WILD-TYPE        9       4      12       10        9
                               vv
clus                            STAGE II STAGE IIA STAGE IIB STAGE IIC
  AMP PEAK  8(6P24.3) MUTATED         17         8         9        11
  AMP PEAK  8(6P24.3) WILD-TYPE        9         6        10         4
                               vv
clus                            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  AMP PEAK  8(6P24.3) MUTATED          20         13         22         27
  AMP PEAK  8(6P24.3) WILD-TYPE        19          2         13         27
                               vv
clus                            STAGE IV
  AMP PEAK  8(6P24.3) MUTATED         12
  AMP PEAK  8(6P24.3) WILD-TYPE        9
D8V4, multiclass
            clus
vv           AMP PEAK  8(6P24.3) MUTATED AMP PEAK  8(6P24.3) WILD-TYPE
  I/II NOS                             4                             9
  STAGE 0                              3                             4
  STAGE I                             17                            12
  STAGE IA                             8                            10
  STAGE IB                            19                             9
  STAGE II                            17                             9
  STAGE IIA                            8                             6
  STAGE IIB                            9                            10
  STAGE IIC                           11                             4
  STAGE III                           20                            19
  STAGE IIIA                          13                             2
  STAGE IIIB                          22                            13
  STAGE IIIC                          27                            27
  STAGE IV                            12                             9
[1] 14  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3 T4
  AMP PEAK  8(6P24.3) MUTATED      31 43 45 47
  AMP PEAK  8(6P24.3) WILD-TYPE    33 30 36 20
D8V5, multiclass
       clus
vv      AMP PEAK  8(6P24.3) MUTATED AMP PEAK  8(6P24.3) WILD-TYPE
  T0+T1                          31                            33
  T2                             43                            30
  T3                             45                            36
  T4                             47                            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  N3
  AMP PEAK  8(6P24.3) MUTATED   100  37  24  25
  AMP PEAK  8(6P24.3) WILD-TYPE  77  28  15  20
D8V6, multiclass
    clus
vv   AMP PEAK  8(6P24.3) MUTATED AMP PEAK  8(6P24.3) WILD-TYPE
  N0                         100                            77
  N1                          37                            28
  N2                          24                            15
  N3                          25                            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"
D8V7, binary
                               cls
clus                              0   1
  AMP PEAK  8(6P24.3) MUTATED   179  13
  AMP PEAK  8(6P24.3) WILD-TYPE 140   9
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(6P24.3) MUTATED    179   13
  AMP PEAK  8(6P24.3) WILD-TYPE  140    9
   clus
vv  AMP PEAK  8(6P24.3) MUTATED AMP PEAK  8(6P24.3) WILD-TYPE
  0                         179                           140
  1                          13                             9
[1] 2 2
[1] FALSE
D8V8, binary
                               cls
clus                             0  1
  AMP PEAK  8(6P24.3) MUTATED   75 56
  AMP PEAK  8(6P24.3) WILD-TYPE 59 34
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(6P24.3) MUTATED     75   56
  AMP PEAK  8(6P24.3) WILD-TYPE   59   34
     clus
vv    AMP PEAK  8(6P24.3) MUTATED AMP PEAK  8(6P24.3) WILD-TYPE
  NO                           75                            59
  YES                          56                            34
[1] 2 2
[1] FALSE
D8V9, binary
                               cls
clus                              0   1
  AMP PEAK  8(6P24.3) MUTATED    28 183
  AMP PEAK  8(6P24.3) WILD-TYPE  19 137
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(6P24.3) MUTATED     28  183
  AMP PEAK  8(6P24.3) WILD-TYPE   19  137
     clus
vv    AMP PEAK  8(6P24.3) MUTATED AMP PEAK  8(6P24.3) WILD-TYPE
  NO                           28                            19
  YES                         183                           137
[1] 2 2
[1] FALSE
D8V10, continuous
D8V11, binary
                               cls
clus                              0   1
  AMP PEAK  8(6P24.3) MUTATED    83 128
  AMP PEAK  8(6P24.3) WILD-TYPE  55 101
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(6P24.3) MUTATED     83  128
  AMP PEAK  8(6P24.3) WILD-TYPE   55  101
        clus
vv       AMP PEAK  8(6P24.3) MUTATED AMP PEAK  8(6P24.3) WILD-TYPE
  FEMALE                          83                            55
  MALE                           128                           101
[1] 2 2
[1] FALSE
D8V12, binary
                               cls
clus                              0   1
  AMP PEAK  8(6P24.3) MUTATED   188  22
  AMP PEAK  8(6P24.3) WILD-TYPE 131  25
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(6P24.3) MUTATED    188   22
  AMP PEAK  8(6P24.3) WILD-TYPE  131   25
     clus
vv    AMP PEAK  8(6P24.3) MUTATED AMP PEAK  8(6P24.3) WILD-TYPE
  NO                          188                           131
  YES                          22                            25
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  8(6P24.3) MUTATED       3                         1   202
  AMP PEAK  8(6P24.3) WILD-TYPE     2                         0   151
D8V13, multiclass
                           clus
vv                          AMP PEAK  8(6P24.3) MUTATED
  ASIAN                                               3
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                             202
                           clus
vv                          AMP PEAK  8(6P24.3) WILD-TYPE
  ASIAN                                                 2
  BLACK OR AFRICAN AMERICAN                             0
  WHITE                                               151
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V14, binary
                               cls
clus                              0   1
  AMP PEAK  8(6P24.3) MUTATED     4 204
  AMP PEAK  8(6P24.3) WILD-TYPE   3 148
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(6P24.3) MUTATED      4  204
  AMP PEAK  8(6P24.3) WILD-TYPE    3  148
                        clus
vv                       AMP PEAK  8(6P24.3) MUTATED
  HISPANIC OR LATINO                               4
  NOT HISPANIC OR LATINO                         204
                        clus
vv                       AMP PEAK  8(6P24.3) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           148
[1] 2 2
[1] FALSE

Clustering(9) Variable = AMP PEAK  9(6Q12) MUTATION ANALYSIS
D9V1, survival
                             sevent
clus2                           0   1
  AMP PEAK  9(6Q12) MUTATED    26  33
  AMP PEAK  9(6Q12) WILD-TYPE 102  91
  AMP PEAK  9(6Q12) MUTATED AMP PEAK  9(6Q12) WILD-TYPE 
                         59                         193 
  AMP PEAK  9(6Q12) MUTATED AMP PEAK  9(6Q12) WILD-TYPE 
                         33                          91 
$`AMP PEAK  9(6Q12) MUTATED`
TCGA-D3-A2JF TCGA-D3-A1Q3 TCGA-D3-A1Q7 TCGA-D3-A2J8 TCGA-D3-A3CC TCGA-D3-A3MU 
       62.07        15.72       133.25        62.86        40.01        23.67 
TCGA-D3-A51E TCGA-D3-A5GU TCGA-D9-A1X3 TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1I1 
      173.85       124.08        10.78        69.21        76.34        68.68 
TCGA-DA-A95V TCGA-DA-A95X TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17Y TCGA-EE-A181 
       72.10        65.03        52.41        18.21        24.89        20.38 
TCGA-EE-A183 TCGA-EE-A2GB TCGA-EE-A2GN TCGA-EE-A2MI TCGA-EE-A2MS TCGA-EE-A2MT 
       26.24        26.14        93.63       171.85       143.93        23.51 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AD TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-EE-A3J8 
       53.26       124.31         4.41        67.89        45.90         3.35 
TCGA-ER-A199 TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P 
        7.82        39.81        11.47        59.84        42.51       120.76 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A3ET 
       49.71        47.18        22.36        16.87        10.19        68.52 
TCGA-ER-A3EV TCGA-FS-A1Z0 TCGA-FS-A1ZM TCGA-FS-A1ZW TCGA-FS-A4F8 TCGA-FW-A3TU 
       15.48       195.98        78.61        23.21       173.19        55.59 
TCGA-GF-A4EO TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A8LK TCGA-GN-A9SD TCGA-W3-AA1Q 
       18.25        17.06        42.48        43.23        59.41        44.05 
TCGA-W3-AA1R TCGA-W3-AA1V TCGA-W3-AA21 TCGA-WE-A8ZQ TCGA-XV-AB01 
       79.99         8.09        92.84        62.89         6.61 

$`AMP PEAK  9(6Q12) WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A3C8 TCGA-D3-A8GI TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A20H 
        9.76        38.76        13.41        33.24        31.96       166.75 
TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-FR-A729 
      269.03        52.90       134.40        27.35        19.04       216.43 
TCGA-FW-A3R5 TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 
       36.95        52.73         7.40        60.46        12.99        14.83 
TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q8 TCGA-D3-A1QA 
        8.42        31.89       110.93        49.35        19.04        76.41 
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC 
       62.60        25.64        45.99        15.75       168.00        86.30 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP 
      107.61        36.30       171.58        64.83        66.08        43.53 
TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR 
       58.06       140.98        59.70        24.53         9.34        90.21 
TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL 
       30.67       144.46        31.76        62.70        11.34        42.05 
TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GJ TCGA-D3-A8GK 
       45.70       177.86        78.21        23.61       179.97       120.00 
TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GP TCGA-D3-A8GR TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       69.53        70.62       135.12        36.53        15.02        16.90 
TCGA-D9-A4Z6 TCGA-D9-A6EG TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 
       18.44        22.85       138.67       150.61       110.53        60.10 
TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-DA-A95W 
       64.83        58.85        30.44       225.11         8.71         0.76 
TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EE-A17X TCGA-EE-A182 
       14.14        12.30         3.91        16.41        13.15         0.00 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
       75.55        79.20        75.22        76.14        12.99         0.26 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T 
       44.28        47.41        47.74        27.16        61.12       346.49 
TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GE TCGA-EE-A2GH 
      185.19       115.43        30.02        77.98        12.95       201.60 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GP TCGA-EE-A2GR 
       68.65        10.62        32.48        18.35         0.76         0.20 
TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
       71.31        81.99       103.13        15.25         5.75        23.77 
TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
      209.79        94.19        63.25        89.26       104.78       145.45 
TCGA-EE-A2MP TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J4 
      227.01       122.73        64.04        54.51         6.28       111.85 
TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A19A 
      168.85        19.86       135.98        34.45        10.49         4.54 
TCGA-ER-A19B TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19W TCGA-ER-A1A1 
       53.29       184.60       150.12        99.06       146.63        73.05 
TCGA-ER-A2ND TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A3YN 
        4.70        28.67       173.29        32.05        74.47         4.50 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FS-A1YW 
      174.21         4.14        26.20         5.65        10.06       171.78 
TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE 
       49.74         8.35        27.62       312.07        32.78        43.92 
TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU 
        7.82        36.33       130.95       136.27        35.28         4.47 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F9 TCGA-FS-A4FD 
        5.29         3.06        30.90        66.67        13.28        80.68 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 
       11.54        19.30         9.90         1.91        53.29       117.93 
TCGA-GN-A265 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-LH-A9QB 
       96.92         7.59       120.53        34.49        46.92        85.05 
TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A825 
      297.01         7.23         0.20         0.33       174.12         1.97 
TCGA-W3-A828 TCGA-W3-AA1W TCGA-WE-A8K1 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO 
      120.07       185.13        47.54        65.42        12.69        21.90 
TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-YG-AA3O 
       10.95        48.39         1.94        37.32        24.99        28.21 
TCGA-Z2-AA3S 
       91.23 

  AMP PEAK  9(6Q12) MUTATED AMP PEAK  9(6Q12) WILD-TYPE 
                       3.35                        0.00 
  AMP PEAK  9(6Q12) MUTATED AMP PEAK  9(6Q12) WILD-TYPE 
                     195.98                      346.49 
  AMP PEAK  9(6Q12) MUTATED AMP PEAK  9(6Q12) WILD-TYPE 
                      47.18                       45.99 
[1] "3.4 - 196.0 (47.2)" "0.0 - 346.5 (46.0)"
[1] "hr=" "1.4"
D9V2, survival
                             sevent
clus2                           0   1
  AMP PEAK  9(6Q12) MUTATED    36  43
  AMP PEAK  9(6Q12) WILD-TYPE 130 149
  AMP PEAK  9(6Q12) MUTATED AMP PEAK  9(6Q12) WILD-TYPE 
                         79                         279 
  AMP PEAK  9(6Q12) MUTATED AMP PEAK  9(6Q12) WILD-TYPE 
                         43                         149 
$`AMP PEAK  9(6Q12) MUTATED`
TCGA-D3-A2JF TCGA-EE-A184 TCGA-D3-A1Q3 TCGA-D3-A1Q7 TCGA-D3-A2J8 TCGA-D3-A2J9 
       62.07        68.15        16.67       133.25        65.49        23.77 
TCGA-D3-A3CC TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A5GO TCGA-D3-A5GU TCGA-D9-A149 
       86.93        39.75       174.84       137.92       125.19        54.67 
TCGA-D9-A1JW TCGA-D9-A1X3 TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1I1 
        3.65        18.12         9.90        77.56        76.57       222.51 
TCGA-DA-A95V TCGA-DA-A95X TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17Y TCGA-EE-A181 
       72.10        73.94        58.92        36.46        27.22        33.73 
TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A2GB TCGA-EE-A2GN TCGA-EE-A2GT TCGA-EE-A2ME 
       26.89       133.81        59.28       102.12        44.88       103.27 
TCGA-EE-A2MI TCGA-EE-A2MN TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA 
      204.66        47.54       162.48        71.21        53.26       124.31 
TCGA-EE-A3AD TCGA-EE-A3J3 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA 
       28.77       172.18        36.95        64.08        34.32        53.19 
TCGA-ER-A199 TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P 
        9.17        48.89        12.59        61.05        44.09       162.08 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A3ET 
       50.89        49.48        43.82        20.15        28.83        93.01 
TCGA-ER-A3EV TCGA-FR-A8YD TCGA-FS-A1Z0 TCGA-FS-A1ZA TCGA-FS-A1ZM TCGA-FS-A1ZW 
       46.98        36.26       202.65        27.72       101.26        49.48 
TCGA-FS-A4F8 TCGA-FW-A3TU TCGA-GF-A4EO TCGA-GF-A6C9 TCGA-GN-A266 TCGA-GN-A267 
      174.84        55.59        19.43        15.78        10.13        64.44 
TCGA-GN-A268 TCGA-GN-A8LK TCGA-GN-A8LL TCGA-GN-A9SD TCGA-W3-AA1Q TCGA-W3-AA1R 
       62.79        50.10        21.37        59.41        69.07       111.09 
TCGA-W3-AA1V TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8ZQ TCGA-WE-A8ZX TCGA-XV-AB01 
       42.08       105.04        24.03        63.22        35.80        13.25 
TCGA-YG-AA3P 
       14.43 

$`AMP PEAK  9(6Q12) WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-D3-A8GI TCGA-EB-A5SG TCGA-EB-A5SH 
       27.65        46.32        13.87        58.52        68.25        54.02 
TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR 
       94.98       168.26         2.60       340.14       126.81       134.40 
TCGA-EE-A3JD TCGA-ER-A193 TCGA-ER-A198 TCGA-FR-A729 TCGA-FS-A1ZF TCGA-FW-A3R5 
       27.35        31.40        50.76       220.80        15.45        36.95 
TCGA-QB-AA9O TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD 
       18.05        61.15        21.40        17.03        66.48        12.99 
TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q8 
       14.93        16.57       112.04       112.57        71.80        28.08 
TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2JA 
       31.59        90.90        95.74        43.43       103.10       115.53 
TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK 
      168.00        86.76        11.87       113.52        42.08        12.10 
TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 
      171.58        66.48        66.08        59.57       130.72        58.06 
TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR 
       46.98       166.52        60.23        24.53         9.34       103.59 
TCGA-D3-A3MV TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
       45.30        55.73        56.35       145.12        32.94        22.62 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS 
       63.81        26.89       125.79       135.75       178.32        18.18 
TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GK 
       30.84        79.59        23.61        26.43       241.38       170.20 
TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR 
       89.13       107.15       161.00       152.75        29.06       129.63 
TCGA-D3-A8GS TCGA-D3-A8GV TCGA-D9-A148 TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 
      117.17       167.70       151.53         7.10        15.39        22.29 
TCGA-D9-A4Z6 TCGA-D9-A6EA TCGA-D9-A6EG TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 
       18.44        25.18        22.95        36.03       144.89        20.38 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA 
      176.55        35.93       135.02        88.87        53.92        65.92 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 
       40.60        68.09        33.93        10.49       225.96        43.36 
TCGA-DA-A95W TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH 
       37.35        14.14        13.02        13.87        10.36        20.35 
TCGA-EB-A5UL TCGA-EB-A5VV TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A182 TCGA-EE-A185 
       29.29         7.04        29.82         8.65        14.70         4.96 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C 
      151.27        91.56        13.55        63.35        85.08        78.97 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N 
       13.97        63.78        72.07        64.64        56.84        18.61 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V 
       56.42        66.74        14.47        61.28       369.93        25.87 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 
      195.02        17.92        46.82       115.96        59.64        39.29 
TCGA-EE-A2A6 TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       86.14        67.43       173.79       220.24        48.72       107.38 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
       54.74        79.66        75.48        13.91        42.77        81.21 
TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
       94.82        21.67       129.27        28.83        19.76        61.51 
TCGA-EE-A2MD TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MJ TCGA-EE-A2MK 
       47.28       268.73       103.20        16.96        96.23       180.39 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A3AB TCGA-EE-A3AC 
      216.66       167.90       248.65        43.23       122.73        64.04 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3JB 
       54.51        13.81        41.59       138.81       127.20       201.80 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A19A 
       51.35       134.33       152.81        35.44        13.94        77.75 
TCGA-ER-A19B TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J 
       98.40        13.02        26.37       302.07       152.35         6.44 
TCGA-ER-A19L TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2ND TCGA-ER-A2NG 
      131.51         8.88       148.18       105.07        23.34        48.99 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3PL TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A3YN 
       41.56       247.04        33.21        12.95       149.03        92.98 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC 
      174.21        15.72        27.85        18.77        38.27        34.82 
TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1Z4 
      104.42       216.92        48.59       228.59        20.91        28.08 
TCGA-FS-A1Z7 TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG 
        7.79        48.85       357.37        53.52        46.45         9.70 
TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR 
       32.75        47.38        23.93        74.73       133.55        11.41 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 
      148.80        53.16        26.56        27.09        27.02        77.82 
TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC 
       50.14        66.67        28.73        34.03        26.73        54.41 
TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 
       80.68        17.46        13.51        19.30         9.90         2.04 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U3 
      139.89       117.93        96.92        32.48        48.00       121.91 
TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-HR-A2OG TCGA-HR-A2OH 
       39.35        10.42        48.89        22.13         0.23        65.88 
TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 TCGA-RP-A694 
      368.78       297.90         7.23         0.20         0.33         0.69 
TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1W TCGA-WE-A8K1 
      228.16        63.02       121.08         4.01       219.16        49.05 
TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-A8ZY 
       17.95       101.33        58.98        70.52        11.80        49.51 
TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-YD-A89C TCGA-YD-A9TA TCGA-YG-AA3O 
       12.16        40.41        24.99         6.90        49.18        37.94 
TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       27.58        96.99        15.98 

  AMP PEAK  9(6Q12) MUTATED AMP PEAK  9(6Q12) WILD-TYPE 
                       3.65                        0.20 
  AMP PEAK  9(6Q12) MUTATED AMP PEAK  9(6Q12) WILD-TYPE 
                     222.51                      369.93 
  AMP PEAK  9(6Q12) MUTATED AMP PEAK  9(6Q12) WILD-TYPE 
                      53.26                       50.76 
[1] "3.6 - 222.5 (53.3)" "0.2 - 369.9 (50.8)"
[1] "hr=" "1.1"
D9V3, continuous
                             vv
clus                          I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB
  AMP PEAK  9(6Q12) MUTATED          1       3       6        4       12
  AMP PEAK  9(6Q12) WILD-TYPE       12       4      23       14       16
                             vv
clus                          STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  AMP PEAK  9(6Q12) MUTATED          7         3         3         6         7
  AMP PEAK  9(6Q12) WILD-TYPE       19        11        16         9        32
                             vv
clus                          STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  AMP PEAK  9(6Q12) MUTATED            6          9          4        0
  AMP PEAK  9(6Q12) WILD-TYPE          9         26         50       21
D9V4, multiclass
            clus
vv           AMP PEAK  9(6Q12) MUTATED AMP PEAK  9(6Q12) WILD-TYPE
  I/II NOS                           1                          12
  STAGE 0                            3                           4
  STAGE I                            6                          23
  STAGE IA                           4                          14
  STAGE IB                          12                          16
  STAGE II                           7                          19
  STAGE IIA                          3                          11
  STAGE IIB                          3                          16
  STAGE IIC                          6                           9
  STAGE III                          7                          32
  STAGE IIIA                         6                           9
  STAGE IIIB                         9                          26
  STAGE IIIC                         4                          50
  STAGE IV                           0                          21
[1] 14  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          T0+T1 T2 T3 T4
  AMP PEAK  9(6Q12) MUTATED      14 19 14 19
  AMP PEAK  9(6Q12) WILD-TYPE    50 54 67 48
D9V5, multiclass
       clus
vv      AMP PEAK  9(6Q12) MUTATED AMP PEAK  9(6Q12) WILD-TYPE
  T0+T1                        14                          50
  T2                           19                          54
  T3                           14                          67
  T4                           19                          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  N3
  AMP PEAK  9(6Q12) MUTATED    42  14   8   5
  AMP PEAK  9(6Q12) WILD-TYPE 135  51  31  40
D9V6, multiclass
    clus
vv   AMP PEAK  9(6Q12) MUTATED AMP PEAK  9(6Q12) WILD-TYPE
  N0                        42                         135
  N1                        14                          51
  N2                         8                          31
  N3                         5                          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"
D9V7, binary
                             cls
clus                            0   1
  AMP PEAK  9(6Q12) MUTATED    72   0
  AMP PEAK  9(6Q12) WILD-TYPE 247  22
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  9(6Q12) MUTATED     72    0
  AMP PEAK  9(6Q12) WILD-TYPE  247   22
   clus
vv  AMP PEAK  9(6Q12) MUTATED AMP PEAK  9(6Q12) WILD-TYPE
  0                        72                         247
  1                         0                          22
[1] 2 2
[1] FALSE
D9V8, binary
                             cls
clus                           0  1
  AMP PEAK  9(6Q12) MUTATED   35 18
  AMP PEAK  9(6Q12) WILD-TYPE 99 72
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  9(6Q12) MUTATED     35   18
  AMP PEAK  9(6Q12) WILD-TYPE   99   72
     clus
vv    AMP PEAK  9(6Q12) MUTATED AMP PEAK  9(6Q12) WILD-TYPE
  NO                         35                          99
  YES                        18                          72
[1] 2 2
[1] FALSE
D9V9, binary
                             cls
clus                            0   1
  AMP PEAK  9(6Q12) MUTATED    11  70
  AMP PEAK  9(6Q12) WILD-TYPE  36 250
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  9(6Q12) MUTATED     11   70
  AMP PEAK  9(6Q12) WILD-TYPE   36  250
     clus
vv    AMP PEAK  9(6Q12) MUTATED AMP PEAK  9(6Q12) WILD-TYPE
  NO                         11                          36
  YES                        70                         250
[1] 2 2
[1] FALSE
D9V10, continuous
D9V11, binary
                             cls
clus                            0   1
  AMP PEAK  9(6Q12) MUTATED    26  55
  AMP PEAK  9(6Q12) WILD-TYPE 112 174
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  9(6Q12) MUTATED     26   55
  AMP PEAK  9(6Q12) WILD-TYPE  112  174
        clus
vv       AMP PEAK  9(6Q12) MUTATED AMP PEAK  9(6Q12) WILD-TYPE
  FEMALE                        26                         112
  MALE                          55                         174
[1] 2 2
[1] FALSE
D9V12, binary
                             cls
clus                            0   1
  AMP PEAK  9(6Q12) MUTATED    70  11
  AMP PEAK  9(6Q12) WILD-TYPE 249  36
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  9(6Q12) MUTATED     70   11
  AMP PEAK  9(6Q12) WILD-TYPE  249   36
     clus
vv    AMP PEAK  9(6Q12) MUTATED AMP PEAK  9(6Q12) WILD-TYPE
  NO                         70                         249
  YES                        11                          36
[1] 2 2
[1] FALSE
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  9(6Q12) MUTATED       2                         0    76
  AMP PEAK  9(6Q12) WILD-TYPE     3                         1   277
D9V13, multiclass
                           clus
vv                          AMP PEAK  9(6Q12) MUTATED
  ASIAN                                             2
  BLACK OR AFRICAN AMERICAN                         0
  WHITE                                            76
                           clus
vv                          AMP PEAK  9(6Q12) WILD-TYPE
  ASIAN                                               3
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                             277
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V14, binary
                             cls
clus                            0   1
  AMP PEAK  9(6Q12) MUTATED     1  78
  AMP PEAK  9(6Q12) WILD-TYPE   6 274
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  9(6Q12) MUTATED      1   78
  AMP PEAK  9(6Q12) WILD-TYPE    6  274
                        clus
vv                       AMP PEAK  9(6Q12) MUTATED AMP PEAK  9(6Q12) WILD-TYPE
  HISPANIC OR LATINO                             1                           6
  NOT HISPANIC OR LATINO                        78                         274
[1] 2 2
[1] FALSE

Clustering(10) Variable = AMP PEAK 10(7P22.1) MUTATION ANALYSIS
D10V1, survival
                               sevent
clus2                            0  1
  AMP PEAK 10(7P22.1) MUTATED   78 62
  AMP PEAK 10(7P22.1) WILD-TYPE 50 62
  AMP PEAK 10(7P22.1) MUTATED AMP PEAK 10(7P22.1) WILD-TYPE 
                          140                           112 
  AMP PEAK 10(7P22.1) MUTATED AMP PEAK 10(7P22.1) WILD-TYPE 
                           62                            62 
$`AMP PEAK 10(7P22.1) MUTATED`
TCGA-D3-A2JE TCGA-D3-A3C8 TCGA-D3-A8GI TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GO 
        9.76        38.76        13.41        31.96       166.75        52.90 
TCGA-EE-A2MR TCGA-FR-A729 TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-3N-A9WC TCGA-BF-AAP0 
      134.40       216.43        52.73         7.40        60.46        14.83 
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A2JA 
        8.42        15.72        31.89       110.93        49.35        15.75 
TCGA-D3-A2JC TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3CB TCGA-D3-A3CC 
       86.30       171.58        64.83        43.53       140.98        40.01 
TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51J TCGA-D3-A51R TCGA-D3-A5GN 
        9.34        90.21        23.67       144.46        62.70        45.70 
TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GK TCGA-D3-A8GP 
      177.86       124.08        78.21        23.61       120.00       135.12 
TCGA-D9-A3Z3 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I2 
       16.90        69.21        22.85        76.34       138.67       150.61 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F5 TCGA-DA-A95V 
      110.53        60.10        64.83        58.85       225.11        72.10 
TCGA-DA-A95W TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A6L9 
        0.76        12.30         3.91        16.41        52.41        18.21 
TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29P 
       24.89        20.38        76.14        12.99         0.26        27.16 
TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE 
       61.12       346.49       185.19        77.98        26.14        12.95 
TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP 
      201.60        68.65        32.48        18.35        93.63         0.76 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MP 
      103.13        15.25        63.25        89.26       145.45       227.01 
TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE 
      143.93        53.26       124.31       122.73         4.41        54.51 
TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3JB TCGA-ER-A199 
        6.28        67.89       111.85        45.90       168.85         7.82 
TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19M TCGA-ER-A19P 
       53.29        39.81       184.60       150.12        59.84       120.76 
TCGA-ER-A19S TCGA-ER-A2ND TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A3YN 
       47.18         4.70        15.48        32.05        74.47         4.50 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FS-A1YW 
      174.21         4.14        26.20         5.65        10.06       171.78 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZM 
        8.35        27.62       312.07        32.78        43.92        78.61 
TCGA-FS-A1ZQ TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F8 TCGA-FW-A5DY TCGA-GF-A4EO 
      130.95         5.29         3.06       173.19        19.30        18.25 
TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U8 
      117.93        17.06        42.48         7.59       120.53        46.92 
TCGA-GN-A8LK TCGA-GN-A9SD TCGA-QB-A6FS TCGA-RP-A690 TCGA-W3-AA1R TCGA-W3-AA1V 
       43.23        59.41         7.23         0.20        79.99         8.09 
TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8ZM TCGA-WE-A8ZQ TCGA-WE-AA9Y 
      185.13        92.84        47.54        65.42        62.89         1.94 
TCGA-XV-AB01 TCGA-YG-AA3O 
        6.61        28.21 

$`AMP PEAK 10(7P22.1) WILD-TYPE`
TCGA-D3-A2JF TCGA-EB-A5SG TCGA-EE-A2GD TCGA-EE-A3JD TCGA-ER-A193 TCGA-FW-A3R5 
       62.07        33.24       269.03        27.35        19.04        36.95 
TCGA-3N-A9WD TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 
       12.99       133.25        19.04        76.41        62.60        25.64 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JB TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JO 
       45.99        62.86       168.00       107.61        36.30        66.08 
TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51K 
       58.06        59.70        24.53       173.85        30.67        31.76 
TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A8GJ TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GR 
       11.34        42.05       179.97        69.53        70.62        36.53 
TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A4Z6 TCGA-DA-A1I1 TCGA-DA-A3F2 TCGA-DA-A3F8 
       10.78        15.02        18.44        68.68        30.44         8.71 
TCGA-DA-A95X TCGA-DA-A95Y TCGA-EE-A17X TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20C 
       65.03        14.14        13.15         0.00        26.24        75.55 
TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A2A1 
       79.20        75.22        44.28        47.41        47.74       115.43 
TCGA-EE-A2A2 TCGA-EE-A2GK TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M8 
       30.02        10.62         0.20        71.31        81.99         5.75 
TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2ML TCGA-EE-A2MT 
       23.77       209.79        94.19       171.85       104.78        23.51 
TCGA-EE-A3AC TCGA-EE-A3J8 TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 
       64.04         3.35        19.86       135.98        34.45        10.49 
TCGA-ER-A19A TCGA-ER-A19D TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A19W 
        4.54        11.47        99.06        42.51        49.71       146.63 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES 
       73.05        22.36        16.87        10.19        28.67       173.29 
TCGA-ER-A3ET TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZS 
       68.52        49.74       195.98         7.82        36.33       136.27 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F9 
       35.28         4.47        23.21        30.90        66.67        13.28 
TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GN-A262 
       80.68        55.59        11.54         9.90         1.91        53.29 
TCGA-GN-A265 TCGA-GN-A4U4 TCGA-LH-A9QB TCGA-OD-A75X TCGA-RP-A693 TCGA-W3-A824 
       96.92        34.49        85.05       297.01         0.33       174.12 
TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1Q TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT 
        1.97       120.07        44.05        12.69        21.90        10.95 
TCGA-WE-A8ZY TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-Z2-AA3S 
       48.39        37.32        24.99        91.23 

  AMP PEAK 10(7P22.1) MUTATED AMP PEAK 10(7P22.1) WILD-TYPE 
                          0.2                           0.0 
  AMP PEAK 10(7P22.1) MUTATED AMP PEAK 10(7P22.1) WILD-TYPE 
                       346.49                        297.01 
  AMP PEAK 10(7P22.1) MUTATED AMP PEAK 10(7P22.1) WILD-TYPE 
                       52.570                        39.685 
[1] "0.2 - 346.5 (52.6)" "0.0 - 297.0 (39.7)"
[1] "hr=" "1.4"
D10V2, survival
                               sevent
clus2                             0   1
  AMP PEAK 10(7P22.1) MUTATED   101 104
  AMP PEAK 10(7P22.1) WILD-TYPE  65  88
  AMP PEAK 10(7P22.1) MUTATED AMP PEAK 10(7P22.1) WILD-TYPE 
                          205                           153 
  AMP PEAK 10(7P22.1) MUTATED AMP PEAK 10(7P22.1) WILD-TYPE 
                          104                            88 
$`AMP PEAK 10(7P22.1) MUTATED`
TCGA-D3-A2JE TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-D3-A8GI TCGA-EE-A180 TCGA-EE-A20H 
       27.65        46.32        13.87        58.52        94.98       168.26 
TCGA-EE-A29L TCGA-EE-A2GO TCGA-EE-A2MR TCGA-FR-A729 TCGA-QB-AA9O TCGA-WE-A8K5 
        2.60       126.81       134.40       220.80        18.05        61.15 
TCGA-WE-AAA3 TCGA-3N-A9WB TCGA-3N-A9WC TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 
       21.40        17.03        66.48        14.93        16.57        16.67 
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JA 
      112.04       112.57        71.80        31.59        23.77       115.53 
TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3BZ 
       86.76        11.87       171.58        66.48        59.57       130.72 
TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU 
       46.98       166.52        86.93         9.34       103.59        39.75 
TCGA-D3-A51J TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS 
      145.12        22.62        63.81       135.75       178.32        18.18 
TCGA-D3-A5GU TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GK TCGA-D3-A8GN TCGA-D3-A8GP 
      125.19        79.59        23.61       170.20       161.00       152.75 
TCGA-D3-A8GQ TCGA-D3-A8GV TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JX TCGA-D9-A3Z3 
       29.06       167.70       151.53        54.67         7.10        22.29 
TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW 
        9.90        25.18        77.56        22.95        76.57        36.03 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 
      144.89        20.38       176.55        35.93       135.02        88.87 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F5 TCGA-DA-A95V TCGA-DA-A95W 
       53.92        65.92        68.09       225.96        72.10        37.35 
TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5UL TCGA-EB-A5UN 
       13.02        13.87        10.36        20.35        29.29        58.92 
TCGA-EB-A6L9 TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A20B TCGA-EE-A29A 
       36.46        27.22         8.65        33.73       133.81        63.35 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
       78.97        13.97        63.78        18.61        56.42        66.74 
TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A0 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE 
      369.93       195.02        46.82        86.14        59.28       173.79 
TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
      220.24        48.72       107.38        79.66        75.48       102.12 
TCGA-EE-A2GP TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MJ TCGA-EE-A2MK 
       13.91        21.67       129.27        28.83        96.23       180.39 
TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A2MU 
      167.90        47.54       248.65        43.23       162.48        53.26 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG 
      124.31       122.73        28.77        54.51        13.81        41.59 
TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3JB TCGA-ER-A199 
      138.81       172.18       127.20        64.08       201.80         9.17 
TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19E TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J 
       98.40        48.89        13.02       302.07       152.35         6.44 
TCGA-ER-A19M TCGA-ER-A19P TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A2ND TCGA-ER-A3EV 
       61.05       162.08        49.48         8.88        23.34        46.98 
TCGA-ER-A3PL TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       33.21        12.95       149.03        92.98       174.21        15.72 
TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE 
       27.85        18.77        38.27        34.82        36.26       104.42 
TCGA-FS-A1YW TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZC TCGA-FS-A1ZD 
      216.92        20.91        28.08         7.79       357.37        53.52 
TCGA-FS-A1ZE TCGA-FS-A1ZH TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZR 
       46.45        32.75        23.93       101.26       133.55        11.41 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F2 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FW-A3I3 
       27.09        27.02        50.14        28.73       174.84        17.46 
TCGA-FW-A5DY TCGA-GF-A4EO TCGA-GF-A6C9 TCGA-GN-A264 TCGA-GN-A266 TCGA-GN-A267 
       19.30        19.43        15.78       117.93        10.13        64.44 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U7 TCGA-GN-A4U8 
       62.79        32.48        48.00       121.91        10.42        48.89 
TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OG TCGA-HR-A2OH 
       22.13        50.10        21.37        59.41         0.23        65.88 
TCGA-QB-A6FS TCGA-RP-A690 TCGA-W3-AA1O TCGA-W3-AA1R TCGA-W3-AA1V TCGA-W3-AA1W 
        7.23         0.20         4.01       111.09        42.08       219.16 
TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZQ 
      105.04        24.03        49.05        17.95       101.33        63.22 
TCGA-WE-A8ZX TCGA-WE-AA9Y TCGA-XV-AB01 TCGA-YD-A89C TCGA-YD-A9TA TCGA-YG-AA3O 
       35.80        12.16        13.25         6.90        49.18        37.94 
TCGA-YG-AA3P 
       14.43 

$`AMP PEAK 10(7P22.1) WILD-TYPE`
TCGA-D3-A2JF TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A184 TCGA-EE-A2GD TCGA-EE-A3JD 
       62.07        68.25        54.02        68.15       340.14        27.35 
TCGA-ER-A193 TCGA-ER-A198 TCGA-FS-A1ZF TCGA-FW-A3R5 TCGA-3N-A9WD TCGA-D3-A1Q7 
       31.40        50.76        15.45        36.95        12.99       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 
       28.08        90.90        95.74        43.43       103.10        65.49 
TCGA-D3-A2JB TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JO TCGA-D3-A3C6 
      168.00       113.52        42.08        12.10        66.08        58.06 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
       60.23        24.53        45.30       174.84        55.73        56.35 
TCGA-D3-A51K TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GO TCGA-D3-A8GB TCGA-D3-A8GE 
       32.94        26.89       125.79       137.92        30.84        26.43 
TCGA-D3-A8GJ TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A1JW 
      241.38        89.13       107.15       129.63       117.17         3.65 
TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A4Z6 TCGA-DA-A1I1 TCGA-DA-A1IB TCGA-DA-A3F2 
       18.12        15.39        18.44       222.51        40.60        33.93 
TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-DA-A95X TCGA-DA-A95Y TCGA-EB-A5VV TCGA-EE-A17X 
       10.49        43.36        73.94        14.14         7.04        29.82 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I 
       14.70        26.89         4.96       151.27        91.56        13.55 
TCGA-EE-A29B TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29R TCGA-EE-A29S 
       85.08        72.07        64.64        56.84        14.47        61.28 
TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2GC 
       25.87        17.92       115.96        59.64        39.29        67.43 
TCGA-EE-A2GK TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M8 
       54.74        42.77        81.21        44.88        94.82        19.76 
TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH 
       61.51        47.28       103.27       268.73       103.20        16.96 
TCGA-EE-A2MI TCGA-EE-A2ML TCGA-EE-A2MT TCGA-EE-A3AC TCGA-EE-A3J5 TCGA-EE-A3J8 
      204.66       216.66        71.21        64.04        36.95        34.32 
TCGA-EE-A3JA TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 
       53.19        51.35       134.33       152.81        35.44        13.94 
TCGA-ER-A19A TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A19Q 
       77.75        12.59        26.37       131.51        44.09        50.89 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
      148.18       105.07        43.82        20.15        28.83        48.99 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
       41.56       247.04        93.01        48.59       228.59       202.65 
TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZP TCGA-FS-A1ZS 
       27.72        48.85         9.70        47.38        74.73       148.80 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F9 
       53.16        26.56        49.48        77.82        66.67        34.03 
TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV TCGA-GF-A3OT 
       26.73        54.41        80.68        55.59        13.51         9.90 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A4U4 TCGA-LH-A9QB TCGA-OD-A75X 
        2.04       139.89        96.92        39.35       368.78       297.90 
TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1Q 
        0.33         0.69       228.16        63.02       121.08        69.07 
TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AAA0 TCGA-WE-AAA4 
       58.98        70.52        11.80        49.51        40.41        24.99 
TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       27.58        96.99        15.98 

  AMP PEAK 10(7P22.1) MUTATED AMP PEAK 10(7P22.1) WILD-TYPE 
                         0.20                          0.33 
  AMP PEAK 10(7P22.1) MUTATED AMP PEAK 10(7P22.1) WILD-TYPE 
                       369.93                        368.78 
  AMP PEAK 10(7P22.1) MUTATED AMP PEAK 10(7P22.1) WILD-TYPE 
                        50.10                         53.19 
[1] "0.2 - 369.9 (50.1)" "0.3 - 368.8 (53.2)"
[1] "hr=" "1.1"
D10V3, continuous
                               vv
clus                            I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB
  AMP PEAK 10(7P22.1) MUTATED         10       1      17       10       10
  AMP PEAK 10(7P22.1) WILD-TYPE        3       6      12        8       18
                               vv
clus                            STAGE II STAGE IIA STAGE IIB STAGE IIC
  AMP PEAK 10(7P22.1) MUTATED         16         8         8        12
  AMP PEAK 10(7P22.1) WILD-TYPE       10         6        11         3
                               vv
clus                            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  AMP PEAK 10(7P22.1) MUTATED          26         10         20         31
  AMP PEAK 10(7P22.1) WILD-TYPE        13          5         15         23
                               vv
clus                            STAGE IV
  AMP PEAK 10(7P22.1) MUTATED         13
  AMP PEAK 10(7P22.1) WILD-TYPE        8
D10V4, multiclass
            clus
vv           AMP PEAK 10(7P22.1) MUTATED AMP PEAK 10(7P22.1) WILD-TYPE
  I/II NOS                            10                             3
  STAGE 0                              1                             6
  STAGE I                             17                            12
  STAGE IA                            10                             8
  STAGE IB                            10                            18
  STAGE II                            16                            10
  STAGE IIA                            8                             6
  STAGE IIB                            8                            11
  STAGE IIC                           12                             3
  STAGE III                           26                            13
  STAGE IIIA                          10                             5
  STAGE IIIB                          20                            15
  STAGE IIIC                          31                            23
  STAGE IV                            13                             8
[1] 14  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3 T4
  AMP PEAK 10(7P22.1) MUTATED      42 36 45 40
  AMP PEAK 10(7P22.1) WILD-TYPE    22 37 36 27
D10V5, multiclass
       clus
vv      AMP PEAK 10(7P22.1) MUTATED AMP PEAK 10(7P22.1) WILD-TYPE
  T0+T1                          42                            22
  T2                             36                            37
  T3                             45                            36
  T4                             40                            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 N3
  AMP PEAK 10(7P22.1) MUTATED   96 39 21 31
  AMP PEAK 10(7P22.1) WILD-TYPE 81 26 18 14
D10V6, multiclass
    clus
vv   AMP PEAK 10(7P22.1) MUTATED AMP PEAK 10(7P22.1) WILD-TYPE
  N0                          96                            81
  N1                          39                            26
  N2                          21                            18
  N3                          31                            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"
D10V7, binary
                               cls
clus                              0   1
  AMP PEAK 10(7P22.1) MUTATED   180  14
  AMP PEAK 10(7P22.1) WILD-TYPE 139   8
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(7P22.1) MUTATED    180   14
  AMP PEAK 10(7P22.1) WILD-TYPE  139    8
   clus
vv  AMP PEAK 10(7P22.1) MUTATED AMP PEAK 10(7P22.1) WILD-TYPE
  0                         180                           139
  1                          14                             8
[1] 2 2
[1] FALSE
D10V8, binary
                               cls
clus                             0  1
  AMP PEAK 10(7P22.1) MUTATED   77 49
  AMP PEAK 10(7P22.1) WILD-TYPE 57 41
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(7P22.1) MUTATED     77   49
  AMP PEAK 10(7P22.1) WILD-TYPE   57   41
     clus
vv    AMP PEAK 10(7P22.1) MUTATED AMP PEAK 10(7P22.1) WILD-TYPE
  NO                           77                            57
  YES                          49                            41
[1] 2 2
[1] FALSE
D10V9, binary
                               cls
clus                              0   1
  AMP PEAK 10(7P22.1) MUTATED    32 177
  AMP PEAK 10(7P22.1) WILD-TYPE  15 143
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(7P22.1) MUTATED     32  177
  AMP PEAK 10(7P22.1) WILD-TYPE   15  143
     clus
vv    AMP PEAK 10(7P22.1) MUTATED AMP PEAK 10(7P22.1) WILD-TYPE
  NO                           32                            15
  YES                         177                           143
[1] 2 2
[1] FALSE
D10V10, continuous
D10V11, binary
                               cls
clus                              0   1
  AMP PEAK 10(7P22.1) MUTATED    79 130
  AMP PEAK 10(7P22.1) WILD-TYPE  59  99
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(7P22.1) MUTATED     79  130
  AMP PEAK 10(7P22.1) WILD-TYPE   59   99
        clus
vv       AMP PEAK 10(7P22.1) MUTATED AMP PEAK 10(7P22.1) WILD-TYPE
  FEMALE                          79                            59
  MALE                           130                            99
[1] 2 2
[1] FALSE
D10V12, binary
                               cls
clus                              0   1
  AMP PEAK 10(7P22.1) MUTATED   181  27
  AMP PEAK 10(7P22.1) WILD-TYPE 138  20
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(7P22.1) MUTATED    181   27
  AMP PEAK 10(7P22.1) WILD-TYPE  138   20
     clus
vv    AMP PEAK 10(7P22.1) MUTATED AMP PEAK 10(7P22.1) WILD-TYPE
  NO                          181                           138
  YES                          27                            20
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 10(7P22.1) MUTATED       5                         0   198
  AMP PEAK 10(7P22.1) WILD-TYPE     0                         1   155
D10V13, multiclass
                           clus
vv                          AMP PEAK 10(7P22.1) MUTATED
  ASIAN                                               5
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                             198
                           clus
vv                          AMP PEAK 10(7P22.1) WILD-TYPE
  ASIAN                                                 0
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                               155
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V14, binary
                               cls
clus                              0   1
  AMP PEAK 10(7P22.1) MUTATED     5 198
  AMP PEAK 10(7P22.1) WILD-TYPE   2 154
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(7P22.1) MUTATED      5  198
  AMP PEAK 10(7P22.1) WILD-TYPE    2  154
                        clus
vv                       AMP PEAK 10(7P22.1) MUTATED
  HISPANIC OR LATINO                               5
  NOT HISPANIC OR LATINO                         198
                        clus
vv                       AMP PEAK 10(7P22.1) WILD-TYPE
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                           154
[1] 2 2
[1] FALSE

Clustering(11) Variable = AMP PEAK 11(7Q34) MUTATION ANALYSIS
D11V1, survival
                             sevent
clus2                          0  1
  AMP PEAK 11(7Q34) MUTATED   82 70
  AMP PEAK 11(7Q34) WILD-TYPE 46 54
  AMP PEAK 11(7Q34) MUTATED AMP PEAK 11(7Q34) WILD-TYPE 
                        152                         100 
  AMP PEAK 11(7Q34) MUTATED AMP PEAK 11(7Q34) WILD-TYPE 
                         70                          54 
$`AMP PEAK 11(7Q34) MUTATED`
TCGA-D3-A2JE TCGA-D3-A3C8 TCGA-D3-A8GI TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GO 
        9.76        38.76        13.41        31.96       166.75        52.90 
TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-FR-A729 TCGA-WE-A8K5 TCGA-WE-AAA3 
      134.40        27.35        19.04       216.43        52.73         7.40 
TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1QA 
       14.83         8.42        15.72       110.93        49.35        76.41 
TCGA-D3-A2J7 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL 
       45.99        15.75        86.30       107.61        36.30       171.58 
TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE 
       64.83        43.53        58.06       140.98        40.01        59.70 
TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51J TCGA-D3-A51R 
        9.34        90.21        23.67       173.85       144.46        62.70 
TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GK 
       45.70       177.86       124.08        78.21        23.61       120.00 
TCGA-D3-A8GM TCGA-D3-A8GP TCGA-D3-A8GR TCGA-D9-A3Z3 TCGA-D9-A6EC TCGA-D9-A6EG 
       70.62       135.12        36.53        16.90        69.21        22.85 
TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA 
       76.34       138.67       150.61       110.53        60.10        64.83 
TCGA-DA-A1IC TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-DA-A95W TCGA-DA-A95Y TCGA-DA-A95Z 
       58.85       225.11         8.71         0.76        14.14        12.30 
TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17Y TCGA-EE-A181 
        3.91        16.41        52.41        18.21        24.89        20.38 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29M 
        0.00        26.24        76.14         0.26        47.41        47.74 
TCGA-EE-A29P TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE 
       27.16       346.49       185.19        77.98        26.14        12.95 
TCGA-EE-A2GH TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GP TCGA-EE-A2M6 TCGA-EE-A2M7 
      201.60        32.48        18.35         0.76       103.13        15.25 
TCGA-EE-A2M8 TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MS TCGA-EE-A2MU 
        5.75        63.25        89.26       145.45       143.93        53.26 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 
      124.31       122.73        54.51         6.28        67.89       111.85 
TCGA-EE-A3J7 TCGA-EE-A3JB TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19C 
       45.90       168.85        10.49         7.82        53.29        39.81 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19M TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S 
      184.60       150.12        59.84       120.76        49.71        47.18 
TCGA-ER-A2ND TCGA-ER-A2NF TCGA-ER-A3ET TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A3YN 
        4.70        10.19        68.52        32.05        74.47         4.50 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FS-A1Z0 TCGA-FS-A1ZC 
      174.21         4.14         5.65        10.06       195.98       312.07 
TCGA-FS-A1ZD TCGA-FS-A1ZG TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZU 
       32.78         7.82        78.61       130.95       136.27         4.47 
TCGA-FS-A1ZZ TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FW-A5DY TCGA-GF-A4EO TCGA-GN-A264 
        3.06        66.67       173.19        19.30        18.25       117.93 
TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A8LK 
       96.92        17.06        42.48         7.59       120.53        43.23 
TCGA-GN-A9SD TCGA-LH-A9QB TCGA-QB-A6FS TCGA-W3-AA1R TCGA-W3-AA1W TCGA-W3-AA21 
       59.41        85.05         7.23        79.99       185.13        92.84 
TCGA-WE-A8K1 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZQ TCGA-WE-AA9Y TCGA-XV-AB01 
       47.54        65.42        12.69        62.89         1.94         6.61 
TCGA-YG-AA3O TCGA-Z2-AA3S 
       28.21        91.23 

$`AMP PEAK 11(7Q34) WILD-TYPE`
TCGA-D3-A2JF TCGA-EB-A5SG TCGA-EE-A2GD TCGA-FW-A3R5 TCGA-3N-A9WC TCGA-3N-A9WD 
       62.07        33.24       269.03        36.95        60.46        12.99 
TCGA-D3-A1Q4 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J8 
       31.89       133.25        19.04        62.60        25.64        62.86 
TCGA-D3-A2JB TCGA-D3-A2JO TCGA-D3-A3CF TCGA-D3-A51F TCGA-D3-A51K TCGA-D3-A51T 
      168.00        66.08        24.53        30.67        31.76        11.34 
TCGA-D3-A5GL TCGA-D3-A8GJ TCGA-D3-A8GL TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A4Z6 
       42.05       179.97        69.53        10.78        15.02        18.44 
TCGA-DA-A1I1 TCGA-DA-A3F2 TCGA-DA-A95V TCGA-DA-A95X TCGA-EE-A17X TCGA-EE-A20C 
       68.68        30.44        72.10        65.03        13.15        75.55 
TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29Q TCGA-EE-A2A1 
       79.20        75.22        12.99        44.28        61.12       115.43 
TCGA-EE-A2A2 TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GN TCGA-EE-A2GR TCGA-EE-A2GS 
       30.02        68.65        10.62        93.63         0.20        71.31 
TCGA-EE-A2GU TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2ML 
       81.99        23.77       209.79        94.19       171.85       104.78 
TCGA-EE-A2MP TCGA-EE-A2MT TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3J8 TCGA-EE-A3JH 
      227.01        23.51        64.04         4.41         3.35        19.86 
TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A19A TCGA-ER-A19D TCGA-ER-A19L TCGA-ER-A19N 
      135.98        34.45         4.54        11.47        99.06        42.51 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A3ES 
      146.63        73.05        22.36        16.87        28.67       173.29 
TCGA-ER-A3EV TCGA-FR-A7U8 TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1Z4 
       15.48        26.20       171.78        49.74         8.35        27.62 
TCGA-FS-A1ZE TCGA-FS-A1ZJ TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F0 
       43.92        36.33        35.28        23.21         5.29        30.90 
TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV TCGA-GF-A3OT TCGA-GF-A6C8 
       13.28        80.68        55.59        11.54         9.90         1.91 
TCGA-GN-A262 TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-OD-A75X TCGA-RP-A690 TCGA-RP-A693 
       53.29        34.49        46.92       297.01         0.20         0.33 
TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1Q TCGA-W3-AA1V TCGA-WE-A8ZO 
      174.12         1.97       120.07        44.05         8.09        21.90 
TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AAA0 TCGA-WE-AAA4 
       10.95        48.39        37.32        24.99 

  AMP PEAK 11(7Q34) MUTATED AMP PEAK 11(7Q34) WILD-TYPE 
                        0.0                         0.2 
  AMP PEAK 11(7Q34) MUTATED AMP PEAK 11(7Q34) WILD-TYPE 
                     346.49                      297.01 
  AMP PEAK 11(7Q34) MUTATED AMP PEAK 11(7Q34) WILD-TYPE 
                      52.57                       36.64 
[1] "0.0 - 346.5 (52.6)" "0.2 - 297.0 (36.6)"
[1] "hr=" "1.3"
D11V2, survival
                             sevent
clus2                           0   1
  AMP PEAK 11(7Q34) MUTATED   107 112
  AMP PEAK 11(7Q34) WILD-TYPE  59  80
  AMP PEAK 11(7Q34) MUTATED AMP PEAK 11(7Q34) WILD-TYPE 
                        219                         139 
  AMP PEAK 11(7Q34) MUTATED AMP PEAK 11(7Q34) WILD-TYPE 
                        112                          80 
$`AMP PEAK 11(7Q34) MUTATED`
TCGA-D3-A2JE TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-D3-A8GI TCGA-EE-A180 TCGA-EE-A20H 
       27.65        46.32        13.87        58.52        94.98       168.26 
TCGA-EE-A29L TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-ER-A198 
        2.60       126.81       134.40        27.35        31.40        50.76 
TCGA-FR-A729 TCGA-FS-A1ZF TCGA-QB-AA9O TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-BF-AAP0 
      220.80        15.45        18.05        61.15        21.40        14.93 
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q9 TCGA-D3-A1QA 
       16.57        16.67       112.57        71.80        31.59        90.90 
TCGA-D3-A2J7 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG 
      103.10        23.77       115.53        86.76        11.87       113.52 
TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3C7 
       42.08       171.58        66.48        59.57        58.06        46.98 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU 
      166.52        86.93        60.23         9.34       103.59        39.75 
TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51J TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GN 
       45.30       174.84       145.12        22.62        63.81       135.75 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GD 
      178.32        18.18       125.19        30.84        79.59        23.61 
TCGA-D3-A8GK TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR 
      170.20       107.15       161.00       152.75        29.06       129.63 
TCGA-D3-A8GS TCGA-D3-A8GV TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX 
      117.17       167.70       151.53        54.67         3.65         7.10 
TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV 
       22.29         9.90        25.18        77.56        22.95        76.57 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
       36.03       144.89        20.38       176.55        35.93       135.02 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F5 TCGA-DA-A3F8 
       88.87        53.92        65.92        68.09       225.96        43.36 
TCGA-DA-A95W TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UL 
       37.35        14.14        13.02        13.87        20.35        29.29 
TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
       58.92        36.46        27.22        33.73        14.70        26.89 
TCGA-EE-A20B TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29M 
      133.81        63.35        78.97        63.78        64.64        56.84 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A0 TCGA-EE-A2A6 
       18.61        56.42       369.93       195.02        46.82        86.14 
TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GL TCGA-EE-A2GM 
       59.28       173.79       220.24        48.72        79.66        75.48 
TCGA-EE-A2GP TCGA-EE-A2GT TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MH 
       13.91        44.88       129.27        28.83        19.76        16.96 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A2MU 
       96.23       180.39       167.90        43.23       162.48        53.26 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH 
      124.31       122.73        54.51        13.81        41.59       138.81 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3JB TCGA-ER-A197 
      172.18       127.20        36.95        64.08       201.80        13.94 
TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19E TCGA-ER-A19G TCGA-ER-A19H 
        9.17        98.40        48.89        13.02       302.07       152.35 
TCGA-ER-A19J TCGA-ER-A19M TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T 
        6.44        61.05       162.08        50.89        49.48         8.88 
TCGA-ER-A2ND TCGA-ER-A2NF TCGA-ER-A3ET TCGA-ER-A3PL TCGA-ER-A42K TCGA-ER-A42L 
       23.34        28.83        93.01        33.21        12.95       149.03 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC 
       92.98       174.21        15.72        18.77        38.27        34.82 
TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YX TCGA-FS-A1Z0 TCGA-FS-A1Z7 TCGA-FS-A1ZC 
       36.26       104.42        48.59       202.65         7.79       357.37 
TCGA-FS-A1ZD TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZR 
       53.52         9.70        32.75       101.26       133.55        11.41 
TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZZ TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 
      148.80        26.56        27.02        50.14        66.67        28.73 
TCGA-FS-A4F8 TCGA-FW-A3I3 TCGA-FW-A5DY TCGA-GF-A4EO TCGA-GF-A6C9 TCGA-GN-A264 
      174.84        17.46        19.30        19.43        15.78       117.93 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
       96.92        10.13        64.44        62.79        32.48        48.00 
TCGA-GN-A4U3 TCGA-GN-A4U7 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A9SD TCGA-HR-A2OG 
      121.91        10.42        22.13        50.10        59.41         0.23 
TCGA-HR-A2OH TCGA-LH-A9QB TCGA-QB-A6FS TCGA-W3-AA1O TCGA-W3-AA1R TCGA-W3-AA1W 
       65.88       368.78         7.23         4.01       111.09       219.16 
TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN 
      105.04        24.03        49.05        17.95       101.33        58.98 
TCGA-WE-A8ZQ TCGA-WE-A8ZX TCGA-WE-AA9Y TCGA-XV-AB01 TCGA-YD-A89C TCGA-YG-AA3O 
       63.22        35.80        12.16        13.25         6.90        37.94 
TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S 
       14.43        27.58        96.99 

$`AMP PEAK 11(7Q34) WILD-TYPE`
TCGA-D3-A2JF TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A184 TCGA-EE-A2GD TCGA-FW-A3R5 
       62.07        68.25        54.02        68.15       340.14        36.95 
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q4 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       17.03        66.48        12.99       112.04       133.25        28.08 
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J8 TCGA-D3-A2JB TCGA-D3-A2JK TCGA-D3-A2JO 
       95.74        43.43        65.49       168.00        12.10        66.08 
TCGA-D3-A3BZ TCGA-D3-A3CF TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51K TCGA-D3-A51T 
      130.72        24.53        55.73        56.35        32.94        26.89 
TCGA-D3-A5GL TCGA-D3-A5GO TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GL TCGA-D9-A1X3 
      125.79       137.92        26.43       241.38        89.13        18.12 
TCGA-D9-A3Z1 TCGA-D9-A4Z6 TCGA-DA-A1I1 TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F3 
       15.39        18.44       222.51        40.60        33.93        10.49 
TCGA-DA-A95V TCGA-DA-A95X TCGA-EB-A44R TCGA-EB-A5VV TCGA-EE-A17X TCGA-EE-A17Z 
       72.10        73.94        10.36         7.04        29.82         8.65 
TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29B TCGA-EE-A29D 
        4.96       151.27        91.56        13.55        85.08        13.97 
TCGA-EE-A29G TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29X 
       72.07        66.74        14.47        61.28        25.87        17.92 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2GC TCGA-EE-A2GJ TCGA-EE-A2GK 
      115.96        59.64        39.29        67.43       107.38        54.74 
TCGA-EE-A2GN TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2MC 
      102.12        42.77        81.21        94.82        21.67        61.51 
TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2ML 
       47.28       103.27       268.73       103.20       204.66       216.66 
TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MT TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3J8 
       47.54       248.65        71.21        64.04        28.77        34.32 
TCGA-EE-A3JA TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A19A 
       53.19        51.35       134.33       152.81        35.44        77.75 
TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A19W TCGA-ER-A1A1 
       12.59        26.37       131.51        44.09       148.18       105.07 
TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3EV 
       43.82        20.15        48.99        41.56       247.04        46.98 
TCGA-FR-A7U8 TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZA 
       27.85       216.92       228.59        20.91        28.08        27.72 
TCGA-FS-A1ZB TCGA-FS-A1ZE TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZT 
       48.85        46.45        47.38        23.93        74.73        53.16 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F0 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC 
       49.48        27.09        77.82        34.03        26.73        54.41 
TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GN-A262 
       80.68        55.59        13.51         9.90         2.04       139.89 
TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-GN-A8LL TCGA-OD-A75X TCGA-RP-A690 TCGA-RP-A693 
       39.35        48.89        21.37       297.90         0.20         0.33 
TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1Q TCGA-W3-AA1V 
        0.69       228.16        63.02       121.08        69.07        42.08 
TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-YD-A9TA 
       70.52        11.80        49.51        40.41        24.99        49.18 
TCGA-Z2-AA3V 
       15.98 

  AMP PEAK 11(7Q34) MUTATED AMP PEAK 11(7Q34) WILD-TYPE 
                       0.23                        0.20 
  AMP PEAK 11(7Q34) MUTATED AMP PEAK 11(7Q34) WILD-TYPE 
                     369.93                      340.14 
  AMP PEAK 11(7Q34) MUTATED AMP PEAK 11(7Q34) WILD-TYPE 
                      53.52                       49.51 
[1] "0.2 - 369.9 (53.5)" "0.2 - 340.1 (49.5)"
[1] "hr=" "1.2"
D11V3, continuous
                             vv
clus                          I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB
  AMP PEAK 11(7Q34) MUTATED         13       3      16       11       13
  AMP PEAK 11(7Q34) WILD-TYPE        0       4      13        7       15
                             vv
clus                          STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  AMP PEAK 11(7Q34) MUTATED         15         7         8        12        29
  AMP PEAK 11(7Q34) WILD-TYPE       11         7        11         3        10
                             vv
clus                          STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  AMP PEAK 11(7Q34) MUTATED           12         24         31       12
  AMP PEAK 11(7Q34) WILD-TYPE          3         11         23        9
D11V4, multiclass
            clus
vv           AMP PEAK 11(7Q34) MUTATED AMP PEAK 11(7Q34) WILD-TYPE
  I/II NOS                          13                           0
  STAGE 0                            3                           4
  STAGE I                           16                          13
  STAGE IA                          11                           7
  STAGE IB                          13                          15
  STAGE II                          15                          11
  STAGE IIA                          7                           7
  STAGE IIB                          8                          11
  STAGE IIC                         12                           3
  STAGE III                         29                          10
  STAGE IIIA                        12                           3
  STAGE IIIB                        24                          11
  STAGE IIIC                        31                          23
  STAGE IV                          12                           9
[1] 14  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          T0+T1 T2 T3 T4
  AMP PEAK 11(7Q34) MUTATED      44 38 52 42
  AMP PEAK 11(7Q34) WILD-TYPE    20 35 29 25
D11V5, multiclass
       clus
vv      AMP PEAK 11(7Q34) MUTATED AMP PEAK 11(7Q34) WILD-TYPE
  T0+T1                        44                          20
  T2                           38                          35
  T3                           52                          29
  T4                           42                          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"
                             vv
clus                           N0  N1  N2  N3
  AMP PEAK 11(7Q34) MUTATED   104  45  25  31
  AMP PEAK 11(7Q34) WILD-TYPE  73  20  14  14
D11V6, multiclass
    clus
vv   AMP PEAK 11(7Q34) MUTATED AMP PEAK 11(7Q34) WILD-TYPE
  N0                       104                          73
  N1                        45                          20
  N2                        25                          14
  N3                        31                          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"
D11V7, binary
                             cls
clus                            0   1
  AMP PEAK 11(7Q34) MUTATED   199  13
  AMP PEAK 11(7Q34) WILD-TYPE 120   9
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 11(7Q34) MUTATED    199   13
  AMP PEAK 11(7Q34) WILD-TYPE  120    9
   clus
vv  AMP PEAK 11(7Q34) MUTATED AMP PEAK 11(7Q34) WILD-TYPE
  0                       199                         120
  1                        13                           9
[1] 2 2
[1] FALSE
D11V8, binary
                             cls
clus                           0  1
  AMP PEAK 11(7Q34) MUTATED   87 53
  AMP PEAK 11(7Q34) WILD-TYPE 47 37
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 11(7Q34) MUTATED     87   53
  AMP PEAK 11(7Q34) WILD-TYPE   47   37
     clus
vv    AMP PEAK 11(7Q34) MUTATED AMP PEAK 11(7Q34) WILD-TYPE
  NO                         87                          47
  YES                        53                          37
[1] 2 2
[1] FALSE
D11V9, binary
                             cls
clus                            0   1
  AMP PEAK 11(7Q34) MUTATED    31 194
  AMP PEAK 11(7Q34) WILD-TYPE  16 126
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 11(7Q34) MUTATED     31  194
  AMP PEAK 11(7Q34) WILD-TYPE   16  126
     clus
vv    AMP PEAK 11(7Q34) MUTATED AMP PEAK 11(7Q34) WILD-TYPE
  NO                         31                          16
  YES                       194                         126
[1] 2 2
[1] FALSE
D11V10, continuous
D11V11, binary
                             cls
clus                            0   1
  AMP PEAK 11(7Q34) MUTATED    93 132
  AMP PEAK 11(7Q34) WILD-TYPE  45  97
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 11(7Q34) MUTATED     93  132
  AMP PEAK 11(7Q34) WILD-TYPE   45   97
        clus
vv       AMP PEAK 11(7Q34) MUTATED AMP PEAK 11(7Q34) WILD-TYPE
  FEMALE                        93                          45
  MALE                         132                          97
[1] 2 2
[1] FALSE
D11V12, binary
                             cls
clus                            0   1
  AMP PEAK 11(7Q34) MUTATED   194  31
  AMP PEAK 11(7Q34) WILD-TYPE 125  16
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 11(7Q34) MUTATED    194   31
  AMP PEAK 11(7Q34) WILD-TYPE  125   16
     clus
vv    AMP PEAK 11(7Q34) MUTATED AMP PEAK 11(7Q34) WILD-TYPE
  NO                        194                         125
  YES                        31                          16
[1] 2 2
[1] FALSE
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 11(7Q34) MUTATED       4                         0   214
  AMP PEAK 11(7Q34) WILD-TYPE     1                         1   139
D11V13, multiclass
                           clus
vv                          AMP PEAK 11(7Q34) MUTATED
  ASIAN                                             4
  BLACK OR AFRICAN AMERICAN                         0
  WHITE                                           214
                           clus
vv                          AMP PEAK 11(7Q34) WILD-TYPE
  ASIAN                                               1
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                             139
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V14, binary
                             cls
clus                            0   1
  AMP PEAK 11(7Q34) MUTATED     4 214
  AMP PEAK 11(7Q34) WILD-TYPE   3 138
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 11(7Q34) MUTATED      4  214
  AMP PEAK 11(7Q34) WILD-TYPE    3  138
                        clus
vv                       AMP PEAK 11(7Q34) MUTATED AMP PEAK 11(7Q34) WILD-TYPE
  HISPANIC OR LATINO                             4                           3
  NOT HISPANIC OR LATINO                       214                         138
[1] 2 2
[1] FALSE

Clustering(12) Variable = AMP PEAK 12(8Q24.21) MUTATION ANALYSIS
D12V1, survival
                                sevent
clus2                             0  1
  AMP PEAK 12(8Q24.21) MUTATED   71 66
  AMP PEAK 12(8Q24.21) WILD-TYPE 57 58
  AMP PEAK 12(8Q24.21) MUTATED AMP PEAK 12(8Q24.21) WILD-TYPE 
                           137                            115 
  AMP PEAK 12(8Q24.21) MUTATED AMP PEAK 12(8Q24.21) WILD-TYPE 
                            66                             58 
$`AMP PEAK 12(8Q24.21) MUTATED`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A8GI TCGA-EB-A5SG TCGA-EE-A2GD TCGA-EE-A2GO 
        9.76        62.07        13.41        33.24       269.03        52.90 
TCGA-EE-A2MR TCGA-FR-A729 TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-3N-A9WC TCGA-3N-A9WD 
      134.40       216.43        52.73         7.40        60.46        12.99 
TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q6 TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
        8.42        31.89        49.35        62.60        25.64        45.99 
TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 
       15.75        86.30        64.83        66.08        43.53        58.06 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU 
      140.98        40.01        59.70         9.34        90.21        23.67 
TCGA-D3-A51E TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GU 
      173.85       144.46        31.76        45.70       177.86       124.08 
TCGA-D3-A8GJ TCGA-D3-A8GP TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HY TCGA-DA-A1I1 
      179.97       135.12        69.21        22.85       138.67        68.68 
TCGA-DA-A1I2 TCGA-DA-A3F5 TCGA-DA-A95V TCGA-DA-A95W TCGA-DA-A95Y TCGA-DA-A95Z 
      150.61       225.11        72.10         0.76        14.14        12.30 
TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A6L9 TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A29C 
        3.91        16.41        18.21        24.89        20.38        76.14 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29T TCGA-EE-A2GE TCGA-EE-A2GH 
        0.26        44.28        47.41       346.49        12.95       201.60 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2M6 
       32.48        18.35        93.63         0.76        71.31       103.13 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MF TCGA-EE-A2MJ TCGA-EE-A2MP TCGA-EE-A3AA 
       15.25         5.75       209.79        63.25       227.01       124.31 
TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 
      122.73         4.41        54.51        67.89       111.85        45.90 
TCGA-ER-A197 TCGA-ER-A19C TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M 
       10.49        39.81       184.60       150.12        99.06        59.84 
TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NF 
       42.51        49.71        47.18        22.36         4.70        10.19 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A42L TCGA-FR-A44A TCGA-FR-A7U8 
      173.29        68.52        15.48        74.47       174.21        26.20 
TCGA-FR-A7UA TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1ZC 
        5.65       171.78        49.74       195.98        27.62       312.07 
TCGA-FS-A1ZD TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU 
       32.78        78.61       130.95       136.27        35.28         4.47 
TCGA-FS-A1ZY TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4FD TCGA-FW-A3TV TCGA-GF-A3OT 
        5.29        66.67       173.19        80.68        11.54         9.90 
TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-GN-A9SD 
       17.06         7.59       120.53        34.49        46.92        59.41 
TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 
      297.01         7.23         0.33       174.12         1.97       120.07 
TCGA-W3-AA1V TCGA-W3-AA21 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ 
        8.09        92.84        65.42        12.69        21.90        62.89 
TCGA-WE-A8ZT TCGA-WE-AAA0 TCGA-XV-AB01 TCGA-YG-AA3O TCGA-Z2-AA3S 
       10.95        37.32         6.61        28.21        91.23 

$`AMP PEAK 12(8Q24.21) WILD-TYPE`
TCGA-D3-A3C8 TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A3JD TCGA-ER-A193 TCGA-FW-A3R5 
       38.76        31.96       166.75        27.35        19.04        36.95 
TCGA-BF-AAP0 TCGA-D3-A1Q3 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA 
       14.83        15.72       110.93       133.25        19.04        76.41 
TCGA-D3-A2J8 TCGA-D3-A2JB TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A3CF 
       62.86       168.00       107.61        36.30       171.58        24.53 
TCGA-D3-A51F TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A8GC TCGA-D3-A8GD 
       30.67        62.70        11.34        42.05        78.21        23.61 
TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GR TCGA-D9-A1X3 TCGA-D9-A3Z1 
      120.00        69.53        70.62        36.53        10.78        15.02 
TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-DA-A1HV TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA 
       16.90        18.44        76.34       110.53        60.10        64.83 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F8 TCGA-DA-A95X TCGA-EB-A5UN TCGA-EE-A17X 
       58.85        30.44         8.71        65.03        52.41        13.15 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29D 
        0.00        26.24        75.55        79.20        75.22        12.99 
TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A2 
       47.74        27.16        61.12       185.19       115.43        30.02 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GR TCGA-EE-A2GU 
       77.98        26.14        68.65        10.62         0.20        81.99 
TCGA-EE-A2MC TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
       23.77        94.19       171.85        89.26       104.78       145.45 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AC TCGA-EE-A3AF TCGA-EE-A3J8 
      143.93        23.51        53.26        64.04         6.28         3.35 
TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A199 TCGA-ER-A19A 
      168.85        19.86       135.98        34.45         7.82         4.54 
TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19P TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NE 
       53.29        11.47       120.76       146.63        73.05        16.87 
TCGA-ER-A2NG TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A69P TCGA-FR-A8YC TCGA-FS-A1Z3 
       28.67        32.05         4.50         4.14        10.06         8.35 
TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZW TCGA-FS-A1ZZ TCGA-FS-A4F0 
       43.92         7.82        36.33        23.21         3.06        30.90 
TCGA-FS-A4F9 TCGA-FW-A3TU TCGA-FW-A5DY TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 
       13.28        55.59        19.30        18.25         1.91        53.29 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A268 TCGA-GN-A8LK TCGA-LH-A9QB TCGA-RP-A690 
      117.93        96.92        42.48        43.23        85.05         0.20 
TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1W TCGA-WE-A8K1 TCGA-WE-A8ZY TCGA-WE-AA9Y 
       44.05        79.99       185.13        47.54        48.39         1.94 
TCGA-WE-AAA4 
       24.99 

  AMP PEAK 12(8Q24.21) MUTATED AMP PEAK 12(8Q24.21) WILD-TYPE 
                          0.26                           0.00 
  AMP PEAK 12(8Q24.21) MUTATED AMP PEAK 12(8Q24.21) WILD-TYPE 
                        346.49                         185.19 
  AMP PEAK 12(8Q24.21) MUTATED AMP PEAK 12(8Q24.21) WILD-TYPE 
                         49.71                          42.05 
[1] "0.3 - 346.5 (49.7)" "0.0 - 185.2 (42.0)"
[1] "hr=" "1.4"
D12V2, survival
                                sevent
clus2                              0   1
  AMP PEAK 12(8Q24.21) MUTATED    87 100
  AMP PEAK 12(8Q24.21) WILD-TYPE  79  92
  AMP PEAK 12(8Q24.21) MUTATED AMP PEAK 12(8Q24.21) WILD-TYPE 
                           187                            171 
  AMP PEAK 12(8Q24.21) MUTATED AMP PEAK 12(8Q24.21) WILD-TYPE 
                           100                             92 
$`AMP PEAK 12(8Q24.21) MUTATED`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A3ML TCGA-D3-A8GI TCGA-EB-A5SG TCGA-EB-A5SH 
       27.65        62.07        13.87        58.52        68.25        54.02 
TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR TCGA-ER-A198 TCGA-FR-A729 
        2.60       340.14       126.81       134.40        50.76       220.80 
TCGA-QB-AA9O TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 
       18.05        61.15        21.40        66.48        12.99        16.57 
TCGA-D3-A1Q4 TCGA-D3-A1Q6 TCGA-D3-A1Q9 TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
      112.04        71.80        31.59        95.74        43.43       103.10 
TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 
      115.53        86.76        66.48        66.08        59.57        58.06 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU 
      166.52        86.93        60.23         9.34       103.59        39.75 
TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A5GN 
       45.30       174.84       145.12        32.94        22.62       135.75 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GJ TCGA-D3-A8GP TCGA-D9-A1JW 
      178.32        18.18       125.19       241.38       152.75         3.65 
TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 
       25.18        77.56        22.95        36.03       144.89        20.38 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A95V 
      222.51       176.55        35.93        10.49       225.96        72.10 
TCGA-DA-A95W TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH 
       37.35        14.14        13.02        13.87        10.36        20.35 
TCGA-EB-A6L9 TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A20B TCGA-EE-A29C 
       36.46        27.22         8.65        33.73       133.81        78.97 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T 
       63.78        72.07        64.64        14.47        61.28       369.93 
TCGA-EE-A29V TCGA-EE-A2A5 TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GL TCGA-EE-A2GM 
       25.87        39.29       173.79       220.24        79.66        75.48 
TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
      102.12        13.91        81.21       129.27        28.83        19.76 
TCGA-EE-A2MF TCGA-EE-A2MH TCGA-EE-A2MJ TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A3AA 
      268.73        16.96        96.23        47.54       248.65       124.31 
TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J4 
      122.73        28.77        54.51        41.59       172.18       127.20 
TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-ER-A197 TCGA-ER-A19C TCGA-ER-A19G 
       36.95        64.08        53.19        13.94        48.89       302.07 
TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19Q 
      152.35         6.44       131.51        61.05        44.09        50.89 
TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NF TCGA-ER-A3ES 
       49.48         8.88        43.82        23.34        28.83       247.04 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A42L TCGA-FR-A44A TCGA-FR-A7U8 TCGA-FR-A7U9 
       93.01        46.98       149.03       174.21        27.85        18.77 
TCGA-FR-A7UA TCGA-FR-A8YD TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
       38.27        36.26       216.92        48.59       228.59       202.65 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZK TCGA-FS-A1ZM 
       28.08         7.79       357.37        53.52        23.93       101.26 
TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU 
       74.73       133.55        11.41       148.80        53.16        26.56 
TCGA-FS-A1ZY TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4FB 
       27.09        50.14        66.67        28.73       174.84        26.73 
TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TV TCGA-GF-A3OT TCGA-GN-A266 TCGA-GN-A267 
       80.68        17.46        13.51         9.90        10.13        64.44 
TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-GN-A8LL 
       32.48        48.00       121.91        39.35        48.89        21.37 
TCGA-GN-A9SD TCGA-HR-A2OH TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 
       59.41        65.88       297.90         7.23         0.33         0.69 
TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1V TCGA-W3-AA21 TCGA-WE-A8K6 
      228.16        63.02       121.08        42.08       105.04        17.95 
TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX 
      101.33        58.98        70.52        63.22        11.80        35.80 
TCGA-WE-AAA0 TCGA-XV-AB01 TCGA-YD-A9TA TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-AA3S 
       40.41        13.25        49.18        37.94        14.43        96.99 
TCGA-Z2-AA3V 
       15.98 

$`AMP PEAK 12(8Q24.21) WILD-TYPE`
TCGA-D3-A3C8 TCGA-EE-A180 TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A3JD TCGA-ER-A193 
       46.32        94.98        68.15       168.26        27.35        31.40 
TCGA-FS-A1ZF TCGA-FW-A3R5 TCGA-3N-A9WB TCGA-BF-AAP0 TCGA-D3-A1Q3 TCGA-D3-A1Q5 
       15.45        36.95        17.03        14.93        16.67       112.57 
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JB 
      133.25        28.08        90.90        65.49        23.77       168.00 
TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A3BZ 
       11.87       113.52        42.08        12.10       171.58       130.72 
TCGA-D3-A3C7 TCGA-D3-A3CF TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51R TCGA-D3-A51T 
       46.98        24.53        55.73        56.35        63.81        26.89 
TCGA-D3-A5GL TCGA-D3-A5GO TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GE 
      125.79       137.92        30.84        79.59        23.61        26.43 
TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GQ TCGA-D3-A8GR 
      170.20        89.13       107.15       161.00        29.06       129.63 
TCGA-D3-A8GS TCGA-D3-A8GV TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JX TCGA-D9-A1X3 
      117.17       167.70       151.53        54.67         7.10        18.12 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-DA-A1HV TCGA-DA-A1I5 
       15.39        22.29        18.44         9.90        76.57       135.02 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       88.87        53.92        65.92        40.60        68.09        33.93 
TCGA-DA-A3F8 TCGA-DA-A95X TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EE-A17X 
       43.36        73.94        29.29        58.92         7.04        29.82 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I 
       14.70        26.89         4.96       151.27        91.56        13.55 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P 
       63.35        85.08        13.97        56.84        18.61        56.42 
TCGA-EE-A29Q TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
       66.74       195.02        17.92        46.82       115.96        59.64 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
       86.14        59.28        67.43        48.72       107.38        54.74 
TCGA-EE-A2GR TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2MC TCGA-EE-A2MD 
       42.77        44.88        94.82        21.67        61.51        47.28 
TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
      103.27       103.20       204.66       180.39       216.66       167.90 
TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AC TCGA-EE-A3AF 
       43.23       162.48        71.21        53.26        64.04        13.81 
TCGA-EE-A3AH TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
      138.81        34.32       201.80        51.35       134.33       152.81 
TCGA-ER-A195 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19E 
       35.44         9.17        77.75        98.40        12.59        13.02 
TCGA-ER-A19F TCGA-ER-A19P TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NE TCGA-ER-A2NG 
       26.37       162.08       148.18       105.07        20.15        48.99 
TCGA-ER-A2NH TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A69P TCGA-FR-A8YC 
       41.56        33.21        12.95        92.98        15.72        34.82 
TCGA-FR-A8YE TCGA-FS-A1Z3 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZE TCGA-FS-A1ZG 
      104.42        20.91        27.72        48.85        46.45         9.70 
TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZW TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F9 
       32.75        47.38        49.48        27.02        77.82        34.03 
TCGA-FS-A4FC TCGA-FW-A3TU TCGA-FW-A5DY TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 
       54.41        55.59        19.30        19.43         2.04        15.78 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A268 TCGA-GN-A4U7 TCGA-GN-A4U9 
      139.89       117.93        96.92        62.79        10.42        22.13 
TCGA-GN-A8LK TCGA-HR-A2OG TCGA-LH-A9QB TCGA-RP-A690 TCGA-W3-AA1O TCGA-W3-AA1Q 
       50.10         0.23       368.78         0.20         4.01        69.07 
TCGA-W3-AA1R TCGA-W3-AA1W TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8ZY TCGA-WE-AA9Y 
      111.09       219.16        24.03        49.05        49.51        12.16 
TCGA-WE-AAA4 TCGA-YD-A89C TCGA-Z2-A8RT 
       24.99         6.90        27.58 

  AMP PEAK 12(8Q24.21) MUTATED AMP PEAK 12(8Q24.21) WILD-TYPE 
                          0.33                           0.20 
  AMP PEAK 12(8Q24.21) MUTATED AMP PEAK 12(8Q24.21) WILD-TYPE 
                        369.93                         368.78 
  AMP PEAK 12(8Q24.21) MUTATED AMP PEAK 12(8Q24.21) WILD-TYPE 
                         53.52                          49.51 
[1] "0.3 - 369.9 (53.5)" "0.2 - 368.8 (49.5)"
[1] "hr=" "1.2"
D12V3, continuous
                                vv
clus                             I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB
  AMP PEAK 12(8Q24.21) MUTATED          6       1      18        9       12
  AMP PEAK 12(8Q24.21) WILD-TYPE        7       6      11        9       16
                                vv
clus                             STAGE II STAGE IIA STAGE IIB STAGE IIC
  AMP PEAK 12(8Q24.21) MUTATED         16         8         6         9
  AMP PEAK 12(8Q24.21) WILD-TYPE       10         6        13         6
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  AMP PEAK 12(8Q24.21) MUTATED          28         10         19         22
  AMP PEAK 12(8Q24.21) WILD-TYPE        11          5         16         32
                                vv
clus                             STAGE IV
  AMP PEAK 12(8Q24.21) MUTATED         11
  AMP PEAK 12(8Q24.21) WILD-TYPE       10
D12V4, multiclass
            clus
vv           AMP PEAK 12(8Q24.21) MUTATED AMP PEAK 12(8Q24.21) WILD-TYPE
  I/II NOS                              6                              7
  STAGE 0                               1                              6
  STAGE I                              18                             11
  STAGE IA                              9                              9
  STAGE IB                             12                             16
  STAGE II                             16                             10
  STAGE IIA                             8                              6
  STAGE IIB                             6                             13
  STAGE IIC                             9                              6
  STAGE III                            28                             11
  STAGE IIIA                           10                              5
  STAGE IIIB                           19                             16
  STAGE IIIC                           22                             32
  STAGE IV                             11                             10
[1] 14  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  AMP PEAK 12(8Q24.21) MUTATED      40 41 40 33
  AMP PEAK 12(8Q24.21) WILD-TYPE    24 32 41 34
D12V5, multiclass
       clus
vv      AMP PEAK 12(8Q24.21) MUTATED AMP PEAK 12(8Q24.21) WILD-TYPE
  T0+T1                           40                             24
  T2                              41                             32
  T3                              40                             41
  T4                              33                             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 N3
  AMP PEAK 12(8Q24.21) MUTATED   87 39 23 21
  AMP PEAK 12(8Q24.21) WILD-TYPE 90 26 16 24
D12V6, multiclass
    clus
vv   AMP PEAK 12(8Q24.21) MUTATED AMP PEAK 12(8Q24.21) WILD-TYPE
  N0                           87                             90
  N1                           39                             26
  N2                           23                             16
  N3                           21                             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"
D12V7, binary
                                cls
clus                               0   1
  AMP PEAK 12(8Q24.21) MUTATED   169  11
  AMP PEAK 12(8Q24.21) WILD-TYPE 150  11
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(8Q24.21) MUTATED    169   11
  AMP PEAK 12(8Q24.21) WILD-TYPE  150   11
   clus
vv  AMP PEAK 12(8Q24.21) MUTATED AMP PEAK 12(8Q24.21) WILD-TYPE
  0                          169                            150
  1                           11                             11
[1] 2 2
[1] FALSE
D12V8, binary
                                cls
clus                              0  1
  AMP PEAK 12(8Q24.21) MUTATED   66 45
  AMP PEAK 12(8Q24.21) WILD-TYPE 68 45
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(8Q24.21) MUTATED     66   45
  AMP PEAK 12(8Q24.21) WILD-TYPE   68   45
     clus
vv    AMP PEAK 12(8Q24.21) MUTATED AMP PEAK 12(8Q24.21) WILD-TYPE
  NO                            66                             68
  YES                           45                             45
[1] 2 2
[1] FALSE
D12V9, binary
                                cls
clus                               0   1
  AMP PEAK 12(8Q24.21) MUTATED    27 165
  AMP PEAK 12(8Q24.21) WILD-TYPE  20 155
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(8Q24.21) MUTATED     27  165
  AMP PEAK 12(8Q24.21) WILD-TYPE   20  155
     clus
vv    AMP PEAK 12(8Q24.21) MUTATED AMP PEAK 12(8Q24.21) WILD-TYPE
  NO                            27                             20
  YES                          165                            155
[1] 2 2
[1] FALSE
D12V10, continuous
D12V11, binary
                                cls
clus                               0   1
  AMP PEAK 12(8Q24.21) MUTATED    69 123
  AMP PEAK 12(8Q24.21) WILD-TYPE  69 106
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(8Q24.21) MUTATED     69  123
  AMP PEAK 12(8Q24.21) WILD-TYPE   69  106
        clus
vv       AMP PEAK 12(8Q24.21) MUTATED AMP PEAK 12(8Q24.21) WILD-TYPE
  FEMALE                           69                             69
  MALE                            123                            106
[1] 2 2
[1] FALSE
D12V12, binary
                                cls
clus                               0   1
  AMP PEAK 12(8Q24.21) MUTATED   170  22
  AMP PEAK 12(8Q24.21) WILD-TYPE 149  25
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(8Q24.21) MUTATED    170   22
  AMP PEAK 12(8Q24.21) WILD-TYPE  149   25
     clus
vv    AMP PEAK 12(8Q24.21) MUTATED AMP PEAK 12(8Q24.21) WILD-TYPE
  NO                           170                            149
  YES                           22                             25
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 12(8Q24.21) MUTATED       5                         0   181
  AMP PEAK 12(8Q24.21) WILD-TYPE     0                         1   172
D12V13, multiclass
                           clus
vv                          AMP PEAK 12(8Q24.21) MUTATED
  ASIAN                                                5
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                              181
                           clus
vv                          AMP PEAK 12(8Q24.21) WILD-TYPE
  ASIAN                                                  0
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                172
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V14, binary
                                cls
clus                               0   1
  AMP PEAK 12(8Q24.21) MUTATED     4 184
  AMP PEAK 12(8Q24.21) WILD-TYPE   3 168
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(8Q24.21) MUTATED      4  184
  AMP PEAK 12(8Q24.21) WILD-TYPE    3  168
                        clus
vv                       AMP PEAK 12(8Q24.21) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                          184
                        clus
vv                       AMP PEAK 12(8Q24.21) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            168
[1] 2 2
[1] FALSE

Clustering(13) Variable = AMP PEAK 13(11Q13.3) MUTATION ANALYSIS
D13V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 13(11Q13.3) MUTATED    22  23
  AMP PEAK 13(11Q13.3) WILD-TYPE 106 101
  AMP PEAK 13(11Q13.3) MUTATED AMP PEAK 13(11Q13.3) WILD-TYPE 
                            45                            207 
  AMP PEAK 13(11Q13.3) MUTATED AMP PEAK 13(11Q13.3) WILD-TYPE 
                            23                            101 
$`AMP PEAK 13(11Q13.3) MUTATED`
TCGA-D3-A2JF TCGA-EE-A180 TCGA-FR-A729 TCGA-D3-A2J6 TCGA-D3-A2JB TCGA-D3-A2JC 
       62.07        31.96       216.43        25.64       168.00        86.30 
TCGA-D3-A2JP TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A51E TCGA-D9-A3Z3 
       43.53       140.98        59.70        24.53       173.85        16.90 
TCGA-D9-A6EC TCGA-DA-A95V TCGA-DA-A95Y TCGA-EB-A44Q TCGA-EB-A6L9 TCGA-EE-A20F 
       69.21        72.10        14.14         3.91        18.21        79.20 
TCGA-EE-A29W TCGA-EE-A2GB TCGA-EE-A2GH TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2MC 
      185.19        26.14       201.60         0.76         0.20        23.77 
TCGA-EE-A2MM TCGA-EE-A3JB TCGA-EE-A3JI TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19Q 
      145.45       168.85       135.98        59.84        42.51        49.71 
TCGA-ER-A19W TCGA-ER-A2NF TCGA-ER-A3ES TCGA-ER-A3ET TCGA-FS-A1YW TCGA-FS-A1ZD 
      146.63        10.19       173.29        68.52       171.78        32.78 
TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A4FD TCGA-GF-A4EO TCGA-GN-A268 
      130.95       136.27        35.28        80.68        18.25        42.48 
TCGA-WE-A8K1 TCGA-WE-A8ZN TCGA-WE-A8ZQ 
       47.54        12.69        62.89 

$`AMP PEAK 13(11Q13.3) WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A3C8 TCGA-D3-A8GI TCGA-EB-A5SG TCGA-EE-A20H TCGA-EE-A2GD 
        9.76        38.76        13.41        33.24       166.75       269.03 
TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-FW-A3R5 TCGA-WE-A8K5 
       52.90       134.40        27.35        19.04        36.95        52.73 
TCGA-WE-AAA3 TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 
        7.40        60.46        12.99        14.83         8.42        15.72 
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA 
       31.89       110.93        49.35       133.25        19.04        76.41 
TCGA-D3-A1QB TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JG TCGA-D3-A2JH 
       62.60        45.99        62.86        15.75       107.61        36.30 
TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3MO 
      171.58        64.83        66.08        58.06        40.01         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R 
       90.21        23.67        30.67       144.46        31.76        62.70 
TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D3-A8GC 
       11.34        42.05        45.70       177.86       124.08        78.21 
TCGA-D3-A8GD TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GP 
       23.61       179.97       120.00        69.53        70.62       135.12 
TCGA-D3-A8GR TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A4Z6 TCGA-D9-A6EG TCGA-DA-A1HV 
       36.53        10.78        15.02        18.44        22.85        76.34 
TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA 
      138.67        68.68       150.61       110.53        60.10        64.83 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-DA-A95W TCGA-DA-A95X 
       58.85        30.44       225.11         8.71         0.76        65.03 
TCGA-DA-A95Z TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A181 
       12.30        16.41        52.41        13.15        24.89        20.38 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D 
        0.00        26.24        75.55        75.22        76.14        12.99 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q 
        0.26        44.28        47.41        47.74        27.16        61.12 
TCGA-EE-A29T TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GE TCGA-EE-A2GJ 
      346.49       115.43        30.02        77.98        12.95        68.65 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GS TCGA-EE-A2GU 
       10.62        32.48        18.35        93.63        71.31        81.99 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI 
      103.13        15.25         5.75       209.79        94.19       171.85 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT 
       63.25        89.26       104.78       227.01       143.93        23.51 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
       53.26       124.31       122.73        64.04         4.41        54.51 
TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JH 
        6.28        67.89       111.85        45.90         3.35        19.86 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C 
       34.45        10.49         7.82         4.54        53.29        39.81 
TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19P TCGA-ER-A19S 
       11.47       184.60       150.12        99.06       120.76        47.18 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A3EV 
       73.05        22.36         4.70        16.87        28.67        15.48 
TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7U8 
       32.05        74.47         4.50       174.21         4.14        26.20 
TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 
        5.65        10.06        49.74       195.98         8.35        27.62 
TCGA-FS-A1ZC TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZU 
      312.07        43.92         7.82        36.33        78.61         4.47 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 
       23.21         5.29         3.06        30.90        66.67       173.19 
TCGA-FS-A4F9 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 
       13.28        55.59        11.54        19.30         9.90         1.91 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A4U3 
       53.29       117.93        96.92        17.06         7.59       120.53 
TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-GN-A8LK TCGA-GN-A9SD TCGA-LH-A9QB TCGA-OD-A75X 
       34.49        46.92        43.23        59.41        85.05       297.01 
TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 
        7.23         0.20         0.33       174.12         1.97       120.07 
TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8ZM 
       44.05        79.99         8.09       185.13        92.84        65.42 
TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 
       21.90        10.95        48.39         1.94        37.32        24.99 
TCGA-XV-AB01 TCGA-YG-AA3O TCGA-Z2-AA3S 
        6.61        28.21        91.23 

  AMP PEAK 13(11Q13.3) MUTATED AMP PEAK 13(11Q13.3) WILD-TYPE 
                           0.2                            0.0 
  AMP PEAK 13(11Q13.3) MUTATED AMP PEAK 13(11Q13.3) WILD-TYPE 
                        216.43                         346.49 
  AMP PEAK 13(11Q13.3) MUTATED AMP PEAK 13(11Q13.3) WILD-TYPE 
                         59.84                          44.28 
[1] "0.2 - 216.4 (59.8)" "0.0 - 346.5 (44.3)"
[1] "hr=" "1.2"
D13V2, survival
                                sevent
clus2                              0   1
  AMP PEAK 13(11Q13.3) MUTATED    27  39
  AMP PEAK 13(11Q13.3) WILD-TYPE 139 153
  AMP PEAK 13(11Q13.3) MUTATED AMP PEAK 13(11Q13.3) WILD-TYPE 
                            66                            292 
  AMP PEAK 13(11Q13.3) MUTATED AMP PEAK 13(11Q13.3) WILD-TYPE 
                            39                            153 
$`AMP PEAK 13(11Q13.3) MUTATED`
TCGA-D3-A2JF TCGA-EB-A5SH TCGA-EE-A180 TCGA-FR-A729 TCGA-D3-A1Q9 TCGA-D3-A2J6 
       62.07        54.02        94.98       220.80        31.59        43.43 
TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JP TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3CF 
      168.00        86.76        59.57       166.52        60.23        24.53 
TCGA-D3-A51E TCGA-D3-A8GB TCGA-D9-A3Z3 TCGA-D9-A6EC TCGA-DA-A3F3 TCGA-DA-A95V 
      174.84        30.84        22.29        77.56        10.49        72.10 
TCGA-DA-A95Y TCGA-EB-A44Q TCGA-EB-A6L9 TCGA-EE-A20F TCGA-EE-A29W TCGA-EE-A29X 
       14.14        13.87        36.46        91.56       195.02        17.92 
TCGA-EE-A2GB TCGA-EE-A2GH TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2M5 TCGA-EE-A2MC 
       59.28       220.24        13.91        42.77        21.67        61.51 
TCGA-EE-A2MM TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JI TCGA-ER-A19M TCGA-ER-A19N 
      167.90        53.19       201.80       152.81        61.05        44.09 
TCGA-ER-A19Q TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A2NF TCGA-ER-A3ES TCGA-ER-A3ET 
       50.89         8.88       148.18        28.83       247.04        93.01 
TCGA-ER-A42K TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1ZB TCGA-FS-A1ZD TCGA-FS-A1ZK 
       12.95       216.92        48.59        48.85        53.52        23.93 
TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A4F2 TCGA-FS-A4FD TCGA-GF-A4EO 
      133.55       148.80        53.16        50.14        80.68        19.43 
TCGA-GN-A266 TCGA-GN-A268 TCGA-GN-A26D TCGA-GN-A4U7 TCGA-GN-A8LL TCGA-WE-A8K1 
       10.13        62.79        48.00        10.42        21.37        49.05 
TCGA-WE-A8K6 TCGA-WE-A8ZN TCGA-WE-A8ZQ TCGA-WE-A8ZX TCGA-YG-AA3P TCGA-Z2-AA3V 
       17.95        58.98        63.22        35.80        14.43        15.98 

$`AMP PEAK 13(11Q13.3) WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-D3-A8GI TCGA-EB-A5SG TCGA-EE-A184 
       27.65        46.32        13.87        58.52        68.25        68.15 
TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD 
      168.26         2.60       340.14       126.81       134.40        27.35 
TCGA-ER-A193 TCGA-ER-A198 TCGA-FS-A1ZF TCGA-FW-A3R5 TCGA-QB-AA9O TCGA-WE-A8K5 
       31.40        50.76        15.45        36.95        18.05        61.15 
TCGA-WE-AAA3 TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 
       21.40        17.03        66.48        12.99        14.93        16.57 
TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       16.67       112.04       112.57        71.80       133.25        28.08 
TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA 
       90.90        95.74       103.10        65.49        23.77       115.53 
TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       11.87       113.52        42.08        12.10       171.58        66.48 
TCGA-D3-A2JO TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CC TCGA-D3-A3MO 
       66.08       130.72        58.06        46.98        86.93         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
      103.59        39.75        45.30        55.73        56.35       145.12 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN 
       32.94        22.62        63.81        26.89       125.79       135.75 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GC TCGA-D3-A8GD 
      137.92       178.32        18.18       125.19        79.59        23.61 
TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GN 
       26.43       241.38       170.20        89.13       107.15       161.00 
TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D3-A8GV TCGA-D9-A148 
      152.75        29.06       129.63       117.17       167.70       151.53 
TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A4Z6 
       54.67         3.65         7.10        18.12        15.39        18.44 
TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY 
        9.90        25.18        22.95        76.57        36.03       144.89 
TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 
       20.38       222.51       176.55        35.93       135.02        88.87 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 
       53.92        65.92        40.60        68.09        33.93       225.96 
TCGA-DA-A3F8 TCGA-DA-A95W TCGA-DA-A95X TCGA-DA-A95Z TCGA-EB-A44R TCGA-EB-A5KH 
       43.36        37.35        73.94        13.02        10.36        20.35 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
       29.29        58.92         7.04        29.82        27.22         8.65 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C 
       33.73        14.70        26.89         4.96       133.81       151.27 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
       13.55        63.35        85.08        78.97        13.97        63.78 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
       72.07        64.64        56.84        18.61        56.42        66.74 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A2A0 TCGA-EE-A2A1 
       14.47        61.28       369.93        25.87        46.82       115.96 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GI 
       59.64        39.29        86.14        67.43       173.79        48.72 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GS 
      107.38        54.74        79.66        75.48       102.12        81.21 
TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MD 
       44.88        94.82       129.27        28.83        19.76        47.28 
TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ 
      103.27       268.73       103.20        16.96       204.66        96.23 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MS 
      180.39       216.66        47.54       248.65        43.23       162.48 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
       71.21        53.26       124.31       122.73        64.04        28.77 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 
       54.51        13.81        41.59       138.81       172.18       127.20 
TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A195 
       36.95        64.08        34.32        51.35       134.33        35.44 
TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D 
       13.94         9.17        77.75        98.40        48.89        12.59 
TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L 
       13.02        26.37       302.07       152.35         6.44       131.51 
TCGA-ER-A19P TCGA-ER-A19S TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
      162.08        49.48       105.07        43.82        23.34        20.15 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A3YN 
       48.99        41.56        46.98        33.21       149.03        92.98 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC 
      174.21        15.72        27.85        18.77        38.27        34.82 
TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 
       36.26       104.42       228.59       202.65        20.91        28.08 
TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZC TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZH 
        7.79        27.72       357.37        46.45         9.70        32.75 
TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZU TCGA-FS-A1ZW 
       47.38       101.26        74.73        11.41        26.56        49.48 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 
       27.09        27.02        77.82        66.67        28.73       174.84 
TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV 
       34.03        26.73        54.41        17.46        55.59        13.51 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 
       19.30         9.90         2.04        15.78       139.89       117.93 
TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 
       96.92        64.44        32.48       121.91        39.35        48.89 
TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A9SD TCGA-HR-A2OG TCGA-HR-A2OH TCGA-LH-A9QB 
       22.13        50.10        59.41         0.23        65.88       368.78 
TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 
      297.90         7.23         0.20         0.33         0.69       228.16 
TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1V 
       63.02       121.08         4.01        69.07       111.09        42.08 
TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8ZM TCGA-WE-A8ZO TCGA-WE-A8ZT 
      219.16       105.04        24.03       101.33        70.52        11.80 
TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-XV-AB01 TCGA-YD-A89C 
       49.51        12.16        40.41        24.99        13.25         6.90 
TCGA-YD-A9TA TCGA-YG-AA3O TCGA-Z2-A8RT TCGA-Z2-AA3S 
       49.18        37.94        27.58        96.99 

  AMP PEAK 13(11Q13.3) MUTATED AMP PEAK 13(11Q13.3) WILD-TYPE 
                          8.88                           0.20 
  AMP PEAK 13(11Q13.3) MUTATED AMP PEAK 13(11Q13.3) WILD-TYPE 
                        247.04                         369.93 
  AMP PEAK 13(11Q13.3) MUTATED AMP PEAK 13(11Q13.3) WILD-TYPE 
                        53.175                         51.055 
[1] "8.9 - 247.0 (53.2)" "0.2 - 369.9 (51.1)"
[1] "hr=" "1.1"
D13V3, continuous
                                vv
clus                             I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB
  AMP PEAK 13(11Q13.3) MUTATED          6       2       9        2        4
  AMP PEAK 13(11Q13.3) WILD-TYPE        7       5      20       16       24
                                vv
clus                             STAGE II STAGE IIA STAGE IIB STAGE IIC
  AMP PEAK 13(11Q13.3) MUTATED          3         2         4         5
  AMP PEAK 13(11Q13.3) WILD-TYPE       23        12        15        10
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  AMP PEAK 13(11Q13.3) MUTATED           6          2          9          9
  AMP PEAK 13(11Q13.3) WILD-TYPE        33         13         26         45
                                vv
clus                             STAGE IV
  AMP PEAK 13(11Q13.3) MUTATED          1
  AMP PEAK 13(11Q13.3) WILD-TYPE       20
D13V4, multiclass
            clus
vv           AMP PEAK 13(11Q13.3) MUTATED AMP PEAK 13(11Q13.3) WILD-TYPE
  I/II NOS                              6                              7
  STAGE 0                               2                              5
  STAGE I                               9                             20
  STAGE IA                              2                             16
  STAGE IB                              4                             24
  STAGE II                              3                             23
  STAGE IIA                             2                             12
  STAGE IIB                             4                             15
  STAGE IIC                             5                             10
  STAGE III                             6                             33
  STAGE IIIA                            2                             13
  STAGE IIIB                            9                             26
  STAGE IIIC                            9                             45
  STAGE IV                              1                             20
[1] 14  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  AMP PEAK 13(11Q13.3) MUTATED      10 18 10 17
  AMP PEAK 13(11Q13.3) WILD-TYPE    54 55 71 50
D13V5, multiclass
       clus
vv      AMP PEAK 13(11Q13.3) MUTATED AMP PEAK 13(11Q13.3) WILD-TYPE
  T0+T1                           10                             54
  T2                              18                             55
  T3                              10                             71
  T4                              17                             50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2  N3
  AMP PEAK 13(11Q13.3) MUTATED    38  11   3  11
  AMP PEAK 13(11Q13.3) WILD-TYPE 139  54  36  34
D13V6, multiclass
    clus
vv   AMP PEAK 13(11Q13.3) MUTATED AMP PEAK 13(11Q13.3) WILD-TYPE
  N0                           38                            139
  N1                           11                             54
  N2                            3                             36
  N3                           11                             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"
D13V7, binary
                                cls
clus                               0   1
  AMP PEAK 13(11Q13.3) MUTATED    62   1
  AMP PEAK 13(11Q13.3) WILD-TYPE 257  21
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 13(11Q13.3) MUTATED     62    1
  AMP PEAK 13(11Q13.3) WILD-TYPE  257   21
   clus
vv  AMP PEAK 13(11Q13.3) MUTATED AMP PEAK 13(11Q13.3) WILD-TYPE
  0                           62                            257
  1                            1                             21
[1] 2 2
[1] FALSE
D13V8, binary
                                cls
clus                               0   1
  AMP PEAK 13(11Q13.3) MUTATED    24  17
  AMP PEAK 13(11Q13.3) WILD-TYPE 110  73
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 13(11Q13.3) MUTATED     24   17
  AMP PEAK 13(11Q13.3) WILD-TYPE  110   73
     clus
vv    AMP PEAK 13(11Q13.3) MUTATED AMP PEAK 13(11Q13.3) WILD-TYPE
  NO                            24                            110
  YES                           17                             73
[1] 2 2
[1] FALSE
D13V9, binary
                                cls
clus                               0   1
  AMP PEAK 13(11Q13.3) MUTATED     8  61
  AMP PEAK 13(11Q13.3) WILD-TYPE  39 259
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 13(11Q13.3) MUTATED      8   61
  AMP PEAK 13(11Q13.3) WILD-TYPE   39  259
     clus
vv    AMP PEAK 13(11Q13.3) MUTATED AMP PEAK 13(11Q13.3) WILD-TYPE
  NO                             8                             39
  YES                           61                            259
[1] 2 2
[1] FALSE
D13V10, continuous
D13V11, binary
                                cls
clus                               0   1
  AMP PEAK 13(11Q13.3) MUTATED    28  41
  AMP PEAK 13(11Q13.3) WILD-TYPE 110 188
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 13(11Q13.3) MUTATED     28   41
  AMP PEAK 13(11Q13.3) WILD-TYPE  110  188
        clus
vv       AMP PEAK 13(11Q13.3) MUTATED AMP PEAK 13(11Q13.3) WILD-TYPE
  FEMALE                           28                            110
  MALE                             41                            188
[1] 2 2
[1] FALSE
D13V12, binary
                                cls
clus                               0   1
  AMP PEAK 13(11Q13.3) MUTATED    56  13
  AMP PEAK 13(11Q13.3) WILD-TYPE 263  34
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 13(11Q13.3) MUTATED     56   13
  AMP PEAK 13(11Q13.3) WILD-TYPE  263   34
     clus
vv    AMP PEAK 13(11Q13.3) MUTATED AMP PEAK 13(11Q13.3) WILD-TYPE
  NO                            56                            263
  YES                           13                             34
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 13(11Q13.3) MUTATED       2                         1    63
  AMP PEAK 13(11Q13.3) WILD-TYPE     3                         0   290
D13V13, multiclass
                           clus
vv                          AMP PEAK 13(11Q13.3) MUTATED
  ASIAN                                                2
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                               63
                           clus
vv                          AMP PEAK 13(11Q13.3) WILD-TYPE
  ASIAN                                                  3
  BLACK OR AFRICAN AMERICAN                              0
  WHITE                                                290
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V14, binary
                                cls
clus                               0   1
  AMP PEAK 13(11Q13.3) MUTATED     1  68
  AMP PEAK 13(11Q13.3) WILD-TYPE   6 284
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 13(11Q13.3) MUTATED      1   68
  AMP PEAK 13(11Q13.3) WILD-TYPE    6  284
                        clus
vv                       AMP PEAK 13(11Q13.3) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           68
                        clus
vv                       AMP PEAK 13(11Q13.3) WILD-TYPE
  HISPANIC OR LATINO                                  6
  NOT HISPANIC OR LATINO                            284
[1] 2 2
[1] FALSE

Clustering(14) Variable = AMP PEAK 14(12Q14.1) MUTATION ANALYSIS
D14V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 14(12Q14.1) MUTATED    15  25
  AMP PEAK 14(12Q14.1) WILD-TYPE 113  99
  AMP PEAK 14(12Q14.1) MUTATED AMP PEAK 14(12Q14.1) WILD-TYPE 
                            40                            212 
  AMP PEAK 14(12Q14.1) MUTATED AMP PEAK 14(12Q14.1) WILD-TYPE 
                            25                             99 
$`AMP PEAK 14(12Q14.1) MUTATED`
TCGA-EE-A180 TCGA-FR-A729 TCGA-D3-A1Q1 TCGA-D3-A1Q6 TCGA-D3-A2J6 TCGA-D3-A2JN 
       31.96       216.43         8.42        49.35        25.64        64.83 
TCGA-D3-A2JO TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A5GN TCGA-D3-A5GU 
       66.08        58.06        40.01        24.53        45.70       124.08 
TCGA-DA-A1HV TCGA-DA-A3F5 TCGA-DA-A95V TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q 
       76.34       225.11        72.10        14.14        12.30         3.91 
TCGA-EE-A17Y TCGA-EE-A29D TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GH TCGA-EE-A2MS 
       24.89        12.99        77.98        26.14       201.60       143.93 
TCGA-ER-A197 TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19M TCGA-ER-A2NE TCGA-ER-A3ET 
       10.49        53.29        39.81        59.84        16.87        68.52 
TCGA-ER-A3PL TCGA-FS-A1ZE TCGA-FS-A1ZM TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 
       32.05        43.92        78.61       117.93        17.06        42.48 
TCGA-GN-A26A TCGA-W3-A825 TCGA-W3-AA1V TCGA-YG-AA3O 
        7.59         1.97         8.09        28.21 

$`AMP PEAK 14(12Q14.1) WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A8GI TCGA-EB-A5SG TCGA-EE-A20H 
        9.76        62.07        38.76        13.41        33.24       166.75 
TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-FW-A3R5 
      269.03        52.90       134.40        27.35        19.04        36.95 
TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q3 
       52.73         7.40        60.46        12.99        14.83        15.72 
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB 
       31.89       110.93       133.25        19.04        76.41        62.60 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JG 
       45.99        62.86        15.75       168.00        86.30       107.61 
TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JP TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3MO 
       36.30       171.58        43.53       140.98        59.70         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K 
       90.21        23.67       173.85        30.67       144.46        31.76 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GR TCGA-D3-A8GC TCGA-D3-A8GD 
       62.70        11.34        42.05       177.86        78.21        23.61 
TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GP TCGA-D3-A8GR 
      179.97       120.00        69.53        70.62       135.12        36.53 
TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6EC TCGA-D9-A6EG 
       10.78        15.02        16.90        18.44        69.21        22.85 
TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA 
      138.67        68.68       150.61       110.53        60.10        64.83 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F8 TCGA-DA-A95W TCGA-DA-A95X TCGA-EB-A5KH 
       58.85        30.44         8.71         0.76        65.03        16.41 
TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
       52.41        18.21        13.15        20.38         0.00        26.24 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G 
       75.55        79.20        75.22        76.14         0.26        44.28 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W 
       47.41        47.74        27.16        61.12       346.49       185.19 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2GE TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
      115.43        30.02        12.95        68.65        10.62        32.48 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU 
       18.35        93.63         0.76         0.20        71.31        81.99 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MG 
      103.13        15.25         5.75        23.77       209.79        94.19 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP 
      171.85        63.25        89.26       104.78       145.45       227.01 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
       23.51        53.26       124.31       122.73        64.04         4.41 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 
       54.51         6.28        67.89       111.85        45.90         3.35 
TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A199 TCGA-ER-A19A 
      168.85        19.86       135.98        34.45         7.82         4.54 
TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A19P 
       11.47       184.60       150.12        99.06        42.51       120.76 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       49.71        47.18       146.63        73.05        22.36         4.70 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3EV TCGA-ER-A42L TCGA-FR-A3YN 
       10.19        28.67       173.29        15.48        74.47         4.50 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FS-A1YW 
      174.21         4.14        26.20         5.65        10.06       171.78 
TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD 
       49.74       195.98         8.35        27.62       312.07        32.78 
TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU 
        7.82        36.33       130.95       136.27        35.28         4.47 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 
       23.21         5.29         3.06        30.90        66.67       173.19 
TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
       13.28        80.68        55.59        11.54        19.30         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A4U3 TCGA-GN-A4U4 
       18.25         1.91        53.29        96.92       120.53        34.49 
TCGA-GN-A4U8 TCGA-GN-A8LK TCGA-GN-A9SD TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS 
       46.92        43.23        59.41        85.05       297.01         7.23 
TCGA-RP-A690 TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A828 TCGA-W3-AA1Q TCGA-W3-AA1R 
        0.20         0.33       174.12       120.07        44.05        79.99 
TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO 
      185.13        92.84        47.54        65.42        12.69        21.90 
TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 
       62.89        10.95        48.39         1.94        37.32        24.99 
TCGA-XV-AB01 TCGA-Z2-AA3S 
        6.61        91.23 

  AMP PEAK 14(12Q14.1) MUTATED AMP PEAK 14(12Q14.1) WILD-TYPE 
                          1.97                           0.00 
  AMP PEAK 14(12Q14.1) MUTATED AMP PEAK 14(12Q14.1) WILD-TYPE 
                        225.11                         346.49 
  AMP PEAK 14(12Q14.1) MUTATED AMP PEAK 14(12Q14.1) WILD-TYPE 
                        41.245                         47.475 
[1] "2.0 - 225.1 (41.2)" "0.0 - 346.5 (47.5)"
[1] "hr=" "1.6"
D14V2, survival
                                sevent
clus2                              0   1
  AMP PEAK 14(12Q14.1) MUTATED    21  36
  AMP PEAK 14(12Q14.1) WILD-TYPE 145 156
  AMP PEAK 14(12Q14.1) MUTATED AMP PEAK 14(12Q14.1) WILD-TYPE 
                            57                            301 
  AMP PEAK 14(12Q14.1) MUTATED AMP PEAK 14(12Q14.1) WILD-TYPE 
                            36                            156 
$`AMP PEAK 14(12Q14.1) MUTATED`
TCGA-EE-A180 TCGA-FR-A729 TCGA-FS-A1ZF TCGA-QB-AA9O TCGA-D3-A1Q1 TCGA-D3-A1Q6 
       94.98       220.80        15.45        18.05        16.57        71.80 
TCGA-D3-A1Q9 TCGA-D3-A2J6 TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A3BZ TCGA-D3-A3C6 
       31.59        43.43        66.48        66.08       130.72        58.06 
TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3MV TCGA-D3-A5GN TCGA-D3-A5GS TCGA-D3-A5GU 
       86.93        24.53        45.30       135.75        18.18       125.19 
TCGA-D3-A8GV TCGA-D9-A6E9 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A3F5 TCGA-DA-A95V 
      167.70         9.90        76.57        36.03       225.96        72.10 
TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5UL TCGA-EE-A17Y TCGA-EE-A17Z 
       14.14        13.02        13.87        29.29        27.22         8.65 
TCGA-EE-A29D TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GH TCGA-EE-A2M5 TCGA-EE-A2MS 
       13.97        86.14        59.28       220.24        21.67       162.48 
TCGA-EE-A3J5 TCGA-EE-A3JE TCGA-ER-A197 TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19M 
       36.95        51.35        13.94        98.40        48.89        61.05 
TCGA-ER-A2NE TCGA-ER-A3ET TCGA-ER-A3PL TCGA-FS-A1ZE TCGA-FS-A1ZK TCGA-FS-A1ZM 
       20.15        93.01        33.21        46.45        23.93       101.26 
TCGA-FS-A4F5 TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
       28.73       117.93        64.44        62.79        32.48        48.00 
TCGA-W3-A825 TCGA-W3-AA1V TCGA-YG-AA3O 
       63.02        42.08        37.94 

$`AMP PEAK 14(12Q14.1) WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-D3-A8GI TCGA-EB-A5SG 
       27.65        62.07        46.32        13.87        58.52        68.25 
TCGA-EB-A5SH TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2GO 
       54.02        68.15       168.26         2.60       340.14       126.81 
TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-ER-A198 TCGA-FW-A3R5 TCGA-WE-A8K5 
      134.40        27.35        31.40        50.76        36.95        61.15 
TCGA-WE-AAA3 TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q3 
       21.40        17.03        66.48        12.99        14.93        16.67 
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB 
      112.04       112.57       133.25        28.08        90.90        95.74 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC 
      103.10        65.49        23.77       115.53       168.00        86.76 
TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JP 
       11.87       113.52        42.08        12.10       171.58        59.57 
TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU 
       46.98       166.52        60.23         9.34       103.59        39.75 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
      174.84        55.73        56.35       145.12        32.94        22.62 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A8GB 
       63.81        26.89       125.79       137.92       178.32        30.84 
TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL 
       79.59        23.61        26.43       241.38       170.20        89.13 
TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS 
      107.15       161.00       152.75        29.06       129.63       117.17 
TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A1X3 TCGA-D9-A3Z1 
      151.53        54.67         3.65         7.10        18.12        15.39 
TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HY 
       22.29        18.44        25.18        77.56        22.95       144.89 
TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 
       20.38       222.51       176.55        35.93       135.02        88.87 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
       53.92        65.92        40.60        68.09        33.93        10.49 
TCGA-DA-A3F8 TCGA-DA-A95W TCGA-DA-A95X TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5UN 
       43.36        37.35        73.94        10.36        20.35        58.92 
TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
        7.04        36.46        29.82        33.73        14.70        26.89 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29A 
        4.96       133.81       151.27        91.56        13.55        63.35 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M 
       85.08        78.97        63.78        72.07        64.64        56.84 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T 
       18.61        56.42        66.74        14.47        61.28       369.93 
TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
       25.87       195.02        17.92        46.82       115.96        59.64 
TCGA-EE-A2A5 TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
       39.29        67.43       173.79        48.72       107.38        54.74 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
       79.66        75.48       102.12        13.91        42.77        81.21 
TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
       44.88        94.82       129.27        28.83        19.76        61.51 
TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
       47.28       103.27       268.73       103.20        16.96       204.66 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP 
       96.23       180.39       216.66       167.90        47.54       248.65 
TCGA-EE-A2MQ TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC 
       43.23        71.21        53.26       124.31       122.73        64.04 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 
       28.77        54.51        13.81        41.59       138.81       172.18 
TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JH 
      127.20        64.08        34.32        53.19       201.80       134.33 
TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19D TCGA-ER-A19E 
      152.81        35.44         9.17        77.75        12.59        13.02 
TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19N 
       26.37       302.07       152.35         6.44       131.51        44.09 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 
      162.08        50.89        49.48         8.88       148.18       105.07 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES 
       43.82        23.34        28.83        48.99        41.56       247.04 
TCGA-ER-A3EV TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       46.98        12.95       149.03        92.98       174.21        15.72 
TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE 
       27.85        18.77        38.27        34.82        36.26       104.42 
TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 
      216.92        48.59       228.59       202.65        20.91        28.08 
TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZG 
        7.79        27.72        48.85       357.37        53.52         9.70 
TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS 
       32.75        47.38        74.73       133.55        11.41       148.80 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 
       53.16        26.56        49.48        27.09        27.02        77.82 
TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC 
       50.14        66.67       174.84        34.03        26.73        54.41 
TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
       80.68        17.46        55.59        13.51        19.30         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A266 
       19.43         2.04        15.78       139.89        96.92        10.13 
TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK 
      121.91        39.35        10.42        48.89        22.13        50.10 
TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OG TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X 
       21.37        59.41         0.23        65.88       368.78       297.90 
TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A828 
        7.23         0.20         0.33         0.69       228.16       121.08 
TCGA-W3-AA1O TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8JZ 
        4.01        69.07       111.09       219.16       105.04        24.03 
TCGA-WE-A8K1 TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ 
       49.05        17.95       101.33        58.98        70.52        63.22 
TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 
       11.80        35.80        49.51        12.16        40.41        24.99 
TCGA-XV-AB01 TCGA-YD-A89C TCGA-YD-A9TA TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S 
       13.25         6.90        49.18        14.43        27.58        96.99 
TCGA-Z2-AA3V 
       15.98 

  AMP PEAK 14(12Q14.1) MUTATED AMP PEAK 14(12Q14.1) WILD-TYPE 
                          8.65                           0.20 
  AMP PEAK 14(12Q14.1) MUTATED AMP PEAK 14(12Q14.1) WILD-TYPE 
                        225.96                         369.93 
  AMP PEAK 14(12Q14.1) MUTATED AMP PEAK 14(12Q14.1) WILD-TYPE 
                         48.00                          53.26 
[1] "8.7 - 226.0 (48.0)" "0.2 - 369.9 (53.3)"
[1] "hr=" "1.4"
D14V3, continuous
                                vv
clus                             I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB
  AMP PEAK 14(12Q14.1) MUTATED          2       1       6        1        4
  AMP PEAK 14(12Q14.1) WILD-TYPE       11       6      23       17       24
                                vv
clus                             STAGE II STAGE IIA STAGE IIB STAGE IIC
  AMP PEAK 14(12Q14.1) MUTATED          4         0         4         6
  AMP PEAK 14(12Q14.1) WILD-TYPE       22        14        15         9
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  AMP PEAK 14(12Q14.1) MUTATED           6          4          8          6
  AMP PEAK 14(12Q14.1) WILD-TYPE        33         11         27         48
                                vv
clus                             STAGE IV
  AMP PEAK 14(12Q14.1) MUTATED          3
  AMP PEAK 14(12Q14.1) WILD-TYPE       18
D14V4, multiclass
            clus
vv           AMP PEAK 14(12Q14.1) MUTATED AMP PEAK 14(12Q14.1) WILD-TYPE
  I/II NOS                              2                             11
  STAGE 0                               1                              6
  STAGE I                               6                             23
  STAGE IA                              1                             17
  STAGE IB                              4                             24
  STAGE II                              4                             22
  STAGE IIA                             0                             14
  STAGE IIB                             4                             15
  STAGE IIC                             6                              9
  STAGE III                             6                             33
  STAGE IIIA                            4                             11
  STAGE IIIB                            8                             27
  STAGE IIIC                            6                             48
  STAGE IV                              3                             18
[1] 14  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  AMP PEAK 14(12Q14.1) MUTATED      10  9 11 17
  AMP PEAK 14(12Q14.1) WILD-TYPE    54 64 70 50
D14V5, multiclass
       clus
vv      AMP PEAK 14(12Q14.1) MUTATED AMP PEAK 14(12Q14.1) WILD-TYPE
  T0+T1                           10                             54
  T2                               9                             64
  T3                              11                             70
  T4                              17                             50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2  N3
  AMP PEAK 14(12Q14.1) MUTATED    31  15   4   5
  AMP PEAK 14(12Q14.1) WILD-TYPE 146  50  35  40
D14V6, multiclass
    clus
vv   AMP PEAK 14(12Q14.1) MUTATED AMP PEAK 14(12Q14.1) WILD-TYPE
  N0                           31                            146
  N1                           15                             50
  N2                            4                             35
  N3                            5                             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"
D14V7, binary
                                cls
clus                               0   1
  AMP PEAK 14(12Q14.1) MUTATED    51   3
  AMP PEAK 14(12Q14.1) WILD-TYPE 268  19
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 14(12Q14.1) MUTATED     51    3
  AMP PEAK 14(12Q14.1) WILD-TYPE  268   19
   clus
vv  AMP PEAK 14(12Q14.1) MUTATED AMP PEAK 14(12Q14.1) WILD-TYPE
  0                           51                            268
  1                            3                             19
[1] 2 2
[1] FALSE
D14V8, binary
                                cls
clus                               0   1
  AMP PEAK 14(12Q14.1) MUTATED    22  18
  AMP PEAK 14(12Q14.1) WILD-TYPE 112  72
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 14(12Q14.1) MUTATED     22   18
  AMP PEAK 14(12Q14.1) WILD-TYPE  112   72
     clus
vv    AMP PEAK 14(12Q14.1) MUTATED AMP PEAK 14(12Q14.1) WILD-TYPE
  NO                            22                            112
  YES                           18                             72
[1] 2 2
[1] FALSE
D14V9, binary
                                cls
clus                               0   1
  AMP PEAK 14(12Q14.1) MUTATED     4  54
  AMP PEAK 14(12Q14.1) WILD-TYPE  43 266
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 14(12Q14.1) MUTATED      4   54
  AMP PEAK 14(12Q14.1) WILD-TYPE   43  266
     clus
vv    AMP PEAK 14(12Q14.1) MUTATED AMP PEAK 14(12Q14.1) WILD-TYPE
  NO                             4                             43
  YES                           54                            266
[1] 2 2
[1] FALSE
D14V10, continuous
D14V11, binary
                                cls
clus                               0   1
  AMP PEAK 14(12Q14.1) MUTATED    22  36
  AMP PEAK 14(12Q14.1) WILD-TYPE 116 193
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 14(12Q14.1) MUTATED     22   36
  AMP PEAK 14(12Q14.1) WILD-TYPE  116  193
        clus
vv       AMP PEAK 14(12Q14.1) MUTATED AMP PEAK 14(12Q14.1) WILD-TYPE
  FEMALE                           22                            116
  MALE                             36                            193
[1] 2 2
[1] FALSE
D14V12, binary
                                cls
clus                               0   1
  AMP PEAK 14(12Q14.1) MUTATED    51   7
  AMP PEAK 14(12Q14.1) WILD-TYPE 268  40
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 14(12Q14.1) MUTATED     51    7
  AMP PEAK 14(12Q14.1) WILD-TYPE  268   40
     clus
vv    AMP PEAK 14(12Q14.1) MUTATED AMP PEAK 14(12Q14.1) WILD-TYPE
  NO                            51                            268
  YES                            7                             40
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 14(12Q14.1) MUTATED       2                         0    55
  AMP PEAK 14(12Q14.1) WILD-TYPE     3                         1   298
D14V13, multiclass
                           clus
vv                          AMP PEAK 14(12Q14.1) MUTATED
  ASIAN                                                2
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                               55
                           clus
vv                          AMP PEAK 14(12Q14.1) WILD-TYPE
  ASIAN                                                  3
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                298
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V14, binary
                                cls
clus                               0   1
  AMP PEAK 14(12Q14.1) MUTATED     2  55
  AMP PEAK 14(12Q14.1) WILD-TYPE   5 297
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 14(12Q14.1) MUTATED      2   55
  AMP PEAK 14(12Q14.1) WILD-TYPE    5  297
                        clus
vv                       AMP PEAK 14(12Q14.1) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           55
                        clus
vv                       AMP PEAK 14(12Q14.1) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                            297
[1] 2 2
[1] FALSE

Clustering(15) Variable = AMP PEAK 15(12Q15) MUTATION ANALYSIS
D15V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 15(12Q15) MUTATED    16  26
  AMP PEAK 15(12Q15) WILD-TYPE 112  98
  AMP PEAK 15(12Q15) MUTATED AMP PEAK 15(12Q15) WILD-TYPE 
                          42                          210 
  AMP PEAK 15(12Q15) MUTATED AMP PEAK 15(12Q15) WILD-TYPE 
                          26                           98 
$`AMP PEAK 15(12Q15) MUTATED`
TCGA-EE-A180 TCGA-D3-A1Q1 TCGA-D3-A1Q6 TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A3C6 
       31.96         8.42        49.35        64.83        66.08        58.06 
TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GU TCGA-D9-A1X3 
       40.01        24.53        42.05        45.70       124.08        10.78 
TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A3F5 TCGA-DA-A95V TCGA-DA-A95Y TCGA-DA-A95Z 
       69.21        76.34       225.11        72.10        14.14        12.30 
TCGA-EE-A17Y TCGA-EE-A29D TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GH TCGA-EE-A2MS 
       24.89        12.99        77.98        26.14       201.60       143.93 
TCGA-EE-A3JI TCGA-ER-A197 TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19G TCGA-ER-A19H 
      135.98        10.49        53.29        39.81       184.60       150.12 
TCGA-ER-A2NE TCGA-ER-A3ET TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-GN-A267 TCGA-GN-A268 
       16.87        68.52        78.61       130.95        17.06        42.48 
TCGA-GN-A26A TCGA-GN-A8LK TCGA-W3-A825 TCGA-W3-AA1V TCGA-WE-A8ZY TCGA-YG-AA3O 
        7.59        43.23         1.97         8.09        48.39        28.21 

$`AMP PEAK 15(12Q15) WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A8GI TCGA-EB-A5SG TCGA-EE-A20H 
        9.76        62.07        38.76        13.41        33.24       166.75 
TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-FR-A729 
      269.03        52.90       134.40        27.35        19.04       216.43 
TCGA-FW-A3R5 TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 
       36.95        52.73         7.40        60.46        12.99        14.83 
TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA 
       15.72        31.89       110.93       133.25        19.04        76.41 
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB 
       62.60        25.64        45.99        62.86        15.75       168.00 
TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JP TCGA-D3-A3CB 
       86.30       107.61        36.30       171.58        43.53       140.98 
TCGA-D3-A3CE TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F 
       59.70         9.34        90.21        23.67       173.85        30.67 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GR TCGA-D3-A8GC 
      144.46        31.76        62.70        11.34       177.86        78.21 
TCGA-D3-A8GD TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GP 
       23.61       179.97       120.00        69.53        70.62       135.12 
TCGA-D3-A8GR TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6EG TCGA-DA-A1HY 
       36.53        15.02        16.90        18.44        22.85       138.67 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC 
       68.68       150.61       110.53        60.10        64.83        58.85 
TCGA-DA-A3F2 TCGA-DA-A3F8 TCGA-DA-A95W TCGA-DA-A95X TCGA-EB-A44Q TCGA-EB-A5KH 
       30.44         8.71         0.76        65.03         3.91        16.41 
TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
       52.41        18.21        13.15        20.38         0.00        26.24 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G 
       75.55        79.20        75.22        76.14         0.26        44.28 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W 
       47.41        47.74        27.16        61.12       346.49       185.19 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2GE TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
      115.43        30.02        12.95        68.65        10.62        32.48 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU 
       18.35        93.63         0.76         0.20        71.31        81.99 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MG 
      103.13        15.25         5.75        23.77       209.79        94.19 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP 
      171.85        63.25        89.26       104.78       145.45       227.01 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
       23.51        53.26       124.31       122.73        64.04         4.41 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 
       54.51         6.28        67.89       111.85        45.90         3.35 
TCGA-EE-A3JB TCGA-EE-A3JH TCGA-ER-A195 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19D 
      168.85        19.86        34.45         7.82         4.54        11.47 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S 
       99.06        59.84        42.51       120.76        49.71        47.18 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NF TCGA-ER-A2NG 
      146.63        73.05        22.36         4.70        10.19        28.67 
TCGA-ER-A3ES TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A 
      173.29        15.48        32.05        74.47         4.50       174.21 
TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FS-A1YW TCGA-FS-A1YY 
        4.14        26.20         5.65        10.06       171.78        49.74 
TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE 
      195.98         8.35        27.62       312.07        32.78        43.92 
TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW 
        7.82        36.33       136.27        35.28         4.47        23.21 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 
        5.29         3.06        30.90        66.67       173.19        13.28 
TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
       80.68        55.59        11.54        19.30         9.90        18.25 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A4U3 TCGA-GN-A4U4 
        1.91        53.29       117.93        96.92       120.53        34.49 
TCGA-GN-A4U8 TCGA-GN-A9SD TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 
       46.92        59.41        85.05       297.01         7.23         0.20 
TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A828 TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1W 
        0.33       174.12       120.07        44.05        79.99       185.13 
TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ 
       92.84        47.54        65.42        12.69        21.90        62.89 
TCGA-WE-A8ZT TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-XV-AB01 TCGA-Z2-AA3S 
       10.95         1.94        37.32        24.99         6.61        91.23 

  AMP PEAK 15(12Q15) MUTATED AMP PEAK 15(12Q15) WILD-TYPE 
                        1.97                         0.00 
  AMP PEAK 15(12Q15) MUTATED AMP PEAK 15(12Q15) WILD-TYPE 
                      225.11                       346.49 
  AMP PEAK 15(12Q15) MUTATED AMP PEAK 15(12Q15) WILD-TYPE 
                      44.465                       47.050 
[1] "2.0 - 225.1 (44.5)" "0.0 - 346.5 (47.0)"
[1] "hr=" "1.4"
D15V2, survival
                              sevent
clus2                            0   1
  AMP PEAK 15(12Q15) MUTATED    22  35
  AMP PEAK 15(12Q15) WILD-TYPE 144 157
  AMP PEAK 15(12Q15) MUTATED AMP PEAK 15(12Q15) WILD-TYPE 
                          57                          301 
  AMP PEAK 15(12Q15) MUTATED AMP PEAK 15(12Q15) WILD-TYPE 
                          35                          157 
$`AMP PEAK 15(12Q15) MUTATED`
TCGA-EE-A180 TCGA-QB-AA9O TCGA-D3-A1Q1 TCGA-D3-A1Q6 TCGA-D3-A1Q9 TCGA-D3-A2JN 
       94.98        18.05        16.57        71.80        31.59        66.48 
TCGA-D3-A2JO TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3MV 
       66.08       130.72        58.06        86.93        24.53        45.30 
TCGA-D3-A51H TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GV 
       56.35       125.79       135.75        18.18       125.19       167.70 
TCGA-D9-A1X3 TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A3F5 TCGA-DA-A95V 
       18.12        77.56        76.57        36.03       225.96        72.10 
TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A5UL TCGA-EE-A17Y TCGA-EE-A29D TCGA-EE-A2A6 
       14.14        13.02        29.29        27.22        13.97        86.14 
TCGA-EE-A2GB TCGA-EE-A2GH TCGA-EE-A2M5 TCGA-EE-A2MS TCGA-EE-A3J5 TCGA-EE-A3JE 
       59.28       220.24        21.67       162.48        36.95        51.35 
TCGA-EE-A3JI TCGA-ER-A197 TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19G TCGA-ER-A19H 
      152.81        13.94        98.40        48.89       302.07       152.35 
TCGA-ER-A2NE TCGA-ER-A3ET TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A4F5 
       20.15        93.01        23.93       101.26       133.55        28.73 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A8LK TCGA-W3-A825 
       64.44        62.79        32.48        48.00        50.10        63.02 
TCGA-W3-AA1V TCGA-WE-A8ZY TCGA-YG-AA3O 
       42.08        49.51        37.94 

$`AMP PEAK 15(12Q15) WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-D3-A8GI TCGA-EB-A5SG 
       27.65        62.07        46.32        13.87        58.52        68.25 
TCGA-EB-A5SH TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2GO 
       54.02        68.15       168.26         2.60       340.14       126.81 
TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-ER-A198 TCGA-FR-A729 TCGA-FS-A1ZF 
      134.40        27.35        31.40        50.76       220.80        15.45 
TCGA-FW-A3R5 TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD 
       36.95        61.15        21.40        17.03        66.48        12.99 
TCGA-BF-AAP0 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       14.93        16.67       112.04       112.57       133.25        28.08 
TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 
       90.90        95.74        43.43       103.10        65.49        23.77 
TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH 
      115.53       168.00        86.76        11.87       113.52        42.08 
TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JP TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CE 
       12.10       171.58        59.57        46.98       166.52        60.23 
TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51J 
        9.34       103.59        39.75       174.84        55.73       145.12 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GO TCGA-D3-A5GR 
       32.94        22.62        63.81        26.89       137.92       178.32 
TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GK 
       30.84        79.59        23.61        26.43       241.38       170.20 
TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR 
       89.13       107.15       161.00       152.75        29.06       129.63 
TCGA-D3-A8GS TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 
      117.17       151.53        54.67         3.65         7.10        15.39 
TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EG TCGA-DA-A1HY 
       22.29        18.44         9.90        25.18        22.95       144.89 
TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 
       20.38       222.51       176.55        35.93       135.02        88.87 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
       53.92        65.92        40.60        68.09        33.93        10.49 
TCGA-DA-A3F8 TCGA-DA-A95W TCGA-DA-A95X TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH 
       43.36        37.35        73.94        13.87        10.36        20.35 
TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 
       58.92         7.04        36.46        29.82         8.65        33.73 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F 
       14.70        26.89         4.96       133.81       151.27        91.56 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G 
       13.55        63.35        85.08        78.97        63.78        72.07 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
       64.64        56.84        18.61        56.42        66.74        14.47 
TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 
       61.28       369.93        25.87       195.02        17.92        46.82 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GI 
      115.96        59.64        39.29        67.43       173.79        48.72 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP 
      107.38        54.74        79.66        75.48       102.12        13.91 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 
       42.77        81.21        44.88        94.82       129.27        28.83 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG 
       19.76        61.51        47.28       103.27       268.73       103.20 
TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
       16.96       204.66        96.23       180.39       216.66       167.90 
TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA 
       47.54       248.65        43.23        71.21        53.26       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG 
      122.73        64.04        28.77        54.51        13.81        41.59 
TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA 
      138.81       172.18       127.20        64.08        34.32        53.19 
TCGA-EE-A3JB TCGA-EE-A3JH TCGA-ER-A195 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19D 
      201.80       134.33        35.44         9.17        77.75        12.59 
TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
       13.02        26.37         6.44       131.51        61.05        44.09 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 
      162.08        50.89        49.48         8.88       148.18       105.07 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES 
       43.82        23.34        28.83        48.99        41.56       247.04 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A 
       46.98        33.21        12.95       149.03        92.98       174.21 
TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD 
       15.72        27.85        18.77        38.27        34.82        36.26 
TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
      104.42       216.92        48.59       228.59       202.65        20.91 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD 
       28.08         7.79        27.72        48.85       357.37        53.52 
TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZP TCGA-FS-A1ZR 
       46.45         9.70        32.75        47.38        74.73        11.41 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ 
      148.80        53.16        26.56        49.48        27.09        27.02 
TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB 
       77.82        50.14        66.67       174.84        34.03        26.73 
TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
       54.41        80.68        17.46        55.59        13.51        19.30 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 
        9.90        19.43         2.04        15.78       139.89       117.93 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 
       96.92        10.13       121.91        39.35        10.42        48.89 
TCGA-GN-A4U9 TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OG TCGA-HR-A2OH TCGA-LH-A9QB 
       22.13        21.37        59.41         0.23        65.88       368.78 
TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 
      297.90         7.23         0.20         0.33         0.69       228.16 
TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1W TCGA-W3-AA21 
      121.08         4.01        69.07       111.09       219.16       105.04 
TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO 
       24.03        49.05        17.95       101.33        58.98        70.52 
TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 
       63.22        11.80        35.80        12.16        40.41        24.99 
TCGA-XV-AB01 TCGA-YD-A89C TCGA-YD-A9TA TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S 
       13.25         6.90        49.18        14.43        27.58        96.99 
TCGA-Z2-AA3V 
       15.98 

  AMP PEAK 15(12Q15) MUTATED AMP PEAK 15(12Q15) WILD-TYPE 
                       13.02                         0.20 
  AMP PEAK 15(12Q15) MUTATED AMP PEAK 15(12Q15) WILD-TYPE 
                      302.07                       369.93 
  AMP PEAK 15(12Q15) MUTATED AMP PEAK 15(12Q15) WILD-TYPE 
                       58.06                        50.76 
[1] "13.0 - 302.1 (58.1)" "0.2 - 369.9 (50.8)" 
[1] "hr=" "1.2"
D15V3, continuous
                              vv
clus                           I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB
  AMP PEAK 15(12Q15) MUTATED          3       1       6        1        5
  AMP PEAK 15(12Q15) WILD-TYPE       10       6      23       17       23
                              vv
clus                           STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  AMP PEAK 15(12Q15) MUTATED          4         1         2         4         6
  AMP PEAK 15(12Q15) WILD-TYPE       22        13        17        11        33
                              vv
clus                           STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  AMP PEAK 15(12Q15) MUTATED            4          8          6        3
  AMP PEAK 15(12Q15) WILD-TYPE         11         27         48       18
D15V4, multiclass
            clus
vv           AMP PEAK 15(12Q15) MUTATED AMP PEAK 15(12Q15) WILD-TYPE
  I/II NOS                            3                           10
  STAGE 0                             1                            6
  STAGE I                             6                           23
  STAGE IA                            1                           17
  STAGE IB                            5                           23
  STAGE II                            4                           22
  STAGE IIA                           1                           13
  STAGE IIB                           2                           17
  STAGE IIC                           4                           11
  STAGE III                           6                           33
  STAGE IIIA                          4                           11
  STAGE IIIB                          8                           27
  STAGE IIIC                          6                           48
  STAGE IV                            3                           18
[1] 14  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           T0+T1 T2 T3 T4
  AMP PEAK 15(12Q15) MUTATED      11 10 10 15
  AMP PEAK 15(12Q15) WILD-TYPE    53 63 71 52
D15V5, multiclass
       clus
vv      AMP PEAK 15(12Q15) MUTATED AMP PEAK 15(12Q15) WILD-TYPE
  T0+T1                         11                           53
  T2                            10                           63
  T3                            10                           71
  T4                            15                           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  N3
  AMP PEAK 15(12Q15) MUTATED    29  15   5   5
  AMP PEAK 15(12Q15) WILD-TYPE 148  50  34  40
D15V6, multiclass
    clus
vv   AMP PEAK 15(12Q15) MUTATED AMP PEAK 15(12Q15) WILD-TYPE
  N0                         29                          148
  N1                         15                           50
  N2                          5                           34
  N3                          5                           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"
D15V7, binary
                              cls
clus                             0   1
  AMP PEAK 15(12Q15) MUTATED    51   3
  AMP PEAK 15(12Q15) WILD-TYPE 268  19
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 15(12Q15) MUTATED     51    3
  AMP PEAK 15(12Q15) WILD-TYPE  268   19
   clus
vv  AMP PEAK 15(12Q15) MUTATED AMP PEAK 15(12Q15) WILD-TYPE
  0                         51                          268
  1                          3                           19
[1] 2 2
[1] FALSE
D15V8, binary
                              cls
clus                             0   1
  AMP PEAK 15(12Q15) MUTATED    23  15
  AMP PEAK 15(12Q15) WILD-TYPE 111  75
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 15(12Q15) MUTATED     23   15
  AMP PEAK 15(12Q15) WILD-TYPE  111   75
     clus
vv    AMP PEAK 15(12Q15) MUTATED AMP PEAK 15(12Q15) WILD-TYPE
  NO                          23                          111
  YES                         15                           75
[1] 2 2
[1] FALSE
D15V9, binary
                              cls
clus                             0   1
  AMP PEAK 15(12Q15) MUTATED     4  55
  AMP PEAK 15(12Q15) WILD-TYPE  43 265
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 15(12Q15) MUTATED      4   55
  AMP PEAK 15(12Q15) WILD-TYPE   43  265
     clus
vv    AMP PEAK 15(12Q15) MUTATED AMP PEAK 15(12Q15) WILD-TYPE
  NO                           4                           43
  YES                         55                          265
[1] 2 2
[1] FALSE
D15V10, continuous
D15V11, binary
                              cls
clus                             0   1
  AMP PEAK 15(12Q15) MUTATED    19  40
  AMP PEAK 15(12Q15) WILD-TYPE 119 189
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 15(12Q15) MUTATED     19   40
  AMP PEAK 15(12Q15) WILD-TYPE  119  189
        clus
vv       AMP PEAK 15(12Q15) MUTATED AMP PEAK 15(12Q15) WILD-TYPE
  FEMALE                         19                          119
  MALE                           40                          189
[1] 2 2
[1] FALSE
D15V12, binary
                              cls
clus                             0   1
  AMP PEAK 15(12Q15) MUTATED    48  11
  AMP PEAK 15(12Q15) WILD-TYPE 271  36
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 15(12Q15) MUTATED     48   11
  AMP PEAK 15(12Q15) WILD-TYPE  271   36
     clus
vv    AMP PEAK 15(12Q15) MUTATED AMP PEAK 15(12Q15) WILD-TYPE
  NO                          48                          271
  YES                         11                           36
[1] 2 2
[1] FALSE
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 15(12Q15) MUTATED       1                         0    57
  AMP PEAK 15(12Q15) WILD-TYPE     4                         1   296
D15V13, multiclass
                           clus
vv                          AMP PEAK 15(12Q15) MUTATED
  ASIAN                                              1
  BLACK OR AFRICAN AMERICAN                          0
  WHITE                                             57
                           clus
vv                          AMP PEAK 15(12Q15) WILD-TYPE
  ASIAN                                                4
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                              296
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V14, binary
                              cls
clus                             0   1
  AMP PEAK 15(12Q15) MUTATED     2  56
  AMP PEAK 15(12Q15) WILD-TYPE   5 296
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 15(12Q15) MUTATED      2   56
  AMP PEAK 15(12Q15) WILD-TYPE    5  296
                        clus
vv                       AMP PEAK 15(12Q15) MUTATED
  HISPANIC OR LATINO                              2
  NOT HISPANIC OR LATINO                         56
                        clus
vv                       AMP PEAK 15(12Q15) WILD-TYPE
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                          296
[1] 2 2
[1] FALSE

Clustering(16) Variable = AMP PEAK 16(13Q31.3) MUTATION ANALYSIS
D16V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 16(13Q31.3) MUTATED    25  49
  AMP PEAK 16(13Q31.3) WILD-TYPE 103  75
  AMP PEAK 16(13Q31.3) MUTATED AMP PEAK 16(13Q31.3) WILD-TYPE 
                            74                            178 
  AMP PEAK 16(13Q31.3) MUTATED AMP PEAK 16(13Q31.3) WILD-TYPE 
                            49                             75 
$`AMP PEAK 16(13Q31.3) MUTATED`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A8GI TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A20H 
        9.76        62.07        13.41        33.24        31.96       166.75 
TCGA-FR-A729 TCGA-WE-AAA3 TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q6 
      216.43         7.40        12.99         8.42        15.72        49.35 
TCGA-D3-A2J6 TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A51T 
       25.64        43.53        58.06        40.01        59.70        11.34 
TCGA-D3-A5GU TCGA-D3-A8GD TCGA-D3-A8GL TCGA-D3-A8GM TCGA-DA-A1I7 TCGA-DA-A95W 
      124.08        23.61        69.53        70.62        60.10         0.76 
TCGA-EE-A17Y TCGA-EE-A29B TCGA-EE-A29G TCGA-EE-A29P TCGA-EE-A2GB TCGA-EE-A2GH 
       24.89        75.22        44.28        27.16        26.14       201.60 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2M7 TCGA-EE-A2MF TCGA-EE-A2MP 
       18.35        93.63         0.76        15.25       209.79       227.01 
TCGA-EE-A3AA TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-EE-A3JI TCGA-ER-A197 
      124.31         6.28        67.89        45.90       135.98        10.49 
TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19L TCGA-ER-A19M 
        7.82        53.29        39.81        11.47        99.06        59.84 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19S TCGA-ER-A2NC TCGA-ER-A3PL TCGA-FR-A69P 
       42.51       120.76        47.18        22.36        32.05         4.14 
TCGA-FR-A7U8 TCGA-FR-A8YC TCGA-FS-A1YW TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 
       26.20        10.06       171.78       195.98         8.35        27.62 
TCGA-FS-A1ZE TCGA-FS-A1ZQ TCGA-FS-A1ZT TCGA-FS-A1ZY TCGA-FS-A4FD TCGA-FW-A3TU 
       43.92       130.95        35.28         5.29        80.68        55.59 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A8LK TCGA-OD-A75X TCGA-W3-A824 TCGA-W3-A825 
       17.06        42.48        43.23       297.01       174.12         1.97 
TCGA-W3-AA1V TCGA-XV-AB01 
        8.09         6.61 

$`AMP PEAK 16(13Q31.3) WILD-TYPE`
TCGA-D3-A3C8 TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 
       38.76       269.03        52.90       134.40        27.35        19.04 
TCGA-FW-A3R5 TCGA-WE-A8K5 TCGA-3N-A9WC TCGA-BF-AAP0 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
       36.95        52.73        60.46        14.83        31.89       110.93 
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J7 TCGA-D3-A2J8 
      133.25        19.04        76.41        62.60        45.99        62.86 
TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL 
       15.75       168.00        86.30       107.61        36.30       171.58 
TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A3CB TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR 
       64.83        66.08       140.98        24.53         9.34        90.21 
TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R 
       23.67       173.85        30.67       144.46        31.76        62.70 
TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A8GC TCGA-D3-A8GJ TCGA-D3-A8GK 
       42.05        45.70       177.86        78.21       179.97       120.00 
TCGA-D3-A8GP TCGA-D3-A8GR TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 
      135.12        36.53        10.78        15.02        16.90        18.44 
TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 
       69.21        22.85        76.34       138.67        68.68       150.61 
TCGA-DA-A1I5 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 
      110.53        64.83        58.85        30.44       225.11         8.71 
TCGA-DA-A95V TCGA-DA-A95X TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5KH 
       72.10        65.03        14.14        12.30         3.91        16.41 
TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
       52.41        18.21        13.15        20.38         0.00        26.24 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H 
       75.55        79.20        76.14        12.99         0.26        47.41 
TCGA-EE-A29M TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A2 
       47.74        61.12       346.49       185.19       115.43        30.02 
TCGA-EE-A2A6 TCGA-EE-A2GE TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GR 
       77.98        12.95        68.65        10.62        32.48         0.20 
TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MG 
       71.31        81.99       103.13         5.75        23.77        94.19 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MS 
      171.85        63.25        89.26       104.78       145.45       143.93 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
       23.51        53.26       122.73        64.04         4.41        54.51 
TCGA-EE-A3J4 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH TCGA-ER-A195 TCGA-ER-A19A 
      111.85         3.35       168.85        19.86        34.45         4.54 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19Q TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2ND 
      184.60       150.12        49.71       146.63        73.05         4.70 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       16.87        10.19        28.67       173.29        68.52        15.48 
TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A7UA TCGA-FS-A1YY TCGA-FS-A1ZC 
       74.47         4.50       174.21         5.65        49.74       312.07 
TCGA-FS-A1ZD TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZS TCGA-FS-A1ZU 
       32.78         7.82        36.33        78.61       136.27         4.47 
TCGA-FS-A1ZW TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 
       23.21         3.06        30.90        66.67       173.19        13.28 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 
       11.54        19.30         9.90        18.25         1.91        53.29 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 
      117.93        96.92         7.59       120.53        34.49        46.92 
TCGA-GN-A9SD TCGA-LH-A9QB TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 TCGA-W3-A828 
       59.41        85.05         7.23         0.20         0.33       120.07 
TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8ZM 
       44.05        79.99       185.13        92.84        47.54        65.42 
TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y 
       12.69        21.90        62.89        10.95        48.39         1.94 
TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-Z2-AA3S 
       37.32        24.99        28.21        91.23 

  AMP PEAK 16(13Q31.3) MUTATED AMP PEAK 16(13Q31.3) WILD-TYPE 
                          0.76                           0.00 
  AMP PEAK 16(13Q31.3) MUTATED AMP PEAK 16(13Q31.3) WILD-TYPE 
                        297.01                         346.49 
  AMP PEAK 16(13Q31.3) MUTATED AMP PEAK 16(13Q31.3) WILD-TYPE 
                        41.245                         51.075 
[1] "0.8 - 297.0 (41.2)" "0.0 - 346.5 (51.1)"
[1] "hr=" "1.7"
D16V2, survival
                                sevent
clus2                              0   1
  AMP PEAK 16(13Q31.3) MUTATED    35  64
  AMP PEAK 16(13Q31.3) WILD-TYPE 131 128
  AMP PEAK 16(13Q31.3) MUTATED AMP PEAK 16(13Q31.3) WILD-TYPE 
                            99                            259 
  AMP PEAK 16(13Q31.3) MUTATED AMP PEAK 16(13Q31.3) WILD-TYPE 
                            64                            128 
$`AMP PEAK 16(13Q31.3) MUTATED`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A8GI TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A184 
       27.65        62.07        58.52        68.25        94.98        68.15 
TCGA-EE-A20H TCGA-EE-A29L TCGA-FR-A729 TCGA-QB-AA9O TCGA-WE-AAA3 TCGA-3N-A9WD 
      168.26         2.60       220.80        18.05        21.40        12.99 
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q6 TCGA-D3-A2J6 TCGA-D3-A2JP TCGA-D3-A3C6 
       16.57        16.67        71.80        43.43        59.57        58.06 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A51T TCGA-D3-A5GO TCGA-D3-A5GU TCGA-D3-A8GD 
       86.93        60.23        26.89       137.92       125.19        23.61 
TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D9-A6EA TCGA-DA-A1I7 TCGA-DA-A3F3 TCGA-DA-A95W 
       89.13       107.15        25.18        88.87        10.49        37.35 
TCGA-EB-A44R TCGA-EE-A17Y TCGA-EE-A20B TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29G 
       10.36        27.22       133.81        63.35        85.08        72.07 
TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A2A5 TCGA-EE-A2GB TCGA-EE-A2GH TCGA-EE-A2GM 
       56.42        14.47        39.29        59.28       220.24        75.48 
TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2M7 TCGA-EE-A2MF TCGA-EE-A2MP TCGA-EE-A3AA 
      102.12        13.91        28.83       268.73       248.65       124.31 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-EE-A3JI 
       13.81        41.59       172.18        64.08        53.19       152.81 
TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E 
       13.94         9.17        98.40        48.89        12.59        13.02 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19S TCGA-ER-A19T 
      131.51        61.05        44.09       162.08        49.48         8.88 
TCGA-ER-A2NC TCGA-ER-A3PL TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A8YC TCGA-FS-A1YW 
       43.82        33.21        15.72        27.85        34.82       216.92 
TCGA-FS-A1YX TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZE 
       48.59       202.65        20.91        28.08         7.79        46.45 
TCGA-FS-A1ZQ TCGA-FS-A1ZT TCGA-FS-A1ZY TCGA-FS-A4F2 TCGA-FS-A4FD TCGA-FW-A3TU 
      133.55        53.16        27.09        50.14        80.68        55.59 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-HR-A2OG TCGA-OD-A75X 
       64.44        62.79        22.13        50.10         0.23       297.90 
TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-AA1V TCGA-WE-A8K6 TCGA-WE-A8ZX TCGA-XV-AB01 
      228.16        63.02        42.08        17.95        35.80        13.25 
TCGA-YD-A89C TCGA-YD-A9TA TCGA-Z2-A8RT 
        6.90        49.18        27.58 

$`AMP PEAK 16(13Q31.3) WILD-TYPE`
TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SH TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR 
       46.32        13.87        54.02       340.14       126.81       134.40 
TCGA-EE-A3JD TCGA-ER-A193 TCGA-ER-A198 TCGA-FS-A1ZF TCGA-FW-A3R5 TCGA-WE-A8K5 
       27.35        31.40        50.76        15.45        36.95        61.15 
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-BF-AAP0 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 
       17.03        66.48        14.93       112.04       112.57       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J7 TCGA-D3-A2J8 
       28.08        31.59        90.90        95.74       103.10        65.49 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG 
       23.77       115.53       168.00        86.76        11.87       113.52 
TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A3BZ 
       42.08        12.10       171.58        66.48        66.08       130.72 
TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU 
       46.98       166.52        24.53         9.34       103.59        39.75 
TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K 
       45.30       174.84        55.73        56.35       145.12        32.94 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS 
       22.62        63.81       125.79       135.75       178.32        18.18 
TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GN 
       30.84        79.59        26.43       241.38       170.20       161.00 
TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D3-A8GV TCGA-D9-A148 
      152.75        29.06       129.63       117.17       167.70       151.53 
TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       54.67         3.65         7.10        18.12        15.39        22.29 
TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW 
       18.44         9.90        77.56        22.95        76.57        36.03 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
      144.89        20.38       222.51       176.55        35.93       135.02 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 
       53.92        65.92        40.60        68.09        33.93       225.96 
TCGA-DA-A3F8 TCGA-DA-A95V TCGA-DA-A95X TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q 
       43.36        72.10        73.94        14.14        13.02        13.87 
TCGA-EB-A5KH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X 
       20.35        29.29        58.92         7.04        36.46        29.82 
TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20C 
        8.65        33.73        14.70        26.89         4.96       151.27 
TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H 
       91.56        13.55        78.97        13.97        63.78        64.64 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V 
       56.84        18.61        66.74        61.28       369.93        25.87 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 
      195.02        17.92        46.82       115.96        59.64        86.14 
TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       67.43       173.79        48.72       107.38        54.74        79.66 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 
       42.77        81.21        44.88        94.82        21.67       129.27 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH 
       19.76        61.51        47.28       103.27       103.20        16.96 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN 
      204.66        96.23       180.39       216.66       167.90        47.54 
TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC 
       43.23       162.48        71.21        53.26       122.73        64.04 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J8 
       28.77        54.51       138.81       127.20        36.95        34.32 
TCGA-EE-A3JB TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A195 TCGA-ER-A19A TCGA-ER-A19F 
      201.80        51.35       134.33        35.44        77.75        26.37 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19Q TCGA-ER-A19W TCGA-ER-A1A1 
      302.07       152.35         6.44        50.89       148.18       105.07 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES 
       23.34        20.15        28.83        48.99        41.56       247.04 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A 
       93.01        46.98        12.95       149.03        92.98       174.21 
TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YY TCGA-FS-A1ZA 
       18.77        38.27        36.26       104.42       228.59        27.72 
TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ 
       48.85       357.37        53.52         9.70        32.75        47.38 
TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZU 
       23.93       101.26        74.73        11.41       148.80        26.56 
TCGA-FS-A1ZW TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 
       49.48        27.02        77.82        66.67        28.73       174.84 
TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-FW-A3TV TCGA-FW-A5DY 
       34.03        26.73        54.41        17.46        13.51        19.30 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 
        9.90        19.43         2.04        15.78       139.89       117.93 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U4 
       96.92        10.13        32.48        48.00       121.91        39.35 
TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OH TCGA-LH-A9QB 
       10.42        48.89        21.37        59.41        65.88       368.78 
TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A828 TCGA-W3-AA1O 
        7.23         0.20         0.33         0.69       121.08         4.01 
TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K1 
       69.07       111.09       219.16       105.04        24.03        49.05 
TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZY 
      101.33        58.98        70.52        63.22        11.80        49.51 
TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-AA3S 
       12.16        40.41        24.99        37.94        14.43        96.99 
TCGA-Z2-AA3V 
       15.98 

  AMP PEAK 16(13Q31.3) MUTATED AMP PEAK 16(13Q31.3) WILD-TYPE 
                          0.23                           0.20 
  AMP PEAK 16(13Q31.3) MUTATED AMP PEAK 16(13Q31.3) WILD-TYPE 
                        297.90                         369.93 
  AMP PEAK 16(13Q31.3) MUTATED AMP PEAK 16(13Q31.3) WILD-TYPE 
                         50.10                          53.52 
[1] "0.2 - 297.9 (50.1)" "0.2 - 369.9 (53.5)"
[1] "hr=" "1.4"
D16V3, continuous
                                vv
clus                             I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB
  AMP PEAK 16(13Q31.3) MUTATED          3       1      11        4       12
  AMP PEAK 16(13Q31.3) WILD-TYPE       10       6      18       14       16
                                vv
clus                             STAGE II STAGE IIA STAGE IIB STAGE IIC
  AMP PEAK 16(13Q31.3) MUTATED          6         1         7         6
  AMP PEAK 16(13Q31.3) WILD-TYPE       20        13        12         9
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  AMP PEAK 16(13Q31.3) MUTATED           6          4         11         17
  AMP PEAK 16(13Q31.3) WILD-TYPE        33         11         24         37
                                vv
clus                             STAGE IV
  AMP PEAK 16(13Q31.3) MUTATED          4
  AMP PEAK 16(13Q31.3) WILD-TYPE       17
D16V4, multiclass
            clus
vv           AMP PEAK 16(13Q31.3) MUTATED AMP PEAK 16(13Q31.3) WILD-TYPE
  I/II NOS                              3                             10
  STAGE 0                               1                              6
  STAGE I                              11                             18
  STAGE IA                              4                             14
  STAGE IB                             12                             16
  STAGE II                              6                             20
  STAGE IIA                             1                             13
  STAGE IIB                             7                             12
  STAGE IIC                             6                              9
  STAGE III                             6                             33
  STAGE IIIA                            4                             11
  STAGE IIIB                           11                             24
  STAGE IIIC                           17                             37
  STAGE IV                              4                             17
[1] 14  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  AMP PEAK 16(13Q31.3) MUTATED      17 26 15 22
  AMP PEAK 16(13Q31.3) WILD-TYPE    47 47 66 45
D16V5, multiclass
       clus
vv      AMP PEAK 16(13Q31.3) MUTATED AMP PEAK 16(13Q31.3) WILD-TYPE
  T0+T1                           17                             47
  T2                              26                             47
  T3                              15                             66
  T4                              22                             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  N3
  AMP PEAK 16(13Q31.3) MUTATED    52  17   7  14
  AMP PEAK 16(13Q31.3) WILD-TYPE 125  48  32  31
D16V6, multiclass
    clus
vv   AMP PEAK 16(13Q31.3) MUTATED AMP PEAK 16(13Q31.3) WILD-TYPE
  N0                           52                            125
  N1                           17                             48
  N2                            7                             32
  N3                           14                             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"
D16V7, binary
                                cls
clus                               0   1
  AMP PEAK 16(13Q31.3) MUTATED    90   4
  AMP PEAK 16(13Q31.3) WILD-TYPE 229  18
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(13Q31.3) MUTATED     90    4
  AMP PEAK 16(13Q31.3) WILD-TYPE  229   18
   clus
vv  AMP PEAK 16(13Q31.3) MUTATED AMP PEAK 16(13Q31.3) WILD-TYPE
  0                           90                            229
  1                            4                             18
[1] 2 2
[1] FALSE
D16V8, binary
                                cls
clus                               0   1
  AMP PEAK 16(13Q31.3) MUTATED    33  27
  AMP PEAK 16(13Q31.3) WILD-TYPE 101  63
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(13Q31.3) MUTATED     33   27
  AMP PEAK 16(13Q31.3) WILD-TYPE  101   63
     clus
vv    AMP PEAK 16(13Q31.3) MUTATED AMP PEAK 16(13Q31.3) WILD-TYPE
  NO                            33                            101
  YES                           27                             63
[1] 2 2
[1] FALSE
D16V9, binary
                                cls
clus                               0   1
  AMP PEAK 16(13Q31.3) MUTATED    15  89
  AMP PEAK 16(13Q31.3) WILD-TYPE  32 231
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(13Q31.3) MUTATED     15   89
  AMP PEAK 16(13Q31.3) WILD-TYPE   32  231
     clus
vv    AMP PEAK 16(13Q31.3) MUTATED AMP PEAK 16(13Q31.3) WILD-TYPE
  NO                            15                             32
  YES                           89                            231
[1] 2 2
[1] FALSE
D16V10, continuous
D16V11, binary
                                cls
clus                               0   1
  AMP PEAK 16(13Q31.3) MUTATED    38  66
  AMP PEAK 16(13Q31.3) WILD-TYPE 100 163
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(13Q31.3) MUTATED     38   66
  AMP PEAK 16(13Q31.3) WILD-TYPE  100  163
        clus
vv       AMP PEAK 16(13Q31.3) MUTATED AMP PEAK 16(13Q31.3) WILD-TYPE
  FEMALE                           38                            100
  MALE                             66                            163
[1] 2 2
[1] FALSE
D16V12, binary
                                cls
clus                               0   1
  AMP PEAK 16(13Q31.3) MUTATED    93  11
  AMP PEAK 16(13Q31.3) WILD-TYPE 226  36
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(13Q31.3) MUTATED     93   11
  AMP PEAK 16(13Q31.3) WILD-TYPE  226   36
     clus
vv    AMP PEAK 16(13Q31.3) MUTATED AMP PEAK 16(13Q31.3) WILD-TYPE
  NO                            93                            226
  YES                           11                             36
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 16(13Q31.3) MUTATED       2                         0   101
  AMP PEAK 16(13Q31.3) WILD-TYPE     3                         1   252
D16V13, multiclass
                           clus
vv                          AMP PEAK 16(13Q31.3) MUTATED
  ASIAN                                                2
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                              101
                           clus
vv                          AMP PEAK 16(13Q31.3) WILD-TYPE
  ASIAN                                                  3
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                252
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V14, binary
                                cls
clus                               0   1
  AMP PEAK 16(13Q31.3) MUTATED     1  99
  AMP PEAK 16(13Q31.3) WILD-TYPE   6 253
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(13Q31.3) MUTATED      1   99
  AMP PEAK 16(13Q31.3) WILD-TYPE    6  253
                        clus
vv                       AMP PEAK 16(13Q31.3) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           99
                        clus
vv                       AMP PEAK 16(13Q31.3) WILD-TYPE
  HISPANIC OR LATINO                                  6
  NOT HISPANIC OR LATINO                            253
[1] 2 2
[1] FALSE

Clustering(17) Variable = AMP PEAK 17(15Q26.2) MUTATION ANALYSIS
D17V1, survival
                                sevent
clus2                             0  1
  AMP PEAK 17(15Q26.2) MUTATED   39 40
  AMP PEAK 17(15Q26.2) WILD-TYPE 89 84
  AMP PEAK 17(15Q26.2) MUTATED AMP PEAK 17(15Q26.2) WILD-TYPE 
                            79                            173 
  AMP PEAK 17(15Q26.2) MUTATED AMP PEAK 17(15Q26.2) WILD-TYPE 
                            40                             84 
$`AMP PEAK 17(15Q26.2) MUTATED`
TCGA-D3-A2JF TCGA-D3-A8GI TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GO TCGA-EE-A2MR 
       62.07        13.41        31.96       166.75        52.90       134.40 
TCGA-ER-A193 TCGA-FR-A729 TCGA-FW-A3R5 TCGA-D3-A1Q5 TCGA-D3-A2JA TCGA-D3-A2JC 
       19.04       216.43        36.95       110.93        15.75        86.30 
TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3MU TCGA-D3-A51E 
      171.58        64.83       140.98        59.70        23.67       173.85 
TCGA-D3-A51K TCGA-D3-A8GD TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D9-A3Z3 TCGA-DA-A1HV 
       31.76        23.61        69.53        70.62        16.90        76.34 
TCGA-DA-A1I7 TCGA-DA-A3F5 TCGA-EB-A44Q TCGA-EE-A17Y TCGA-EE-A183 TCGA-EE-A20F 
       60.10       225.11         3.91        24.89        26.24        79.20 
TCGA-EE-A29D TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2GH TCGA-EE-A2GM 
       12.99       346.49       185.19       115.43       201.60        18.35 
TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MJ 
       93.63         0.76        81.99       103.13        15.25        63.25 
TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AE TCGA-EE-A3AF 
      227.01       143.93       124.31       122.73        54.51         6.28 
TCGA-EE-A3J3 TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19M 
       67.89        19.86       135.98        39.81        11.47        59.84 
TCGA-ER-A19P TCGA-ER-A19S TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A42L TCGA-FR-A44A 
      120.76        47.18        68.52        15.48        74.47       174.21 
TCGA-FR-A69P TCGA-FR-A8YC TCGA-FS-A1Z3 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZJ 
        4.14        10.06         8.35       312.07        32.78        36.33 
TCGA-FS-A1ZQ TCGA-FS-A1ZY TCGA-FS-A4FD TCGA-GF-A4EO TCGA-GN-A264 TCGA-GN-A265 
      130.95         5.29        80.68        18.25       117.93        96.92 
TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A8LK TCGA-GN-A9SD TCGA-W3-A825 TCGA-WE-A8ZQ 
       17.06         7.59        43.23        59.41         1.97        62.89 
TCGA-XV-AB01 
        6.61 

$`AMP PEAK 17(15Q26.2) WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A2GD TCGA-EE-A3JD TCGA-WE-A8K5 
        9.76        38.76        33.24       269.03        27.35        52.73 
TCGA-WE-AAA3 TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 
        7.40        60.46        12.99        14.83         8.42        15.72 
TCGA-D3-A1Q4 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB 
       31.89        49.35       133.25        19.04        76.41        62.60 
TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JB TCGA-D3-A2JG TCGA-D3-A2JH 
       25.64        45.99        62.86       168.00       107.61        36.30 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3MO 
       66.08        43.53        58.06        40.01        24.53         9.34 
TCGA-D3-A3MR TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL 
       90.21        30.67       144.46        62.70        11.34        42.05 
TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D3-A8GC TCGA-D3-A8GJ TCGA-D3-A8GK 
       45.70       177.86       124.08        78.21       179.97       120.00 
TCGA-D3-A8GP TCGA-D3-A8GR TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A4Z6 TCGA-D9-A6EC 
      135.12        36.53        10.78        15.02        18.44        69.21 
TCGA-D9-A6EG TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1IA 
       22.85       138.67        68.68       150.61       110.53        64.83 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F8 TCGA-DA-A95V TCGA-DA-A95W TCGA-DA-A95X 
       58.85        30.44         8.71        72.10         0.76        65.03 
TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X 
       14.14        12.30        16.41        52.41        18.21        13.15 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A20C TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E 
       20.38         0.00        75.55        75.22        76.14         0.26 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A2A2 
       44.28        47.41        47.74        27.16        61.12        30.02 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       77.98        26.14        12.95        68.65        10.62        32.48 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MG 
        0.20        71.31         5.75        23.77       209.79        94.19 
TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MT TCGA-EE-A2MU 
      171.85        89.26       104.78       145.45        23.51        53.26 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB 
       64.04         4.41       111.85        45.90         3.35       168.85 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19G 
       34.45        10.49         7.82         4.54        53.29       184.60 
TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A19W TCGA-ER-A1A1 
      150.12        99.06        42.51        49.71       146.63        73.05 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES 
       22.36         4.70        16.87        10.19        28.67       173.29 
TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FS-A1YW TCGA-FS-A1YY 
       32.05         4.50        26.20         5.65       171.78        49.74 
TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZM TCGA-FS-A1ZS 
      195.98        27.62        43.92         7.82        78.61       136.27 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 
       35.28         4.47        23.21         3.06        30.90        66.67 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
      173.19        13.28        55.59        11.54        19.30         9.90 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A268 TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 
        1.91        53.29        42.48       120.53        34.49        46.92 
TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 TCGA-W3-A824 
       85.05       297.01         7.23         0.20         0.33       174.12 
TCGA-W3-A828 TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 
      120.07        44.05        79.99         8.09       185.13        92.84 
TCGA-WE-A8K1 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-A8ZY 
       47.54        65.42        12.69        21.90        10.95        48.39 
TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-Z2-AA3S 
        1.94        37.32        24.99        28.21        91.23 

  AMP PEAK 17(15Q26.2) MUTATED AMP PEAK 17(15Q26.2) WILD-TYPE 
                          0.76                           0.00 
  AMP PEAK 17(15Q26.2) MUTATED AMP PEAK 17(15Q26.2) WILD-TYPE 
                        346.49                         297.01 
  AMP PEAK 17(15Q26.2) MUTATED AMP PEAK 17(15Q26.2) WILD-TYPE 
                         60.10                          43.53 
[1] "0.8 - 346.5 (60.1)" "0.0 - 297.0 (43.5)"
[1] "hr=" "1.3"
D17V2, survival
                                sevent
clus2                              0   1
  AMP PEAK 17(15Q26.2) MUTATED    54  61
  AMP PEAK 17(15Q26.2) WILD-TYPE 112 131
  AMP PEAK 17(15Q26.2) MUTATED AMP PEAK 17(15Q26.2) WILD-TYPE 
                           115                            243 
  AMP PEAK 17(15Q26.2) MUTATED AMP PEAK 17(15Q26.2) WILD-TYPE 
                            61                            131 
$`AMP PEAK 17(15Q26.2) MUTATED`
TCGA-D3-A2JF TCGA-D3-A8GI TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GO TCGA-EE-A2MR 
       62.07        58.52        94.98       168.26       126.81       134.40 
TCGA-ER-A193 TCGA-FR-A729 TCGA-FW-A3R5 TCGA-D3-A1Q5 TCGA-D3-A1Q9 TCGA-D3-A2J9 
       31.40       220.80        36.95       112.57        31.59        23.77 
TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A3CB 
      115.53        86.76        11.87       171.58        66.48       166.52 
TCGA-D3-A3CE TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51K TCGA-D3-A8GB 
       60.23        39.75        45.30       174.84        32.94        30.84 
TCGA-D3-A8GD TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GQ TCGA-D9-A148 TCGA-D9-A149 
       23.61        89.13       107.15        29.06       151.53        54.67 
TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I7 
       22.29         9.90        25.18        76.57        36.03        88.87 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-EB-A44Q TCGA-EE-A17Y TCGA-EE-A183 TCGA-EE-A20B 
       10.49       225.96        13.87        27.22        26.89       133.81 
TCGA-EE-A20F TCGA-EE-A29D TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A1 
       91.56        13.97       369.93       195.02        17.92       115.96 
TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GU 
      220.24        48.72        75.48       102.12        13.91        94.82 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MD TCGA-EE-A2MJ TCGA-EE-A2MN TCGA-EE-A2MP 
      129.27        28.83        47.28        96.23        47.54       248.65 
TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AE TCGA-EE-A3AF 
       43.23       162.48       124.31       122.73        54.51        13.81 
TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J5 TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A19C 
       41.59       172.18        36.95       134.33       152.81        48.89 
TCGA-ER-A19D TCGA-ER-A19M TCGA-ER-A19P TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A3ET 
       12.59        61.05       162.08        49.48         8.88        93.01 
TCGA-ER-A3EV TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7U9 
       46.98        12.95       149.03       174.21        15.72        18.77 
TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FS-A1Z3 TCGA-FS-A1Z7 TCGA-FS-A1ZC TCGA-FS-A1ZD 
       34.82        36.26        20.91         7.79       357.37        53.52 
TCGA-FS-A1ZJ TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZY TCGA-FS-A4F2 TCGA-FS-A4FD 
       47.38        74.73       133.55        27.09        50.14        80.68 
TCGA-GF-A4EO TCGA-GF-A6C9 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A26A 
       19.43        15.78       117.93        96.92        64.44        32.48 
TCGA-GN-A8LK TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OG TCGA-W3-A825 TCGA-W3-AA1O 
       50.10        21.37        59.41         0.23        63.02         4.01 
TCGA-WE-A8K6 TCGA-WE-A8ZQ TCGA-WE-A8ZX TCGA-XV-AB01 TCGA-YD-A89C TCGA-YD-A9TA 
       17.95        63.22        35.80        13.25         6.90        49.18 
TCGA-Z2-AA3V 
       15.98 

$`AMP PEAK 17(15Q26.2) WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A184 
       27.65        46.32        13.87        68.25        54.02        68.15 
TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A3JD TCGA-ER-A198 TCGA-FS-A1ZF TCGA-QB-AA9O 
        2.60       340.14        27.35        50.76        15.45        18.05 
TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 
       61.15        21.40        17.03        66.48        12.99        14.93 
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       16.57        16.67       112.04        71.80       133.25        28.08 
TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JB 
       90.90        95.74        43.43       103.10        65.49       168.00 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ 
      113.52        42.08        12.10        66.08        59.57       130.72 
TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR 
       58.06        46.98        86.93        24.53         9.34       103.59 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T 
       55.73        56.35       145.12        22.62        63.81        26.89 
TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU 
      125.79       135.75       137.92       178.32        18.18       125.19 
TCGA-D3-A8GC TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GN TCGA-D3-A8GP 
       79.59        26.43       241.38       170.20       161.00       152.75 
TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D3-A8GV TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A1X3 
      129.63       117.17       167.70         3.65         7.10        18.12 
TCGA-D9-A3Z1 TCGA-D9-A4Z6 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HY TCGA-DA-A1I0 
       15.39        18.44        77.56        22.95       144.89        20.38 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A1IA 
      222.51       176.55        35.93       135.02        53.92        65.92 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F8 TCGA-DA-A95V TCGA-DA-A95W 
       40.60        68.09        33.93        43.36        72.10        37.35 
TCGA-DA-A95X TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5UL 
       73.94        14.14        13.02        10.36        20.35        29.29 
TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 
       58.92         7.04        36.46        29.82         8.65        33.73 
TCGA-EE-A182 TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
       14.70         4.96       151.27        13.55        63.35        85.08 
TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N 
       78.97        63.78        72.07        64.64        56.84        18.61 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A2A0 
       56.42        66.74        14.47        61.28        25.87        46.82 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GE 
       59.64        39.29        86.14        59.28        67.43       173.79 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT 
      107.38        54.74        79.66        42.77        81.21        44.88 
TCGA-EE-A2M5 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG 
       21.67        19.76        61.51       103.27       268.73       103.20 
TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MT 
       16.96       204.66       180.39       216.66       167.90        71.21 
TCGA-EE-A2MU TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J7 
       53.26        64.04        28.77       138.81       127.20        64.08 
TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JE TCGA-ER-A195 TCGA-ER-A197 
       34.32        53.19       201.80        51.35        35.44        13.94 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G 
        9.17        77.75        98.40        13.02        26.37       302.07 
TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A19W 
      152.35         6.44       131.51        44.09        50.89       148.18 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
      105.07        43.82        23.34        20.15        28.83        48.99 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A7U8 TCGA-FR-A7UA 
       41.56       247.04        33.21        92.98        27.85        38.27 
TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z4 
      104.42       216.92        48.59       228.59       202.65        28.08 
TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZK 
       27.72        48.85        46.45         9.70        32.75        23.93 
TCGA-FS-A1ZM TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW 
      101.26        11.41       148.80        53.16        26.56        49.48 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 
       27.02        77.82        66.67        28.73       174.84        34.03 
TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
       26.73        54.41        17.46        55.59        13.51        19.30 
TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A266 TCGA-GN-A268 TCGA-GN-A26D 
        9.90         2.04       139.89        10.13        62.79        48.00 
TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-HR-A2OH 
      121.91        39.35        10.42        48.89        22.13        65.88 
TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 TCGA-RP-A694 
      368.78       297.90         7.23         0.20         0.33         0.69 
TCGA-W3-A824 TCGA-W3-A828 TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1V TCGA-W3-AA1W 
      228.16       121.08        69.07       111.09        42.08       219.16 
TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO 
      105.04        24.03        49.05       101.33        58.98        70.52 
TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-YG-AA3O 
       11.80        49.51        12.16        40.41        24.99        37.94 
TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S 
       14.43        27.58        96.99 

  AMP PEAK 17(15Q26.2) MUTATED AMP PEAK 17(15Q26.2) WILD-TYPE 
                          0.23                           0.20 
  AMP PEAK 17(15Q26.2) MUTATED AMP PEAK 17(15Q26.2) WILD-TYPE 
                        369.93                         368.78 
  AMP PEAK 17(15Q26.2) MUTATED AMP PEAK 17(15Q26.2) WILD-TYPE 
                         50.14                          53.16 
[1] "0.2 - 369.9 (50.1)" "0.2 - 368.8 (53.2)"
[1] "hr=" "1.1"
D17V3, continuous
                                vv
clus                             I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB
  AMP PEAK 17(15Q26.2) MUTATED         10       2      12        8        7
  AMP PEAK 17(15Q26.2) WILD-TYPE        3       5      17       10       21
                                vv
clus                             STAGE II STAGE IIA STAGE IIB STAGE IIC
  AMP PEAK 17(15Q26.2) MUTATED         11         3         4         4
  AMP PEAK 17(15Q26.2) WILD-TYPE       15        11        15        11
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  AMP PEAK 17(15Q26.2) MUTATED          12          7         15         13
  AMP PEAK 17(15Q26.2) WILD-TYPE        27          8         20         41
                                vv
clus                             STAGE IV
  AMP PEAK 17(15Q26.2) MUTATED          3
  AMP PEAK 17(15Q26.2) WILD-TYPE       18
D17V4, multiclass
            clus
vv           AMP PEAK 17(15Q26.2) MUTATED AMP PEAK 17(15Q26.2) WILD-TYPE
  I/II NOS                             10                              3
  STAGE 0                               2                              5
  STAGE I                              12                             17
  STAGE IA                              8                             10
  STAGE IB                              7                             21
  STAGE II                             11                             15
  STAGE IIA                             3                             11
  STAGE IIB                             4                             15
  STAGE IIC                             4                             11
  STAGE III                            12                             27
  STAGE IIIA                            7                              8
  STAGE IIIB                           15                             20
  STAGE IIIC                           13                             41
  STAGE IV                              3                             18
[1] 14  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  AMP PEAK 17(15Q26.2) MUTATED      25 24 26 18
  AMP PEAK 17(15Q26.2) WILD-TYPE    39 49 55 49
D17V5, multiclass
       clus
vv      AMP PEAK 17(15Q26.2) MUTATED AMP PEAK 17(15Q26.2) WILD-TYPE
  T0+T1                           25                             39
  T2                              24                             49
  T3                              26                             55
  T4                              18                             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  N3
  AMP PEAK 17(15Q26.2) MUTATED    60  20  14  12
  AMP PEAK 17(15Q26.2) WILD-TYPE 117  45  25  33
D17V6, multiclass
    clus
vv   AMP PEAK 17(15Q26.2) MUTATED AMP PEAK 17(15Q26.2) WILD-TYPE
  N0                           60                            117
  N1                           20                             45
  N2                           14                             25
  N3                           12                             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"
D17V7, binary
                                cls
clus                               0   1
  AMP PEAK 17(15Q26.2) MUTATED   108   4
  AMP PEAK 17(15Q26.2) WILD-TYPE 211  18
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(15Q26.2) MUTATED    108    4
  AMP PEAK 17(15Q26.2) WILD-TYPE  211   18
   clus
vv  AMP PEAK 17(15Q26.2) MUTATED AMP PEAK 17(15Q26.2) WILD-TYPE
  0                          108                            211
  1                            4                             18
[1] 2 2
[1] FALSE
D17V8, binary
                                cls
clus                              0  1
  AMP PEAK 17(15Q26.2) MUTATED   44 22
  AMP PEAK 17(15Q26.2) WILD-TYPE 90 68
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(15Q26.2) MUTATED     44   22
  AMP PEAK 17(15Q26.2) WILD-TYPE   90   68
     clus
vv    AMP PEAK 17(15Q26.2) MUTATED AMP PEAK 17(15Q26.2) WILD-TYPE
  NO                            44                             90
  YES                           22                             68
[1] 2 2
[1] FALSE
D17V9, binary
                                cls
clus                               0   1
  AMP PEAK 17(15Q26.2) MUTATED    18 102
  AMP PEAK 17(15Q26.2) WILD-TYPE  29 218
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(15Q26.2) MUTATED     18  102
  AMP PEAK 17(15Q26.2) WILD-TYPE   29  218
     clus
vv    AMP PEAK 17(15Q26.2) MUTATED AMP PEAK 17(15Q26.2) WILD-TYPE
  NO                            18                             29
  YES                          102                            218
[1] 2 2
[1] FALSE
D17V10, continuous
D17V11, binary
                                cls
clus                               0   1
  AMP PEAK 17(15Q26.2) MUTATED    48  72
  AMP PEAK 17(15Q26.2) WILD-TYPE  90 157
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(15Q26.2) MUTATED     48   72
  AMP PEAK 17(15Q26.2) WILD-TYPE   90  157
        clus
vv       AMP PEAK 17(15Q26.2) MUTATED AMP PEAK 17(15Q26.2) WILD-TYPE
  FEMALE                           48                             90
  MALE                             72                            157
[1] 2 2
[1] FALSE
D17V12, binary
                                cls
clus                               0   1
  AMP PEAK 17(15Q26.2) MUTATED   102  18
  AMP PEAK 17(15Q26.2) WILD-TYPE 217  29
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(15Q26.2) MUTATED    102   18
  AMP PEAK 17(15Q26.2) WILD-TYPE  217   29
     clus
vv    AMP PEAK 17(15Q26.2) MUTATED AMP PEAK 17(15Q26.2) WILD-TYPE
  NO                           102                            217
  YES                           18                             29
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 17(15Q26.2) MUTATED       2                         0   116
  AMP PEAK 17(15Q26.2) WILD-TYPE     3                         1   237
D17V13, multiclass
                           clus
vv                          AMP PEAK 17(15Q26.2) MUTATED
  ASIAN                                                2
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                              116
                           clus
vv                          AMP PEAK 17(15Q26.2) WILD-TYPE
  ASIAN                                                  3
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                237
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V14, binary
                                cls
clus                               0   1
  AMP PEAK 17(15Q26.2) MUTATED     2 116
  AMP PEAK 17(15Q26.2) WILD-TYPE   5 236
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(15Q26.2) MUTATED      2  116
  AMP PEAK 17(15Q26.2) WILD-TYPE    5  236
                        clus
vv                       AMP PEAK 17(15Q26.2) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                          116
                        clus
vv                       AMP PEAK 17(15Q26.2) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                            236
[1] 2 2
[1] FALSE

Clustering(18) Variable = AMP PEAK 18(17Q25.3) MUTATION ANALYSIS
D18V1, survival
                                sevent
clus2                             0  1
  AMP PEAK 18(17Q25.3) MUTATED   42 40
  AMP PEAK 18(17Q25.3) WILD-TYPE 86 84
  AMP PEAK 18(17Q25.3) MUTATED AMP PEAK 18(17Q25.3) WILD-TYPE 
                            82                            170 
  AMP PEAK 18(17Q25.3) MUTATED AMP PEAK 18(17Q25.3) WILD-TYPE 
                            40                             84 
$`AMP PEAK 18(17Q25.3) MUTATED`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-EE-A20H TCGA-EE-A2MR TCGA-WE-AAA3 TCGA-3N-A9WC 
        9.76        62.07       166.75       134.40         7.40        60.46 
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1QA TCGA-D3-A2JB TCGA-D3-A2JC 
        8.42        15.72        31.89        76.41       168.00        86.30 
TCGA-D3-A2JL TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A51T 
      171.58        58.06        40.01        24.53         9.34        11.34 
TCGA-D3-A8GC TCGA-D3-A8GM TCGA-D3-A8GP TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 
       78.21        70.62       135.12        76.34       138.67        68.68 
TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F5 TCGA-DA-A95V TCGA-DA-A95X 
       60.10        64.83        58.85       225.11        72.10        65.03 
TCGA-DA-A95Z TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A20F TCGA-EE-A29D 
       12.30        24.89        20.38         0.00        79.20        12.99 
TCGA-EE-A29H TCGA-EE-A29P TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GH TCGA-EE-A2GM 
       47.41        27.16        77.98        26.14       201.60        18.35 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2M7 TCGA-EE-A2MI TCGA-EE-A2MP TCGA-EE-A2MS 
        0.76         0.20        15.25       171.85       227.01       143.93 
TCGA-EE-A2MT TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A19C 
       23.51        64.04        54.51        19.86       135.98        39.81 
TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A19W TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A3ET 
       42.51        49.71       146.63        22.36        16.87        68.52 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A8YC TCGA-FS-A1YW TCGA-FS-A1ZD 
       15.48        32.05         4.50        10.06       171.78        32.78 
TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A4FD TCGA-GN-A265 
       78.61       130.95        35.28         4.47        80.68        96.92 
TCGA-GN-A268 TCGA-GN-A9SD TCGA-QB-A6FS TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-AA1W 
       42.48        59.41         7.23       174.12         1.97       185.13 
TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-AA9Y TCGA-WE-AAA0 
       92.84        47.54         1.94        37.32 

$`AMP PEAK 18(17Q25.3) WILD-TYPE`
TCGA-D3-A3C8 TCGA-D3-A8GI TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A2GD TCGA-EE-A2GO 
       38.76        13.41        33.24        31.96       269.03        52.90 
TCGA-EE-A3JD TCGA-ER-A193 TCGA-FR-A729 TCGA-FW-A3R5 TCGA-WE-A8K5 TCGA-3N-A9WD 
       27.35        19.04       216.43        36.95        52.73        12.99 
TCGA-BF-AAP0 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QB 
       14.83       110.93        49.35       133.25        19.04        62.60 
TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JG TCGA-D3-A2JH 
       25.64        45.99        62.86        15.75       107.61        36.30 
TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3MR 
       64.83        66.08        43.53       140.98        59.70        90.21 
TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R 
       23.67       173.85        30.67       144.46        31.76        62.70 
TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D3-A8GD TCGA-D3-A8GJ 
       42.05        45.70       177.86       124.08        23.61       179.97 
TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GR TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 
      120.00        69.53        36.53        10.78        15.02        16.90 
TCGA-D9-A4Z6 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A3F2 
       18.44        69.21        22.85       150.61       110.53        30.44 
TCGA-DA-A3F8 TCGA-DA-A95W TCGA-DA-A95Y TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN 
        8.71         0.76        14.14         3.91        16.41        52.41 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A29B TCGA-EE-A29C 
       18.21        13.15        26.24        75.55        75.22        76.14 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29M TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W 
        0.26        44.28        47.74        61.12       346.49       185.19 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2GE TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
      115.43        30.02        12.95        68.65        10.62        32.48 
TCGA-EE-A2GN TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M8 TCGA-EE-A2MC 
       93.63        71.31        81.99       103.13         5.75        23.77 
TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
      209.79        94.19        63.25        89.26       104.78       145.45 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3J3 
       53.26       124.31       122.73         4.41         6.28        67.89 
TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-ER-A195 TCGA-ER-A197 
      111.85        45.90         3.35       168.85        34.45        10.49 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19H 
        7.82         4.54        53.29        11.47       184.60       150.12 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19P TCGA-ER-A19S TCGA-ER-A1A1 TCGA-ER-A2ND 
       99.06        59.84       120.76        47.18        73.05         4.70 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A42L TCGA-FR-A44A TCGA-FR-A69P 
       10.19        28.67       173.29        74.47       174.21         4.14 
TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 
       26.20         5.65        49.74       195.98         8.35        27.62 
TCGA-FS-A1ZC TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZS TCGA-FS-A1ZW 
      312.07        43.92         7.82        36.33       136.27        23.21 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 
        5.29         3.06        30.90        66.67       173.19        13.28 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
       55.59        11.54        19.30         9.90        18.25         1.91 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 
       53.29       117.93        17.06         7.59       120.53        34.49 
TCGA-GN-A4U8 TCGA-GN-A8LK TCGA-LH-A9QB TCGA-OD-A75X TCGA-RP-A690 TCGA-RP-A693 
       46.92        43.23        85.05       297.01         0.20         0.33 
TCGA-W3-A828 TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1V TCGA-WE-A8ZM TCGA-WE-A8ZN 
      120.07        44.05        79.99         8.09        65.42        12.69 
TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AAA4 TCGA-XV-AB01 
       21.90        62.89        10.95        48.39        24.99         6.61 
TCGA-YG-AA3O TCGA-Z2-AA3S 
       28.21        91.23 

  AMP PEAK 18(17Q25.3) MUTATED AMP PEAK 18(17Q25.3) WILD-TYPE 
                           0.0                            0.2 
  AMP PEAK 18(17Q25.3) MUTATED AMP PEAK 18(17Q25.3) WILD-TYPE 
                        227.01                         346.49 
  AMP PEAK 18(17Q25.3) MUTATED AMP PEAK 18(17Q25.3) WILD-TYPE 
                         52.11                          44.99 
[1] "0.0 - 227.0 (52.1)" "0.2 - 346.5 (45.0)"
[1] "hr=" "1"  
D18V2, survival
                                sevent
clus2                              0   1
  AMP PEAK 18(17Q25.3) MUTATED    58  63
  AMP PEAK 18(17Q25.3) WILD-TYPE 108 129
  AMP PEAK 18(17Q25.3) MUTATED AMP PEAK 18(17Q25.3) WILD-TYPE 
                           121                            237 
  AMP PEAK 18(17Q25.3) MUTATED AMP PEAK 18(17Q25.3) WILD-TYPE 
                            63                            129 
$`AMP PEAK 18(17Q25.3) MUTATED`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2MR 
       27.65        62.07        68.15       168.26         2.60       134.40 
TCGA-WE-AAA3 TCGA-3N-A9WB TCGA-3N-A9WC TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
       21.40        17.03        66.48        16.57        16.67       112.04 
TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JL 
       31.59        90.90       168.00        86.76        11.87       171.58 
TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MV 
      130.72        58.06        86.93        24.53         9.34        45.30 
TCGA-D3-A51N TCGA-D3-A51T TCGA-D3-A5GS TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GM 
       22.62        26.89        18.18        30.84        79.59       107.15 
TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D9-A148 TCGA-D9-A1JW TCGA-D9-A6E9 
      161.00       152.75        29.06       151.53         3.65         9.90 
TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC 
       76.57       144.89       222.51        88.87        65.92        68.09 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A95V TCGA-DA-A95X TCGA-DA-A95Z TCGA-EB-A44R 
       10.49       225.96        72.10        73.94        13.02        10.36 
TCGA-EB-A5UL TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A185 TCGA-EE-A20F 
       29.29        27.22        33.73        14.70         4.96        91.56 
TCGA-EE-A29D TCGA-EE-A29H TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A29V 
       13.97        64.64        18.61        56.42        14.47        25.87 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GM 
       86.14        59.28        67.43       220.24        48.72        75.48 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2M7 TCGA-EE-A2MD TCGA-EE-A2MH TCGA-EE-A2MI 
       13.91        42.77        28.83        47.28        16.96       204.66 
TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AC TCGA-EE-A3AE 
       47.54       248.65       162.48        71.21        64.04        54.51 
TCGA-EE-A3J5 TCGA-EE-A3JA TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A19C TCGA-ER-A19F 
       36.95        53.19       134.33       152.81        48.89        26.37 
TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A2NC TCGA-ER-A2NE 
       44.09        50.89         8.88       148.18        43.82        20.15 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A7U9 TCGA-FR-A8YC 
       93.01        46.98        33.21        92.98        18.77        34.82 
TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1ZD TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZQ 
      216.92        48.59        53.52        23.93       101.26       133.55 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-GN-A265 TCGA-GN-A268 
       53.16        26.56        80.68        17.46        96.92        62.79 
TCGA-GN-A26D TCGA-GN-A9SD TCGA-QB-A6FS TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 
       48.00        59.41         7.23         0.69       228.16        63.02 
TCGA-W3-AA1O TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-AA9Y 
        4.01       219.16       105.04        24.03        49.05        12.16 
TCGA-WE-AAA0 
       40.41 

$`AMP PEAK 18(17Q25.3) WILD-TYPE`
TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-D3-A8GI TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A180 
       46.32        13.87        58.52        68.25        54.02        94.98 
TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A3JD TCGA-ER-A193 TCGA-ER-A198 TCGA-FR-A729 
      340.14       126.81        27.35        31.40        50.76       220.80 
TCGA-FS-A1ZF TCGA-FW-A3R5 TCGA-QB-AA9O TCGA-WE-A8K5 TCGA-3N-A9WD TCGA-BF-AAP0 
       15.45        36.95        18.05        61.15        12.99        14.93 
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QB TCGA-D3-A2J6 
      112.57        71.80       133.25        28.08        95.74        43.43 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JG TCGA-D3-A2JH 
      103.10        65.49        23.77       115.53       113.52        42.08 
TCGA-D3-A2JK TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C7 TCGA-D3-A3CB 
       12.10        66.48        66.08        59.57        46.98       166.52 
TCGA-D3-A3CE TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
       60.23       103.59        39.75       174.84        55.73        56.35 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO 
      145.12        32.94        63.81       125.79       135.75       137.92 
TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GK 
      178.32       125.19        23.61        26.43       241.38       170.20 
TCGA-D3-A8GL TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D3-A8GV TCGA-D9-A149 TCGA-D9-A1JX 
       89.13       129.63       117.17       167.70        54.67         7.10 
TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6EA TCGA-D9-A6EC 
       18.12        15.39        22.29        18.44        25.18        77.56 
TCGA-D9-A6EG TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
       22.95        36.03        20.38       176.55        35.93       135.02 
TCGA-DA-A1I8 TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F8 TCGA-DA-A95W TCGA-DA-A95Y 
       53.92        40.60        33.93        43.36        37.35        14.14 
TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X 
       13.87        20.35        58.92         7.04        36.46        29.82 
TCGA-EE-A17Z TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20I TCGA-EE-A29A 
        8.65        26.89       133.81       151.27        13.55        63.35 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29M TCGA-EE-A29Q 
       85.08        78.97        63.78        72.07        56.84        66.74 
TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 
       61.28       369.93       195.02        17.92        46.82       115.96 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2GE TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       59.64        39.29       173.79       107.38        54.74        79.66 
TCGA-EE-A2GN TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 
      102.12        81.21        44.88        94.82        21.67       129.27 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MJ 
       19.76        61.51       103.27       268.73       103.20        96.23 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MQ TCGA-EE-A2MU TCGA-EE-A3AA 
      180.39       216.66       167.90        43.23        53.26       124.31 
TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 
      122.73        28.77        13.81        41.59       138.81       172.18 
TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JE TCGA-ER-A195 
      127.20        64.08        34.32       201.80        51.35        35.44 
TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19E 
       13.94         9.17        77.75        98.40        12.59        13.02 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19P 
      302.07       152.35         6.44       131.51        61.05       162.08 
TCGA-ER-A19S TCGA-ER-A1A1 TCGA-ER-A2ND TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH 
       49.48       105.07        23.34        28.83        48.99        41.56 
TCGA-ER-A3ES TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7U8 
      247.04        12.95       149.03       174.21        15.72        27.85 
TCGA-FR-A7UA TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
       38.27        36.26       104.42       228.59       202.65        20.91 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZE 
       28.08         7.79        27.72        48.85       357.37        46.45 
TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZS 
        9.70        32.75        47.38        74.73        11.41       148.80 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 
       49.48        27.09        27.02        77.82        50.14        66.67 
TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FW-A3TU 
       28.73       174.84        34.03        26.73        54.41        55.59 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 
       13.51        19.30         9.90        19.43         2.04        15.78 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A4U3 
      139.89       117.93        10.13        64.44        32.48       121.91 
TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL 
       39.35        10.42        48.89        22.13        50.10        21.37 
TCGA-HR-A2OG TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X TCGA-RP-A690 TCGA-RP-A693 
        0.23        65.88       368.78       297.90         0.20         0.33 
TCGA-W3-A828 TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1V TCGA-WE-A8K6 TCGA-WE-A8ZM 
      121.08        69.07       111.09        42.08        17.95       101.33 
TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-A8ZY 
       58.98        70.52        63.22        11.80        35.80        49.51 
TCGA-WE-AAA4 TCGA-XV-AB01 TCGA-YD-A89C TCGA-YD-A9TA TCGA-YG-AA3O TCGA-YG-AA3P 
       24.99        13.25         6.90        49.18        37.94        14.43 
TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       27.58        96.99        15.98 

  AMP PEAK 18(17Q25.3) MUTATED AMP PEAK 18(17Q25.3) WILD-TYPE 
                          0.69                           0.20 
  AMP PEAK 18(17Q25.3) MUTATED AMP PEAK 18(17Q25.3) WILD-TYPE 
                        248.65                         369.93 
  AMP PEAK 18(17Q25.3) MUTATED AMP PEAK 18(17Q25.3) WILD-TYPE 
                         50.89                          53.26 
[1] "0.7 - 248.7 (50.9)" "0.2 - 369.9 (53.3)"
[1] "hr=" "1"  
D18V3, continuous
                                vv
clus                             I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB
  AMP PEAK 18(17Q25.3) MUTATED          5       2      12        8       10
  AMP PEAK 18(17Q25.3) WILD-TYPE        8       5      17       10       18
                                vv
clus                             STAGE II STAGE IIA STAGE IIB STAGE IIC
  AMP PEAK 18(17Q25.3) MUTATED          9         2         6         7
  AMP PEAK 18(17Q25.3) WILD-TYPE       17        12        13         8
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  AMP PEAK 18(17Q25.3) MUTATED          13          2         13         19
  AMP PEAK 18(17Q25.3) WILD-TYPE        26         13         22         35
                                vv
clus                             STAGE IV
  AMP PEAK 18(17Q25.3) MUTATED          7
  AMP PEAK 18(17Q25.3) WILD-TYPE       14
D18V4, multiclass
            clus
vv           AMP PEAK 18(17Q25.3) MUTATED AMP PEAK 18(17Q25.3) WILD-TYPE
  I/II NOS                              5                              8
  STAGE 0                               2                              5
  STAGE I                              12                             17
  STAGE IA                              8                             10
  STAGE IB                             10                             18
  STAGE II                              9                             17
  STAGE IIA                             2                             12
  STAGE IIB                             6                             13
  STAGE IIC                             7                              8
  STAGE III                            13                             26
  STAGE IIIA                            2                             13
  STAGE IIIB                           13                             22
  STAGE IIIC                           19                             35
  STAGE IV                              7                             14
[1] 14  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  AMP PEAK 18(17Q25.3) MUTATED      22 31 21 26
  AMP PEAK 18(17Q25.3) WILD-TYPE    42 42 60 41
D18V5, multiclass
       clus
vv      AMP PEAK 18(17Q25.3) MUTATED AMP PEAK 18(17Q25.3) WILD-TYPE
  T0+T1                           22                             42
  T2                              31                             42
  T3                              21                             60
  T4                              26                             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  N3
  AMP PEAK 18(17Q25.3) MUTATED    64  20  16  14
  AMP PEAK 18(17Q25.3) WILD-TYPE 113  45  23  31
D18V6, multiclass
    clus
vv   AMP PEAK 18(17Q25.3) MUTATED AMP PEAK 18(17Q25.3) WILD-TYPE
  N0                           64                            113
  N1                           20                             45
  N2                           16                             23
  N3                           14                             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"
D18V7, binary
                                cls
clus                               0   1
  AMP PEAK 18(17Q25.3) MUTATED   109   8
  AMP PEAK 18(17Q25.3) WILD-TYPE 210  14
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 18(17Q25.3) MUTATED    109    8
  AMP PEAK 18(17Q25.3) WILD-TYPE  210   14
   clus
vv  AMP PEAK 18(17Q25.3) MUTATED AMP PEAK 18(17Q25.3) WILD-TYPE
  0                          109                            210
  1                            8                             14
[1] 2 2
[1] FALSE
D18V8, binary
                                cls
clus                              0  1
  AMP PEAK 18(17Q25.3) MUTATED   41 34
  AMP PEAK 18(17Q25.3) WILD-TYPE 93 56
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 18(17Q25.3) MUTATED     41   34
  AMP PEAK 18(17Q25.3) WILD-TYPE   93   56
     clus
vv    AMP PEAK 18(17Q25.3) MUTATED AMP PEAK 18(17Q25.3) WILD-TYPE
  NO                            41                             93
  YES                           34                             56
[1] 2 2
[1] FALSE
D18V9, binary
                                cls
clus                               0   1
  AMP PEAK 18(17Q25.3) MUTATED    16 106
  AMP PEAK 18(17Q25.3) WILD-TYPE  31 214
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 18(17Q25.3) MUTATED     16  106
  AMP PEAK 18(17Q25.3) WILD-TYPE   31  214
     clus
vv    AMP PEAK 18(17Q25.3) MUTATED AMP PEAK 18(17Q25.3) WILD-TYPE
  NO                            16                             31
  YES                          106                            214
[1] 2 2
[1] FALSE
D18V10, continuous
D18V11, binary
                                cls
clus                               0   1
  AMP PEAK 18(17Q25.3) MUTATED    39  83
  AMP PEAK 18(17Q25.3) WILD-TYPE  99 146
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 18(17Q25.3) MUTATED     39   83
  AMP PEAK 18(17Q25.3) WILD-TYPE   99  146
        clus
vv       AMP PEAK 18(17Q25.3) MUTATED AMP PEAK 18(17Q25.3) WILD-TYPE
  FEMALE                           39                             99
  MALE                             83                            146
[1] 2 2
[1] FALSE
D18V12, binary
                                cls
clus                               0   1
  AMP PEAK 18(17Q25.3) MUTATED   105  17
  AMP PEAK 18(17Q25.3) WILD-TYPE 214  30
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 18(17Q25.3) MUTATED    105   17
  AMP PEAK 18(17Q25.3) WILD-TYPE  214   30
     clus
vv    AMP PEAK 18(17Q25.3) MUTATED AMP PEAK 18(17Q25.3) WILD-TYPE
  NO                           105                            214
  YES                           17                             30
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 18(17Q25.3) MUTATED       2                         1   118
  AMP PEAK 18(17Q25.3) WILD-TYPE     3                         0   235
D18V13, multiclass
                           clus
vv                          AMP PEAK 18(17Q25.3) MUTATED
  ASIAN                                                2
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                              118
                           clus
vv                          AMP PEAK 18(17Q25.3) WILD-TYPE
  ASIAN                                                  3
  BLACK OR AFRICAN AMERICAN                              0
  WHITE                                                235
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V14, binary
                                cls
clus                               0   1
  AMP PEAK 18(17Q25.3) MUTATED     1 119
  AMP PEAK 18(17Q25.3) WILD-TYPE   6 233
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 18(17Q25.3) MUTATED      1  119
  AMP PEAK 18(17Q25.3) WILD-TYPE    6  233
                        clus
vv                       AMP PEAK 18(17Q25.3) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                          119
                        clus
vv                       AMP PEAK 18(17Q25.3) WILD-TYPE
  HISPANIC OR LATINO                                  6
  NOT HISPANIC OR LATINO                            233
[1] 2 2
[1] FALSE

Clustering(19) Variable = AMP PEAK 19(20Q13.33) MUTATION ANALYSIS
D19V1, survival
                                 sevent
clus2                              0  1
  AMP PEAK 19(20Q13.33) MUTATED   67 64
  AMP PEAK 19(20Q13.33) WILD-TYPE 61 60
  AMP PEAK 19(20Q13.33) MUTATED AMP PEAK 19(20Q13.33) WILD-TYPE 
                            131                             121 
  AMP PEAK 19(20Q13.33) MUTATED AMP PEAK 19(20Q13.33) WILD-TYPE 
                             64                              60 
$`AMP PEAK 19(20Q13.33) MUTATED`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A8GI TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GO 
        9.76        62.07        13.41        31.96       166.75        52.90 
TCGA-ER-A193 TCGA-FR-A729 TCGA-WE-AAA3 TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 
       19.04       216.43         7.40        12.99        14.83         8.42 
TCGA-D3-A1Q5 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL 
      110.93        15.75        86.30       107.61        36.30       171.58 
TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE 
       64.83        43.53        58.06       140.98        40.01        59.70 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A5GN 
       90.21        23.67       144.46        31.76        62.70        45.70 
TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GK TCGA-D3-A8GL 
      177.86       124.08        78.21        23.61       120.00        69.53 
TCGA-D3-A8GM TCGA-D3-A8GP TCGA-D9-A3Z3 TCGA-D9-A6EC TCGA-DA-A1I2 TCGA-DA-A1I7 
       70.62       135.12        16.90        69.21       150.61        60.10 
TCGA-DA-A1IA TCGA-DA-A3F5 TCGA-DA-A95Z TCGA-EB-A6L9 TCGA-EE-A17Y TCGA-EE-A183 
       64.83       225.11        12.30        18.21        24.89        26.24 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29P TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 
       12.99         0.26        27.16       346.49       185.19       115.43 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GM TCGA-EE-A2GN 
       77.98        26.14        12.95       201.60        18.35        93.63 
TCGA-EE-A2GP TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
        0.76        81.99       103.13        15.25         5.75        23.77 
TCGA-EE-A2MG TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA 
       94.19       227.01       143.93        23.51        53.26       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3J3 TCGA-EE-A3J7 
      122.73        64.04         4.41        54.51        67.89        45.90 
TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19B 
      168.85        19.86       135.98        10.49         7.82        53.29 
TCGA-ER-A19G TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19P TCGA-ER-A19W TCGA-ER-A2NC 
      184.60        99.06        59.84       120.76       146.63        22.36 
TCGA-ER-A2ND TCGA-ER-A2NG TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
        4.70        28.67        32.05         4.50       174.21         4.14 
TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG 
      195.98        27.62       312.07        32.78        43.92         7.82 
TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU 
       36.33        78.61       130.95       136.27        35.28         4.47 
TCGA-FS-A1ZY TCGA-FS-A4F8 TCGA-FS-A4FD TCGA-GF-A4EO TCGA-GN-A264 TCGA-GN-A265 
        5.29       173.19        80.68        18.25       117.93        96.92 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A8LK TCGA-GN-A9SD TCGA-LH-A9QB 
       17.06        42.48         7.59        43.23        59.41        85.05 
TCGA-OD-A75X TCGA-QB-A6FS TCGA-W3-A825 TCGA-W3-AA1R TCGA-W3-AA1W TCGA-W3-AA21 
      297.01         7.23         1.97        79.99       185.13        92.84 
TCGA-WE-A8ZM TCGA-WE-A8ZQ TCGA-WE-A8ZY TCGA-XV-AB01 TCGA-YG-AA3O 
       65.42        62.89        48.39         6.61        28.21 

$`AMP PEAK 19(20Q13.33) WILD-TYPE`
TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A2GD TCGA-EE-A2MR TCGA-EE-A3JD TCGA-FW-A3R5 
       38.76        33.24       269.03       134.40        27.35        36.95 
TCGA-WE-A8K5 TCGA-3N-A9WC TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       52.73        60.46        15.72        31.89        49.35       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 
       19.04        76.41        62.60        25.64        45.99        62.86 
TCGA-D3-A2JB TCGA-D3-A2JO TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A51E TCGA-D3-A51F 
      168.00        66.08        24.53         9.34       173.85        30.67 
TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A8GJ TCGA-D3-A8GR TCGA-D9-A1X3 TCGA-D9-A3Z1 
       11.34        42.05       179.97        36.53        10.78        15.02 
TCGA-D9-A4Z6 TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I5 
       18.44        22.85        76.34       138.67        68.68       110.53 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F8 TCGA-DA-A95V TCGA-DA-A95W TCGA-DA-A95X 
       58.85        30.44         8.71        72.10         0.76        65.03 
TCGA-DA-A95Y TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A181 
       14.14         3.91        16.41        52.41        13.15        20.38 
TCGA-EE-A182 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29G 
        0.00        75.55        79.20        75.22        76.14        44.28 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29Q TCGA-EE-A2A2 TCGA-EE-A2GJ TCGA-EE-A2GK 
       47.41        47.74        61.12        30.02        68.65        10.62 
TCGA-EE-A2GL TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2MF TCGA-EE-A2MI TCGA-EE-A2MJ 
       32.48         0.20        71.31       209.79       171.85        63.25 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A3AF TCGA-EE-A3J4 TCGA-EE-A3J8 
       89.26       104.78       145.45         6.28       111.85         3.35 
TCGA-ER-A195 TCGA-ER-A19A TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19H TCGA-ER-A19N 
       34.45         4.54        39.81        11.47       150.12        42.51 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A1A1 TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A3ES 
       49.71        47.18        73.05        16.87        10.19       173.29 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A42L TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FR-A8YC 
       68.52        15.48        74.47        26.20         5.65        10.06 
TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1ZW TCGA-FS-A1ZZ TCGA-FS-A4F0 
      171.78        49.74         8.35        23.21         3.06        30.90 
TCGA-FS-A4F4 TCGA-FS-A4F9 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
       66.67        13.28        55.59        11.54        19.30         9.90 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-RP-A690 
        1.91        53.29       120.53        34.49        46.92         0.20 
TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A828 TCGA-W3-AA1Q TCGA-W3-AA1V TCGA-WE-A8K1 
        0.33       174.12       120.07        44.05         8.09        47.54 
TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 
       12.69        21.90        10.95         1.94        37.32        24.99 
TCGA-Z2-AA3S 
       91.23 

  AMP PEAK 19(20Q13.33) MUTATED AMP PEAK 19(20Q13.33) WILD-TYPE 
                           0.26                            0.00 
  AMP PEAK 19(20Q13.33) MUTATED AMP PEAK 19(20Q13.33) WILD-TYPE 
                         346.49                          269.03 
  AMP PEAK 19(20Q13.33) MUTATED AMP PEAK 19(20Q13.33) WILD-TYPE 
                          58.06                           39.81 
[1] "0.3 - 346.5 (58.1)" "0.0 - 269.0 (39.8)"
[1] "hr=" "1.4"
D19V2, survival
                                 sevent
clus2                              0  1
  AMP PEAK 19(20Q13.33) MUTATED   83 99
  AMP PEAK 19(20Q13.33) WILD-TYPE 83 93
  AMP PEAK 19(20Q13.33) MUTATED AMP PEAK 19(20Q13.33) WILD-TYPE 
                            182                             176 
  AMP PEAK 19(20Q13.33) MUTATED AMP PEAK 19(20Q13.33) WILD-TYPE 
                             99                              93 
$`AMP PEAK 19(20Q13.33) MUTATED`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A8GI TCGA-EB-A5SH TCGA-EE-A180 TCGA-EE-A184 
       27.65        62.07        58.52        54.02        94.98        68.15 
TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GO TCGA-ER-A193 TCGA-FR-A729 TCGA-QB-AA9O 
      168.26         2.60       126.81        31.40       220.80        18.05 
TCGA-WE-AAA3 TCGA-3N-A9WB TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q5 
       21.40        17.03        12.99        14.93        16.57       112.57 
TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG 
       31.59        23.77       115.53        86.76        11.87       113.52 
TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CB 
       42.08       171.58        66.48        59.57        58.06       166.52 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51J 
       86.93        60.23       103.59        39.75        45.30       145.12 
TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GU 
       32.94        63.81       135.75       137.92       178.32       125.19 
TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GP 
       79.59        23.61       170.20        89.13       107.15       152.75 
TCGA-D3-A8GQ TCGA-D9-A148 TCGA-D9-A1JX TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA 
       29.06       151.53         7.10        22.29         9.90        25.18 
TCGA-D9-A6EC TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I7 TCGA-DA-A1IA 
       77.56        36.03        20.38       176.55        88.87        65.92 
TCGA-DA-A3F5 TCGA-DA-A95Z TCGA-EB-A5UL TCGA-EB-A6L9 TCGA-EE-A17Y TCGA-EE-A183 
      225.96        13.02        29.29        36.46        27.22        26.89 
TCGA-EE-A20B TCGA-EE-A29A TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29P TCGA-EE-A29R 
      133.81        63.35        13.97        63.78        56.42        14.47 
TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-EE-A2A6 
      369.93       195.02        17.92       115.96        39.29        86.14 
TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GM TCGA-EE-A2GN 
       59.28       173.79       220.24        48.72        75.48       102.12 
TCGA-EE-A2GP TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
       13.91        94.82        21.67       129.27        28.83        19.76 
TCGA-EE-A2MC TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT 
       61.51       103.20        16.96       248.65       162.48        71.21 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
       53.26       124.31       122.73        64.04        28.77        54.51 
TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-EE-A3JB 
       41.59       172.18        36.95        64.08        53.19       201.80 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19E 
      134.33       152.81        13.94         9.17        98.40        13.02 
TCGA-ER-A19G TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19P TCGA-ER-A19T 
      302.07         6.44       131.51        61.05       162.08         8.88 
TCGA-ER-A19W TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NG TCGA-ER-A3PL TCGA-ER-A42K 
      148.18        43.82        23.34        48.99        33.21        12.95 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A8YD TCGA-FS-A1YX TCGA-FS-A1Z0 
       92.98       174.21        15.72        36.26        48.59       202.65 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE 
       28.08         7.79        27.72       357.37        53.52        46.45 
TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS 
        9.70        47.38        23.93       101.26       133.55       148.80 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A4F2 TCGA-FS-A4F5 TCGA-FS-A4F8 
       53.16        26.56        27.09        50.14        28.73       174.84 
TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-GF-A4EO TCGA-GF-A6C9 TCGA-GN-A264 TCGA-GN-A265 
       80.68        17.46        19.43        15.78       117.93        96.92 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U7 TCGA-GN-A4U9 
       64.44        62.79        32.48        48.00        10.42        22.13 
TCGA-GN-A8LK TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X 
       50.10        21.37        59.41        65.88       368.78       297.90 
TCGA-QB-A6FS TCGA-W3-A825 TCGA-W3-AA1R TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8JZ 
        7.23        63.02       111.09       219.16       105.04        24.03 
TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZQ TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-XV-AB01 
       17.95       101.33        63.22        35.80        49.51        13.25 
TCGA-YG-AA3O TCGA-YG-AA3P 
       37.94        14.43 

$`AMP PEAK 19(20Q13.33) WILD-TYPE`
TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SG TCGA-EE-A2GD TCGA-EE-A2MR TCGA-EE-A3JD 
       46.32        13.87        68.25       340.14       134.40        27.35 
TCGA-ER-A198 TCGA-FS-A1ZF TCGA-FW-A3R5 TCGA-WE-A8K5 TCGA-3N-A9WC TCGA-D3-A1Q3 
       50.76        15.45        36.95        61.15        66.48        16.67 
TCGA-D3-A1Q4 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB 
      112.04        71.80       133.25        28.08        90.90        95.74 
TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JB TCGA-D3-A2JK TCGA-D3-A2JO 
       43.43       103.10        65.49       168.00        12.10        66.08 
TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A51E TCGA-D3-A51F 
      130.72        46.98        24.53         9.34       174.84        55.73 
TCGA-D3-A51H TCGA-D3-A51N TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GS TCGA-D3-A8GB 
       56.35        22.62        26.89       125.79        18.18        30.84 
TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GN TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D3-A8GV 
       26.43       241.38       161.00       129.63       117.17       167.70 
TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A4Z6 TCGA-D9-A6EG 
       54.67         3.65        18.12        15.39        18.44        22.95 
TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I8 
       76.57       144.89       222.51        35.93       135.02        53.92 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-DA-A95V 
       40.60        68.09        33.93        10.49        43.36        72.10 
TCGA-DA-A95W TCGA-DA-A95X TCGA-DA-A95Y TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH 
       37.35        73.94        14.14        13.87        10.36        20.35 
TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 
       58.92         7.04        29.82         8.65        33.73        14.70 
TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29B TCGA-EE-A29C 
        4.96       151.27        91.56        13.55        85.08        78.97 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29S 
       72.07        64.64        56.84        18.61        66.74        61.28 
TCGA-EE-A29V TCGA-EE-A2A0 TCGA-EE-A2A2 TCGA-EE-A2GC TCGA-EE-A2GJ TCGA-EE-A2GK 
       25.87        46.82        59.64        67.43       107.38        54.74 
TCGA-EE-A2GL TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2MD TCGA-EE-A2ME 
       79.66        42.77        81.21        44.88        47.28       103.27 
TCGA-EE-A2MF TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
      268.73       204.66        96.23       180.39       216.66       167.90 
TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J8 
       47.54        43.23        13.81       138.81       127.20        34.32 
TCGA-EE-A3JE TCGA-ER-A195 TCGA-ER-A19A TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19F 
       51.35        35.44        77.75        48.89        12.59        26.37 
TCGA-ER-A19H TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A1A1 TCGA-ER-A2NE 
      152.35        44.09        50.89        49.48       105.07        20.15 
TCGA-ER-A2NF TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A42L 
       28.83        41.56       247.04        93.01        46.98       149.03 
TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YE TCGA-FS-A1YW 
       27.85        18.77        38.27        34.82       104.42       216.92 
TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1ZB TCGA-FS-A1ZH TCGA-FS-A1ZP TCGA-FS-A1ZR 
      228.59        20.91        48.85        32.75        74.73        11.41 
TCGA-FS-A1ZW TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F9 TCGA-FS-A4FB 
       49.48        27.02        77.82        66.67        34.03        26.73 
TCGA-FS-A4FC TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 
       54.41        55.59        13.51        19.30         9.90         2.04 
TCGA-GN-A262 TCGA-GN-A266 TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-HR-A2OG 
      139.89        10.13       121.91        39.35        48.89         0.23 
TCGA-RP-A690 TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A828 TCGA-W3-AA1O 
        0.20         0.33         0.69       228.16       121.08         4.01 
TCGA-W3-AA1Q TCGA-W3-AA1V TCGA-WE-A8K1 TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT 
       69.07        42.08        49.05        58.98        70.52        11.80 
TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-YD-A89C TCGA-YD-A9TA TCGA-Z2-A8RT 
       12.16        40.41        24.99         6.90        49.18        27.58 
TCGA-Z2-AA3S TCGA-Z2-AA3V 
       96.99        15.98 

  AMP PEAK 19(20Q13.33) MUTATED AMP PEAK 19(20Q13.33) WILD-TYPE 
                            2.6                             0.2 
  AMP PEAK 19(20Q13.33) MUTATED AMP PEAK 19(20Q13.33) WILD-TYPE 
                         369.93                          340.14 
  AMP PEAK 19(20Q13.33) MUTATED AMP PEAK 19(20Q13.33) WILD-TYPE 
                          58.29                           48.89 
[1] "2.6 - 369.9 (58.3)" "0.2 - 340.1 (48.9)"
[1] "hr=" "1.1"
D19V3, continuous
                                 vv
clus                              I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB
  AMP PEAK 19(20Q13.33) MUTATED          9       3      19       10       17
  AMP PEAK 19(20Q13.33) WILD-TYPE        4       4      10        8       11
                                 vv
clus                              STAGE II STAGE IIA STAGE IIB STAGE IIC
  AMP PEAK 19(20Q13.33) MUTATED         12         6         5         9
  AMP PEAK 19(20Q13.33) WILD-TYPE       14         8        14         6
                                 vv
clus                              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  AMP PEAK 19(20Q13.33) MUTATED          22          9         20         26
  AMP PEAK 19(20Q13.33) WILD-TYPE        17          6         15         28
                                 vv
clus                              STAGE IV
  AMP PEAK 19(20Q13.33) MUTATED          7
  AMP PEAK 19(20Q13.33) WILD-TYPE       14
D19V4, multiclass
            clus
vv           AMP PEAK 19(20Q13.33) MUTATED AMP PEAK 19(20Q13.33) WILD-TYPE
  I/II NOS                               9                               4
  STAGE 0                                3                               4
  STAGE I                               19                              10
  STAGE IA                              10                               8
  STAGE IB                              17                              11
  STAGE II                              12                              14
  STAGE IIA                              6                               8
  STAGE IIB                              5                              14
  STAGE IIC                              9                               6
  STAGE III                             22                              17
  STAGE IIIA                             9                               6
  STAGE IIIB                            20                              15
  STAGE IIIC                            26                              28
  STAGE IV                               7                              14
[1] 14  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              T0+T1 T2 T3 T4
  AMP PEAK 19(20Q13.33) MUTATED      37 44 33 37
  AMP PEAK 19(20Q13.33) WILD-TYPE    27 29 48 30
D19V5, multiclass
       clus
vv      AMP PEAK 19(20Q13.33) MUTATED AMP PEAK 19(20Q13.33) WILD-TYPE
  T0+T1                            37                              27
  T2                               44                              29
  T3                               33                              48
  T4                               37                              30
[1] 4 2
[1] 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 N3
  AMP PEAK 19(20Q13.33) MUTATED   93 36 17 24
  AMP PEAK 19(20Q13.33) WILD-TYPE 84 29 22 21
D19V6, multiclass
    clus
vv   AMP PEAK 19(20Q13.33) MUTATED AMP PEAK 19(20Q13.33) WILD-TYPE
  N0                            93                              84
  N1                            36                              29
  N2                            17                              22
  N3                            24                              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"
D19V7, binary
                                 cls
clus                                0   1
  AMP PEAK 19(20Q13.33) MUTATED   169   8
  AMP PEAK 19(20Q13.33) WILD-TYPE 150  14
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 19(20Q13.33) MUTATED    169    8
  AMP PEAK 19(20Q13.33) WILD-TYPE  150   14
   clus
vv  AMP PEAK 19(20Q13.33) MUTATED AMP PEAK 19(20Q13.33) WILD-TYPE
  0                           169                             150
  1                             8                              14
[1] 2 2
[1] FALSE
D19V8, binary
                                 cls
clus                               0  1
  AMP PEAK 19(20Q13.33) MUTATED   75 41
  AMP PEAK 19(20Q13.33) WILD-TYPE 59 49
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 19(20Q13.33) MUTATED     75   41
  AMP PEAK 19(20Q13.33) WILD-TYPE   59   49
     clus
vv    AMP PEAK 19(20Q13.33) MUTATED AMP PEAK 19(20Q13.33) WILD-TYPE
  NO                             75                              59
  YES                            41                              49
[1] 2 2
[1] FALSE
D19V9, binary
                                 cls
clus                                0   1
  AMP PEAK 19(20Q13.33) MUTATED    23 165
  AMP PEAK 19(20Q13.33) WILD-TYPE  24 155
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 19(20Q13.33) MUTATED     23  165
  AMP PEAK 19(20Q13.33) WILD-TYPE   24  155
     clus
vv    AMP PEAK 19(20Q13.33) MUTATED AMP PEAK 19(20Q13.33) WILD-TYPE
  NO                             23                              24
  YES                           165                             155
[1] 2 2
[1] FALSE
D19V10, continuous
D19V11, binary
                                 cls
clus                                0   1
  AMP PEAK 19(20Q13.33) MUTATED    71 117
  AMP PEAK 19(20Q13.33) WILD-TYPE  67 112
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 19(20Q13.33) MUTATED     71  117
  AMP PEAK 19(20Q13.33) WILD-TYPE   67  112
        clus
vv       AMP PEAK 19(20Q13.33) MUTATED AMP PEAK 19(20Q13.33) WILD-TYPE
  FEMALE                            71                              67
  MALE                             117                             112
[1] 2 2
[1] FALSE
D19V12, binary
                                 cls
clus                                0   1
  AMP PEAK 19(20Q13.33) MUTATED   164  24
  AMP PEAK 19(20Q13.33) WILD-TYPE 155  23
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 19(20Q13.33) MUTATED    164   24
  AMP PEAK 19(20Q13.33) WILD-TYPE  155   23
     clus
vv    AMP PEAK 19(20Q13.33) MUTATED AMP PEAK 19(20Q13.33) WILD-TYPE
  NO                            164                             155
  YES                            24                              23
[1] 2 2
[1] FALSE
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 19(20Q13.33) MUTATED       2                         0   181
  AMP PEAK 19(20Q13.33) WILD-TYPE     3                         1   172
D19V13, multiclass
                           clus
vv                          AMP PEAK 19(20Q13.33) MUTATED
  ASIAN                                                 2
  BLACK OR AFRICAN AMERICAN                             0
  WHITE                                               181
                           clus
vv                          AMP PEAK 19(20Q13.33) WILD-TYPE
  ASIAN                                                   3
  BLACK OR AFRICAN AMERICAN                               1
  WHITE                                                 172
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V14, binary
                                 cls
clus                                0   1
  AMP PEAK 19(20Q13.33) MUTATED     4 180
  AMP PEAK 19(20Q13.33) WILD-TYPE   3 172
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 19(20Q13.33) MUTATED      4  180
  AMP PEAK 19(20Q13.33) WILD-TYPE    3  172
                        clus
vv                       AMP PEAK 19(20Q13.33) MUTATED
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           180
                        clus
vv                       AMP PEAK 19(20Q13.33) WILD-TYPE
  HISPANIC OR LATINO                                   3
  NOT HISPANIC OR LATINO                             172
[1] 2 2
[1] FALSE

Clustering(20) Variable = AMP PEAK 20(22Q13.2) MUTATION ANALYSIS
D20V1, survival
                                sevent
clus2                             0  1
  AMP PEAK 20(22Q13.2) MUTATED   54 51
  AMP PEAK 20(22Q13.2) WILD-TYPE 74 73
  AMP PEAK 20(22Q13.2) MUTATED AMP PEAK 20(22Q13.2) WILD-TYPE 
                           105                            147 
  AMP PEAK 20(22Q13.2) MUTATED AMP PEAK 20(22Q13.2) WILD-TYPE 
                            51                             73 
$`AMP PEAK 20(22Q13.2) MUTATED`
TCGA-D3-A2JE TCGA-D3-A8GI TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GO 
        9.76        13.41        33.24        31.96       166.75        52.90 
TCGA-EE-A2MR TCGA-EE-A3JD TCGA-FR-A729 TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-3N-A9WD 
      134.40        27.35       216.43        52.73         7.40        12.99 
TCGA-D3-A1Q1 TCGA-D3-A2J7 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JL 
        8.42        45.99        15.75       168.00        86.30       171.58 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3MO 
       66.08        43.53        58.06        40.01        59.70         9.34 
TCGA-D3-A3MU TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A8GC 
       23.67        11.34        42.05        45.70       177.86        78.21 
TCGA-D3-A8GJ TCGA-D3-A8GM TCGA-D9-A3Z1 TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HY 
      179.97        70.62        15.02        69.21        76.34       138.67 
TCGA-DA-A1I1 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A3F5 TCGA-DA-A95V TCGA-DA-A95Z 
       68.68        60.10        64.83       225.11        72.10        12.30 
TCGA-EB-A5KH TCGA-EB-A6L9 TCGA-EE-A17Y TCGA-EE-A29M TCGA-EE-A29Q TCGA-EE-A29W 
       16.41        18.21        24.89        47.74        61.12       185.19 
TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GH TCGA-EE-A2GM TCGA-EE-A2GN 
       30.02        77.98        26.14       201.60        18.35        93.63 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MJ TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA 
      103.13        15.25        63.25       143.93        53.26       124.31 
TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3J7 TCGA-EE-A3JB TCGA-ER-A19B 
      122.73         4.41        54.51        45.90       168.85        53.29 
TCGA-ER-A19C TCGA-ER-A19G TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19W TCGA-ER-A2NF 
       39.81       184.60        99.06        59.84       146.63        10.19 
TCGA-ER-A2NG TCGA-ER-A3ET TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7UA 
       28.67        68.52         4.50       174.21         4.14         5.65 
TCGA-FS-A1YY TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZM TCGA-FS-A1ZQ 
       49.74        32.78        43.92         7.82        78.61       130.95 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F4 
      136.27        35.28         4.47        23.21         5.29        66.67 
TCGA-FS-A4FD TCGA-FW-A3TU TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 
       80.68        55.59       117.93        96.92        17.06        42.48 
TCGA-GN-A26A TCGA-GN-A8LK TCGA-QB-A6FS TCGA-W3-AA1R TCGA-WE-A8K1 TCGA-WE-A8ZM 
        7.59        43.23         7.23        79.99        47.54        65.42 
TCGA-WE-A8ZY TCGA-XV-AB01 TCGA-YG-AA3O 
       48.39         6.61        28.21 

$`AMP PEAK 20(22Q13.2) WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EE-A2GD TCGA-ER-A193 TCGA-FW-A3R5 TCGA-3N-A9WC 
       62.07        38.76       269.03        19.04        36.95        60.46 
TCGA-BF-AAP0 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       14.83        15.72        31.89       110.93        49.35       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J8 TCGA-D3-A2JG 
       19.04        76.41        62.60        25.64        62.86       107.61 
TCGA-D3-A2JH TCGA-D3-A2JN TCGA-D3-A3CB TCGA-D3-A3CF TCGA-D3-A3MR TCGA-D3-A51E 
       36.30        64.83       140.98        24.53        90.21       173.85 
TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A5GU TCGA-D3-A8GD 
       30.67       144.46        31.76        62.70       124.08        23.61 
TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GP TCGA-D3-A8GR TCGA-D9-A1X3 TCGA-D9-A3Z3 
      120.00        69.53       135.12        36.53        10.78        16.90 
TCGA-D9-A4Z6 TCGA-D9-A6EG TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1IC TCGA-DA-A3F2 
       18.44        22.85       150.61       110.53        58.85        30.44 
TCGA-DA-A3F8 TCGA-DA-A95W TCGA-DA-A95X TCGA-DA-A95Y TCGA-EB-A44Q TCGA-EB-A5UN 
        8.71         0.76        65.03        14.14         3.91        52.41 
TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A20F 
       13.15        20.38         0.00        26.24        75.55        79.20 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H 
       75.22        76.14        12.99         0.26        44.28        47.41 
TCGA-EE-A29P TCGA-EE-A29T TCGA-EE-A2A1 TCGA-EE-A2GE TCGA-EE-A2GJ TCGA-EE-A2GK 
       27.16       346.49       115.43        12.95        68.65        10.62 
TCGA-EE-A2GL TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M8 
       32.48         0.76         0.20        71.31        81.99         5.75 
TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML 
       23.77       209.79        94.19       171.85        89.26       104.78 
TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MT TCGA-EE-A3AC TCGA-EE-A3AF TCGA-EE-A3J3 
      145.45       227.01        23.51        64.04         6.28        67.89 
TCGA-EE-A3J4 TCGA-EE-A3J8 TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 
      111.85         3.35        19.86       135.98        34.45        10.49 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19D TCGA-ER-A19H TCGA-ER-A19N TCGA-ER-A19P 
        7.82         4.54        11.47       150.12        42.51       120.76 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
       49.71        47.18        73.05        22.36         4.70        16.87 
TCGA-ER-A3ES TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A7U8 TCGA-FR-A8YC 
      173.29        15.48        32.05        74.47        26.20        10.06 
TCGA-FS-A1YW TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZJ 
      171.78       195.98         8.35        27.62       312.07        36.33 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FW-A3TV TCGA-FW-A5DY 
        3.06        30.90       173.19        13.28        11.54        19.30 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A4U3 TCGA-GN-A4U4 
        9.90        18.25         1.91        53.29       120.53        34.49 
TCGA-GN-A4U8 TCGA-GN-A9SD TCGA-LH-A9QB TCGA-OD-A75X TCGA-RP-A690 TCGA-RP-A693 
       46.92        59.41        85.05       297.01         0.20         0.33 
TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1Q TCGA-W3-AA1V TCGA-W3-AA1W 
      174.12         1.97       120.07        44.05         8.09       185.13 
TCGA-W3-AA21 TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-AA9Y 
       92.84        12.69        21.90        62.89        10.95         1.94 
TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-Z2-AA3S 
       37.32        24.99        91.23 

  AMP PEAK 20(22Q13.2) MUTATED AMP PEAK 20(22Q13.2) WILD-TYPE 
                          4.14                           0.00 
  AMP PEAK 20(22Q13.2) MUTATED AMP PEAK 20(22Q13.2) WILD-TYPE 
                        225.11                         346.49 
  AMP PEAK 20(22Q13.2) MUTATED AMP PEAK 20(22Q13.2) WILD-TYPE 
                         52.73                          37.32 
[1] "4.1 - 225.1 (52.7)" "0.0 - 346.5 (37.3)"
[1] "hr=" "1"  
D20V2, survival
                                sevent
clus2                              0   1
  AMP PEAK 20(22Q13.2) MUTATED    66  83
  AMP PEAK 20(22Q13.2) WILD-TYPE 100 109
  AMP PEAK 20(22Q13.2) MUTATED AMP PEAK 20(22Q13.2) WILD-TYPE 
                           149                            209 
  AMP PEAK 20(22Q13.2) MUTATED AMP PEAK 20(22Q13.2) WILD-TYPE 
                            83                            109 
$`AMP PEAK 20(22Q13.2) MUTATED`
TCGA-D3-A2JE TCGA-D3-A8GI TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A180 TCGA-EE-A184 
       27.65        58.52        68.25        54.02        94.98        68.15 
TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-FR-A729 
      168.26         2.60       126.81       134.40        27.35       220.80 
TCGA-QB-AA9O TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q9 
       18.05        61.15        21.40        12.99        16.57        31.59 
TCGA-D3-A2J7 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JL TCGA-D3-A2JO 
      103.10       115.53       168.00        86.76       171.58        66.08 
TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3MO TCGA-D3-A3MU 
       59.57        58.06        86.93        60.23         9.34        39.75 
TCGA-D3-A3MV TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS 
       45.30        26.89       125.79       135.75       178.32        18.18 
TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GJ TCGA-D3-A8GM TCGA-D3-A8GQ TCGA-D9-A148 
       30.84        79.59       241.38       107.15        29.06       151.53 
TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HV 
        7.10        15.39         9.90        25.18        77.56        76.57 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I7 TCGA-DA-A1I8 
       36.03       144.89        20.38       222.51        88.87        53.92 
TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A3F5 TCGA-DA-A95V TCGA-DA-A95Z TCGA-EB-A5KH 
       65.92        40.60       225.96        72.10        13.02        20.35 
TCGA-EB-A5UL TCGA-EB-A6L9 TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A29M TCGA-EE-A29N 
       29.29        36.46        27.22         8.65        56.84        18.61 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A2 TCGA-EE-A2A5 
       66.74        14.47       195.02        17.92        59.64        39.29 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GM TCGA-EE-A2GN 
       86.14        59.28       220.24        48.72        75.48       102.12 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2ME TCGA-EE-A2MJ TCGA-EE-A2MN TCGA-EE-A2MQ 
      129.27        28.83       103.27        96.23        47.54        43.23 
TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE 
      162.48        53.26       124.31       122.73        28.77        54.51 
TCGA-EE-A3AG TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3JB TCGA-ER-A19B TCGA-ER-A19C 
       41.59        36.95        64.08       201.80        98.40        48.89 
TCGA-ER-A19G TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A2NF 
      302.07       131.51        61.05         8.88       148.18        28.83 
TCGA-ER-A2NG TCGA-ER-A3ET TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7UA 
       48.99        93.01        92.98       174.21        15.72        38.27 
TCGA-FR-A8YD TCGA-FS-A1YY TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZD TCGA-FS-A1ZE 
       36.26       228.59         7.79        27.72        53.52        46.45 
TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS 
        9.70        32.75        23.93       101.26       133.55       148.80 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F2 TCGA-FS-A4F4 
       53.16        26.56        49.48        27.09        50.14        66.67 
TCGA-FS-A4F5 TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-GN-A264 TCGA-GN-A265 
       28.73        80.68        17.46        55.59       117.93        96.92 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U7 TCGA-GN-A8LK 
       64.44        62.79        32.48        48.00        10.42        50.10 
TCGA-GN-A8LL TCGA-HR-A2OH TCGA-QB-A6FS TCGA-RP-A694 TCGA-W3-AA1R TCGA-WE-A8K1 
       21.37        65.88         7.23         0.69       111.09        49.05 
TCGA-WE-A8ZM TCGA-WE-A8ZY TCGA-XV-AB01 TCGA-YD-A89C TCGA-YG-AA3O 
      101.33        49.51        13.25         6.90        37.94 

$`AMP PEAK 20(22Q13.2) WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EE-A2GD TCGA-ER-A193 TCGA-ER-A198 
       62.07        46.32        13.87       340.14        31.40        50.76 
TCGA-FS-A1ZF TCGA-FW-A3R5 TCGA-3N-A9WB TCGA-3N-A9WC TCGA-BF-AAP0 TCGA-D3-A1Q3 
       15.45        36.95        17.03        66.48        14.93        16.67 
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA 
      112.04       112.57        71.80       133.25        28.08        90.90 
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JG 
       95.74        43.43        65.49        23.77        11.87       113.52 
TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JN TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3CB 
       42.08        12.10        66.48       130.72        46.98       166.52 
TCGA-D3-A3CF TCGA-D3-A3MR TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
       24.53       103.59       174.84        55.73        56.35       145.12 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GO TCGA-D3-A5GU TCGA-D3-A8GD 
       32.94        22.62        63.81       137.92       125.19        23.61 
TCGA-D3-A8GE TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GR 
       26.43       170.20        89.13       161.00       152.75       129.63 
TCGA-D3-A8GS TCGA-D3-A8GV TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1X3 TCGA-D9-A3Z3 
      117.17       167.70        54.67         3.65        18.12        22.29 
TCGA-D9-A4Z6 TCGA-D9-A6EG TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1IC 
       18.44        22.95       176.55        35.93       135.02        68.09 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-DA-A95W TCGA-DA-A95X TCGA-DA-A95Y 
       33.93        10.49        43.36        37.35        73.94        14.14 
TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EE-A17X TCGA-EE-A181 
       13.87        10.36        58.92         7.04        29.82        33.73 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F 
       14.70        26.89         4.96       133.81       151.27        91.56 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
       13.55        63.35        85.08        78.97        13.97        63.78 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29P TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V 
       72.07        64.64        56.42        61.28       369.93        25.87 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GJ TCGA-EE-A2GK 
       46.82       115.96        67.43       173.79       107.38        54.74 
TCGA-EE-A2GL TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU 
       79.66        13.91        42.77        81.21        44.88        94.82 
TCGA-EE-A2M5 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2MF TCGA-EE-A2MG 
       21.67        19.76        61.51        47.28       268.73       103.20 
TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP 
       16.96       204.66       180.39       216.66       167.90       248.65 
TCGA-EE-A2MT TCGA-EE-A3AC TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 
       71.21        64.04        13.81       138.81       172.18       127.20 
TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 
       34.32        53.19        51.35       134.33       152.81        35.44 
TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F 
       13.94         9.17        77.75        12.59        13.02        26.37 
TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S 
      152.35         6.44        44.09       162.08        50.89        49.48 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NH TCGA-ER-A3ES 
      105.07        43.82        23.34        20.15        41.56       247.04 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A7U8 TCGA-FR-A7U9 
       46.98        33.21        12.95       149.03        27.85        18.77 
TCGA-FR-A8YC TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1Z0 TCGA-FS-A1Z3 
       34.82       104.42       216.92        48.59       202.65        20.91 
TCGA-FS-A1Z4 TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZJ TCGA-FS-A1ZP TCGA-FS-A1ZR 
       28.08        48.85       357.37        47.38        74.73        11.41 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC 
       27.02        77.82       174.84        34.03        26.73        54.41 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 
       13.51        19.30         9.90        19.43         2.04        15.78 
TCGA-GN-A262 TCGA-GN-A266 TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-GN-A4U9 
      139.89        10.13       121.91        39.35        48.89        22.13 
TCGA-GN-A9SD TCGA-HR-A2OG TCGA-LH-A9QB TCGA-OD-A75X TCGA-RP-A690 TCGA-RP-A693 
       59.41         0.23       368.78       297.90         0.20         0.33 
TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1Q TCGA-W3-AA1V 
      228.16        63.02       121.08         4.01        69.07        42.08 
TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K6 TCGA-WE-A8ZN TCGA-WE-A8ZO 
      219.16       105.04        24.03        17.95        58.98        70.52 
TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 
       63.22        11.80        35.80        12.16        40.41        24.99 
TCGA-YD-A9TA TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       49.18        14.43        27.58        96.99        15.98 

  AMP PEAK 20(22Q13.2) MUTATED AMP PEAK 20(22Q13.2) WILD-TYPE 
                          0.69                           0.20 
  AMP PEAK 20(22Q13.2) MUTATED AMP PEAK 20(22Q13.2) WILD-TYPE 
                        302.07                         369.93 
  AMP PEAK 20(22Q13.2) MUTATED AMP PEAK 20(22Q13.2) WILD-TYPE 
                         54.02                          49.18 
[1] "0.7 - 302.1 (54.0)" "0.2 - 369.9 (49.2)"
[1] "hr=" "1.1"
D20V3, continuous
                                vv
clus                             I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB
  AMP PEAK 20(22Q13.2) MUTATED          4       3      12        6       11
  AMP PEAK 20(22Q13.2) WILD-TYPE        9       4      17       12       17
                                vv
clus                             STAGE II STAGE IIA STAGE IIB STAGE IIC
  AMP PEAK 20(22Q13.2) MUTATED         10         4         5        10
  AMP PEAK 20(22Q13.2) WILD-TYPE       16        10        14         5
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  AMP PEAK 20(22Q13.2) MUTATED          20          9         14         24
  AMP PEAK 20(22Q13.2) WILD-TYPE        19          6         21         30
                                vv
clus                             STAGE IV
  AMP PEAK 20(22Q13.2) MUTATED          8
  AMP PEAK 20(22Q13.2) WILD-TYPE       13
D20V4, multiclass
            clus
vv           AMP PEAK 20(22Q13.2) MUTATED AMP PEAK 20(22Q13.2) WILD-TYPE
  I/II NOS                              4                              9
  STAGE 0                               3                              4
  STAGE I                              12                             17
  STAGE IA                              6                             12
  STAGE IB                             11                             17
  STAGE II                             10                             16
  STAGE IIA                             4                             10
  STAGE IIB                             5                             14
  STAGE IIC                            10                              5
  STAGE III                            20                             19
  STAGE IIIA                            9                              6
  STAGE IIIB                           14                             21
  STAGE IIIC                           24                             30
  STAGE IV                              8                             13
[1] 14  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  AMP PEAK 20(22Q13.2) MUTATED      27 35 30 29
  AMP PEAK 20(22Q13.2) WILD-TYPE    37 38 51 38
D20V5, multiclass
       clus
vv      AMP PEAK 20(22Q13.2) MUTATED AMP PEAK 20(22Q13.2) WILD-TYPE
  T0+T1                           27                             37
  T2                              35                             38
  T3                              30                             51
  T4                              29                             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  N3
  AMP PEAK 20(22Q13.2) MUTATED    66  29  20  21
  AMP PEAK 20(22Q13.2) WILD-TYPE 111  36  19  24
D20V6, multiclass
    clus
vv   AMP PEAK 20(22Q13.2) MUTATED AMP PEAK 20(22Q13.2) WILD-TYPE
  N0                           66                            111
  N1                           29                             36
  N2                           20                             19
  N3                           21                             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"
D20V7, binary
                                cls
clus                               0   1
  AMP PEAK 20(22Q13.2) MUTATED   131   9
  AMP PEAK 20(22Q13.2) WILD-TYPE 188  13
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(22Q13.2) MUTATED    131    9
  AMP PEAK 20(22Q13.2) WILD-TYPE  188   13
   clus
vv  AMP PEAK 20(22Q13.2) MUTATED AMP PEAK 20(22Q13.2) WILD-TYPE
  0                          131                            188
  1                            9                             13
[1] 2 2
[1] FALSE
D20V8, binary
                                cls
clus                              0  1
  AMP PEAK 20(22Q13.2) MUTATED   57 42
  AMP PEAK 20(22Q13.2) WILD-TYPE 77 48
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(22Q13.2) MUTATED     57   42
  AMP PEAK 20(22Q13.2) WILD-TYPE   77   48
     clus
vv    AMP PEAK 20(22Q13.2) MUTATED AMP PEAK 20(22Q13.2) WILD-TYPE
  NO                            57                             77
  YES                           42                             48
[1] 2 2
[1] FALSE
D20V9, binary
                                cls
clus                               0   1
  AMP PEAK 20(22Q13.2) MUTATED    19 133
  AMP PEAK 20(22Q13.2) WILD-TYPE  28 187
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(22Q13.2) MUTATED     19  133
  AMP PEAK 20(22Q13.2) WILD-TYPE   28  187
     clus
vv    AMP PEAK 20(22Q13.2) MUTATED AMP PEAK 20(22Q13.2) WILD-TYPE
  NO                            19                             28
  YES                          133                            187
[1] 2 2
[1] FALSE
D20V10, continuous
D20V11, binary
                                cls
clus                               0   1
  AMP PEAK 20(22Q13.2) MUTATED    61  91
  AMP PEAK 20(22Q13.2) WILD-TYPE  77 138
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(22Q13.2) MUTATED     61   91
  AMP PEAK 20(22Q13.2) WILD-TYPE   77  138
        clus
vv       AMP PEAK 20(22Q13.2) MUTATED AMP PEAK 20(22Q13.2) WILD-TYPE
  FEMALE                           61                             77
  MALE                             91                            138
[1] 2 2
[1] FALSE
D20V12, binary
                                cls
clus                               0   1
  AMP PEAK 20(22Q13.2) MUTATED   132  20
  AMP PEAK 20(22Q13.2) WILD-TYPE 187  27
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(22Q13.2) MUTATED    132   20
  AMP PEAK 20(22Q13.2) WILD-TYPE  187   27
     clus
vv    AMP PEAK 20(22Q13.2) MUTATED AMP PEAK 20(22Q13.2) WILD-TYPE
  NO                           132                            187
  YES                           20                             27
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 20(22Q13.2) MUTATED       3                         1   146
  AMP PEAK 20(22Q13.2) WILD-TYPE     2                         0   207
D20V13, multiclass
                           clus
vv                          AMP PEAK 20(22Q13.2) MUTATED
  ASIAN                                                3
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                              146
                           clus
vv                          AMP PEAK 20(22Q13.2) WILD-TYPE
  ASIAN                                                  2
  BLACK OR AFRICAN AMERICAN                              0
  WHITE                                                207
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V14, binary
                                cls
clus                               0   1
  AMP PEAK 20(22Q13.2) MUTATED     1 148
  AMP PEAK 20(22Q13.2) WILD-TYPE   6 204
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(22Q13.2) MUTATED      1  148
  AMP PEAK 20(22Q13.2) WILD-TYPE    6  204
                        clus
vv                       AMP PEAK 20(22Q13.2) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                          148
                        clus
vv                       AMP PEAK 20(22Q13.2) WILD-TYPE
  HISPANIC OR LATINO                                  6
  NOT HISPANIC OR LATINO                            204
[1] 2 2
[1] FALSE

Clustering(21) Variable = DEL PEAK  1(1P36.31) MUTATION ANALYSIS
D21V1, survival
                                sevent
clus2                              0   1
  DEL PEAK  1(1P36.31) MUTATED    26  32
  DEL PEAK  1(1P36.31) WILD-TYPE 102  92
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                            58                            194 
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                            32                             92 
$`DEL PEAK  1(1P36.31) MUTATED`
TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GO TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-D3-A1Q1 
       31.96       166.75        52.90        52.73         7.40         8.42 
TCGA-D3-A1Q4 TCGA-D3-A2JO TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A5GN TCGA-D3-A5GR 
       31.89        66.08        58.06        59.70        45.70       177.86 
TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D9-A4Z6 TCGA-DA-A1I2 TCGA-DA-A1I7 TCGA-DA-A3F5 
       69.53        70.62        18.44       150.61        60.10       225.11 
TCGA-DA-A3F8 TCGA-EE-A17Y TCGA-EE-A182 TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29D 
        8.71        24.89         0.00        79.20        75.22        12.99 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GR TCGA-EE-A2MK TCGA-EE-A2MS TCGA-EE-A3AB 
       12.95       201.60         0.20        89.26       143.93       122.73 
TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19G 
        4.41         6.28        67.89        39.81        11.47       184.60 
TCGA-ER-A19S TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A69P 
       47.18         4.70        16.87        15.48        32.05         4.14 
TCGA-FR-A7U8 TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1ZJ TCGA-FS-A1ZT 
       26.20       171.78        49.74       195.98        36.33        35.28 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F8 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV 
       23.21         5.29       173.19        80.68        55.59        11.54 
TCGA-RP-A690 TCGA-WE-A8ZM TCGA-WE-AA9Y TCGA-WE-AAA0 
        0.20        65.42         1.94        37.32 

$`DEL PEAK  1(1P36.31) WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A8GI TCGA-EB-A5SG TCGA-EE-A2GD 
        9.76        62.07        38.76        13.41        33.24       269.03 
TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-FR-A729 TCGA-FW-A3R5 TCGA-3N-A9WC 
      134.40        27.35        19.04       216.43        36.95        60.46 
TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q3 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       12.99        14.83        15.72       110.93        49.35       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 
       19.04        76.41        62.60        25.64        45.99        62.86 
TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL 
       15.75       168.00        86.30       107.61        36.30       171.58 
TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3MO 
       64.83        43.53       140.98        40.01        24.53         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K 
       90.21        23.67       173.85        30.67       144.46        31.76 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GU TCGA-D3-A8GC TCGA-D3-A8GD 
       62.70        11.34        42.05       124.08        78.21        23.61 
TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GP TCGA-D3-A8GR TCGA-D9-A1X3 TCGA-D9-A3Z1 
      179.97       120.00       135.12        36.53        10.78        15.02 
TCGA-D9-A3Z3 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 
       16.90        69.21        22.85        76.34       138.67        68.68 
TCGA-DA-A1I5 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A95V TCGA-DA-A95W 
      110.53        64.83        58.85        30.44        72.10         0.76 
TCGA-DA-A95X TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN 
       65.03        14.14        12.30         3.91        16.41        52.41 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A29C 
       18.21        13.15        20.38        26.24        75.55        76.14 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q 
        0.26        44.28        47.41        47.74        27.16        61.12 
TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB 
      346.49       185.19       115.43        30.02        77.98        26.14 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP 
       68.65        10.62        32.48        18.35        93.63         0.76 
TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
       71.31        81.99       103.13        15.25         5.75        23.77 
TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MM 
      209.79        94.19       171.85        63.25       104.78       145.45 
TCGA-EE-A2MP TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AE 
      227.01        23.51        53.26       124.31        64.04        54.51 
TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI 
      111.85        45.90         3.35       168.85        19.86       135.98 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19H 
       34.45        10.49         7.82         4.54        53.29       150.12 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19W 
       99.06        59.84        42.51       120.76        49.71       146.63 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET 
       73.05        22.36        10.19        28.67       173.29        68.52 
TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FS-A1Z3 
       74.47         4.50       174.21         5.65        10.06         8.35 
TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZM 
       27.62       312.07        32.78        43.92         7.82        78.61 
TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 
      130.95       136.27         4.47         3.06        30.90        66.67 
TCGA-FS-A4F9 TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 
       13.28        19.30         9.90        18.25         1.91        53.29 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 
      117.93        96.92        17.06        42.48         7.59       120.53 
TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-GN-A8LK TCGA-GN-A9SD TCGA-LH-A9QB TCGA-OD-A75X 
       34.49        46.92        43.23        59.41        85.05       297.01 
TCGA-QB-A6FS TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1Q 
        7.23         0.33       174.12         1.97       120.07        44.05 
TCGA-W3-AA1R TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8ZN 
       79.99         8.09       185.13        92.84        47.54        12.69 
TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AAA4 TCGA-XV-AB01 
       21.90        62.89        10.95        48.39        24.99         6.61 
TCGA-YG-AA3O TCGA-Z2-AA3S 
       28.21        91.23 

  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                          0.00                           0.26 
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                        225.11                         346.49 
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                        42.755                         47.165 
[1] "0.0 - 225.1 (42.8)" "0.3 - 346.5 (47.2)"
[1] "hr=" "1.3"
D21V2, survival
                                sevent
clus2                              0   1
  DEL PEAK  1(1P36.31) MUTATED    35  44
  DEL PEAK  1(1P36.31) WILD-TYPE 131 148
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                            79                            279 
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                            44                            148 
$`DEL PEAK  1(1P36.31) MUTATED`
TCGA-EB-A5SH TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GO TCGA-WE-A8K5 TCGA-WE-AAA3 
       54.02        94.98       168.26       126.81        61.15        21.40 
TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A2JK TCGA-D3-A2JO TCGA-D3-A3C6 TCGA-D3-A3CE 
       16.57       112.04        12.10        66.08        58.06        60.23 
TCGA-D3-A3MV TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A8GL TCGA-D3-A8GM 
       45.30       135.75       178.32        18.18        89.13       107.15 
TCGA-D9-A1JX TCGA-D9-A4Z6 TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I7 TCGA-DA-A3F5 
        7.10        18.44        20.38       176.55        88.87       225.96 
TCGA-DA-A3F8 TCGA-EE-A17Y TCGA-EE-A182 TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29D 
       43.36        27.22        14.70        91.56        85.08        13.97 
TCGA-EE-A29R TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GR TCGA-EE-A2M5 
       14.47       173.79       220.24        48.72        42.77        21.67 
TCGA-EE-A2MD TCGA-EE-A2MH TCGA-EE-A2MK TCGA-EE-A2MS TCGA-EE-A3AB TCGA-EE-A3AD 
       47.28        16.96       180.39       162.48       122.73        28.77 
TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3JA TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19G 
       13.81       172.18        53.19        48.89        12.59       302.07 
TCGA-ER-A19S TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NH TCGA-ER-A3EV TCGA-ER-A3PL 
       49.48        23.34        20.15        41.56        46.98        33.21 
TCGA-ER-A42K TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY 
       12.95        15.72        27.85       216.92        48.59       228.59 
TCGA-FS-A1Z0 TCGA-FS-A1Z7 TCGA-FS-A1ZJ TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A1ZY 
      202.65         7.79        47.38        53.16        49.48        27.09 
TCGA-FS-A4F8 TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV 
      174.84        54.41        80.68        17.46        55.59        13.51 
TCGA-GN-A26D TCGA-RP-A690 TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-AA9Y TCGA-WE-AAA0 
       48.00         0.20        17.95       101.33        12.16        40.41 
TCGA-YG-AA3P 
       14.43 

$`DEL PEAK  1(1P36.31) WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-D3-A8GI TCGA-EB-A5SG 
       27.65        62.07        46.32        13.87        58.52        68.25 
TCGA-EE-A184 TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 
       68.15         2.60       340.14       134.40        27.35        31.40 
TCGA-ER-A198 TCGA-FR-A729 TCGA-FS-A1ZF TCGA-FW-A3R5 TCGA-QB-AA9O TCGA-3N-A9WB 
       50.76       220.80        15.45        36.95        18.05        17.03 
TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q3 TCGA-D3-A1Q5 TCGA-D3-A1Q6 
       66.48        12.99        14.93        16.67       112.57        71.80 
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 
      133.25        28.08        31.59        90.90        95.74        43.43 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC 
      103.10        65.49        23.77       115.53       168.00        86.76 
TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JP 
       11.87       113.52        42.08       171.58        66.48        59.57 
TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3MO 
      130.72        46.98       166.52        86.93        24.53         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
      103.59        39.75       174.84        55.73        56.35       145.12 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GO 
       32.94        22.62        63.81        26.89       125.79       137.92 
TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GJ 
      125.19        30.84        79.59        23.61        26.43       241.38 
TCGA-D3-A8GK TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS 
      170.20       161.00       152.75        29.06       129.63       117.17 
TCGA-D3-A8GV TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1X3 TCGA-D9-A3Z1 
      167.70       151.53        54.67         3.65        18.12        15.39 
TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV 
       22.29         9.90        25.18        77.56        22.95        76.57 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I8 
       36.03       144.89       222.51        35.93       135.02        53.92 
TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A95V 
       65.92        40.60        68.09        33.93        10.49        72.10 
TCGA-DA-A95W TCGA-DA-A95X TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A44R 
       37.35        73.94        14.14        13.02        13.87        10.36 
TCGA-EB-A5KH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X 
       20.35        29.29        58.92         7.04        36.46        29.82 
TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C 
        8.65        33.73        26.89         4.96       133.81       151.27 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H 
       13.55        63.35        78.97        63.78        72.07        64.64 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29T 
       56.84        18.61        56.42        66.74        61.28       369.93 
TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
       25.87       195.02        17.92        46.82       115.96        59.64 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GJ TCGA-EE-A2GK 
       39.29        86.14        59.28        67.43       107.38        54.74 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2GT 
       79.66        75.48       102.12        13.91        81.21        44.88 
TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2ME 
       94.82       129.27        28.83        19.76        61.51       103.27 
TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MM 
      268.73       103.20       204.66        96.23       216.66       167.90 
TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA 
       47.54       248.65        43.23        71.21        53.26       124.31 
TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J5 
       64.04        54.51        41.59       138.81       127.20        36.95 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
       64.08        34.32       201.80        51.35       134.33       152.81 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19E 
       35.44        13.94         9.17        77.75        98.40        13.02 
TCGA-ER-A19F TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
       26.37       152.35         6.44       131.51        61.05        44.09 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
      162.08        50.89         8.88       148.18       105.07        43.82 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A42L TCGA-FR-A3YN 
       28.83        48.99       247.04        93.01       149.03        92.98 
TCGA-FR-A44A TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE 
      174.21        18.77        38.27        34.82        36.26       104.42 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD 
       20.91        28.08        27.72        48.85       357.37        53.52 
TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP 
       46.45         9.70        32.75        23.93       101.26        74.73 
TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZZ TCGA-FS-A4F0 
      133.55        11.41       148.80        26.56        27.02        77.82 
TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FW-A5DY 
       50.14        66.67        28.73        34.03        26.73        19.30 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 
        9.90        19.43         2.04        15.78       139.89       117.93 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 
       96.92        10.13        64.44        62.79        32.48       121.91 
TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL 
       39.35        10.42        48.89        22.13        50.10        21.37 
TCGA-GN-A9SD TCGA-HR-A2OG TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS 
       59.41         0.23        65.88       368.78       297.90         7.23 
TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O 
        0.33         0.69       228.16        63.02       121.08         4.01 
TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8JZ 
       69.07       111.09        42.08       219.16       105.04        24.03 
TCGA-WE-A8K1 TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX 
       49.05        58.98        70.52        63.22        11.80        35.80 
TCGA-WE-A8ZY TCGA-WE-AAA4 TCGA-XV-AB01 TCGA-YD-A89C TCGA-YD-A9TA TCGA-YG-AA3O 
       49.51        24.99        13.25         6.90        49.18        37.94 
TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       27.58        96.99        15.98 

  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                          0.20                           0.23 
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                        302.07                         369.93 
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                         48.59                          54.67 
[1] "0.2 - 302.1 (48.6)" "0.2 - 369.9 (54.7)"
[1] "hr=" "1.1"
D21V3, continuous
                                vv
clus                             I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB
  DEL PEAK  1(1P36.31) MUTATED          1       1      11        3        5
  DEL PEAK  1(1P36.31) WILD-TYPE       12       6      18       15       23
                                vv
clus                             STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK  1(1P36.31) MUTATED          4         2         4         1
  DEL PEAK  1(1P36.31) WILD-TYPE       22        12        15        14
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK  1(1P36.31) MUTATED          11          0          9         18
  DEL PEAK  1(1P36.31) WILD-TYPE        28         15         26         36
                                vv
clus                             STAGE IV
  DEL PEAK  1(1P36.31) MUTATED          5
  DEL PEAK  1(1P36.31) WILD-TYPE       16
D21V4, multiclass
            clus
vv           DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE
  I/II NOS                              1                             12
  STAGE 0                               1                              6
  STAGE I                              11                             18
  STAGE IA                              3                             15
  STAGE IB                              5                             23
  STAGE II                              4                             22
  STAGE IIA                             2                             12
  STAGE IIB                             4                             15
  STAGE IIC                             1                             14
  STAGE III                            11                             28
  STAGE IIIA                            0                             15
  STAGE IIIB                            9                             26
  STAGE IIIC                           18                             36
  STAGE IV                              5                             16
[1] 14  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  DEL PEAK  1(1P36.31) MUTATED      18 21 14 15
  DEL PEAK  1(1P36.31) WILD-TYPE    46 52 67 52
D21V5, multiclass
       clus
vv      DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE
  T0+T1                           18                             46
  T2                              21                             52
  T3                              14                             67
  T4                              15                             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  N3
  DEL PEAK  1(1P36.31) MUTATED    39  16   8  12
  DEL PEAK  1(1P36.31) WILD-TYPE 138  49  31  33
D21V6, multiclass
    clus
vv   DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE
  N0                           39                            138
  N1                           16                             49
  N2                            8                             31
  N3                           12                             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"
D21V7, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.31) MUTATED    70   5
  DEL PEAK  1(1P36.31) WILD-TYPE 249  17
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.31) MUTATED     70    5
  DEL PEAK  1(1P36.31) WILD-TYPE  249   17
   clus
vv  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE
  0                           70                            249
  1                            5                             17
[1] 2 2
[1] FALSE
D21V8, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.31) MUTATED    31  21
  DEL PEAK  1(1P36.31) WILD-TYPE 103  69
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.31) MUTATED     31   21
  DEL PEAK  1(1P36.31) WILD-TYPE  103   69
     clus
vv    DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE
  NO                            31                            103
  YES                           21                             69
[1] 2 2
[1] FALSE
D21V9, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.31) MUTATED    10  71
  DEL PEAK  1(1P36.31) WILD-TYPE  37 249
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.31) MUTATED     10   71
  DEL PEAK  1(1P36.31) WILD-TYPE   37  249
     clus
vv    DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE
  NO                            10                             37
  YES                           71                            249
[1] 2 2
[1] FALSE
D21V10, continuous
D21V11, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.31) MUTATED    35  46
  DEL PEAK  1(1P36.31) WILD-TYPE 103 183
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.31) MUTATED     35   46
  DEL PEAK  1(1P36.31) WILD-TYPE  103  183
        clus
vv       DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE
  FEMALE                           35                            103
  MALE                             46                            183
[1] 2 2
[1] FALSE
D21V12, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.31) MUTATED    68  12
  DEL PEAK  1(1P36.31) WILD-TYPE 251  35
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.31) MUTATED     68   12
  DEL PEAK  1(1P36.31) WILD-TYPE  251   35
     clus
vv    DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE
  NO                            68                            251
  YES                           12                             35
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  1(1P36.31) MUTATED       1                         0    79
  DEL PEAK  1(1P36.31) WILD-TYPE     4                         1   274
D21V13, multiclass
                           clus
vv                          DEL PEAK  1(1P36.31) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                               79
                           clus
vv                          DEL PEAK  1(1P36.31) WILD-TYPE
  ASIAN                                                  4
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                274
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V14, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.31) MUTATED     1  79
  DEL PEAK  1(1P36.31) WILD-TYPE   6 273
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.31) MUTATED      1   79
  DEL PEAK  1(1P36.31) WILD-TYPE    6  273
                        clus
vv                       DEL PEAK  1(1P36.31) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           79
                        clus
vv                       DEL PEAK  1(1P36.31) WILD-TYPE
  HISPANIC OR LATINO                                  6
  NOT HISPANIC OR LATINO                            273
[1] 2 2
[1] FALSE

Clustering(22) Variable = DEL PEAK  2(1P22.1) MUTATION ANALYSIS
D22V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  2(1P22.1) MUTATED   30 35
  DEL PEAK  2(1P22.1) WILD-TYPE 98 89
  DEL PEAK  2(1P22.1) MUTATED DEL PEAK  2(1P22.1) WILD-TYPE 
                           65                           187 
  DEL PEAK  2(1P22.1) MUTATED DEL PEAK  2(1P22.1) WILD-TYPE 
                           35                            89 
$`DEL PEAK  2(1P22.1) MUTATED`
TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GO TCGA-ER-A193 TCGA-WE-A8K5 TCGA-WE-AAA3 
       31.96       166.75        52.90        19.04        52.73         7.40 
TCGA-BF-AAP0 TCGA-D3-A1Q4 TCGA-D3-A1Q8 TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2JC 
       14.83        31.89        19.04        25.64        45.99        86.30 
TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3MO TCGA-D3-A5GN 
       64.83        66.08        40.01        59.70         9.34        45.70 
TCGA-D3-A5GR TCGA-D3-A8GR TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-DA-A1I2 TCGA-DA-A1I7 
      177.86        36.53        16.90        18.44       150.61        60.10 
TCGA-DA-A1IA TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-DA-A95V TCGA-DA-A95Y TCGA-EE-A17Y 
       64.83       225.11         8.71        72.10        14.14        24.89 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29T TCGA-EE-A2GE TCGA-EE-A2GR TCGA-EE-A2MK 
       76.14        12.99       346.49        12.95         0.20        89.26 
TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3J3 TCGA-ER-A197 
      227.01       143.93       122.73         4.41        67.89        10.49 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19S TCGA-ER-A2ND 
       39.81        11.47        99.06        59.84        47.18         4.70 
TCGA-ER-A2NG TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A69P TCGA-FS-A1Z0 TCGA-FS-A1ZJ 
       28.67        15.48        32.05         4.14       195.98        36.33 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A4F8 TCGA-FW-A3TV TCGA-GN-A262 
      136.27        35.28        23.21       173.19        11.54        53.29 
TCGA-GN-A8LK TCGA-W3-A825 TCGA-WE-A8ZM TCGA-WE-A8ZQ TCGA-WE-AA9Y 
       43.23         1.97        65.42        62.89         1.94 

$`DEL PEAK  2(1P22.1) WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A8GI TCGA-EB-A5SG TCGA-EE-A2GD 
        9.76        62.07        38.76        13.41        33.24       269.03 
TCGA-EE-A2MR TCGA-EE-A3JD TCGA-FR-A729 TCGA-FW-A3R5 TCGA-3N-A9WC TCGA-3N-A9WD 
      134.40        27.35       216.43        36.95        60.46        12.99 
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1QA 
        8.42        15.72       110.93        49.35       133.25        76.41 
TCGA-D3-A1QB TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JG TCGA-D3-A2JH 
       62.60        62.86        15.75       168.00       107.61        36.30 
TCGA-D3-A2JL TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CF TCGA-D3-A3MR 
      171.58        43.53        58.06       140.98        24.53        90.21 
TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R 
       23.67       173.85        30.67       144.46        31.76        62.70 
TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GU TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GJ 
       11.34        42.05       124.08        78.21        23.61       179.97 
TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GP TCGA-D9-A1X3 TCGA-D9-A3Z1 
      120.00        69.53        70.62       135.12        10.78        15.02 
TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I5 
       69.21        22.85        76.34       138.67        68.68       110.53 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A95W TCGA-DA-A95X TCGA-DA-A95Z TCGA-EB-A44Q 
       58.85        30.44         0.76        65.03        12.30         3.91 
TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A182 
       16.41        52.41        18.21        13.15        20.38         0.00 
TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29E TCGA-EE-A29G 
       26.24        75.55        79.20        75.22         0.26        44.28 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29W TCGA-EE-A2A1 
       47.41        47.74        27.16        61.12       185.19       115.43 
TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK 
       30.02        77.98        26.14       201.60        68.65        10.62 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2GU 
       32.48        18.35        93.63         0.76        71.31        81.99 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MG 
      103.13        15.25         5.75        23.77       209.79        94.19 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MT TCGA-EE-A2MU 
      171.85        63.25       104.78       145.45        23.51        53.26 
TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J4 TCGA-EE-A3J7 
      124.31        64.04        54.51         6.28       111.85        45.90 
TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A199 
        3.35       168.85        19.86       135.98        34.45         7.82 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19N TCGA-ER-A19P 
        4.54        53.29       184.60       150.12        42.51       120.76 
TCGA-ER-A19Q TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF 
       49.71       146.63        73.05        22.36        16.87        10.19 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A7U8 
      173.29        68.52        74.47         4.50       174.21        26.20 
TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1Z4 
        5.65        10.06       171.78        49.74         8.35        27.62 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZM TCGA-FS-A1ZQ 
      312.07        32.78        43.92         7.82        78.61       130.95 
TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F9 
        4.47         5.29         3.06        30.90        66.67        13.28 
TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
       80.68        55.59        19.30         9.90        18.25         1.91 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 
      117.93        96.92        17.06        42.48         7.59       120.53 
TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-GN-A9SD TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS 
       34.49        46.92        59.41        85.05       297.01         7.23 
TCGA-RP-A690 TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A828 TCGA-W3-AA1Q TCGA-W3-AA1R 
        0.20         0.33       174.12       120.07        44.05        79.99 
TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8ZN TCGA-WE-A8ZO 
        8.09       185.13        92.84        47.54        12.69        21.90 
TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-XV-AB01 TCGA-YG-AA3O 
       10.95        48.39        37.32        24.99         6.61        28.21 
TCGA-Z2-AA3S 
       91.23 

  DEL PEAK  2(1P22.1) MUTATED DEL PEAK  2(1P22.1) WILD-TYPE 
                          0.2                           0.0 
  DEL PEAK  2(1P22.1) MUTATED DEL PEAK  2(1P22.1) WILD-TYPE 
                       346.49                        312.07 
  DEL PEAK  2(1P22.1) MUTATED DEL PEAK  2(1P22.1) WILD-TYPE 
                        40.01                         47.74 
[1] "0.2 - 346.5 (40.0)" "0.0 - 312.1 (47.7)"
[1] "hr=" "1.2"
D22V2, survival
                               sevent
clus2                             0   1
  DEL PEAK  2(1P22.1) MUTATED    42  52
  DEL PEAK  2(1P22.1) WILD-TYPE 124 140
  DEL PEAK  2(1P22.1) MUTATED DEL PEAK  2(1P22.1) WILD-TYPE 
                           94                           264 
  DEL PEAK  2(1P22.1) MUTATED DEL PEAK  2(1P22.1) WILD-TYPE 
                           52                           140 
$`DEL PEAK  2(1P22.1) MUTATED`
TCGA-EB-A5SH TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GO TCGA-ER-A193 TCGA-QB-AA9O 
       54.02        94.98       168.26       126.81        31.40        18.05 
TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-BF-AAP0 TCGA-D3-A1Q4 TCGA-D3-A1Q8 TCGA-D3-A1Q9 
       61.15        21.40        14.93       112.04        28.08        31.59 
TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JN TCGA-D3-A2JO 
       43.43       103.10        86.76        11.87        66.48        66.08 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3MO TCGA-D3-A3MV TCGA-D3-A5GN TCGA-D3-A5GR 
       86.93        60.23         9.34        45.30       135.75       178.32 
TCGA-D3-A5GS TCGA-D3-A8GB TCGA-D3-A8GR TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-DA-A1I0 
       18.18        30.84       129.63        22.29        18.44        20.38 
TCGA-DA-A1I2 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A3F5 TCGA-DA-A3F8 
      176.55        88.87        53.92        65.92       225.96        43.36 
TCGA-DA-A95V TCGA-DA-A95Y TCGA-EB-A44R TCGA-EB-A5UL TCGA-EE-A17Y TCGA-EE-A20B 
       72.10        14.14        10.36        29.29        27.22       133.81 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29R TCGA-EE-A29T TCGA-EE-A2GC TCGA-EE-A2GE 
       78.97        13.97        14.47       369.93        67.43       173.79 
TCGA-EE-A2GR TCGA-EE-A2MK TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A3AB TCGA-EE-A3AD 
       42.77       180.39       248.65       162.48       122.73        28.77 
TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-ER-A197 TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19L 
      138.81       172.18        13.94        48.89        12.59       131.51 
TCGA-ER-A19M TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A2ND TCGA-ER-A2NG TCGA-ER-A2NH 
       61.05        49.48         8.88        23.34        48.99        41.56 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A69P TCGA-FS-A1YX TCGA-FS-A1Z0 
       46.98        33.21        12.95        15.72        48.59       202.65 
TCGA-FS-A1Z7 TCGA-FS-A1ZJ TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A4F8 
        7.79        47.38       148.80        53.16        49.48       174.84 
TCGA-FW-A3TV TCGA-GN-A262 TCGA-GN-A26D TCGA-GN-A4U7 TCGA-GN-A4U9 TCGA-GN-A8LK 
       13.51       139.89        48.00        10.42        22.13        50.10 
TCGA-GN-A8LL TCGA-HR-A2OH TCGA-W3-A825 TCGA-WE-A8JZ TCGA-WE-A8ZM TCGA-WE-A8ZQ 
       21.37        65.88        63.02        24.03       101.33        63.22 
TCGA-WE-AA9Y TCGA-YD-A9TA TCGA-YG-AA3P TCGA-Z2-A8RT 
       12.16        49.18        14.43        27.58 

$`DEL PEAK  2(1P22.1) WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-D3-A8GI TCGA-EB-A5SG 
       27.65        62.07        46.32        13.87        58.52        68.25 
TCGA-EE-A184 TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A198 
       68.15         2.60       340.14       134.40        27.35        50.76 
TCGA-FR-A729 TCGA-FS-A1ZF TCGA-FW-A3R5 TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD 
      220.80        15.45        36.95        17.03        66.48        12.99 
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1QA 
       16.57        16.67       112.57        71.80       133.25        90.90 
TCGA-D3-A1QB TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JG 
       95.74        65.49        23.77       115.53       168.00       113.52 
TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 
       42.08        12.10       171.58        59.57       130.72        58.06 
TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CF TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E 
       46.98       166.52        24.53       103.59        39.75       174.84 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R 
       55.73        56.35       145.12        32.94        22.62        63.81 
TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GO TCGA-D3-A5GU TCGA-D3-A8GC TCGA-D3-A8GD 
       26.89       125.79       137.92       125.19        79.59        23.61 
TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GN 
       26.43       241.38       170.20        89.13       107.15       161.00 
TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GS TCGA-D3-A8GV TCGA-D9-A148 TCGA-D9-A149 
      152.75        29.06       117.17       167.70       151.53        54.67 
TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A6E9 TCGA-D9-A6EA 
        3.65         7.10        18.12        15.39         9.90        25.18 
TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I1 
       77.56        22.95        76.57        36.03       144.89       222.51 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
       35.93       135.02        40.60        68.09        33.93        10.49 
TCGA-DA-A95W TCGA-DA-A95X TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN 
       37.35        73.94        13.02        13.87        20.35        58.92 
TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 
        7.04        36.46        29.82         8.65        33.73        14.70 
TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29A 
       26.89         4.96       151.27        91.56        13.55        63.35 
TCGA-EE-A29B TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N 
       85.08        63.78        72.07        64.64        56.84        18.61 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X 
       56.42        66.74        61.28        25.87       195.02        17.92 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
       46.82       115.96        59.64        39.29        86.14        59.28 
TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
      220.24        48.72       107.38        54.74        79.66        75.48 
TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 
      102.12        13.91        81.21        44.88        94.82        21.67 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME 
      129.27        28.83        19.76        61.51        47.28       103.27 
TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2ML 
      268.73       103.20        16.96       204.66        96.23       216.66 
TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA 
      167.90        47.54        43.23        71.21        53.26       124.31 
TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3J4 TCGA-EE-A3J5 
       64.04        54.51        13.81        41.59       127.20        36.95 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JE TCGA-EE-A3JH 
       64.08        34.32        53.19       201.80        51.35       134.33 
TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19E 
      152.81        35.44         9.17        77.75        98.40        13.02 
TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19N TCGA-ER-A19P 
       26.37       302.07       152.35         6.44        44.09       162.08 
TCGA-ER-A19Q TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF 
       50.89       148.18       105.07        43.82        20.15        28.83 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A7U8 
      247.04        93.01       149.03        92.98       174.21        27.85 
TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW 
       18.77        38.27        34.82        36.26       104.42       216.92 
TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC 
      228.59        20.91        28.08        27.72        48.85       357.37 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZK TCGA-FS-A1ZM 
       53.52        46.45         9.70        32.75        23.93       101.26 
TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A1ZZ 
       74.73       133.55        11.41        26.56        27.09        27.02 
TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F9 TCGA-FS-A4FB 
       77.82        50.14        66.67        28.73        34.03        26.73 
TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A5DY TCGA-GF-A3OT 
       54.41        80.68        17.46        55.59        19.30         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
       19.43         2.04        15.78       117.93        96.92        10.13 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 
       64.44        62.79        32.48       121.91        39.35        48.89 
TCGA-GN-A9SD TCGA-HR-A2OG TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 
       59.41         0.23       368.78       297.90         7.23         0.20 
TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1Q 
        0.33         0.69       228.16       121.08         4.01        69.07 
TCGA-W3-AA1R TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K6 
      111.09        42.08       219.16       105.04        49.05        17.95 
TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AAA0 
       58.98        70.52        11.80        35.80        49.51        40.41 
TCGA-WE-AAA4 TCGA-XV-AB01 TCGA-YD-A89C TCGA-YG-AA3O TCGA-Z2-AA3S TCGA-Z2-AA3V 
       24.99        13.25         6.90        37.94        96.99        15.98 

  DEL PEAK  2(1P22.1) MUTATED DEL PEAK  2(1P22.1) WILD-TYPE 
                         7.79                          0.20 
  DEL PEAK  2(1P22.1) MUTATED DEL PEAK  2(1P22.1) WILD-TYPE 
                       369.93                        368.78 
  DEL PEAK  2(1P22.1) MUTATED DEL PEAK  2(1P22.1) WILD-TYPE 
                       49.085                        54.460 
[1] "7.8 - 369.9 (49.1)" "0.2 - 368.8 (54.5)"
[1] "hr=" "1.1"
D22V3, continuous
                               vv
clus                            I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB
  DEL PEAK  2(1P22.1) MUTATED          1       1      10        1        5
  DEL PEAK  2(1P22.1) WILD-TYPE       12       6      19       17       23
                               vv
clus                            STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK  2(1P22.1) MUTATED          6         1         5         6
  DEL PEAK  2(1P22.1) WILD-TYPE       20        13        14         9
                               vv
clus                            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK  2(1P22.1) MUTATED          14          0         15         18
  DEL PEAK  2(1P22.1) WILD-TYPE        25         15         20         36
                               vv
clus                            STAGE IV
  DEL PEAK  2(1P22.1) MUTATED          7
  DEL PEAK  2(1P22.1) WILD-TYPE       14
D22V4, multiclass
            clus
vv           DEL PEAK  2(1P22.1) MUTATED DEL PEAK  2(1P22.1) WILD-TYPE
  I/II NOS                             1                            12
  STAGE 0                              1                             6
  STAGE I                             10                            19
  STAGE IA                             1                            17
  STAGE IB                             5                            23
  STAGE II                             6                            20
  STAGE IIA                            1                            13
  STAGE IIB                            5                            14
  STAGE IIC                            6                             9
  STAGE III                           14                            25
  STAGE IIIA                           0                            15
  STAGE IIIB                          15                            20
  STAGE IIIC                          18                            36
  STAGE IV                             7                            14
[1] 14  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3 T4
  DEL PEAK  2(1P22.1) MUTATED      16 22 21 23
  DEL PEAK  2(1P22.1) WILD-TYPE    48 51 60 44
D22V5, multiclass
       clus
vv      DEL PEAK  2(1P22.1) MUTATED DEL PEAK  2(1P22.1) WILD-TYPE
  T0+T1                          16                            48
  T2                             22                            51
  T3                             21                            60
  T4                             23                            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  N3
  DEL PEAK  2(1P22.1) MUTATED    38  22  12  14
  DEL PEAK  2(1P22.1) WILD-TYPE 139  43  27  31
D22V6, multiclass
    clus
vv   DEL PEAK  2(1P22.1) MUTATED DEL PEAK  2(1P22.1) WILD-TYPE
  N0                          38                           139
  N1                          22                            43
  N2                          12                            27
  N3                          14                            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"
D22V7, binary
                               cls
clus                              0   1
  DEL PEAK  2(1P22.1) MUTATED    80   7
  DEL PEAK  2(1P22.1) WILD-TYPE 239  15
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P22.1) MUTATED     80    7
  DEL PEAK  2(1P22.1) WILD-TYPE  239   15
   clus
vv  DEL PEAK  2(1P22.1) MUTATED DEL PEAK  2(1P22.1) WILD-TYPE
  0                          80                           239
  1                           7                            15
[1] 2 2
[1] FALSE
D22V8, binary
                               cls
clus                              0   1
  DEL PEAK  2(1P22.1) MUTATED    29  31
  DEL PEAK  2(1P22.1) WILD-TYPE 105  59
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P22.1) MUTATED     29   31
  DEL PEAK  2(1P22.1) WILD-TYPE  105   59
     clus
vv    DEL PEAK  2(1P22.1) MUTATED DEL PEAK  2(1P22.1) WILD-TYPE
  NO                           29                           105
  YES                          31                            59
[1] 2 2
[1] FALSE
D22V9, binary
                               cls
clus                              0   1
  DEL PEAK  2(1P22.1) MUTATED    10  87
  DEL PEAK  2(1P22.1) WILD-TYPE  37 233
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P22.1) MUTATED     10   87
  DEL PEAK  2(1P22.1) WILD-TYPE   37  233
     clus
vv    DEL PEAK  2(1P22.1) MUTATED DEL PEAK  2(1P22.1) WILD-TYPE
  NO                           10                            37
  YES                          87                           233
[1] 2 2
[1] FALSE
D22V10, continuous
D22V11, binary
                               cls
clus                              0   1
  DEL PEAK  2(1P22.1) MUTATED    45  52
  DEL PEAK  2(1P22.1) WILD-TYPE  93 177
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P22.1) MUTATED     45   52
  DEL PEAK  2(1P22.1) WILD-TYPE   93  177
        clus
vv       DEL PEAK  2(1P22.1) MUTATED DEL PEAK  2(1P22.1) WILD-TYPE
  FEMALE                          45                            93
  MALE                            52                           177
[1] 2 2
[1] FALSE
D22V12, binary
                               cls
clus                              0   1
  DEL PEAK  2(1P22.1) MUTATED    87  10
  DEL PEAK  2(1P22.1) WILD-TYPE 232  37
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P22.1) MUTATED     87   10
  DEL PEAK  2(1P22.1) WILD-TYPE  232   37
     clus
vv    DEL PEAK  2(1P22.1) MUTATED DEL PEAK  2(1P22.1) WILD-TYPE
  NO                           87                           232
  YES                          10                            37
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  2(1P22.1) MUTATED       2                         0    91
  DEL PEAK  2(1P22.1) WILD-TYPE     3                         1   262
D22V13, multiclass
                           clus
vv                          DEL PEAK  2(1P22.1) MUTATED
  ASIAN                                               2
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                              91
                           clus
vv                          DEL PEAK  2(1P22.1) WILD-TYPE
  ASIAN                                                 3
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                               262
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V14, binary
                               cls
clus                              0   1
  DEL PEAK  2(1P22.1) MUTATED     2  92
  DEL PEAK  2(1P22.1) WILD-TYPE   5 260
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P22.1) MUTATED      2   92
  DEL PEAK  2(1P22.1) WILD-TYPE    5  260
                        clus
vv                       DEL PEAK  2(1P22.1) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          92
                        clus
vv                       DEL PEAK  2(1P22.1) WILD-TYPE
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                           260
[1] 2 2
[1] FALSE

Clustering(23) Variable = DEL PEAK  3(2Q37.3) MUTATION ANALYSIS
D23V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  3(2Q37.3) MUTATED    26  39
  DEL PEAK  3(2Q37.3) WILD-TYPE 102  85
  DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE 
                           65                           187 
  DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE 
                           39                            85 
$`DEL PEAK  3(2Q37.3) MUTATED`
TCGA-EE-A180 TCGA-EE-A20H TCGA-ER-A193 TCGA-WE-A8K5 TCGA-D3-A1QA TCGA-D3-A2JC 
       31.96       166.75        19.04        52.73        76.41        86.30 
TCGA-D3-A2JG TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51K 
      107.61        58.06       140.98        90.21        23.67        31.76 
TCGA-D3-A51T TCGA-D3-A8GD TCGA-D3-A8GM TCGA-D9-A1X3 TCGA-DA-A1IA TCGA-DA-A95V 
       11.34        23.61        70.62        10.78        64.83        72.10 
TCGA-DA-A95W TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
        0.76        75.55        79.20        76.14        12.99         0.26 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A2GH TCGA-EE-A2GR TCGA-EE-A2MJ TCGA-EE-A2MK 
       27.16        61.12       201.60         0.20        63.25        89.26 
TCGA-EE-A2MS TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3JI TCGA-ER-A197 TCGA-ER-A19C 
      143.93         6.28        67.89       135.98        10.49        39.81 
TCGA-ER-A19P TCGA-ER-A19W TCGA-ER-A2ND TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL 
      120.76       146.63         4.70        68.52        15.48        32.05 
TCGA-FR-A44A TCGA-FR-A8YC TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1ZJ 
      174.21        10.06       171.78        49.74       195.98        36.33 
TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FW-A3TU 
       78.61       130.95         3.06        30.90        66.67        55.59 
TCGA-GN-A264 TCGA-GN-A267 TCGA-W3-A824 TCGA-W3-A828 TCGA-W3-AA21 TCGA-WE-A8ZM 
      117.93        17.06       174.12       120.07        92.84        65.42 
TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-YG-AA3O TCGA-Z2-AA3S 
       48.39         1.94        37.32        28.21        91.23 

$`DEL PEAK  3(2Q37.3) WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A8GI TCGA-EB-A5SG TCGA-EE-A2GD 
        9.76        62.07        38.76        13.41        33.24       269.03 
TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-FR-A729 TCGA-FW-A3R5 TCGA-WE-AAA3 
       52.90       134.40        27.35       216.43        36.95         7.40 
TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
       60.46        12.99        14.83         8.42        15.72        31.89 
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QB TCGA-D3-A2J6 
      110.93        49.35       133.25        19.04        62.60        25.64 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JH TCGA-D3-A2JL 
       45.99        62.86        15.75       168.00        36.30       171.58 
TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF 
       64.83        66.08        43.53        40.01        59.70        24.53 
TCGA-D3-A3MO TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51R TCGA-D3-A5GL 
        9.34       173.85        30.67       144.46        62.70        42.05 
TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D3-A8GC TCGA-D3-A8GJ TCGA-D3-A8GK 
       45.70       177.86       124.08        78.21       179.97       120.00 
TCGA-D3-A8GL TCGA-D3-A8GP TCGA-D3-A8GR TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 
       69.53       135.12        36.53        15.02        16.90        18.44 
TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 
       69.21        22.85        76.34       138.67        68.68       150.61 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 
      110.53        60.10        58.85        30.44       225.11         8.71 
TCGA-DA-A95X TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN 
       65.03        14.14        12.30         3.91        16.41        52.41 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
       18.21        13.15        24.89        20.38         0.00        26.24 
TCGA-EE-A29B TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29T TCGA-EE-A29W 
       75.22        44.28        47.41        47.74       346.49       185.19 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GJ 
      115.43        30.02        77.98        26.14        12.95        68.65 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GS 
       10.62        32.48        18.35        93.63         0.76        71.31 
TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MF 
       81.99       103.13        15.25         5.75        23.77       209.79 
TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MT 
       94.19       171.85       104.78       145.45       227.01        23.51 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
       53.26       124.31       122.73        64.04         4.41        54.51 
TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH TCGA-ER-A195 
      111.85        45.90         3.35       168.85        19.86        34.45 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19H 
        7.82         4.54        53.29        11.47       184.60       150.12 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A1A1 
       99.06        59.84        42.51        49.71        47.18        73.05 
TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A42L 
       22.36        16.87        10.19        28.67       173.29        74.47 
TCGA-FR-A3YN TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FS-A1Z3 TCGA-FS-A1Z4 
        4.50         4.14        26.20         5.65         8.35        27.62 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZS TCGA-FS-A1ZT 
      312.07        32.78        43.92         7.82       136.27        35.28 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FD 
        4.47        23.21         5.29       173.19        13.28        80.68 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 
       11.54        19.30         9.90        18.25         1.91        53.29 
TCGA-GN-A265 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 
       96.92        42.48         7.59       120.53        34.49        46.92 
TCGA-GN-A8LK TCGA-GN-A9SD TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 
       43.23        59.41        85.05       297.01         7.23         0.20 
TCGA-RP-A693 TCGA-W3-A825 TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1V TCGA-W3-AA1W 
        0.33         1.97        44.05        79.99         8.09       185.13 
TCGA-WE-A8K1 TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-AAA4 
       47.54        12.69        21.90        62.89        10.95        24.99 
TCGA-XV-AB01 
        6.61 

  DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE 
                          0.2                           0.0 
  DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE 
                       201.60                        346.49 
  DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE 
                        63.25                         43.53 
[1] "0.2 - 201.6 (63.2)" "0.0 - 346.5 (43.5)"
[1] "hr=" "1.3"
D23V2, survival
                               sevent
clus2                             0   1
  DEL PEAK  3(2Q37.3) MUTATED    36  53
  DEL PEAK  3(2Q37.3) WILD-TYPE 130 139
  DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE 
                           89                           269 
  DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE 
                           53                           139 
$`DEL PEAK  3(2Q37.3) MUTATED`
TCGA-EE-A180 TCGA-EE-A20H TCGA-ER-A193 TCGA-WE-A8K5 TCGA-D3-A1QA TCGA-D3-A2JC 
       94.98       168.26        31.40        61.15        90.90        86.76 
TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3MR 
       11.87       113.52        12.10        58.06       166.52       103.59 
TCGA-D3-A3MU TCGA-D3-A51K TCGA-D3-A51T TCGA-D3-A8GD TCGA-D3-A8GM TCGA-D9-A148 
       39.75        32.94        26.89        23.61       107.15       151.53 
TCGA-D9-A149 TCGA-D9-A1X3 TCGA-D9-A6EA TCGA-DA-A1I0 TCGA-DA-A1IA TCGA-DA-A95V 
       54.67        18.12        25.18        20.38        65.92        72.10 
TCGA-DA-A95W TCGA-EB-A44R TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I 
       37.35        10.36       133.81       151.27        91.56        13.55 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A2GC 
       78.97        13.97        63.78        56.42        66.74        67.43 
TCGA-EE-A2GH TCGA-EE-A2GR TCGA-EE-A2MH TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2MS 
      220.24        42.77        16.96        96.23       180.39       162.48 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3JA TCGA-EE-A3JE TCGA-EE-A3JI 
       13.81        41.59       172.18        53.19        51.35       152.81 
TCGA-ER-A197 TCGA-ER-A19C TCGA-ER-A19P TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A2ND 
       13.94        48.89       162.08         8.88       148.18        23.34 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A44A TCGA-FR-A8YC TCGA-FS-A1YW 
       93.01        46.98        33.21       174.21        34.82       216.92 
TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ 
       48.59       228.59       202.65        47.38       101.26       133.55 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-GN-A264 
       27.02        77.82        66.67        17.46        55.59       117.93 
TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A26D TCGA-GN-A8LL TCGA-HR-A2OG TCGA-HR-A2OH 
       10.13        64.44        48.00        21.37         0.23        65.88 
TCGA-W3-A824 TCGA-W3-A828 TCGA-W3-AA21 TCGA-WE-A8ZM TCGA-WE-A8ZY TCGA-WE-AA9Y 
      228.16       121.08       105.04       101.33        49.51        12.16 
TCGA-WE-AAA0 TCGA-YD-A9TA TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-AA3S 
       40.41        49.18        37.94        14.43        96.99 

$`DEL PEAK  3(2Q37.3) WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-D3-A8GI TCGA-EB-A5SG 
       27.65        62.07        46.32        13.87        58.52        68.25 
TCGA-EB-A5SH TCGA-EE-A184 TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR 
       54.02        68.15         2.60       340.14       126.81       134.40 
TCGA-EE-A3JD TCGA-ER-A198 TCGA-FR-A729 TCGA-FS-A1ZF TCGA-FW-A3R5 TCGA-QB-AA9O 
       27.35        50.76       220.80        15.45        36.95        18.05 
TCGA-WE-AAA3 TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 
       21.40        17.03        66.48        12.99        14.93        16.57 
TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       16.67       112.04       112.57        71.80       133.25        28.08 
TCGA-D3-A1Q9 TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 
       31.59        95.74        43.43       103.10        65.49        23.77 
TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
      115.53       168.00        42.08       171.58        66.48        66.08 
TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF 
       59.57       130.72        46.98        86.93        60.23        24.53 
TCGA-D3-A3MO TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
        9.34        45.30       174.84        55.73        56.35       145.12 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR 
       22.62        63.81       125.79       135.75       137.92       178.32 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GE TCGA-D3-A8GJ 
       18.18       125.19        30.84        79.59        26.43       241.38 
TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR 
      170.20        89.13       161.00       152.75        29.06       129.63 
TCGA-D3-A8GS TCGA-D3-A8GV TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 
      117.17       167.70         3.65         7.10        15.39        22.29 
TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW 
       18.44         9.90        77.56        22.95        76.57        36.03 
TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 
      144.89       222.51       176.55        35.93       135.02        88.87 
TCGA-DA-A1I8 TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 
       53.92        40.60        68.09        33.93        10.49       225.96 
TCGA-DA-A3F8 TCGA-DA-A95X TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5KH 
       43.36        73.94        14.14        13.02        13.87        20.35 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
       29.29        58.92         7.04        36.46        29.82        27.22 
TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A29A 
        8.65        33.73        14.70        26.89         4.96        63.35 
TCGA-EE-A29B TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29R 
       85.08        72.07        64.64        56.84        18.61        14.47 
TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 
       61.28       369.93        25.87       195.02        17.92        46.82 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE 
      115.96        59.64        39.29        86.14        59.28       173.79 
TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
       48.72       107.38        54.74        79.66        75.48       102.12 
TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 
       13.91        81.21        44.88        94.82        21.67       129.27 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF 
       28.83        19.76        61.51        47.28       103.27       268.73 
TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP 
      103.20       204.66       216.66       167.90        47.54       248.65 
TCGA-EE-A2MQ TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC 
       43.23        71.21        53.26       124.31       122.73        64.04 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 
       28.77        54.51       138.81       127.20        36.95        64.08 
TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH TCGA-ER-A195 TCGA-ER-A199 TCGA-ER-A19A 
       34.32       201.80       134.33        35.44         9.17        77.75 
TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H 
       98.40        12.59        13.02        26.37       302.07       152.35 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A19S 
        6.44       131.51        61.05        44.09        50.89        49.48 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH 
      105.07        43.82        20.15        28.83        48.99        41.56 
TCGA-ER-A3ES TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A69P TCGA-FR-A7U8 
      247.04        12.95       149.03        92.98        15.72        27.85 
TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1Z3 TCGA-FS-A1Z4 
       18.77        38.27        36.26       104.42        20.91        28.08 
TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE 
        7.79        27.72        48.85       357.37        53.52        46.45 
TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZS 
        9.70        32.75        23.93        74.73        11.41       148.80 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F2 TCGA-FS-A4F5 
       53.16        26.56        49.48        27.09        50.14        28.73 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3TV 
      174.84        34.03        26.73        54.41        80.68        13.51 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 
       19.30         9.90        19.43         2.04        15.78       139.89 
TCGA-GN-A265 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 
       96.92        62.79        32.48       121.91        39.35        10.42 
TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A9SD TCGA-LH-A9QB TCGA-OD-A75X 
       48.89        22.13        50.10        59.41       368.78       297.90 
TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A825 TCGA-W3-AA1O 
        7.23         0.20         0.33         0.69        63.02         4.01 
TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1V TCGA-W3-AA1W TCGA-WE-A8JZ TCGA-WE-A8K1 
       69.07       111.09        42.08       219.16        24.03        49.05 
TCGA-WE-A8K6 TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX 
       17.95        58.98        70.52        63.22        11.80        35.80 
TCGA-WE-AAA4 TCGA-XV-AB01 TCGA-YD-A89C TCGA-Z2-A8RT TCGA-Z2-AA3V 
       24.99        13.25         6.90        27.58        15.98 

  DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE 
                         0.23                          0.20 
  DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE 
                       228.59                        369.93 
  DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE 
                        58.06                         49.48 
[1] "0.2 - 228.6 (58.1)" "0.2 - 369.9 (49.5)"
[1] "hr=" "1.1"
D23V3, continuous
                               vv
clus                            I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB
  DEL PEAK  3(2Q37.3) MUTATED          3       1       9        3        6
  DEL PEAK  3(2Q37.3) WILD-TYPE       10       6      20       15       22
                               vv
clus                            STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK  3(2Q37.3) MUTATED          6         2         8         4
  DEL PEAK  3(2Q37.3) WILD-TYPE       20        12        11        11
                               vv
clus                            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK  3(2Q37.3) MUTATED           9          4          9          9
  DEL PEAK  3(2Q37.3) WILD-TYPE        30         11         26         45
                               vv
clus                            STAGE IV
  DEL PEAK  3(2Q37.3) MUTATED          7
  DEL PEAK  3(2Q37.3) WILD-TYPE       14
D23V4, multiclass
            clus
vv           DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE
  I/II NOS                             3                            10
  STAGE 0                              1                             6
  STAGE I                              9                            20
  STAGE IA                             3                            15
  STAGE IB                             6                            22
  STAGE II                             6                            20
  STAGE IIA                            2                            12
  STAGE IIB                            8                            11
  STAGE IIC                            4                            11
  STAGE III                            9                            30
  STAGE IIIA                           4                            11
  STAGE IIIB                           9                            26
  STAGE IIIC                           9                            45
  STAGE IV                             7                            14
[1] 14  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3 T4
  DEL PEAK  3(2Q37.3) MUTATED      10 19 21 22
  DEL PEAK  3(2Q37.3) WILD-TYPE    54 54 60 45
D23V5, multiclass
       clus
vv      DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE
  T0+T1                          10                            54
  T2                             19                            54
  T3                             21                            60
  T4                             22                            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  N3
  DEL PEAK  3(2Q37.3) MUTATED    48  14   9   9
  DEL PEAK  3(2Q37.3) WILD-TYPE 129  51  30  36
D23V6, multiclass
    clus
vv   DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE
  N0                          48                           129
  N1                          14                            51
  N2                           9                            30
  N3                           9                            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"
D23V7, binary
                               cls
clus                              0   1
  DEL PEAK  3(2Q37.3) MUTATED    73   8
  DEL PEAK  3(2Q37.3) WILD-TYPE 246  14
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2Q37.3) MUTATED     73    8
  DEL PEAK  3(2Q37.3) WILD-TYPE  246   14
   clus
vv  DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE
  0                          73                           246
  1                           8                            14
[1] 2 2
[1] FALSE
D23V8, binary
                               cls
clus                             0  1
  DEL PEAK  3(2Q37.3) MUTATED   39 22
  DEL PEAK  3(2Q37.3) WILD-TYPE 95 68
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2Q37.3) MUTATED     39   22
  DEL PEAK  3(2Q37.3) WILD-TYPE   95   68
     clus
vv    DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE
  NO                           39                            95
  YES                          22                            68
[1] 2 2
[1] FALSE
D23V9, binary
                               cls
clus                              0   1
  DEL PEAK  3(2Q37.3) MUTATED     7  86
  DEL PEAK  3(2Q37.3) WILD-TYPE  40 234
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2Q37.3) MUTATED      7   86
  DEL PEAK  3(2Q37.3) WILD-TYPE   40  234
     clus
vv    DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE
  NO                            7                            40
  YES                          86                           234
[1] 2 2
[1] FALSE
D23V10, continuous
D23V11, binary
                               cls
clus                              0   1
  DEL PEAK  3(2Q37.3) MUTATED    35  58
  DEL PEAK  3(2Q37.3) WILD-TYPE 103 171
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2Q37.3) MUTATED     35   58
  DEL PEAK  3(2Q37.3) WILD-TYPE  103  171
        clus
vv       DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE
  FEMALE                          35                           103
  MALE                            58                           171
[1] 2 2
[1] FALSE
D23V12, binary
                               cls
clus                              0   1
  DEL PEAK  3(2Q37.3) MUTATED    76  17
  DEL PEAK  3(2Q37.3) WILD-TYPE 243  30
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2Q37.3) MUTATED     76   17
  DEL PEAK  3(2Q37.3) WILD-TYPE  243   30
     clus
vv    DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE
  NO                           76                           243
  YES                          17                            30
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  3(2Q37.3) MUTATED       1                         0    88
  DEL PEAK  3(2Q37.3) WILD-TYPE     4                         1   265
D23V13, multiclass
                           clus
vv                          DEL PEAK  3(2Q37.3) MUTATED
  ASIAN                                               1
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                              88
                           clus
vv                          DEL PEAK  3(2Q37.3) WILD-TYPE
  ASIAN                                                 4
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                               265
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V14, binary
                               cls
clus                              0   1
  DEL PEAK  3(2Q37.3) MUTATED     5  84
  DEL PEAK  3(2Q37.3) WILD-TYPE   2 268
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2Q37.3) MUTATED      5   84
  DEL PEAK  3(2Q37.3) WILD-TYPE    2  268
                        clus
vv                       DEL PEAK  3(2Q37.3) MUTATED
  HISPANIC OR LATINO                               5
  NOT HISPANIC OR LATINO                          84
                        clus
vv                       DEL PEAK  3(2Q37.3) WILD-TYPE
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                           268
[1] 2 2
[1] FALSE

Clustering(24) Variable = DEL PEAK  4(3P25.1) MUTATION ANALYSIS
D24V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  4(3P25.1) MUTATED    27  24
  DEL PEAK  4(3P25.1) WILD-TYPE 101 100
  DEL PEAK  4(3P25.1) MUTATED DEL PEAK  4(3P25.1) WILD-TYPE 
                           51                           201 
  DEL PEAK  4(3P25.1) MUTATED DEL PEAK  4(3P25.1) WILD-TYPE 
                           24                           100 
$`DEL PEAK  4(3P25.1) MUTATED`
TCGA-FR-A729 TCGA-BF-AAP0 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A2J7 
      216.43        14.83        31.89       110.93       133.25        45.99 
TCGA-D3-A2JN TCGA-D3-A3C6 TCGA-D3-A5GL TCGA-D3-A5GU TCGA-D3-A8GP TCGA-D9-A1X3 
       64.83        58.06        42.05       124.08       135.12        10.78 
TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A95Y TCGA-EE-A17Y TCGA-EE-A20C 
      150.61       110.53        60.10        14.14        24.89        75.55 
TCGA-EE-A20F TCGA-EE-A29G TCGA-EE-A29P TCGA-EE-A2GH TCGA-EE-A2M6 TCGA-EE-A2M7 
       79.20        44.28        27.16       201.60       103.13        15.25 
TCGA-EE-A2MF TCGA-EE-A3AA TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-EE-A3JB TCGA-ER-A195 
      209.79       124.31        67.89        45.90       168.85        34.45 
TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A2ND TCGA-ER-A2NG 
      150.12        99.06        49.71        47.18         4.70        28.67 
TCGA-FR-A44A TCGA-FR-A7UA TCGA-FS-A1Z4 TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A4F8 
      174.21         5.65        27.62        78.61       130.95       173.19 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A267 TCGA-RP-A690 
       55.59        11.54         1.91        53.29        17.06         0.20 
TCGA-W3-AA21 TCGA-WE-AAA4 TCGA-Z2-AA3S 
       92.84        24.99        91.23 

$`DEL PEAK  4(3P25.1) WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A8GI TCGA-EB-A5SG TCGA-EE-A180 
        9.76        62.07        38.76        13.41        33.24        31.96 
TCGA-EE-A20H TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 
      166.75       269.03        52.90       134.40        27.35        19.04 
TCGA-FW-A3R5 TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 
       36.95        52.73         7.40        60.46        12.99         8.42 
TCGA-D3-A1Q3 TCGA-D3-A1Q6 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 
       15.72        49.35        19.04        76.41        62.60        25.64 
TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A2JH 
       62.86        15.75       168.00        86.30       107.61        36.30 
TCGA-D3-A2JL TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE 
      171.58        66.08        43.53       140.98        40.01        59.70 
TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F 
       24.53         9.34        90.21        23.67       173.85        30.67 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GR 
      144.46        31.76        62.70        11.34        45.70       177.86 
TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM 
       78.21        23.61       179.97       120.00        69.53        70.62 
TCGA-D3-A8GR TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6EC TCGA-D9-A6EG 
       36.53        15.02        16.90        18.44        69.21        22.85 
TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 
       76.34       138.67        68.68        64.83        58.85        30.44 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-DA-A95V TCGA-DA-A95W TCGA-DA-A95X TCGA-DA-A95Z 
      225.11         8.71        72.10         0.76        65.03        12.30 
TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A181 
        3.91        16.41        52.41        18.21        13.15        20.38 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
        0.00        26.24        75.22        76.14        12.99         0.26 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 
       47.41        47.74        61.12       346.49       185.19       115.43 
TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GJ TCGA-EE-A2GK 
       30.02        77.98        26.14        12.95        68.65        10.62 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
       32.48        18.35        93.63         0.76         0.20        71.31 
TCGA-EE-A2GU TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ 
       81.99         5.75        23.77        94.19       171.85        63.25 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT 
       89.26       104.78       145.45       227.01       143.93        23.51 
TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
       53.26       122.73        64.04         4.41        54.51         6.28 
TCGA-EE-A3J4 TCGA-EE-A3J8 TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A197 TCGA-ER-A199 
      111.85         3.35        19.86       135.98        10.49         7.82 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19M 
        4.54        53.29        39.81        11.47       184.60        59.84 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE 
       42.51       120.76       146.63        73.05        22.36        16.87 
TCGA-ER-A2NF TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42L 
       10.19       173.29        68.52        15.48        32.05        74.47 
TCGA-FR-A3YN TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A8YC TCGA-FS-A1YW TCGA-FS-A1YY 
        4.50         4.14        26.20        10.06       171.78        49.74 
TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG 
      195.98         8.35       312.07        32.78        43.92         7.82 
TCGA-FS-A1ZJ TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
       36.33       136.27        35.28         4.47        23.21         5.29 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A5DY 
        3.06        30.90        66.67        13.28        80.68        19.30 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A268 TCGA-GN-A26A 
        9.90        18.25       117.93        96.92        42.48         7.59 
TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-GN-A8LK TCGA-GN-A9SD TCGA-LH-A9QB 
      120.53        34.49        46.92        43.23        59.41        85.05 
TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 
      297.01         7.23         0.33       174.12         1.97       120.07 
TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1V TCGA-W3-AA1W TCGA-WE-A8K1 TCGA-WE-A8ZM 
       44.05        79.99         8.09       185.13        47.54        65.42 
TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y 
       12.69        21.90        62.89        10.95        48.39         1.94 
TCGA-WE-AAA0 TCGA-XV-AB01 TCGA-YG-AA3O 
       37.32         6.61        28.21 

  DEL PEAK  4(3P25.1) MUTATED DEL PEAK  4(3P25.1) WILD-TYPE 
                          0.2                           0.0 
  DEL PEAK  4(3P25.1) MUTATED DEL PEAK  4(3P25.1) WILD-TYPE 
                       216.43                        346.49 
  DEL PEAK  4(3P25.1) MUTATED DEL PEAK  4(3P25.1) WILD-TYPE 
                        58.06                         43.23 
[1] "0.2 - 216.4 (58.1)" "0.0 - 346.5 (43.2)"
[1] "hr=" "1.3"
D24V2, survival
                               sevent
clus2                             0   1
  DEL PEAK  4(3P25.1) MUTATED    35  34
  DEL PEAK  4(3P25.1) WILD-TYPE 131 158
  DEL PEAK  4(3P25.1) MUTATED DEL PEAK  4(3P25.1) WILD-TYPE 
                           69                           289 
  DEL PEAK  4(3P25.1) MUTATED DEL PEAK  4(3P25.1) WILD-TYPE 
                           34                           158 
$`DEL PEAK  4(3P25.1) MUTATED`
TCGA-FR-A729 TCGA-BF-AAP0 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A2J7 
      220.80        14.93       112.04       112.57       133.25       103.10 
TCGA-D3-A2JN TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A5GL TCGA-D3-A5GU TCGA-D3-A8GB 
       66.48        58.06        46.98       125.79       125.19        30.84 
TCGA-D3-A8GP TCGA-D9-A1X3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-DA-A1HW TCGA-DA-A1I2 
      152.75        18.12         9.90        25.18        36.03       176.55 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A95Y TCGA-EB-A44R TCGA-EB-A5UL TCGA-EE-A17Y 
      135.02        88.87        14.14        10.36        29.29        27.22 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29G TCGA-EE-A29P TCGA-EE-A29V TCGA-EE-A2GH 
      151.27        91.56        72.07        56.42        25.87       220.24 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MD TCGA-EE-A2MF TCGA-EE-A2MH TCGA-EE-A3AA 
      129.27        28.83        47.28       268.73        16.96       124.31 
TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-EE-A3JB TCGA-ER-A195 TCGA-ER-A19E TCGA-ER-A19H 
      172.18        64.08       201.80        35.44        13.02       152.35 
TCGA-ER-A19L TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A2ND TCGA-ER-A2NG TCGA-FR-A44A 
      131.51        50.89        49.48        23.34        48.99       174.21 
TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FS-A1YX TCGA-FS-A1Z4 TCGA-FS-A1ZM TCGA-FS-A1ZQ 
       18.77        38.27        48.59        28.08       101.26       133.55 
TCGA-FS-A4F8 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 
      174.84        55.59        13.51         2.04        15.78       139.89 
TCGA-GN-A267 TCGA-GN-A4U9 TCGA-RP-A690 TCGA-W3-AA1O TCGA-W3-AA21 TCGA-WE-A8ZX 
       64.44        22.13         0.20         4.01       105.04        35.80 
TCGA-WE-AAA4 TCGA-YG-AA3P TCGA-Z2-AA3S 
       24.99        14.43        96.99 

$`DEL PEAK  4(3P25.1) WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-D3-A8GI TCGA-EB-A5SG 
       27.65        62.07        46.32        13.87        58.52        68.25 
TCGA-EB-A5SH TCGA-EE-A180 TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD 
       54.02        94.98        68.15       168.26         2.60       340.14 
TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-ER-A198 TCGA-FS-A1ZF 
      126.81       134.40        27.35        31.40        50.76        15.45 
TCGA-FW-A3R5 TCGA-QB-AA9O TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-3N-A9WB TCGA-3N-A9WC 
       36.95        18.05        61.15        21.40        17.03        66.48 
TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q6 TCGA-D3-A1Q8 TCGA-D3-A1Q9 
       12.99        16.57        16.67        71.80        28.08        31.59 
TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA 
       90.90        95.74        43.43        65.49        23.77       115.53 
TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK 
      168.00        86.76        11.87       113.52        42.08        12.10 
TCGA-D3-A2JL TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3CB TCGA-D3-A3CC 
      171.58        66.08        59.57       130.72       166.52        86.93 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV 
       60.23        24.53         9.34       103.59        39.75        45.30 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
      174.84        55.73        56.35       145.12        32.94        22.62 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       63.81        26.89       135.75       137.92       178.32        18.18 
TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL 
       79.59        23.61        26.43       241.38       170.20        89.13 
TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D3-A8GV 
      107.15       161.00        29.06       129.63       117.17       167.70 
TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 
      151.53        54.67         3.65         7.10        15.39        22.29 
TCGA-D9-A4Z6 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I0 
       18.44        77.56        22.95        76.57       144.89        20.38 
TCGA-DA-A1I1 TCGA-DA-A1I4 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
      222.51        35.93        53.92        65.92        40.60        68.09 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-DA-A95V TCGA-DA-A95W 
       33.93        10.49       225.96        43.36        72.10        37.35 
TCGA-DA-A95X TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A5VV 
       73.94        13.02        13.87        20.35        58.92         7.04 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
       36.46        29.82         8.65        33.73        14.70        26.89 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C 
        4.96       133.81        13.55        63.35        85.08        78.97 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29Q 
       13.97        63.78        64.64        56.84        18.61        66.74 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 
       14.47        61.28       369.93       195.02        17.92        46.82 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
      115.96        59.64        39.29        86.14        59.28        67.43 
TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
      173.79        48.72       107.38        54.74        79.66        75.48 
TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU 
      102.12        13.91        42.77        81.21        44.88        94.82 
TCGA-EE-A2M5 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MI 
       21.67        19.76        61.51       103.27       103.20       204.66 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP 
       96.23       180.39       216.66       167.90        47.54       248.65 
TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC 
       43.23       162.48        71.21        53.26       122.73        64.04 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J4 
       28.77        54.51        13.81        41.59       138.81       127.20 
TCGA-EE-A3J5 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
       36.95        34.32        53.19        51.35       134.33       152.81 
TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D 
       13.94         9.17        77.75        98.40        48.89        12.59 
TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19J TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P 
       26.37       302.07         6.44        61.05        44.09       162.08 
TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF 
        8.88       148.18       105.07        43.82        20.15        28.83 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K 
       41.56       247.04        93.01        46.98        33.21        12.95 
TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A8YC TCGA-FR-A8YD 
      149.03        92.98        15.72        27.85        34.82        36.26 
TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z7 
      104.42       216.92       228.59       202.65        20.91         7.79 
TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG 
       27.72        48.85       357.37        53.52        46.45         9.70 
TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZS 
       32.75        47.38        23.93        74.73        11.41       148.80 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 
       53.16        26.56        49.48        27.09        27.02        77.82 
TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC 
       50.14        66.67        28.73        34.03        26.73        54.41 
TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GN-A264 
       80.68        17.46        19.30         9.90        19.43       117.93 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U3 
       96.92        10.13        62.79        32.48        48.00       121.91 
TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A8LK TCGA-GN-A8LL TCGA-GN-A9SD 
       39.35        10.42        48.89        50.10        21.37        59.41 
TCGA-HR-A2OG TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A693 
        0.23        65.88       368.78       297.90         7.23         0.33 
TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1Q TCGA-W3-AA1R 
        0.69       228.16        63.02       121.08        69.07       111.09 
TCGA-W3-AA1V TCGA-W3-AA1W TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K6 TCGA-WE-A8ZM 
       42.08       219.16        24.03        49.05        17.95       101.33 
TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y 
       58.98        70.52        63.22        11.80        49.51        12.16 
TCGA-WE-AAA0 TCGA-XV-AB01 TCGA-YD-A89C TCGA-YD-A9TA TCGA-YG-AA3O TCGA-Z2-A8RT 
       40.41        13.25         6.90        49.18        37.94        27.58 
TCGA-Z2-AA3V 
       15.98 

  DEL PEAK  4(3P25.1) MUTATED DEL PEAK  4(3P25.1) WILD-TYPE 
                         0.20                          0.23 
  DEL PEAK  4(3P25.1) MUTATED DEL PEAK  4(3P25.1) WILD-TYPE 
                       268.73                        369.93 
  DEL PEAK  4(3P25.1) MUTATED DEL PEAK  4(3P25.1) WILD-TYPE 
                        55.59                         51.35 
[1] "0.2 - 268.7 (55.6)" "0.2 - 369.9 (51.4)"
[1] "hr=" "1.2"
D24V3, continuous
                               vv
clus                            I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB
  DEL PEAK  4(3P25.1) MUTATED          2       1      10        1        7
  DEL PEAK  4(3P25.1) WILD-TYPE       11       6      19       17       21
                               vv
clus                            STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK  4(3P25.1) MUTATED          3         0         2         2
  DEL PEAK  4(3P25.1) WILD-TYPE       23        14        17        13
                               vv
clus                            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK  4(3P25.1) MUTATED          10          3          8          9
  DEL PEAK  4(3P25.1) WILD-TYPE        29         12         27         45
                               vv
clus                            STAGE IV
  DEL PEAK  4(3P25.1) MUTATED          2
  DEL PEAK  4(3P25.1) WILD-TYPE       19
D24V4, multiclass
            clus
vv           DEL PEAK  4(3P25.1) MUTATED DEL PEAK  4(3P25.1) WILD-TYPE
  I/II NOS                             2                            11
  STAGE 0                              1                             6
  STAGE I                             10                            19
  STAGE IA                             1                            17
  STAGE IB                             7                            21
  STAGE II                             3                            23
  STAGE IIA                            0                            14
  STAGE IIB                            2                            17
  STAGE IIC                            2                            13
  STAGE III                           10                            29
  STAGE IIIA                           3                            12
  STAGE IIIB                           8                            27
  STAGE IIIC                           9                            45
  STAGE IV                             2                            19
[1] 14  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3 T4
  DEL PEAK  4(3P25.1) MUTATED      16 14 12 10
  DEL PEAK  4(3P25.1) WILD-TYPE    48 59 69 57
D24V5, multiclass
       clus
vv      DEL PEAK  4(3P25.1) MUTATED DEL PEAK  4(3P25.1) WILD-TYPE
  T0+T1                          16                            48
  T2                             14                            59
  T3                             12                            69
  T4                             10                            57
[1] 4 2
[1] 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  N3
  DEL PEAK  4(3P25.1) MUTATED    32  13  10   6
  DEL PEAK  4(3P25.1) WILD-TYPE 145  52  29  39
D24V6, multiclass
    clus
vv   DEL PEAK  4(3P25.1) MUTATED DEL PEAK  4(3P25.1) WILD-TYPE
  N0                          32                           145
  N1                          13                            52
  N2                          10                            29
  N3                           6                            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"
D24V7, binary
                               cls
clus                              0   1
  DEL PEAK  4(3P25.1) MUTATED    60   2
  DEL PEAK  4(3P25.1) WILD-TYPE 259  20
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(3P25.1) MUTATED     60    2
  DEL PEAK  4(3P25.1) WILD-TYPE  259   20
   clus
vv  DEL PEAK  4(3P25.1) MUTATED DEL PEAK  4(3P25.1) WILD-TYPE
  0                          60                           259
  1                           2                            20
[1] 2 2
[1] FALSE
D24V8, binary
                               cls
clus                              0   1
  DEL PEAK  4(3P25.1) MUTATED    25  14
  DEL PEAK  4(3P25.1) WILD-TYPE 109  76
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(3P25.1) MUTATED     25   14
  DEL PEAK  4(3P25.1) WILD-TYPE  109   76
     clus
vv    DEL PEAK  4(3P25.1) MUTATED DEL PEAK  4(3P25.1) WILD-TYPE
  NO                           25                           109
  YES                          14                            76
[1] 2 2
[1] FALSE
D24V9, binary
                               cls
clus                              0   1
  DEL PEAK  4(3P25.1) MUTATED     9  62
  DEL PEAK  4(3P25.1) WILD-TYPE  38 258
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(3P25.1) MUTATED      9   62
  DEL PEAK  4(3P25.1) WILD-TYPE   38  258
     clus
vv    DEL PEAK  4(3P25.1) MUTATED DEL PEAK  4(3P25.1) WILD-TYPE
  NO                            9                            38
  YES                          62                           258
[1] 2 2
[1] FALSE
D24V10, continuous
D24V11, binary
                               cls
clus                              0   1
  DEL PEAK  4(3P25.1) MUTATED    31  40
  DEL PEAK  4(3P25.1) WILD-TYPE 107 189
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(3P25.1) MUTATED     31   40
  DEL PEAK  4(3P25.1) WILD-TYPE  107  189
        clus
vv       DEL PEAK  4(3P25.1) MUTATED DEL PEAK  4(3P25.1) WILD-TYPE
  FEMALE                          31                           107
  MALE                            40                           189
[1] 2 2
[1] FALSE
D24V12, binary
                               cls
clus                              0   1
  DEL PEAK  4(3P25.1) MUTATED    60  10
  DEL PEAK  4(3P25.1) WILD-TYPE 259  37
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(3P25.1) MUTATED     60   10
  DEL PEAK  4(3P25.1) WILD-TYPE  259   37
     clus
vv    DEL PEAK  4(3P25.1) MUTATED DEL PEAK  4(3P25.1) WILD-TYPE
  NO                           60                           259
  YES                          10                            37
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  4(3P25.1) MUTATED       2                         0    68
  DEL PEAK  4(3P25.1) WILD-TYPE     3                         1   285
D24V13, multiclass
                           clus
vv                          DEL PEAK  4(3P25.1) MUTATED
  ASIAN                                               2
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                              68
                           clus
vv                          DEL PEAK  4(3P25.1) WILD-TYPE
  ASIAN                                                 3
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                               285
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V14, binary
                               cls
clus                              0   1
  DEL PEAK  4(3P25.1) MUTATED     1  69
  DEL PEAK  4(3P25.1) WILD-TYPE   6 283
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(3P25.1) MUTATED      1   69
  DEL PEAK  4(3P25.1) WILD-TYPE    6  283
                        clus
vv                       DEL PEAK  4(3P25.1) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          69
                        clus
vv                       DEL PEAK  4(3P25.1) WILD-TYPE
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                           283
[1] 2 2
[1] FALSE

Clustering(25) Variable = DEL PEAK  5(3Q13.31) MUTATION ANALYSIS
D25V1, survival
                                sevent
clus2                              0   1
  DEL PEAK  5(3Q13.31) MUTATED    19  28
  DEL PEAK  5(3Q13.31) WILD-TYPE 109  96
  DEL PEAK  5(3Q13.31) MUTATED DEL PEAK  5(3Q13.31) WILD-TYPE 
                            47                            205 
  DEL PEAK  5(3Q13.31) MUTATED DEL PEAK  5(3Q13.31) WILD-TYPE 
                            28                             96 
$`DEL PEAK  5(3Q13.31) MUTATED`
TCGA-D3-A2JE TCGA-EE-A180 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A2JG TCGA-D3-A5GR 
        9.76        31.96       110.93       133.25       107.61       177.86 
TCGA-D3-A5GU TCGA-D3-A8GP TCGA-D3-A8GR TCGA-D9-A1X3 TCGA-DA-A1I2 TCGA-DA-A1I5 
      124.08       135.12        36.53        10.78       150.61       110.53 
TCGA-DA-A1I7 TCGA-DA-A95V TCGA-DA-A95Y TCGA-EE-A17Y TCGA-EE-A20C TCGA-EE-A29G 
       60.10        72.10        14.14        24.89        75.55        44.28 
TCGA-EE-A29H TCGA-EE-A29P TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GN TCGA-EE-A2MS 
       47.41        27.16       201.60        68.65        93.63       143.93 
TCGA-EE-A3AC TCGA-EE-A3J3 TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A19H 
       64.04        67.89       135.98        34.45        10.49       150.12 
TCGA-ER-A19S TCGA-ER-A3EV TCGA-FR-A8YC TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A4F8 
       47.18        15.48        10.06        36.33        78.61       173.19 
TCGA-FS-A4FD TCGA-FW-A3TU TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 
       80.68        55.59        53.29       117.93        17.06        42.48 
TCGA-W3-AA1R TCGA-W3-AA1V TCGA-WE-A8K1 TCGA-WE-AAA4 TCGA-Z2-AA3S 
       79.99         8.09        47.54        24.99        91.23 

$`DEL PEAK  5(3Q13.31) WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A8GI TCGA-EB-A5SG TCGA-EE-A20H TCGA-EE-A2GD 
       62.07        38.76        13.41        33.24       166.75       269.03 
TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-FR-A729 TCGA-FW-A3R5 
       52.90       134.40        27.35        19.04       216.43        36.95 
TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 
       52.73         7.40        60.46        12.99        14.83         8.42 
TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q6 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB 
       15.72        31.89        49.35        19.04        76.41        62.60 
TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC 
       25.64        45.99        62.86        15.75       168.00        86.30 
TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 
       36.30       171.58        64.83        66.08        43.53        58.06 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR 
      140.98        40.01        59.70        24.53         9.34        90.21 
TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R 
       23.67       173.85        30.67       144.46        31.76        62.70 
TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GJ 
       11.34        42.05        45.70        78.21        23.61       179.97 
TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 
      120.00        69.53        70.62        15.02        16.90        18.44 
TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1IA 
       69.21        22.85        76.34       138.67        68.68        64.83 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-DA-A95W TCGA-DA-A95X 
       58.85        30.44       225.11         8.71         0.76        65.03 
TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X 
       12.30         3.91        16.41        52.41        18.21        13.15 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29C 
       20.38         0.00        26.24        79.20        75.22        76.14 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29M TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W 
       12.99         0.26        47.74        61.12       346.49       185.19 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GK 
      115.43        30.02        77.98        26.14        12.95        10.62 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU 
       32.48        18.35         0.76         0.20        71.31        81.99 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MG 
      103.13        15.25         5.75        23.77       209.79        94.19 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP 
      171.85        63.25        89.26       104.78       145.45       227.01 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE 
       23.51        53.26       124.31       122.73         4.41        54.51 
TCGA-EE-A3AF TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH 
        6.28       111.85        45.90         3.35       168.85        19.86 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19G 
        7.82         4.54        53.29        39.81        11.47       184.60 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19W 
       99.06        59.84        42.51       120.76        49.71       146.63 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
       73.05        22.36         4.70        16.87        10.19        28.67 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A 
      173.29        68.52        32.05        74.47         4.50       174.21 
TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 
        4.14        26.20         5.65       171.78        49.74       195.98 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG 
        8.35        27.62       312.07        32.78        43.92         7.82 
TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
      130.95       136.27        35.28         4.47        23.21         5.29 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F9 TCGA-FW-A3TV TCGA-FW-A5DY 
        3.06        30.90        66.67        13.28        11.54        19.30 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A265 TCGA-GN-A26A TCGA-GN-A4U3 
        9.90        18.25         1.91        96.92         7.59       120.53 
TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-GN-A8LK TCGA-GN-A9SD TCGA-LH-A9QB TCGA-OD-A75X 
       34.49        46.92        43.23        59.41        85.05       297.01 
TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 
        7.23         0.20         0.33       174.12         1.97       120.07 
TCGA-W3-AA1Q TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO 
       44.05       185.13        92.84        65.42        12.69        21.90 
TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-XV-AB01 
       62.89        10.95        48.39         1.94        37.32         6.61 
TCGA-YG-AA3O 
       28.21 

  DEL PEAK  5(3Q13.31) MUTATED DEL PEAK  5(3Q13.31) WILD-TYPE 
                          8.09                           0.00 
  DEL PEAK  5(3Q13.31) MUTATED DEL PEAK  5(3Q13.31) WILD-TYPE 
                        201.60                         346.49 
  DEL PEAK  5(3Q13.31) MUTATED DEL PEAK  5(3Q13.31) WILD-TYPE 
                         64.04                          43.23 
[1] "8.1 - 201.6 (64.0)" "0.0 - 346.5 (43.2)"
[1] "hr=" "1.1"
D25V2, survival
                                sevent
clus2                              0   1
  DEL PEAK  5(3Q13.31) MUTATED    25  35
  DEL PEAK  5(3Q13.31) WILD-TYPE 141 157
  DEL PEAK  5(3Q13.31) MUTATED DEL PEAK  5(3Q13.31) WILD-TYPE 
                            60                            298 
  DEL PEAK  5(3Q13.31) MUTATED DEL PEAK  5(3Q13.31) WILD-TYPE 
                            35                            157 
$`DEL PEAK  5(3Q13.31) MUTATED`
TCGA-D3-A2JE TCGA-EE-A180 TCGA-ER-A198 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A2JG 
       27.65        94.98        50.76       112.57       133.25       113.52 
TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D3-A8GP TCGA-D3-A8GR TCGA-D9-A1X3 TCGA-D9-A6E9 
      178.32       125.19       152.75       129.63        18.12         9.90 
TCGA-D9-A6EA TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A95V TCGA-DA-A95Y 
       25.18       176.55       135.02        88.87        72.10        14.14 
TCGA-EB-A44R TCGA-EE-A17Y TCGA-EE-A20C TCGA-EE-A20I TCGA-EE-A29G TCGA-EE-A29H 
       10.36        27.22       151.27        13.55        72.07        64.64 
TCGA-EE-A29P TCGA-EE-A29X TCGA-EE-A2GC TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GN 
       56.42        17.92        67.43       220.24       107.38       102.12 
TCGA-EE-A2MS TCGA-EE-A3AC TCGA-EE-A3J3 TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 
      162.48        64.04       172.18       152.81        35.44        13.94 
TCGA-ER-A19H TCGA-ER-A19S TCGA-ER-A3EV TCGA-FR-A7U9 TCGA-FR-A8YC TCGA-FS-A1YX 
      152.35        49.48        46.98        18.77        34.82        48.59 
TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A4F8 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-GN-A262 
       47.38       101.26       174.84        80.68        55.59       139.89 
TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A4U9 TCGA-GN-A8LL TCGA-W3-AA1R 
      117.93        64.44        62.79        22.13        21.37       111.09 
TCGA-W3-AA1V TCGA-WE-A8K1 TCGA-WE-A8ZX TCGA-WE-AAA4 TCGA-YG-AA3P TCGA-Z2-AA3S 
       42.08        49.05        35.80        24.99        14.43        96.99 

$`DEL PEAK  5(3Q13.31) WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-D3-A8GI TCGA-EB-A5SG TCGA-EB-A5SH 
       62.07        46.32        13.87        58.52        68.25        54.02 
TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR 
       68.15       168.26         2.60       340.14       126.81       134.40 
TCGA-EE-A3JD TCGA-ER-A193 TCGA-FR-A729 TCGA-FS-A1ZF TCGA-FW-A3R5 TCGA-QB-AA9O 
       27.35        31.40       220.80        15.45        36.95        18.05 
TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 
       61.15        21.40        17.03        66.48        12.99        14.93 
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q6 TCGA-D3-A1Q8 TCGA-D3-A1Q9 
       16.57        16.67       112.04        71.80        28.08        31.59 
TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 
       90.90        95.74        43.43       103.10        65.49        23.77 
TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JH TCGA-D3-A2JK 
      115.53       168.00        86.76        11.87        42.08        12.10 
TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 
      171.58        66.48        66.08        59.57       130.72        58.06 
TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO 
       46.98       166.52        86.93        60.23        24.53         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
      103.59        39.75        45.30       174.84        55.73        56.35 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL 
      145.12        32.94        22.62        63.81        26.89       125.79 
TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GS TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GD 
      135.75       137.92        18.18        30.84        79.59        23.61 
TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GN 
       26.43       241.38       170.20        89.13       107.15       161.00 
TCGA-D3-A8GQ TCGA-D3-A8GS TCGA-D3-A8GV TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW 
       29.06       117.17       167.70       151.53        54.67         3.65 
TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6EC TCGA-D9-A6EG 
        7.10        15.39        22.29        18.44        77.56        22.95 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I4 
       76.57        36.03       144.89        20.38       222.51        35.93 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
       53.92        65.92        40.60        68.09        33.93        10.49 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-DA-A95W TCGA-DA-A95X TCGA-DA-A95Z TCGA-EB-A44Q 
      225.96        43.36        37.35        73.94        13.02        13.87 
TCGA-EB-A5KH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X 
       20.35        29.29        58.92         7.04        36.46        29.82 
TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B 
        8.65        33.73        14.70        26.89         4.96       133.81 
TCGA-EE-A20F TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
       91.56        63.35        85.08        78.97        13.97        63.78 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T 
       56.84        18.61        66.74        14.47        61.28       369.93 
TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 
       25.87       195.02        46.82       115.96        59.64        39.29 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GK TCGA-EE-A2GL 
       86.14        59.28       173.79        48.72        54.74        79.66 
TCGA-EE-A2GM TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU 
       75.48        13.91        42.77        81.21        44.88        94.82 
TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD 
       21.67       129.27        28.83        19.76        61.51        47.28 
TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ 
      103.27       268.73       103.20        16.96       204.66        96.23 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ 
      180.39       216.66       167.90        47.54       248.65        43.23 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE 
       71.21        53.26       124.31       122.73        28.77        54.51 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 
       13.81        41.59       138.81       127.20        36.95        64.08 
TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A199 
       34.32        53.19       201.80        51.35       134.33         9.17 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F 
       77.75        98.40        48.89        12.59        13.02        26.37 
TCGA-ER-A19G TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P 
      302.07         6.44       131.51        61.05        44.09       162.08 
TCGA-ER-A19Q TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       50.89         8.88       148.18       105.07        43.82        23.34 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
       20.15        28.83        48.99        41.56       247.04        93.01 
TCGA-ER-A3PL TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       33.21        12.95       149.03        92.98       174.21        15.72 
TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YY 
       27.85        38.27        36.26       104.42       216.92       228.59 
TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB 
      202.65        20.91        28.08         7.79        27.72        48.85 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZK 
      357.37        53.52        46.45         9.70        32.75        23.93 
TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU 
       74.73       133.55        11.41       148.80        53.16        26.56 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 
       49.48        27.09        27.02        77.82        50.14        66.67 
TCGA-FS-A4F5 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-FW-A3TV 
       28.73        34.03        26.73        54.41        17.46        13.51 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A265 
       19.30         9.90        19.43         2.04        15.78        96.92 
TCGA-GN-A266 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 
       10.13        32.48        48.00       121.91        39.35        10.42 
TCGA-GN-A4U8 TCGA-GN-A8LK TCGA-GN-A9SD TCGA-HR-A2OG TCGA-HR-A2OH TCGA-LH-A9QB 
       48.89        50.10        59.41         0.23        65.88       368.78 
TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 
      297.90         7.23         0.20         0.33         0.69       228.16 
TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1Q TCGA-W3-AA1W TCGA-W3-AA21 
       63.02       121.08         4.01        69.07       219.16       105.04 
TCGA-WE-A8JZ TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ 
       24.03        17.95       101.33        58.98        70.52        63.22 
TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-XV-AB01 TCGA-YD-A89C 
       11.80        49.51        12.16        40.41        13.25         6.90 
TCGA-YD-A9TA TCGA-YG-AA3O TCGA-Z2-A8RT TCGA-Z2-AA3V 
       49.18        37.94        27.58        15.98 

  DEL PEAK  5(3Q13.31) MUTATED DEL PEAK  5(3Q13.31) WILD-TYPE 
                           9.9                            0.2 
  DEL PEAK  5(3Q13.31) MUTATED DEL PEAK  5(3Q13.31) WILD-TYPE 
                        220.24                         369.93 
  DEL PEAK  5(3Q13.31) MUTATED DEL PEAK  5(3Q13.31) WILD-TYPE 
                        64.540                         49.495 
[1] "9.9 - 220.2 (64.5)" "0.2 - 369.9 (49.5)"
[1] "hr=" "1"  
D25V3, continuous
                                vv
clus                             I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB
  DEL PEAK  5(3Q13.31) MUTATED          2       2       5        3        4
  DEL PEAK  5(3Q13.31) WILD-TYPE       11       5      24       15       24
                                vv
clus                             STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK  5(3Q13.31) MUTATED          3         1         4         4
  DEL PEAK  5(3Q13.31) WILD-TYPE       23        13        15        11
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK  5(3Q13.31) MUTATED           7          4          5          7
  DEL PEAK  5(3Q13.31) WILD-TYPE        32         11         30         47
                                vv
clus                             STAGE IV
  DEL PEAK  5(3Q13.31) MUTATED          2
  DEL PEAK  5(3Q13.31) WILD-TYPE       19
D25V4, multiclass
            clus
vv           DEL PEAK  5(3Q13.31) MUTATED DEL PEAK  5(3Q13.31) WILD-TYPE
  I/II NOS                              2                             11
  STAGE 0                               2                              5
  STAGE I                               5                             24
  STAGE IA                              3                             15
  STAGE IB                              4                             24
  STAGE II                              3                             23
  STAGE IIA                             1                             13
  STAGE IIB                             4                             15
  STAGE IIC                             4                             11
  STAGE III                             7                             32
  STAGE IIIA                            4                             11
  STAGE IIIB                            5                             30
  STAGE IIIC                            7                             47
  STAGE IV                              2                             19
[1] 14  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  DEL PEAK  5(3Q13.31) MUTATED      10 12 10 14
  DEL PEAK  5(3Q13.31) WILD-TYPE    54 61 71 53
D25V5, multiclass
       clus
vv      DEL PEAK  5(3Q13.31) MUTATED DEL PEAK  5(3Q13.31) WILD-TYPE
  T0+T1                           10                             54
  T2                              12                             61
  T3                              10                             71
  T4                              14                             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  N3
  DEL PEAK  5(3Q13.31) MUTATED    33   7   8   7
  DEL PEAK  5(3Q13.31) WILD-TYPE 144  58  31  38
D25V6, multiclass
    clus
vv   DEL PEAK  5(3Q13.31) MUTATED DEL PEAK  5(3Q13.31) WILD-TYPE
  N0                           33                            144
  N1                            7                             58
  N2                            8                             31
  N3                            7                             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"
D25V7, binary
                                cls
clus                               0   1
  DEL PEAK  5(3Q13.31) MUTATED    53   2
  DEL PEAK  5(3Q13.31) WILD-TYPE 266  20
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  5(3Q13.31) MUTATED     53    2
  DEL PEAK  5(3Q13.31) WILD-TYPE  266   20
   clus
vv  DEL PEAK  5(3Q13.31) MUTATED DEL PEAK  5(3Q13.31) WILD-TYPE
  0                           53                            266
  1                            2                             20
[1] 2 2
[1] FALSE
D25V8, binary
                                cls
clus                               0   1
  DEL PEAK  5(3Q13.31) MUTATED    21  16
  DEL PEAK  5(3Q13.31) WILD-TYPE 113  74
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  5(3Q13.31) MUTATED     21   16
  DEL PEAK  5(3Q13.31) WILD-TYPE  113   74
     clus
vv    DEL PEAK  5(3Q13.31) MUTATED DEL PEAK  5(3Q13.31) WILD-TYPE
  NO                            21                            113
  YES                           16                             74
[1] 2 2
[1] FALSE
D25V9, binary
                                cls
clus                               0   1
  DEL PEAK  5(3Q13.31) MUTATED     4  58
  DEL PEAK  5(3Q13.31) WILD-TYPE  43 262
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  5(3Q13.31) MUTATED      4   58
  DEL PEAK  5(3Q13.31) WILD-TYPE   43  262
     clus
vv    DEL PEAK  5(3Q13.31) MUTATED DEL PEAK  5(3Q13.31) WILD-TYPE
  NO                             4                             43
  YES                           58                            262
[1] 2 2
[1] FALSE
D25V10, continuous
D25V11, binary
                                cls
clus                               0   1
  DEL PEAK  5(3Q13.31) MUTATED    24  38
  DEL PEAK  5(3Q13.31) WILD-TYPE 114 191
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  5(3Q13.31) MUTATED     24   38
  DEL PEAK  5(3Q13.31) WILD-TYPE  114  191
        clus
vv       DEL PEAK  5(3Q13.31) MUTATED DEL PEAK  5(3Q13.31) WILD-TYPE
  FEMALE                           24                            114
  MALE                             38                            191
[1] 2 2
[1] FALSE
D25V12, binary
                                cls
clus                               0   1
  DEL PEAK  5(3Q13.31) MUTATED    57   5
  DEL PEAK  5(3Q13.31) WILD-TYPE 262  42
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  5(3Q13.31) MUTATED     57    5
  DEL PEAK  5(3Q13.31) WILD-TYPE  262   42
     clus
vv    DEL PEAK  5(3Q13.31) MUTATED DEL PEAK  5(3Q13.31) WILD-TYPE
  NO                            57                            262
  YES                            5                             42
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  5(3Q13.31) MUTATED       2                         0    59
  DEL PEAK  5(3Q13.31) WILD-TYPE     3                         1   294
D25V13, multiclass
                           clus
vv                          DEL PEAK  5(3Q13.31) MUTATED
  ASIAN                                                2
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                               59
                           clus
vv                          DEL PEAK  5(3Q13.31) WILD-TYPE
  ASIAN                                                  3
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                294
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V14, binary
                                cls
clus                               0   1
  DEL PEAK  5(3Q13.31) MUTATED     2  59
  DEL PEAK  5(3Q13.31) WILD-TYPE   5 293
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  5(3Q13.31) MUTATED      2   59
  DEL PEAK  5(3Q13.31) WILD-TYPE    5  293
                        clus
vv                       DEL PEAK  5(3Q13.31) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           59
                        clus
vv                       DEL PEAK  5(3Q13.31) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                            293
[1] 2 2
[1] FALSE

Clustering(26) Variable = DEL PEAK  6(4P16.3) MUTATION ANALYSIS
D26V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  6(4P16.3) MUTATED   29 33
  DEL PEAK  6(4P16.3) WILD-TYPE 99 91
  DEL PEAK  6(4P16.3) MUTATED DEL PEAK  6(4P16.3) WILD-TYPE 
                           62                           190 
  DEL PEAK  6(4P16.3) MUTATED DEL PEAK  6(4P16.3) WILD-TYPE 
                           33                            91 
$`DEL PEAK  6(4P16.3) MUTATED`
TCGA-D3-A2JE TCGA-D3-A8GI TCGA-EE-A180 TCGA-EE-A2GO TCGA-ER-A193 TCGA-D3-A1Q1 
        9.76        13.41        31.96        52.90        19.04         8.42 
TCGA-D3-A1Q4 TCGA-D3-A1QA TCGA-D3-A2J6 TCGA-D3-A2JA TCGA-D3-A2JN TCGA-D3-A2JO 
       31.89        76.41        25.64        15.75        64.83        66.08 
TCGA-D3-A3CC TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51F TCGA-D3-A8GC 
       40.01         9.34        90.21        23.67        30.67        78.21 
TCGA-D3-A8GM TCGA-D9-A1X3 TCGA-D9-A4Z6 TCGA-D9-A6EC TCGA-DA-A3F8 TCGA-DA-A95X 
       70.62        10.78        18.44        69.21         8.71        65.03 
TCGA-EB-A5KH TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D 
       16.41        75.55        79.20        75.22        76.14        12.99 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29W TCGA-EE-A2GH TCGA-EE-A2GM TCGA-EE-A2M6 
       47.41        47.74       185.19       201.60        18.35       103.13 
TCGA-EE-A2MM TCGA-EE-A2MS TCGA-EE-A3AB TCGA-EE-A3J8 TCGA-ER-A197 TCGA-ER-A19D 
      145.45       143.93       122.73         3.35        10.49        11.47 
TCGA-ER-A19S TCGA-ER-A2ND TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A42L TCGA-FR-A7U8 
       47.18         4.70        10.19        28.67        74.47        26.20 
TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FW-A3TU TCGA-GF-A6C8 
      195.98        27.62        66.67       173.19        55.59         1.91 
TCGA-GN-A262 TCGA-GN-A268 TCGA-GN-A4U3 TCGA-W3-A825 TCGA-W3-AA1R TCGA-W3-AA1V 
       53.29        42.48       120.53         1.97        79.99         8.09 
TCGA-WE-AA9Y TCGA-YG-AA3O 
        1.94        28.21 

$`DEL PEAK  6(4P16.3) WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A20H TCGA-EE-A2GD TCGA-EE-A2MR 
       62.07        38.76        33.24       166.75       269.03       134.40 
TCGA-EE-A3JD TCGA-FR-A729 TCGA-FW-A3R5 TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-3N-A9WC 
       27.35       216.43        36.95        52.73         7.40        60.46 
TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q3 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       12.99        14.83        15.72       110.93        49.35       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1QB TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JB TCGA-D3-A2JC 
       19.04        62.60        45.99        62.86       168.00        86.30 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CB 
      107.61        36.30       171.58        43.53        58.06       140.98 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A51E TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R 
       59.70        24.53       173.85       144.46        31.76        62.70 
TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D3-A8GD 
       11.34        42.05        45.70       177.86       124.08        23.61 
TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GP TCGA-D3-A8GR TCGA-D9-A3Z1 
      179.97       120.00        69.53       135.12        36.53        15.02 
TCGA-D9-A3Z3 TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 
       16.90        22.85        76.34       138.67        68.68       150.61 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 
      110.53        60.10        64.83        58.85        30.44       225.11 
TCGA-DA-A95V TCGA-DA-A95W TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5UN 
       72.10         0.76        14.14        12.30         3.91        52.41 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
       18.21        13.15        24.89        20.38         0.00        26.24 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A2A1 
        0.26        44.28        27.16        61.12       346.49       115.43 
TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GJ TCGA-EE-A2GK 
       30.02        77.98        26.14        12.95        68.65        10.62 
TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU 
       32.48        93.63         0.76         0.20        71.31        81.99 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI 
       15.25         5.75        23.77       209.79        94.19       171.85 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MP TCGA-EE-A2MT TCGA-EE-A2MU 
       63.25        89.26       104.78       227.01        23.51        53.26 
TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J3 
      124.31        64.04         4.41        54.51         6.28        67.89 
TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 
      111.85        45.90       168.85        19.86       135.98        34.45 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19G TCGA-ER-A19H 
        7.82         4.54        53.29        39.81       184.60       150.12 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19W 
       99.06        59.84        42.51       120.76        49.71       146.63 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       73.05        22.36        16.87       173.29        68.52        15.48 
TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7UA TCGA-FR-A8YC 
       32.05         4.50       174.21         4.14         5.65        10.06 
TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE 
      171.78        49.74         8.35       312.07        32.78        43.92 
TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT 
        7.82        36.33        78.61       130.95       136.27        35.28 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F9 
        4.47        23.21         5.29         3.06        30.90        13.28 
TCGA-FS-A4FD TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GN-A264 
       80.68        11.54        19.30         9.90        18.25       117.93 
TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-GN-A8LK 
       96.92        17.06         7.59        34.49        46.92        43.23 
TCGA-GN-A9SD TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 
       59.41        85.05       297.01         7.23         0.20         0.33 
TCGA-W3-A824 TCGA-W3-A828 TCGA-W3-AA1Q TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 
      174.12       120.07        44.05       185.13        92.84        47.54 
TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZY 
       65.42        12.69        21.90        62.89        10.95        48.39 
TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-XV-AB01 TCGA-Z2-AA3S 
       37.32        24.99         6.61        91.23 

  DEL PEAK  6(4P16.3) MUTATED DEL PEAK  6(4P16.3) WILD-TYPE 
                         1.91                          0.00 
  DEL PEAK  6(4P16.3) MUTATED DEL PEAK  6(4P16.3) WILD-TYPE 
                       201.60                        346.49 
  DEL PEAK  6(4P16.3) MUTATED DEL PEAK  6(4P16.3) WILD-TYPE 
                       41.245                        47.230 
[1] "1.9 - 201.6 (41.2)" "0.0 - 346.5 (47.2)"
[1] "hr=" "1.4"
D26V2, survival
                               sevent
clus2                             0   1
  DEL PEAK  6(4P16.3) MUTATED    41  48
  DEL PEAK  6(4P16.3) WILD-TYPE 125 144
  DEL PEAK  6(4P16.3) MUTATED DEL PEAK  6(4P16.3) WILD-TYPE 
                           89                           269 
  DEL PEAK  6(4P16.3) MUTATED DEL PEAK  6(4P16.3) WILD-TYPE 
                           48                           144 
$`DEL PEAK  6(4P16.3) MUTATED`
TCGA-D3-A2JE TCGA-D3-A8GI TCGA-EE-A180 TCGA-EE-A29L TCGA-EE-A2GO TCGA-ER-A193 
       27.65        58.52        94.98         2.60       126.81        31.40 
TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1QA TCGA-D3-A2J6 TCGA-D3-A2JA TCGA-D3-A2JN 
       16.57       112.04        90.90        43.43       115.53        66.48 
TCGA-D3-A2JO TCGA-D3-A3CC TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV 
       66.08        86.93         9.34       103.59        39.75        45.30 
TCGA-D3-A51F TCGA-D3-A5GO TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GM TCGA-D9-A148 
       55.73       137.92        30.84        79.59       107.15       151.53 
TCGA-D9-A149 TCGA-D9-A1X3 TCGA-D9-A4Z6 TCGA-D9-A6EC TCGA-DA-A1HW TCGA-DA-A3F8 
       54.67        18.12        18.44        77.56        36.03        43.36 
TCGA-DA-A95X TCGA-EB-A44R TCGA-EB-A5KH TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F 
       73.94        10.36        20.35       133.81       151.27        91.56 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29W 
       85.08        78.97        13.97        64.64        56.84       195.02 
TCGA-EE-A2A5 TCGA-EE-A2GH TCGA-EE-A2GM TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2MM 
       39.29       220.24        75.48        21.67       129.27       167.90 
TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A3AB TCGA-EE-A3AG TCGA-EE-A3J8 TCGA-EE-A3JE 
       43.23       162.48       122.73        41.59        34.32        51.35 
TCGA-ER-A197 TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A2ND 
       13.94        12.59        13.02        49.48         8.88        23.34 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A42L TCGA-FR-A7U8 TCGA-FS-A1Z0 
       28.83        48.99        41.56       149.03        27.85       202.65 
TCGA-FS-A1Z4 TCGA-FS-A1ZA TCGA-FS-A1ZR TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4FB 
       28.08        27.72        11.41        66.67       174.84        26.73 
TCGA-FW-A3TU TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A266 TCGA-GN-A268 
       55.59         2.04        15.78       139.89        10.13        62.79 
TCGA-GN-A4U3 TCGA-GN-A8LL TCGA-W3-A825 TCGA-W3-AA1R TCGA-W3-AA1V TCGA-WE-A8JZ 
      121.91        21.37        63.02       111.09        42.08        24.03 
TCGA-WE-A8K6 TCGA-WE-A8ZX TCGA-WE-AA9Y TCGA-YG-AA3O TCGA-Z2-A8RT 
       17.95        35.80        12.16        37.94        27.58 

$`DEL PEAK  6(4P16.3) WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A184 
       62.07        46.32        13.87        68.25        54.02        68.15 
TCGA-EE-A20H TCGA-EE-A2GD TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A198 TCGA-FR-A729 
      168.26       340.14       134.40        27.35        50.76       220.80 
TCGA-FS-A1ZF TCGA-FW-A3R5 TCGA-QB-AA9O TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-3N-A9WB 
       15.45        36.95        18.05        61.15        21.40        17.03 
TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q3 TCGA-D3-A1Q5 TCGA-D3-A1Q6 
       66.48        12.99        14.93        16.67       112.57        71.80 
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QB TCGA-D3-A2J7 TCGA-D3-A2J8 
      133.25        28.08        31.59        95.74       103.10        65.49 
TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH 
       23.77       168.00        86.76        11.87       113.52        42.08 
TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 
       12.10       171.58        59.57       130.72        58.06        46.98 
TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A51E TCGA-D3-A51H TCGA-D3-A51J 
      166.52        60.23        24.53       174.84        56.35       145.12 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN 
       32.94        22.62        63.81        26.89       125.79       135.75 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GJ 
      178.32        18.18       125.19        23.61        26.43       241.38 
TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR 
      170.20        89.13       161.00       152.75        29.06       129.63 
TCGA-D3-A8GS TCGA-D3-A8GV TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 
      117.17       167.70         3.65         7.10        15.39        22.29 
TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I0 
        9.90        25.18        22.95        76.57       144.89        20.38 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
      222.51       176.55        35.93       135.02        88.87        53.92 
TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 
       65.92        40.60        68.09        33.93        10.49       225.96 
TCGA-DA-A95V TCGA-DA-A95W TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5UL 
       72.10        37.35        14.14        13.02        13.87        29.29 
TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
       58.92         7.04        36.46        29.82        27.22         8.65 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20I TCGA-EE-A29A 
       33.73        14.70        26.89         4.96        13.55        63.35 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
       63.78        72.07        18.61        56.42        66.74        14.47 
TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 
       61.28       369.93        25.87        17.92        46.82       115.96 
TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GI 
       59.64        86.14        59.28        67.43       173.79        48.72 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR 
      107.38        54.74        79.66       102.12        13.91        42.77 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
       81.21        44.88        94.82        28.83        19.76        61.51 
TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
       47.28       103.27       268.73       103.20        16.96       204.66 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MT 
       96.23       180.39       216.66        47.54       248.65        71.21 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
       53.26       124.31        64.04        28.77        54.51        13.81 
TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3JA 
      138.81       172.18       127.20        36.95        64.08        53.19 
TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A199 TCGA-ER-A19A 
      201.80       134.33       152.81        35.44         9.17        77.75 
TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J 
       98.40        48.89        26.37       302.07       152.35         6.44 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19W 
      131.51        61.05        44.09       162.08        50.89       148.18 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
      105.07        43.82        20.15       247.04        93.01        46.98 
TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7U9 
       33.21        12.95        92.98       174.21        15.72        18.77 
TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YX 
       38.27        34.82        36.26       104.42       216.92        48.59 
TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1Z7 TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD 
      228.59        20.91         7.79        48.85       357.37        53.52 
TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM 
       46.45         9.70        32.75        47.38        23.93       101.26 
TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW 
       74.73       133.55       148.80        53.16        26.56        49.48 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F5 TCGA-FS-A4F9 
       27.09        27.02        77.82        50.14        28.73        34.03 
TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
       54.41        80.68        17.46        13.51        19.30         9.90 
TCGA-GF-A4EO TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A26D 
       19.43       117.93        96.92        64.44        32.48        48.00 
TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A9SD 
       39.35        10.42        48.89        22.13        50.10        59.41 
TCGA-HR-A2OG TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 
        0.23        65.88       368.78       297.90         7.23         0.20 
TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1Q 
        0.33         0.69       228.16       121.08         4.01        69.07 
TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO 
      219.16       105.04        49.05       101.33        58.98        70.52 
TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-XV-AB01 
       63.22        11.80        49.51        40.41        24.99        13.25 
TCGA-YD-A89C TCGA-YD-A9TA TCGA-YG-AA3P TCGA-Z2-AA3S TCGA-Z2-AA3V 
        6.90        49.18        14.43        96.99        15.98 

  DEL PEAK  6(4P16.3) MUTATED DEL PEAK  6(4P16.3) WILD-TYPE 
                         2.04                          0.20 
  DEL PEAK  6(4P16.3) MUTATED DEL PEAK  6(4P16.3) WILD-TYPE 
                       220.24                        369.93 
  DEL PEAK  6(4P16.3) MUTATED DEL PEAK  6(4P16.3) WILD-TYPE 
                        48.99                         53.26 
[1] "2.0 - 220.2 (49.0)" "0.2 - 369.9 (53.3)"
[1] "hr=" "1.2"
D26V3, continuous
                               vv
clus                            I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB
  DEL PEAK  6(4P16.3) MUTATED          1       2       7        3        7
  DEL PEAK  6(4P16.3) WILD-TYPE       12       5      22       15       21
                               vv
clus                            STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK  6(4P16.3) MUTATED         10         0         7         3
  DEL PEAK  6(4P16.3) WILD-TYPE       16        14        12        12
                               vv
clus                            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK  6(4P16.3) MUTATED           9          5         13         14
  DEL PEAK  6(4P16.3) WILD-TYPE        30         10         22         40
                               vv
clus                            STAGE IV
  DEL PEAK  6(4P16.3) MUTATED          2
  DEL PEAK  6(4P16.3) WILD-TYPE       19
D26V4, multiclass
            clus
vv           DEL PEAK  6(4P16.3) MUTATED DEL PEAK  6(4P16.3) WILD-TYPE
  I/II NOS                             1                            12
  STAGE 0                              2                             5
  STAGE I                              7                            22
  STAGE IA                             3                            15
  STAGE IB                             7                            21
  STAGE II                            10                            16
  STAGE IIA                            0                            14
  STAGE IIB                            7                            12
  STAGE IIC                            3                            12
  STAGE III                            9                            30
  STAGE IIIA                           5                            10
  STAGE IIIB                          13                            22
  STAGE IIIC                          14                            40
  STAGE IV                             2                            19
[1] 14  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3 T4
  DEL PEAK  6(4P16.3) MUTATED      15 18 25 14
  DEL PEAK  6(4P16.3) WILD-TYPE    49 55 56 53
D26V5, multiclass
       clus
vv      DEL PEAK  6(4P16.3) MUTATED DEL PEAK  6(4P16.3) WILD-TYPE
  T0+T1                          15                            49
  T2                             18                            55
  T3                             25                            56
  T4                             14                            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  N3
  DEL PEAK  6(4P16.3) MUTATED    39  20  10  13
  DEL PEAK  6(4P16.3) WILD-TYPE 138  45  29  32
D26V6, multiclass
    clus
vv   DEL PEAK  6(4P16.3) MUTATED DEL PEAK  6(4P16.3) WILD-TYPE
  N0                          39                           138
  N1                          20                            45
  N2                          10                            29
  N3                          13                            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"
D26V7, binary
                               cls
clus                              0   1
  DEL PEAK  6(4P16.3) MUTATED    81   3
  DEL PEAK  6(4P16.3) WILD-TYPE 238  19
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(4P16.3) MUTATED     81    3
  DEL PEAK  6(4P16.3) WILD-TYPE  238   19
   clus
vv  DEL PEAK  6(4P16.3) MUTATED DEL PEAK  6(4P16.3) WILD-TYPE
  0                          81                           238
  1                           3                            19
[1] 2 2
[1] FALSE
D26V8, binary
                               cls
clus                             0  1
  DEL PEAK  6(4P16.3) MUTATED   36 22
  DEL PEAK  6(4P16.3) WILD-TYPE 98 68
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(4P16.3) MUTATED     36   22
  DEL PEAK  6(4P16.3) WILD-TYPE   98   68
     clus
vv    DEL PEAK  6(4P16.3) MUTATED DEL PEAK  6(4P16.3) WILD-TYPE
  NO                           36                            98
  YES                          22                            68
[1] 2 2
[1] FALSE
D26V9, binary
                               cls
clus                              0   1
  DEL PEAK  6(4P16.3) MUTATED    10  81
  DEL PEAK  6(4P16.3) WILD-TYPE  37 239
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(4P16.3) MUTATED     10   81
  DEL PEAK  6(4P16.3) WILD-TYPE   37  239
     clus
vv    DEL PEAK  6(4P16.3) MUTATED DEL PEAK  6(4P16.3) WILD-TYPE
  NO                           10                            37
  YES                          81                           239
[1] 2 2
[1] FALSE
D26V10, continuous
D26V11, binary
                               cls
clus                              0   1
  DEL PEAK  6(4P16.3) MUTATED    33  58
  DEL PEAK  6(4P16.3) WILD-TYPE 105 171
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(4P16.3) MUTATED     33   58
  DEL PEAK  6(4P16.3) WILD-TYPE  105  171
        clus
vv       DEL PEAK  6(4P16.3) MUTATED DEL PEAK  6(4P16.3) WILD-TYPE
  FEMALE                          33                           105
  MALE                            58                           171
[1] 2 2
[1] FALSE
D26V12, binary
                               cls
clus                              0   1
  DEL PEAK  6(4P16.3) MUTATED    78  13
  DEL PEAK  6(4P16.3) WILD-TYPE 241  34
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(4P16.3) MUTATED     78   13
  DEL PEAK  6(4P16.3) WILD-TYPE  241   34
     clus
vv    DEL PEAK  6(4P16.3) MUTATED DEL PEAK  6(4P16.3) WILD-TYPE
  NO                           78                           241
  YES                          13                            34
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  6(4P16.3) MUTATED       2                         0    87
  DEL PEAK  6(4P16.3) WILD-TYPE     3                         1   266
D26V13, multiclass
                           clus
vv                          DEL PEAK  6(4P16.3) MUTATED
  ASIAN                                               2
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                              87
                           clus
vv                          DEL PEAK  6(4P16.3) WILD-TYPE
  ASIAN                                                 3
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                               266
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V14, binary
                               cls
clus                              0   1
  DEL PEAK  6(4P16.3) MUTATED     1  88
  DEL PEAK  6(4P16.3) WILD-TYPE   6 264
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(4P16.3) MUTATED      1   88
  DEL PEAK  6(4P16.3) WILD-TYPE    6  264
                        clus
vv                       DEL PEAK  6(4P16.3) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          88
                        clus
vv                       DEL PEAK  6(4P16.3) WILD-TYPE
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                           264
[1] 2 2
[1] FALSE

Clustering(27) Variable = DEL PEAK  7(4Q34.3) MUTATION ANALYSIS
D27V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  7(4Q34.3) MUTATED   34 38
  DEL PEAK  7(4Q34.3) WILD-TYPE 94 86
  DEL PEAK  7(4Q34.3) MUTATED DEL PEAK  7(4Q34.3) WILD-TYPE 
                           72                           180 
  DEL PEAK  7(4Q34.3) MUTATED DEL PEAK  7(4Q34.3) WILD-TYPE 
                           38                            86 
$`DEL PEAK  7(4Q34.3) MUTATED`
TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GO TCGA-EE-A3JD TCGA-ER-A193 TCGA-WE-AAA3 
       31.96       166.75        52.90        27.35        19.04         7.40 
TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q8 TCGA-D3-A2JA TCGA-D3-A2JN 
       14.83         8.42        31.89        19.04        15.75        64.83 
TCGA-D3-A2JO TCGA-D3-A3CC TCGA-D3-A3MR TCGA-D3-A51F TCGA-D3-A8GC TCGA-D3-A8GM 
       66.08        40.01        90.21        30.67        78.21        70.62 
TCGA-D3-A8GP TCGA-D3-A8GR TCGA-D9-A4Z6 TCGA-D9-A6EC TCGA-DA-A1HY TCGA-DA-A1I7 
      135.12        36.53        18.44        69.21       138.67        60.10 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-DA-A95V TCGA-DA-A95X TCGA-EE-A17Y TCGA-EE-A181 
      225.11         8.71        72.10        65.03        24.89        20.38 
TCGA-EE-A29C TCGA-EE-A29M TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A6 TCGA-EE-A2GH 
       76.14        47.74       346.49       185.19        77.98       201.60 
TCGA-EE-A2GM TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2MM TCGA-EE-A2MT TCGA-EE-A3J4 
       18.35        81.99       103.13       145.45        23.51       111.85 
TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-ER-A197 TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19S 
        3.35       168.85        10.49        53.29        11.47        47.18 
TCGA-ER-A2ND TCGA-ER-A2NG TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A42L TCGA-FR-A7U8 
        4.70        28.67        68.52        15.48        74.47        26.20 
TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ 
      195.98        27.62       312.07        43.92         7.82        36.33 
TCGA-FW-A3TU TCGA-GF-A6C8 TCGA-GN-A4U3 TCGA-GN-A8LK TCGA-W3-A825 TCGA-W3-A828 
       55.59         1.91       120.53        43.23         1.97       120.07 
TCGA-W3-AA1R TCGA-W3-AA1V TCGA-WE-A8ZM TCGA-WE-AA9Y TCGA-YG-AA3O TCGA-Z2-AA3S 
       79.99         8.09        65.42         1.94        28.21        91.23 

$`DEL PEAK  7(4Q34.3) WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A8GI TCGA-EB-A5SG TCGA-EE-A2GD 
        9.76        62.07        38.76        13.41        33.24       269.03 
TCGA-EE-A2MR TCGA-FR-A729 TCGA-FW-A3R5 TCGA-WE-A8K5 TCGA-3N-A9WC TCGA-3N-A9WD 
      134.40       216.43        36.95        52.73        60.46        12.99 
TCGA-D3-A1Q3 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1QA TCGA-D3-A1QB 
       15.72       110.93        49.35       133.25        76.41        62.60 
TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JG 
       25.64        45.99        62.86       168.00        86.30       107.61 
TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CE 
       36.30       171.58        43.53        58.06       140.98        59.70 
TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51J TCGA-D3-A51K 
       24.53         9.34        23.67       173.85       144.46        31.76 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GU 
       62.70        11.34        42.05        45.70       177.86       124.08 
TCGA-D3-A8GD TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D9-A1X3 TCGA-D9-A3Z1 
       23.61       179.97       120.00        69.53        10.78        15.02 
TCGA-D9-A3Z3 TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 
       16.90        22.85        76.34        68.68       150.61       110.53 
TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A95W TCGA-DA-A95Y TCGA-DA-A95Z 
       64.83        58.85        30.44         0.76        14.14        12.30 
TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A182 
        3.91        16.41        52.41        18.21        13.15         0.00 
TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29E 
       26.24        75.55        79.20        75.22        12.99         0.26 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A2A1 TCGA-EE-A2A2 
       44.28        47.41        27.16        61.12       115.43        30.02 
TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN 
       26.14        12.95        68.65        10.62        32.48        93.63 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
        0.76         0.20        71.31        15.25         5.75        23.77 
TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML 
      209.79        94.19       171.85        63.25        89.26       104.78 
TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC 
      227.01       143.93        53.26       124.31       122.73        64.04 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-EE-A3JH 
        4.41        54.51         6.28        67.89        45.90        19.86 
TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19C TCGA-ER-A19G 
      135.98        34.45         7.82         4.54        39.81       184.60 
TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
      150.12        99.06        59.84        42.51       120.76        49.71 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A3ES 
      146.63        73.05        22.36        16.87        10.19       173.29 
TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7UA TCGA-FR-A8YC 
       32.05         4.50       174.21         4.14         5.65        10.06 
TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1ZD TCGA-FS-A1ZM TCGA-FS-A1ZQ 
      171.78        49.74         8.35        32.78        78.61       130.95 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ 
      136.27        35.28         4.47        23.21         5.29         3.06 
TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TV 
       30.90        66.67       173.19        13.28        80.68        11.54 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
       19.30         9.90        18.25        53.29       117.93        96.92 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-GN-A9SD 
       17.06        42.48         7.59        34.49        46.92        59.41 
TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 TCGA-W3-A824 
       85.05       297.01         7.23         0.20         0.33       174.12 
TCGA-W3-AA1Q TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8ZN TCGA-WE-A8ZO 
       44.05       185.13        92.84        47.54        12.69        21.90 
TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-XV-AB01 
       62.89        10.95        48.39        37.32        24.99         6.61 

  DEL PEAK  7(4Q34.3) MUTATED DEL PEAK  7(4Q34.3) WILD-TYPE 
                         1.91                          0.00 
  DEL PEAK  7(4Q34.3) MUTATED DEL PEAK  7(4Q34.3) WILD-TYPE 
                       346.49                        297.01 
  DEL PEAK  7(4Q34.3) MUTATED DEL PEAK  7(4Q34.3) WILD-TYPE 
                       47.460                        45.945 
[1] "1.9 - 346.5 (47.5)" "0.0 - 297.0 (45.9)"
[1] "hr=" "1"  
D27V2, survival
                               sevent
clus2                             0   1
  DEL PEAK  7(4Q34.3) MUTATED    54  55
  DEL PEAK  7(4Q34.3) WILD-TYPE 112 137
  DEL PEAK  7(4Q34.3) MUTATED DEL PEAK  7(4Q34.3) WILD-TYPE 
                          109                           249 
  DEL PEAK  7(4Q34.3) MUTATED DEL PEAK  7(4Q34.3) WILD-TYPE 
                           55                           137 
$`DEL PEAK  7(4Q34.3) MUTATED`
TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GO TCGA-EE-A3JD TCGA-ER-A193 TCGA-FS-A1ZF 
       94.98       168.26       126.81        27.35        31.40        15.45 
TCGA-QB-AA9O TCGA-WE-AAA3 TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q8 
       18.05        21.40        14.93        16.57       112.04        28.08 
TCGA-D3-A2JA TCGA-D3-A2JD TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A3C7 TCGA-D3-A3CC 
      115.53        11.87        66.48        66.08        46.98        86.93 
TCGA-D3-A3MR TCGA-D3-A3MV TCGA-D3-A51F TCGA-D3-A51N TCGA-D3-A8GC TCGA-D3-A8GM 
      103.59        45.30        55.73        22.62        79.59       107.15 
TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GR TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A4Z6 
      161.00       152.75       129.63       151.53        54.67        18.44 
TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I7 TCGA-DA-A3F5 
        9.90        77.56        36.03       144.89        88.87       225.96 
TCGA-DA-A3F8 TCGA-DA-A95V TCGA-DA-A95X TCGA-EB-A44R TCGA-EB-A5UL TCGA-EE-A17Y 
       43.36        72.10        73.94        10.36        29.29        27.22 
TCGA-EE-A181 TCGA-EE-A20B TCGA-EE-A29C TCGA-EE-A29M TCGA-EE-A29T TCGA-EE-A29W 
       33.73       133.81        78.97        56.84       369.93       195.02 
TCGA-EE-A29X TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GM 
       17.92        39.29        86.14       220.24        48.72        75.48 
TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2MM TCGA-EE-A2MQ TCGA-EE-A2MT 
       94.82        21.67       129.27       167.90        43.23        71.21 
TCGA-EE-A3AG TCGA-EE-A3J4 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JE 
       41.59       127.20        34.32        53.19       201.80        51.35 
TCGA-ER-A197 TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19S TCGA-ER-A2ND 
       13.94        98.40        12.59        13.02        49.48        23.34 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A42L TCGA-FR-A7U8 
       48.99        41.56        93.01        46.98       149.03        27.85 
TCGA-FR-A7U9 TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1ZA TCGA-FS-A1ZC TCGA-FS-A1ZE 
       18.77       202.65        28.08        27.72       357.37        46.45 
TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-GF-A6C8 TCGA-GF-A6C9 
        9.70        47.38        17.46        55.59         2.04        15.78 
TCGA-GN-A266 TCGA-GN-A4U3 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL TCGA-HR-A2OH 
       10.13       121.91        22.13        50.10        21.37        65.88 
TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1R TCGA-W3-AA1V TCGA-WE-A8JZ TCGA-WE-A8K6 
       63.02       121.08       111.09        42.08        24.03        17.95 
TCGA-WE-A8ZM TCGA-WE-A8ZX TCGA-WE-AA9Y TCGA-YD-A9TA TCGA-YG-AA3O TCGA-Z2-A8RT 
      101.33        35.80        12.16        49.18        37.94        27.58 
TCGA-Z2-AA3S 
       96.99 

$`DEL PEAK  7(4Q34.3) WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-D3-A8GI TCGA-EB-A5SG 
       27.65        62.07        46.32        13.87        58.52        68.25 
TCGA-EB-A5SH TCGA-EE-A184 TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2MR TCGA-ER-A198 
       54.02        68.15         2.60       340.14       134.40        50.76 
TCGA-FR-A729 TCGA-FW-A3R5 TCGA-WE-A8K5 TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD 
      220.80        36.95        61.15        17.03        66.48        12.99 
TCGA-D3-A1Q3 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A1QA 
       16.67       112.57        71.80       133.25        31.59        90.90 
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JB 
       95.74        43.43       103.10        65.49        23.77       168.00 
TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JP 
       86.76       113.52        42.08        12.10       171.58        59.57 
TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO 
      130.72        58.06       166.52        60.23        24.53         9.34 
TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R 
       39.75       174.84        56.35       145.12        32.94        63.81 
TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       26.89       125.79       135.75       137.92       178.32        18.18 
TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GK 
      125.19        30.84        23.61        26.43       241.38       170.20 
TCGA-D3-A8GL TCGA-D3-A8GQ TCGA-D3-A8GS TCGA-D3-A8GV TCGA-D9-A1JW TCGA-D9-A1JX 
       89.13        29.06       117.17       167.70         3.65         7.10 
TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6EA TCGA-D9-A6EG TCGA-DA-A1HV 
       18.12        15.39        22.29        25.18        22.95        76.57 
TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I8 
       20.38       222.51       176.55        35.93       135.02        53.92 
TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A95W 
       65.92        40.60        68.09        33.93        10.49        37.35 
TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A5VV 
       14.14        13.02        13.87        20.35        58.92         7.04 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 
       36.46        29.82         8.65        14.70        26.89         4.96 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29D 
      151.27        91.56        13.55        63.35        85.08        13.97 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
       63.78        72.07        64.64        18.61        56.42        66.74 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
       14.47        61.28        25.87        46.82       115.96        59.64 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       59.28        67.43       173.79       107.38        54.74        79.66 
TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2M7 
      102.12        13.91        42.77        81.21        44.88        28.83 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG 
       19.76        61.51        47.28       103.27       268.73       103.20 
TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MN 
       16.96       204.66        96.23       180.39       216.66        47.54 
TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC 
      248.65       162.48        53.26       124.31       122.73        64.04 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J5 
       28.77        54.51        13.81       138.81       172.18        36.95 
TCGA-EE-A3J7 TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A199 TCGA-ER-A19A 
       64.08       134.33       152.81        35.44         9.17        77.75 
TCGA-ER-A19C TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L 
       48.89        26.37       302.07       152.35         6.44       131.51 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19T TCGA-ER-A19W 
       61.05        44.09       162.08        50.89         8.88       148.18 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A3ES TCGA-ER-A3PL 
      105.07        43.82        20.15        28.83       247.04        33.21 
TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7UA TCGA-FR-A8YC 
       12.95        92.98       174.21        15.72        38.27        34.82 
TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z3 
       36.26       104.42       216.92        48.59       228.59        20.91 
TCGA-FS-A1Z7 TCGA-FS-A1ZB TCGA-FS-A1ZD TCGA-FS-A1ZH TCGA-FS-A1ZK TCGA-FS-A1ZM 
        7.79        48.85        53.52        32.75        23.93       101.26 
TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU 
       74.73       133.55        11.41       148.80        53.16        26.56 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 
       49.48        27.09        27.02        77.82        50.14        66.67 
TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD 
       28.73       174.84        34.03        26.73        54.41        80.68 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GN-A262 TCGA-GN-A264 
       13.51        19.30         9.90        19.43       139.89       117.93 
TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U4 
       96.92        64.44        62.79        32.48        48.00        39.35 
TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A9SD TCGA-HR-A2OG TCGA-LH-A9QB TCGA-OD-A75X 
       10.42        48.89        59.41         0.23       368.78       297.90 
TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-AA1O 
        7.23         0.20         0.33         0.69       228.16         4.01 
TCGA-W3-AA1Q TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8ZN TCGA-WE-A8ZO 
       69.07       219.16       105.04        49.05        58.98        70.52 
TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-XV-AB01 
       63.22        11.80        49.51        40.41        24.99        13.25 
TCGA-YD-A89C TCGA-YG-AA3P TCGA-Z2-AA3V 
        6.90        14.43        15.98 

  DEL PEAK  7(4Q34.3) MUTATED DEL PEAK  7(4Q34.3) WILD-TYPE 
                         2.04                          0.20 
  DEL PEAK  7(4Q34.3) MUTATED DEL PEAK  7(4Q34.3) WILD-TYPE 
                       369.93                        368.78 
  DEL PEAK  7(4Q34.3) MUTATED DEL PEAK  7(4Q34.3) WILD-TYPE 
                        49.18                         53.92 
[1] "2.0 - 369.9 (49.2)" "0.2 - 368.8 (53.9)"
[1] "hr=" "1.1"
D27V3, continuous
                               vv
clus                            I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB
  DEL PEAK  7(4Q34.3) MUTATED          2       2       8        5       10
  DEL PEAK  7(4Q34.3) WILD-TYPE       11       5      21       13       18
                               vv
clus                            STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK  7(4Q34.3) MUTATED          9         0         4         6
  DEL PEAK  7(4Q34.3) WILD-TYPE       17        14        15         9
                               vv
clus                            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK  7(4Q34.3) MUTATED          12          6         15         17
  DEL PEAK  7(4Q34.3) WILD-TYPE        27          9         20         37
                               vv
clus                            STAGE IV
  DEL PEAK  7(4Q34.3) MUTATED          5
  DEL PEAK  7(4Q34.3) WILD-TYPE       16
D27V4, multiclass
            clus
vv           DEL PEAK  7(4Q34.3) MUTATED DEL PEAK  7(4Q34.3) WILD-TYPE
  I/II NOS                             2                            11
  STAGE 0                              2                             5
  STAGE I                              8                            21
  STAGE IA                             5                            13
  STAGE IB                            10                            18
  STAGE II                             9                            17
  STAGE IIA                            0                            14
  STAGE IIB                            4                            15
  STAGE IIC                            6                             9
  STAGE III                           12                            27
  STAGE IIIA                           6                             9
  STAGE IIIB                          15                            20
  STAGE IIIC                          17                            37
  STAGE IV                             5                            16
[1] 14  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3 T4
  DEL PEAK  7(4Q34.3) MUTATED      19 22 26 17
  DEL PEAK  7(4Q34.3) WILD-TYPE    45 51 55 50
D27V5, multiclass
       clus
vv      DEL PEAK  7(4Q34.3) MUTATED DEL PEAK  7(4Q34.3) WILD-TYPE
  T0+T1                          19                            45
  T2                             22                            51
  T3                             26                            55
  T4                             17                            50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  DEL PEAK  7(4Q34.3) MUTATED    47  25  12  14
  DEL PEAK  7(4Q34.3) WILD-TYPE 130  40  27  31
D27V6, multiclass
    clus
vv   DEL PEAK  7(4Q34.3) MUTATED DEL PEAK  7(4Q34.3) WILD-TYPE
  N0                          47                           130
  N1                          25                            40
  N2                          12                            27
  N3                          14                            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"
D27V7, binary
                               cls
clus                              0   1
  DEL PEAK  7(4Q34.3) MUTATED    96   6
  DEL PEAK  7(4Q34.3) WILD-TYPE 223  16
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(4Q34.3) MUTATED     96    6
  DEL PEAK  7(4Q34.3) WILD-TYPE  223   16
   clus
vv  DEL PEAK  7(4Q34.3) MUTATED DEL PEAK  7(4Q34.3) WILD-TYPE
  0                          96                           223
  1                           6                            16
[1] 2 2
[1] FALSE
D27V8, binary
                               cls
clus                             0  1
  DEL PEAK  7(4Q34.3) MUTATED   38 27
  DEL PEAK  7(4Q34.3) WILD-TYPE 96 63
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(4Q34.3) MUTATED     38   27
  DEL PEAK  7(4Q34.3) WILD-TYPE   96   63
     clus
vv    DEL PEAK  7(4Q34.3) MUTATED DEL PEAK  7(4Q34.3) WILD-TYPE
  NO                           38                            96
  YES                          27                            63
[1] 2 2
[1] FALSE
D27V9, binary
                               cls
clus                              0   1
  DEL PEAK  7(4Q34.3) MUTATED    17  93
  DEL PEAK  7(4Q34.3) WILD-TYPE  30 227
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(4Q34.3) MUTATED     17   93
  DEL PEAK  7(4Q34.3) WILD-TYPE   30  227
     clus
vv    DEL PEAK  7(4Q34.3) MUTATED DEL PEAK  7(4Q34.3) WILD-TYPE
  NO                           17                            30
  YES                          93                           227
[1] 2 2
[1] FALSE
D27V10, continuous
D27V11, binary
                               cls
clus                              0   1
  DEL PEAK  7(4Q34.3) MUTATED    47  63
  DEL PEAK  7(4Q34.3) WILD-TYPE  91 166
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(4Q34.3) MUTATED     47   63
  DEL PEAK  7(4Q34.3) WILD-TYPE   91  166
        clus
vv       DEL PEAK  7(4Q34.3) MUTATED DEL PEAK  7(4Q34.3) WILD-TYPE
  FEMALE                          47                            91
  MALE                            63                           166
[1] 2 2
[1] FALSE
D27V12, binary
                               cls
clus                              0   1
  DEL PEAK  7(4Q34.3) MUTATED    95  15
  DEL PEAK  7(4Q34.3) WILD-TYPE 224  32
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(4Q34.3) MUTATED     95   15
  DEL PEAK  7(4Q34.3) WILD-TYPE  224   32
     clus
vv    DEL PEAK  7(4Q34.3) MUTATED DEL PEAK  7(4Q34.3) WILD-TYPE
  NO                           95                           224
  YES                          15                            32
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  7(4Q34.3) MUTATED       2                         0   105
  DEL PEAK  7(4Q34.3) WILD-TYPE     3                         1   248
D27V13, multiclass
                           clus
vv                          DEL PEAK  7(4Q34.3) MUTATED
  ASIAN                                               2
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                             105
                           clus
vv                          DEL PEAK  7(4Q34.3) WILD-TYPE
  ASIAN                                                 3
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                               248
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V14, binary
                               cls
clus                              0   1
  DEL PEAK  7(4Q34.3) MUTATED     1 106
  DEL PEAK  7(4Q34.3) WILD-TYPE   6 246
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(4Q34.3) MUTATED      1  106
  DEL PEAK  7(4Q34.3) WILD-TYPE    6  246
                        clus
vv                       DEL PEAK  7(4Q34.3) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                         106
                        clus
vv                       DEL PEAK  7(4Q34.3) WILD-TYPE
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                           246
[1] 2 2
[1] FALSE

Clustering(28) Variable = DEL PEAK  8(5P15.31) MUTATION ANALYSIS
D28V1, survival
                                sevent
clus2                              0   1
  DEL PEAK  8(5P15.31) MUTATED    22  30
  DEL PEAK  8(5P15.31) WILD-TYPE 106  94
  DEL PEAK  8(5P15.31) MUTATED DEL PEAK  8(5P15.31) WILD-TYPE 
                            52                            200 
  DEL PEAK  8(5P15.31) MUTATED DEL PEAK  8(5P15.31) WILD-TYPE 
                            30                             94 
$`DEL PEAK  8(5P15.31) MUTATED`
TCGA-EE-A2GD TCGA-3N-A9WD TCGA-D3-A1Q3 TCGA-D3-A2JB TCGA-D3-A2JG TCGA-D3-A2JL 
      269.03        12.99        15.72       168.00       107.61       171.58 
TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A8GR TCGA-D9-A1X3 TCGA-D9-A4Z6 TCGA-DA-A1HV 
       40.01        24.53        36.53        10.78        18.44        76.34 
TCGA-DA-A3F5 TCGA-DA-A95Y TCGA-EB-A44Q TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A29C 
      225.11        14.14         3.91        13.15        24.89        76.14 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A2A2 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH 
       27.16        61.12        30.02        26.14        12.95       201.60 
TCGA-EE-A2GR TCGA-EE-A2MM TCGA-EE-A2MU TCGA-EE-A3J7 TCGA-EE-A3JB TCGA-ER-A199 
        0.20       145.45        53.26        45.90       168.85         7.82 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NG TCGA-FR-A69P TCGA-FS-A1ZD TCGA-FS-A1ZM 
        4.70        16.87        28.67         4.14        32.78        78.61 
TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F8 TCGA-GF-A6C8 TCGA-GN-A262 
       35.28        23.21         5.29       173.19         1.91        53.29 
TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A4U3 TCGA-GN-A8LK TCGA-OD-A75X 
      117.93        17.06        42.48       120.53        43.23       297.01 
TCGA-W3-AA1R TCGA-WE-A8ZM TCGA-WE-A8ZY TCGA-WE-AAA4 
       79.99        65.42        48.39        24.99 

$`DEL PEAK  8(5P15.31) WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A8GI TCGA-EB-A5SG TCGA-EE-A180 
        9.76        62.07        38.76        13.41        33.24        31.96 
TCGA-EE-A20H TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-FR-A729 
      166.75        52.90       134.40        27.35        19.04       216.43 
TCGA-FW-A3R5 TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-3N-A9WC TCGA-BF-AAP0 TCGA-D3-A1Q1 
       36.95        52.73         7.40        60.46        14.83         8.42 
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA 
       31.89       110.93        49.35       133.25        19.04        76.41 
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JC 
       62.60        25.64        45.99        62.86        15.75        86.30 
TCGA-D3-A2JH TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CB 
       36.30        64.83        66.08        43.53        58.06       140.98 
TCGA-D3-A3CE TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F 
       59.70         9.34        90.21        23.67       173.85        30.67 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN 
      144.46        31.76        62.70        11.34        42.05        45.70 
TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GJ TCGA-D3-A8GK 
      177.86       124.08        78.21        23.61       179.97       120.00 
TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GP TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6EC 
       69.53        70.62       135.12        15.02        16.90        69.21 
TCGA-D9-A6EG TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 
       22.85       138.67        68.68       150.61       110.53        60.10 
TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F8 TCGA-DA-A95V TCGA-DA-A95W 
       64.83        58.85        30.44         8.71        72.10         0.76 
TCGA-DA-A95X TCGA-DA-A95Z TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A181 
       65.03        12.30        16.41        52.41        18.21        20.38 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29D 
        0.00        26.24        75.55        79.20        75.22        12.99 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29T TCGA-EE-A29W 
        0.26        44.28        47.41        47.74       346.49       185.19 
TCGA-EE-A2A1 TCGA-EE-A2A6 TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
      115.43        77.98        68.65        10.62        32.48        18.35 
TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 
       93.63         0.76        71.31        81.99       103.13        15.25 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ 
        5.75        23.77       209.79        94.19       171.85        63.25 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AA 
       89.26       104.78       227.01       143.93        23.51       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J3 
      122.73        64.04         4.41        54.51         6.28        67.89 
TCGA-EE-A3J4 TCGA-EE-A3J8 TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 
      111.85         3.35        19.86       135.98        34.45        10.49 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19H 
        4.54        53.29        39.81        11.47       184.60       150.12 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S 
       99.06        59.84        42.51       120.76        49.71        47.18 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NF TCGA-ER-A3ES TCGA-ER-A3ET 
      146.63        73.05        22.36        10.19       173.29        68.52 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A7U8 
       15.48        32.05        74.47         4.50       174.21        26.20 
TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
        5.65        10.06       171.78        49.74       195.98         8.35 
TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZQ 
       27.62       312.07        43.92         7.82        36.33       130.95 
TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F9 
      136.27         4.47         3.06        30.90        66.67        13.28 
TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
       80.68        55.59        11.54        19.30         9.90        18.25 
TCGA-GN-A265 TCGA-GN-A26A TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-GN-A9SD TCGA-LH-A9QB 
       96.92         7.59        34.49        46.92        59.41        85.05 
TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 
        7.23         0.20         0.33       174.12         1.97       120.07 
TCGA-W3-AA1Q TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8ZN 
       44.05         8.09       185.13        92.84        47.54        12.69 
TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-XV-AB01 
       21.90        62.89        10.95         1.94        37.32         6.61 
TCGA-YG-AA3O TCGA-Z2-AA3S 
       28.21        91.23 

  DEL PEAK  8(5P15.31) MUTATED DEL PEAK  8(5P15.31) WILD-TYPE 
                           0.2                            0.0 
  DEL PEAK  8(5P15.31) MUTATED DEL PEAK  8(5P15.31) WILD-TYPE 
                        297.01                         346.49 
  DEL PEAK  8(5P15.31) MUTATED DEL PEAK  8(5P15.31) WILD-TYPE 
                        35.905                         48.545 
[1] "0.2 - 297.0 (35.9)" "0.0 - 346.5 (48.5)"
[1] "hr=" "1.2"
D28V2, survival
                                sevent
clus2                              0   1
  DEL PEAK  8(5P15.31) MUTATED    30  47
  DEL PEAK  8(5P15.31) WILD-TYPE 136 145
  DEL PEAK  8(5P15.31) MUTATED DEL PEAK  8(5P15.31) WILD-TYPE 
                            77                            281 
  DEL PEAK  8(5P15.31) MUTATED DEL PEAK  8(5P15.31) WILD-TYPE 
                            47                            145 
$`DEL PEAK  8(5P15.31) MUTATED`
TCGA-EE-A184 TCGA-EE-A2GD TCGA-3N-A9WD TCGA-D3-A1Q3 TCGA-D3-A2JB TCGA-D3-A2JD 
       68.15       340.14        12.99        16.67       168.00        11.87 
TCGA-D3-A2JG TCGA-D3-A2JL TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3MV TCGA-D3-A5GO 
      113.52       171.58        86.93        24.53        45.30       137.92 
TCGA-D3-A8GB TCGA-D3-A8GN TCGA-D3-A8GR TCGA-D3-A8GV TCGA-D9-A1X3 TCGA-D9-A4Z6 
       30.84       161.00       129.63       167.70        18.12        18.44 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A3F5 TCGA-DA-A95Y TCGA-EB-A44Q TCGA-EB-A44R 
       76.57        36.03       225.96        14.14        13.87        10.36 
TCGA-EB-A5UL TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A185 TCGA-EE-A20I TCGA-EE-A29C 
       29.29        29.82        27.22         4.96        13.55        78.97 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A2A2 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH 
       56.42        66.74        59.64        59.28       173.79       220.24 
TCGA-EE-A2GI TCGA-EE-A2GR TCGA-EE-A2MM TCGA-EE-A2MQ TCGA-EE-A2MU TCGA-EE-A3J5 
       48.72        42.77       167.90        43.23        53.26        36.95 
TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-ER-A199 TCGA-ER-A2ND TCGA-ER-A2NE 
       64.08        53.19       201.80         9.17        23.34        20.15 
TCGA-ER-A2NG TCGA-FR-A69P TCGA-FS-A1ZD TCGA-FS-A1ZM TCGA-FS-A1ZT TCGA-FS-A1ZW 
       48.99        15.72        53.52       101.26        53.16        49.48 
TCGA-FS-A1ZY TCGA-FS-A4F2 TCGA-FS-A4F8 TCGA-FS-A4FB TCGA-FW-A3I3 TCGA-GF-A6C8 
       27.09        50.14       174.84        26.73        17.46         2.04 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26D 
      139.89       117.93        10.13        64.44        62.79        48.00 
TCGA-GN-A4U3 TCGA-GN-A8LK TCGA-GN-A8LL TCGA-HR-A2OG TCGA-HR-A2OH TCGA-OD-A75X 
      121.91        50.10        21.37         0.23        65.88       297.90 
TCGA-W3-AA1R TCGA-WE-A8ZM TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AAA4 
      111.09       101.33        35.80        49.51        24.99 

$`DEL PEAK  8(5P15.31) WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-D3-A8GI TCGA-EB-A5SG 
       27.65        62.07        46.32        13.87        58.52        68.25 
TCGA-EB-A5SH TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GO TCGA-EE-A2MR 
       54.02        94.98       168.26         2.60       126.81       134.40 
TCGA-EE-A3JD TCGA-ER-A193 TCGA-ER-A198 TCGA-FR-A729 TCGA-FS-A1ZF TCGA-FW-A3R5 
       27.35        31.40        50.76       220.80        15.45        36.95 
TCGA-QB-AA9O TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-3N-A9WB TCGA-3N-A9WC TCGA-BF-AAP0 
       18.05        61.15        21.40        17.03        66.48        14.93 
TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       16.57       112.04       112.57        71.80       133.25        28.08 
TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 
       31.59        90.90        95.74        43.43       103.10        65.49 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JN 
       23.77       115.53        86.76        42.08        12.10        66.48 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CB 
       66.08        59.57       130.72        58.06        46.98       166.52 
TCGA-D3-A3CE TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F 
       60.23         9.34       103.59        39.75       174.84        55.73 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T 
       56.35       145.12        32.94        22.62        63.81        26.89 
TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GC 
      125.79       135.75       178.32        18.18       125.19        79.59 
TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM 
       23.61        26.43       241.38       170.20        89.13       107.15 
TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GS TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW 
      152.75        29.06       117.17       151.53        54.67         3.65 
TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC 
        7.10        15.39        22.29         9.90        25.18        77.56 
TCGA-D9-A6EG TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 
       22.95       144.89        20.38       222.51       176.55        35.93 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
      135.02        88.87        53.92        65.92        40.60        68.09 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-DA-A95V TCGA-DA-A95W TCGA-DA-A95X 
       33.93        10.49        43.36        72.10        37.35        73.94 
TCGA-DA-A95Z TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17Z 
       13.02        20.35        58.92         7.04        36.46         8.65 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F 
       33.73        14.70        26.89       133.81       151.27        91.56 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H 
       63.35        85.08        13.97        63.78        72.07        64.64 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V 
       56.84        18.61        14.47        61.28       369.93        25.87 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-EE-A2A6 
      195.02        17.92        46.82       115.96        39.29        86.14 
TCGA-EE-A2GC TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
       67.43       107.38        54.74        79.66        75.48       102.12 
TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 
       13.91        81.21        44.88        94.82        21.67       129.27 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF 
       28.83        19.76        61.51        47.28       103.27       268.73 
TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML 
      103.20        16.96       204.66        96.23       180.39       216.66 
TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AB 
       47.54       248.65       162.48        71.21       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH 
       64.04        28.77        54.51        13.81        41.59       138.81 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J8 TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
      172.18       127.20        34.32        51.35       134.33       152.81 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D 
       35.44        13.94        77.75        98.40        48.89        12.59 
TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L 
       13.02        26.37       302.07       152.35         6.44       131.51 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T 
       61.05        44.09       162.08        50.89        49.48         8.88 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NF TCGA-ER-A2NH TCGA-ER-A3ES 
      148.18       105.07        43.82        28.83        41.56       247.04 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A3YN 
       93.01        46.98        33.21        12.95       149.03        92.98 
TCGA-FR-A44A TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD 
      174.21        27.85        18.77        38.27        34.82        36.26 
TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
      104.42       216.92        48.59       228.59       202.65        20.91 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZE 
       28.08         7.79        27.72        48.85       357.37        46.45 
TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZQ 
        9.70        32.75        47.38        23.93        74.73       133.55 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 
       11.41       148.80        26.56        27.02        77.82        66.67 
TCGA-FS-A4F5 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV 
       28.73        34.03        54.41        80.68        55.59        13.51 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C9 TCGA-GN-A265 TCGA-GN-A26A 
       19.30         9.90        19.43        15.78        96.92        32.48 
TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A9SD TCGA-LH-A9QB 
       39.35        10.42        48.89        22.13        59.41       368.78 
TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 
        7.23         0.20         0.33         0.69       228.16        63.02 
TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1Q TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 
      121.08         4.01        69.07        42.08       219.16       105.04 
TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K6 TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ 
       24.03        49.05        17.95        58.98        70.52        63.22 
TCGA-WE-A8ZT TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-XV-AB01 TCGA-YD-A89C TCGA-YD-A9TA 
       11.80        12.16        40.41        13.25         6.90        49.18 
TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       37.94        14.43        27.58        96.99        15.98 

  DEL PEAK  8(5P15.31) MUTATED DEL PEAK  8(5P15.31) WILD-TYPE 
                          0.23                           0.20 
  DEL PEAK  8(5P15.31) MUTATED DEL PEAK  8(5P15.31) WILD-TYPE 
                        340.14                         369.93 
  DEL PEAK  8(5P15.31) MUTATED DEL PEAK  8(5P15.31) WILD-TYPE 
                         50.10                          54.02 
[1] "0.2 - 340.1 (50.1)" "0.2 - 369.9 (54.0)"
[1] "hr=" "1.2"
D28V3, continuous
                                vv
clus                             I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB
  DEL PEAK  8(5P15.31) MUTATED          4       3       6        3        4
  DEL PEAK  8(5P15.31) WILD-TYPE        9       4      23       15       24
                                vv
clus                             STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK  8(5P15.31) MUTATED          3         2         5         7
  DEL PEAK  8(5P15.31) WILD-TYPE       23        12        14         8
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK  8(5P15.31) MUTATED           7          4         11         11
  DEL PEAK  8(5P15.31) WILD-TYPE        32         11         24         43
                                vv
clus                             STAGE IV
  DEL PEAK  8(5P15.31) MUTATED          2
  DEL PEAK  8(5P15.31) WILD-TYPE       19
D28V4, multiclass
            clus
vv           DEL PEAK  8(5P15.31) MUTATED DEL PEAK  8(5P15.31) WILD-TYPE
  I/II NOS                              4                              9
  STAGE 0                               3                              4
  STAGE I                               6                             23
  STAGE IA                              3                             15
  STAGE IB                              4                             24
  STAGE II                              3                             23
  STAGE IIA                             2                             12
  STAGE IIB                             5                             14
  STAGE IIC                             7                              8
  STAGE III                             7                             32
  STAGE IIIA                            4                             11
  STAGE IIIB                           11                             24
  STAGE IIIC                           11                             43
  STAGE IV                              2                             19
[1] 14  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  DEL PEAK  8(5P15.31) MUTATED       9 16 14 19
  DEL PEAK  8(5P15.31) WILD-TYPE    55 57 67 48
D28V5, multiclass
       clus
vv      DEL PEAK  8(5P15.31) MUTATED DEL PEAK  8(5P15.31) WILD-TYPE
  T0+T1                            9                             55
  T2                              16                             57
  T3                              14                             67
  T4                              19                             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  N3
  DEL PEAK  8(5P15.31) MUTATED    35  19   7   8
  DEL PEAK  8(5P15.31) WILD-TYPE 142  46  32  37
D28V6, multiclass
    clus
vv   DEL PEAK  8(5P15.31) MUTATED DEL PEAK  8(5P15.31) WILD-TYPE
  N0                           35                            142
  N1                           19                             46
  N2                            7                             32
  N3                            8                             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"
D28V7, binary
                                cls
clus                               0   1
  DEL PEAK  8(5P15.31) MUTATED    68   2
  DEL PEAK  8(5P15.31) WILD-TYPE 251  20
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  8(5P15.31) MUTATED     68    2
  DEL PEAK  8(5P15.31) WILD-TYPE  251   20
   clus
vv  DEL PEAK  8(5P15.31) MUTATED DEL PEAK  8(5P15.31) WILD-TYPE
  0                           68                            251
  1                            2                             20
[1] 2 2
[1] FALSE
D28V8, binary
                                cls
clus                               0   1
  DEL PEAK  8(5P15.31) MUTATED    21  27
  DEL PEAK  8(5P15.31) WILD-TYPE 113  63
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  8(5P15.31) MUTATED     21   27
  DEL PEAK  8(5P15.31) WILD-TYPE  113   63
     clus
vv    DEL PEAK  8(5P15.31) MUTATED DEL PEAK  8(5P15.31) WILD-TYPE
  NO                            21                            113
  YES                           27                             63
[1] 2 2
[1] FALSE
D28V9, binary
                                cls
clus                               0   1
  DEL PEAK  8(5P15.31) MUTATED     6  73
  DEL PEAK  8(5P15.31) WILD-TYPE  41 247
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  8(5P15.31) MUTATED      6   73
  DEL PEAK  8(5P15.31) WILD-TYPE   41  247
     clus
vv    DEL PEAK  8(5P15.31) MUTATED DEL PEAK  8(5P15.31) WILD-TYPE
  NO                             6                             41
  YES                           73                            247
[1] 2 2
[1] FALSE
D28V10, continuous
D28V11, binary
                                cls
clus                               0   1
  DEL PEAK  8(5P15.31) MUTATED    35  44
  DEL PEAK  8(5P15.31) WILD-TYPE 103 185
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  8(5P15.31) MUTATED     35   44
  DEL PEAK  8(5P15.31) WILD-TYPE  103  185
        clus
vv       DEL PEAK  8(5P15.31) MUTATED DEL PEAK  8(5P15.31) WILD-TYPE
  FEMALE                           35                            103
  MALE                             44                            185
[1] 2 2
[1] FALSE
D28V12, binary
                                cls
clus                               0   1
  DEL PEAK  8(5P15.31) MUTATED    69  10
  DEL PEAK  8(5P15.31) WILD-TYPE 250  37
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  8(5P15.31) MUTATED     69   10
  DEL PEAK  8(5P15.31) WILD-TYPE  250   37
     clus
vv    DEL PEAK  8(5P15.31) MUTATED DEL PEAK  8(5P15.31) WILD-TYPE
  NO                            69                            250
  YES                           10                             37
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  8(5P15.31) MUTATED       3                         1    73
  DEL PEAK  8(5P15.31) WILD-TYPE     2                         0   280
D28V13, multiclass
                           clus
vv                          DEL PEAK  8(5P15.31) MUTATED
  ASIAN                                                3
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                               73
                           clus
vv                          DEL PEAK  8(5P15.31) WILD-TYPE
  ASIAN                                                  2
  BLACK OR AFRICAN AMERICAN                              0
  WHITE                                                280
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V14, binary
                                cls
clus                               0   1
  DEL PEAK  8(5P15.31) MUTATED     0  75
  DEL PEAK  8(5P15.31) WILD-TYPE   7 277
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  8(5P15.31) MUTATED      0   75
  DEL PEAK  8(5P15.31) WILD-TYPE    7  277
                        clus
vv                       DEL PEAK  8(5P15.31) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           75
                        clus
vv                       DEL PEAK  8(5P15.31) WILD-TYPE
  HISPANIC OR LATINO                                  7
  NOT HISPANIC OR LATINO                            277
[1] 2 2
[1] FALSE

Clustering(29) Variable = DEL PEAK  9(5Q12.1) MUTATION ANALYSIS
D29V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  9(5Q12.1) MUTATED   31 35
  DEL PEAK  9(5Q12.1) WILD-TYPE 97 89
  DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE 
                           66                           186 
  DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE 
                           35                            89 
$`DEL PEAK  9(5Q12.1) MUTATED`
TCGA-D3-A8GI TCGA-EE-A20H TCGA-EE-A2GD TCGA-3N-A9WD TCGA-D3-A1Q8 TCGA-D3-A2JL 
       13.41       166.75       269.03        12.99        19.04       171.58 
TCGA-D3-A2JO TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D9-A3Z1 
       66.08        58.06        40.01        42.05        45.70        15.02 
TCGA-D9-A4Z6 TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IC 
       18.44        69.21        76.34       110.53        60.10        58.85 
TCGA-DA-A3F5 TCGA-DA-A95Y TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A29C TCGA-EE-A29D 
      225.11        14.14        13.15        24.89        76.14        12.99 
TCGA-EE-A29E TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A2A2 TCGA-EE-A2GB TCGA-EE-A2GE 
        0.26        47.74        27.16        30.02        26.14        12.95 
TCGA-EE-A2GH TCGA-EE-A2GM TCGA-EE-A2GR TCGA-EE-A2MJ TCGA-EE-A2MM TCGA-EE-A2MP 
      201.60        18.35         0.20        63.25       145.45       227.01 
TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3J7 TCGA-EE-A3JB TCGA-ER-A199 
      122.73         4.41        54.51        45.90       168.85         7.82 
TCGA-ER-A19B TCGA-ER-A19H TCGA-ER-A2ND TCGA-ER-A2NE TCGA-FR-A44A TCGA-FR-A69P 
       53.29       150.12         4.70        16.87       174.21         4.14 
TCGA-FS-A1ZQ TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F8 TCGA-GF-A6C8 
      130.95        35.28        23.21         5.29       173.19         1.91 
TCGA-GN-A262 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A4U3 TCGA-GN-A8LK TCGA-LH-A9QB 
       53.29        17.06        42.48       120.53        43.23        85.05 
TCGA-OD-A75X TCGA-W3-A825 TCGA-W3-AA1R TCGA-W3-AA1V TCGA-WE-A8ZY TCGA-WE-AAA4 
      297.01         1.97        79.99         8.09        48.39        24.99 

$`DEL PEAK  9(5Q12.1) WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A2GO 
        9.76        62.07        38.76        33.24        31.96        52.90 
TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-FR-A729 TCGA-FW-A3R5 TCGA-WE-A8K5 
      134.40        27.35        19.04       216.43        36.95        52.73 
TCGA-WE-AAA3 TCGA-3N-A9WC TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
        7.40        60.46        14.83         8.42        15.72        31.89 
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 
      110.93        49.35       133.25        76.41        62.60        25.64 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JG 
       45.99        62.86        15.75       168.00        86.30       107.61 
TCGA-D3-A2JH TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3CF 
       36.30        64.83        43.53       140.98        59.70        24.53 
TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51J 
        9.34        90.21        23.67       173.85        30.67       144.46 
TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D3-A8GC 
       31.76        62.70        11.34       177.86       124.08        78.21 
TCGA-D3-A8GD TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GP 
       23.61       179.97       120.00        69.53        70.62       135.12 
TCGA-D3-A8GR TCGA-D9-A1X3 TCGA-D9-A3Z3 TCGA-D9-A6EG TCGA-DA-A1HY TCGA-DA-A1I1 
       36.53        10.78        16.90        22.85       138.67        68.68 
TCGA-DA-A1I2 TCGA-DA-A1IA TCGA-DA-A3F2 TCGA-DA-A3F8 TCGA-DA-A95V TCGA-DA-A95W 
      150.61        64.83        30.44         8.71        72.10         0.76 
TCGA-DA-A95X TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A6L9 
       65.03        12.30         3.91        16.41        52.41        18.21 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29B 
       20.38         0.00        26.24        75.55        79.20        75.22 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 
       44.28        47.41        61.12       346.49       185.19       115.43 
TCGA-EE-A2A6 TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GP 
       77.98        68.65        10.62        32.48        93.63         0.76 
TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
       71.31        81.99       103.13        15.25         5.75        23.77 
TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MS 
      209.79        94.19       171.85        89.26       104.78       143.93 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AF TCGA-EE-A3J3 
       23.51        53.26       124.31        64.04         6.28        67.89 
TCGA-EE-A3J4 TCGA-EE-A3J8 TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 
      111.85         3.35        19.86       135.98        34.45        10.49 
TCGA-ER-A19A TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19L TCGA-ER-A19M 
        4.54        39.81        11.47       184.60        99.06        59.84 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 
       42.51       120.76        49.71        47.18       146.63        73.05 
TCGA-ER-A2NC TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       22.36        10.19        28.67       173.29        68.52        15.48 
TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FR-A8YC 
       32.05        74.47         4.50        26.20         5.65        10.06 
TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZC 
      171.78        49.74       195.98         8.35        27.62       312.07 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZS 
       32.78        43.92         7.82        36.33        78.61       136.27 
TCGA-FS-A1ZU TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F9 TCGA-FS-A4FD 
        4.47         3.06        30.90        66.67        13.28        80.68 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GN-A264 
       55.59        11.54        19.30         9.90        18.25       117.93 
TCGA-GN-A265 TCGA-GN-A26A TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-GN-A9SD TCGA-QB-A6FS 
       96.92         7.59        34.49        46.92        59.41         7.23 
TCGA-RP-A690 TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A828 TCGA-W3-AA1Q TCGA-W3-AA1W 
        0.20         0.33       174.12       120.07        44.05       185.13 
TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ 
       92.84        47.54        65.42        12.69        21.90        62.89 
TCGA-WE-A8ZT TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-XV-AB01 TCGA-YG-AA3O TCGA-Z2-AA3S 
       10.95         1.94        37.32         6.61        28.21        91.23 

  DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE 
                          0.2                           0.0 
  DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE 
                       297.01                        346.49 
  DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE 
                       44.465                        47.295 
[1] "0.2 - 297.0 (44.5)" "0.0 - 346.5 (47.3)"
[1] "hr=" "1.1"
D29V2, survival
                               sevent
clus2                             0   1
  DEL PEAK  9(5Q12.1) MUTATED    41  52
  DEL PEAK  9(5Q12.1) WILD-TYPE 125 140
  DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE 
                           93                           265 
  DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE 
                           52                           140 
$`DEL PEAK  9(5Q12.1) MUTATED`
TCGA-D3-A8GI TCGA-EE-A20H TCGA-EE-A2GD TCGA-QB-AA9O TCGA-3N-A9WD TCGA-D3-A1Q8 
       58.52       168.26       340.14        18.05        12.99        28.08 
TCGA-D3-A1Q9 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JO TCGA-D3-A3C6 
       31.59        11.87        12.10       171.58        66.08        58.06 
TCGA-D3-A3CC TCGA-D3-A3MV TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D9-A148 
       86.93        45.30       125.79       135.75       137.92       151.53 
TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A4Z6 TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW 
        7.10        15.39        18.44        77.56        76.57        36.03 
TCGA-DA-A1I0 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IC TCGA-DA-A3F5 TCGA-DA-A95Y 
       20.38       135.02        88.87        68.09       225.96        14.14 
TCGA-EB-A5UL TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A185 TCGA-EE-A29C TCGA-EE-A29D 
       29.29        29.82        27.22         4.96        78.97        13.97 
TCGA-EE-A29E TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29V TCGA-EE-A2A2 TCGA-EE-A2GB 
       63.78        56.84        56.42        25.87        59.64        59.28 
TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GM TCGA-EE-A2GR 
       67.43       173.79       220.24        48.72        75.48        42.77 
TCGA-EE-A2MJ TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE 
       96.23       167.90       248.65       122.73        28.77        54.51 
TCGA-EE-A3AH TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3JB TCGA-ER-A199 TCGA-ER-A19B 
      138.81        36.95        64.08       201.80         9.17        98.40 
TCGA-ER-A19H TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NH TCGA-FR-A44A TCGA-FR-A69P 
      152.35        23.34        20.15        41.56       174.21        15.72 
TCGA-FS-A1YX TCGA-FS-A1ZK TCGA-FS-A1ZQ TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A1ZY 
       48.59        23.93       133.55        53.16        49.48        27.09 
TCGA-FS-A4F2 TCGA-FS-A4F8 TCGA-FS-A4FB TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A266 
       50.14       174.84        26.73         2.04       139.89        10.13 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A4U3 TCGA-GN-A8LK TCGA-HR-A2OG TCGA-HR-A2OH 
       64.44        62.79       121.91        50.10         0.23        65.88 
TCGA-LH-A9QB TCGA-OD-A75X TCGA-W3-A825 TCGA-W3-AA1R TCGA-W3-AA1V TCGA-WE-A8ZX 
      368.78       297.90        63.02       111.09        42.08        35.80 
TCGA-WE-A8ZY TCGA-WE-AAA4 TCGA-YD-A9TA 
       49.51        24.99        49.18 

$`DEL PEAK  9(5Q12.1) WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SG TCGA-EB-A5SH 
       27.65        62.07        46.32        13.87        68.25        54.02 
TCGA-EE-A180 TCGA-EE-A184 TCGA-EE-A29L TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD 
       94.98        68.15         2.60       126.81       134.40        27.35 
TCGA-ER-A193 TCGA-ER-A198 TCGA-FR-A729 TCGA-FS-A1ZF TCGA-FW-A3R5 TCGA-WE-A8K5 
       31.40        50.76       220.80        15.45        36.95        61.15 
TCGA-WE-AAA3 TCGA-3N-A9WB TCGA-3N-A9WC TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 
       21.40        17.03        66.48        14.93        16.57        16.67 
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1QA TCGA-D3-A1QB 
      112.04       112.57        71.80       133.25        90.90        95.74 
TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB 
       43.43       103.10        65.49        23.77       115.53       168.00 
TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3BZ 
       86.76       113.52        42.08        66.48        59.57       130.72 
TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR 
       46.98       166.52        60.23        24.53         9.34       103.59 
TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K 
       39.75       174.84        55.73        56.35       145.12        32.94 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU 
       22.62        63.81        26.89       178.32        18.18       125.19 
TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GK 
       30.84        79.59        23.61        26.43       241.38       170.20 
TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR 
       89.13       107.15       161.00       152.75        29.06       129.63 
TCGA-D3-A8GS TCGA-D3-A8GV TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1X3 TCGA-D9-A3Z3 
      117.17       167.70        54.67         3.65        18.12        22.29 
TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EG TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 
        9.90        25.18        22.95       144.89       222.51       176.55 
TCGA-DA-A1I4 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F3 
       35.93        53.92        65.92        40.60        33.93        10.49 
TCGA-DA-A3F8 TCGA-DA-A95V TCGA-DA-A95W TCGA-DA-A95X TCGA-DA-A95Z TCGA-EB-A44Q 
       43.36        72.10        37.35        73.94        13.02        13.87 
TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17Z 
       10.36        20.35        58.92         7.04        36.46         8.65 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F 
       33.73        14.70        26.89       133.81       151.27        91.56 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29N 
       13.55        63.35        85.08        72.07        64.64        18.61 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A29X 
       66.74        14.47        61.28       369.93       195.02        17.92 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GJ TCGA-EE-A2GK 
       46.82       115.96        39.29        86.14       107.38        54.74 
TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU 
       79.66       102.12        13.91        81.21        44.88        94.82 
TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD 
       21.67       129.27        28.83        19.76        61.51        47.28 
TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK 
      103.27       268.73       103.20        16.96       204.66       180.39 
TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU 
      216.66        47.54        43.23       162.48        71.21        53.26 
TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J4 
      124.31        64.04        13.81        41.59       172.18       127.20 
TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 
       34.32        53.19        51.35       134.33       152.81        35.44 
TCGA-ER-A197 TCGA-ER-A19A TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F 
       13.94        77.75        48.89        12.59        13.02        26.37 
TCGA-ER-A19G TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P 
      302.07         6.44       131.51        61.05        44.09       162.08 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
       50.89        49.48         8.88       148.18       105.07        43.82 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL 
       28.83        48.99       247.04        93.01        46.98        33.21 
TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA 
       12.95       149.03        92.98        27.85        18.77        38.27 
TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 
       34.82        36.26       104.42       216.92       228.59       202.65 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC 
       20.91        28.08         7.79        27.72        48.85       357.37 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZM 
       53.52        46.45         9.70        32.75        47.38       101.26 
TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZZ TCGA-FS-A4F0 
       74.73        11.41       148.80        26.56        27.02        77.82 
TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 
       66.67        28.73        34.03        54.41        80.68        17.46 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C9 
       55.59        13.51        19.30         9.90        19.43        15.78 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U4 TCGA-GN-A4U7 
      117.93        96.92        32.48        48.00        39.35        10.42 
TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LL TCGA-GN-A9SD TCGA-QB-A6FS TCGA-RP-A690 
       48.89        22.13        21.37        59.41         7.23         0.20 
TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1Q 
        0.33         0.69       228.16       121.08         4.01        69.07 
TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K6 TCGA-WE-A8ZM 
      219.16       105.04        24.03        49.05        17.95       101.33 
TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-AA9Y TCGA-WE-AAA0 
       58.98        70.52        63.22        11.80        12.16        40.41 
TCGA-XV-AB01 TCGA-YD-A89C TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S 
       13.25         6.90        37.94        14.43        27.58        96.99 
TCGA-Z2-AA3V 
       15.98 

  DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE 
                         0.23                          0.20 
  DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE 
                       368.78                        369.93 
  DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE 
                        56.84                         49.48 
[1] "0.2 - 368.8 (56.8)" "0.2 - 369.9 (49.5)"
[1] "hr=" "1.1"
D29V3, continuous
                               vv
clus                            I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB
  DEL PEAK  9(5Q12.1) MUTATED          4       2      10        4        5
  DEL PEAK  9(5Q12.1) WILD-TYPE        9       5      19       14       23
                               vv
clus                            STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK  9(5Q12.1) MUTATED          8         1         5         5
  DEL PEAK  9(5Q12.1) WILD-TYPE       18        13        14        10
                               vv
clus                            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK  9(5Q12.1) MUTATED           9          3         12         15
  DEL PEAK  9(5Q12.1) WILD-TYPE        30         12         23         39
                               vv
clus                            STAGE IV
  DEL PEAK  9(5Q12.1) MUTATED          3
  DEL PEAK  9(5Q12.1) WILD-TYPE       18
D29V4, multiclass
            clus
vv           DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE
  I/II NOS                             4                             9
  STAGE 0                              2                             5
  STAGE I                             10                            19
  STAGE IA                             4                            14
  STAGE IB                             5                            23
  STAGE II                             8                            18
  STAGE IIA                            1                            13
  STAGE IIB                            5                            14
  STAGE IIC                            5                            10
  STAGE III                            9                            30
  STAGE IIIA                           3                            12
  STAGE IIIB                          12                            23
  STAGE IIIC                          15                            39
  STAGE IV                             3                            18
[1] 14  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3 T4
  DEL PEAK  9(5Q12.1) MUTATED      16 19 20 20
  DEL PEAK  9(5Q12.1) WILD-TYPE    48 54 61 47
D29V5, multiclass
       clus
vv      DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE
  T0+T1                          16                            48
  T2                             19                            54
  T3                             20                            61
  T4                             20                            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  N3
  DEL PEAK  9(5Q12.1) MUTATED    45  21   8  12
  DEL PEAK  9(5Q12.1) WILD-TYPE 132  44  31  33
D29V6, multiclass
    clus
vv   DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE
  N0                          45                           132
  N1                          21                            44
  N2                           8                            31
  N3                          12                            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"
D29V7, binary
                               cls
clus                              0   1
  DEL PEAK  9(5Q12.1) MUTATED    85   4
  DEL PEAK  9(5Q12.1) WILD-TYPE 234  18
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(5Q12.1) MUTATED     85    4
  DEL PEAK  9(5Q12.1) WILD-TYPE  234   18
   clus
vv  DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE
  0                          85                           234
  1                           4                            18
[1] 2 2
[1] FALSE
D29V8, binary
                               cls
clus                              0   1
  DEL PEAK  9(5Q12.1) MUTATED    31  25
  DEL PEAK  9(5Q12.1) WILD-TYPE 103  65
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(5Q12.1) MUTATED     31   25
  DEL PEAK  9(5Q12.1) WILD-TYPE  103   65
     clus
vv    DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE
  NO                           31                           103
  YES                          25                            65
[1] 2 2
[1] FALSE
D29V9, binary
                               cls
clus                              0   1
  DEL PEAK  9(5Q12.1) MUTATED     9  88
  DEL PEAK  9(5Q12.1) WILD-TYPE  38 232
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(5Q12.1) MUTATED      9   88
  DEL PEAK  9(5Q12.1) WILD-TYPE   38  232
     clus
vv    DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE
  NO                            9                            38
  YES                          88                           232
[1] 2 2
[1] FALSE
D29V10, continuous
D29V11, binary
                               cls
clus                              0   1
  DEL PEAK  9(5Q12.1) MUTATED    36  61
  DEL PEAK  9(5Q12.1) WILD-TYPE 102 168
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(5Q12.1) MUTATED     36   61
  DEL PEAK  9(5Q12.1) WILD-TYPE  102  168
        clus
vv       DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE
  FEMALE                          36                           102
  MALE                            61                           168
[1] 2 2
[1] FALSE
D29V12, binary
                               cls
clus                              0   1
  DEL PEAK  9(5Q12.1) MUTATED    80  17
  DEL PEAK  9(5Q12.1) WILD-TYPE 239  30
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(5Q12.1) MUTATED     80   17
  DEL PEAK  9(5Q12.1) WILD-TYPE  239   30
     clus
vv    DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE
  NO                           80                           239
  YES                          17                            30
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  9(5Q12.1) MUTATED       1                         0    94
  DEL PEAK  9(5Q12.1) WILD-TYPE     4                         1   259
D29V13, multiclass
                           clus
vv                          DEL PEAK  9(5Q12.1) MUTATED
  ASIAN                                               1
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                              94
                           clus
vv                          DEL PEAK  9(5Q12.1) WILD-TYPE
  ASIAN                                                 4
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                               259
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V14, binary
                               cls
clus                              0   1
  DEL PEAK  9(5Q12.1) MUTATED     0  93
  DEL PEAK  9(5Q12.1) WILD-TYPE   7 259
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(5Q12.1) MUTATED      0   93
  DEL PEAK  9(5Q12.1) WILD-TYPE    7  259
                        clus
vv                       DEL PEAK  9(5Q12.1) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                          93
                        clus
vv                       DEL PEAK  9(5Q12.1) WILD-TYPE
  HISPANIC OR LATINO                                 7
  NOT HISPANIC OR LATINO                           259
[1] 2 2
[1] FALSE

Clustering(30) Variable = DEL PEAK 10(5Q31.3) MUTATION ANALYSIS
D30V1, survival
                               sevent
clus2                            0  1
  DEL PEAK 10(5Q31.3) MUTATED   40 47
  DEL PEAK 10(5Q31.3) WILD-TYPE 88 77
  DEL PEAK 10(5Q31.3) MUTATED DEL PEAK 10(5Q31.3) WILD-TYPE 
                           87                           165 
  DEL PEAK 10(5Q31.3) MUTATED DEL PEAK 10(5Q31.3) WILD-TYPE 
                           47                            77 
$`DEL PEAK 10(5Q31.3) MUTATED`
TCGA-D3-A8GI TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GD TCGA-EE-A2MR TCGA-3N-A9WD 
       13.41        31.96       166.75       269.03       134.40        12.99 
TCGA-BF-AAP0 TCGA-D3-A1Q3 TCGA-D3-A1Q8 TCGA-D3-A2JG TCGA-D3-A2JL TCGA-D3-A2JO 
       14.83        15.72        19.04       107.61       171.58        66.08 
TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A8GJ 
       58.06        40.01        24.53        42.05        45.70       179.97 
TCGA-D3-A8GM TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A4Z6 TCGA-D9-A6EC TCGA-DA-A1HV 
       70.62        10.78        15.02        18.44        69.21        76.34 
TCGA-DA-A1HY TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A3F5 TCGA-DA-A95V TCGA-DA-A95Y 
      138.67       110.53        60.10       225.11        72.10        14.14 
TCGA-EB-A5KH TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G 
       16.41        13.15        24.89        76.14         0.26        44.28 
TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A2A2 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH 
       47.74        27.16        30.02        26.14        12.95       201.60 
TCGA-EE-A2GJ TCGA-EE-A2GM TCGA-EE-A2GR TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MG 
       68.65        18.35         0.20       103.13        15.25        94.19 
TCGA-EE-A2MJ TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE 
       63.25       145.45       227.01       122.73         4.41        54.51 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A199 
       45.90         3.35       168.85       135.98        34.45         7.82 
TCGA-ER-A19B TCGA-ER-A19H TCGA-ER-A19Q TCGA-ER-A2ND TCGA-ER-A2NE TCGA-FR-A44A 
       53.29       150.12        49.71         4.70        16.87       174.21 
TCGA-FR-A69P TCGA-FS-A1ZC TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZT TCGA-FS-A1ZW 
        4.14       312.07        78.61       130.95        35.28        23.21 
TCGA-FS-A4F0 TCGA-FS-A4F8 TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A267 TCGA-GN-A268 
       30.90       173.19         1.91        53.29        17.06        42.48 
TCGA-GN-A4U3 TCGA-GN-A8LK TCGA-OD-A75X TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1R 
      120.53        43.23       297.01         1.97       120.07        79.99 
TCGA-WE-A8ZM TCGA-WE-A8ZY TCGA-WE-AAA4 
       65.42        48.39        24.99 

$`DEL PEAK 10(5Q31.3) WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A2GO TCGA-EE-A3JD 
        9.76        62.07        38.76        33.24        52.90        27.35 
TCGA-ER-A193 TCGA-FR-A729 TCGA-FW-A3R5 TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-3N-A9WC 
       19.04       216.43        36.95        52.73         7.40        60.46 
TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1QA 
        8.42        31.89       110.93        49.35       133.25        76.41 
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB 
       62.60        25.64        45.99        62.86        15.75       168.00 
TCGA-D3-A2JC TCGA-D3-A2JH TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3CB TCGA-D3-A3CE 
       86.30        36.30        64.83        43.53       140.98        59.70 
TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51J 
        9.34        90.21        23.67       173.85        30.67       144.46 
TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D3-A8GC 
       31.76        62.70        11.34       177.86       124.08        78.21 
TCGA-D3-A8GD TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GP TCGA-D3-A8GR TCGA-D9-A3Z3 
       23.61       120.00        69.53       135.12        36.53        16.90 
TCGA-D9-A6EG TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 
       22.85        68.68       150.61        64.83        58.85        30.44 
TCGA-DA-A3F8 TCGA-DA-A95W TCGA-DA-A95X TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5UN 
        8.71         0.76        65.03        12.30         3.91        52.41 
TCGA-EB-A6L9 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A20F 
       18.21        20.38         0.00        26.24        75.55        79.20 
TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29H TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W 
       75.22        12.99        47.41        61.12       346.49       185.19 
TCGA-EE-A2A1 TCGA-EE-A2A6 TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GP 
      115.43        77.98        10.62        32.48        93.63         0.76 
TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MI 
       71.31        81.99         5.75        23.77       209.79       171.85 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA 
       89.26       104.78       143.93        23.51        53.26       124.31 
TCGA-EE-A3AC TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3JH TCGA-ER-A197 
       64.04         6.28        67.89       111.85        19.86        10.49 
TCGA-ER-A19A TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19L TCGA-ER-A19M 
        4.54        39.81        11.47       184.60        99.06        59.84 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
       42.51       120.76        47.18       146.63        73.05        22.36 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL 
       10.19        28.67       173.29        68.52        15.48        32.05 
TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FS-A1YW 
       74.47         4.50        26.20         5.65        10.06       171.78 
TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZD TCGA-FS-A1ZE 
       49.74       195.98         8.35        27.62        32.78        43.92 
TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A1ZZ 
        7.82        36.33       136.27         4.47         5.29         3.06 
TCGA-FS-A4F4 TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
       66.67        13.28        80.68        55.59        11.54        19.30 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A26A TCGA-GN-A4U4 
        9.90        18.25       117.93        96.92         7.59        34.49 
TCGA-GN-A4U8 TCGA-GN-A9SD TCGA-LH-A9QB TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 
       46.92        59.41        85.05         7.23         0.20         0.33 
TCGA-W3-A824 TCGA-W3-AA1Q TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 
      174.12        44.05         8.09       185.13        92.84        47.54 
TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-AA9Y TCGA-WE-AAA0 
       12.69        21.90        62.89        10.95         1.94        37.32 
TCGA-XV-AB01 TCGA-YG-AA3O TCGA-Z2-AA3S 
        6.61        28.21        91.23 

  DEL PEAK 10(5Q31.3) MUTATED DEL PEAK 10(5Q31.3) WILD-TYPE 
                          0.2                           0.0 
  DEL PEAK 10(5Q31.3) MUTATED DEL PEAK 10(5Q31.3) WILD-TYPE 
                       312.07                        346.49 
  DEL PEAK 10(5Q31.3) MUTATED DEL PEAK 10(5Q31.3) WILD-TYPE 
                        47.74                         45.99 
[1] "0.2 - 312.1 (47.7)" "0.0 - 346.5 (46.0)"
[1] "hr=" "1"  
D30V2, survival
                               sevent
clus2                             0   1
  DEL PEAK 10(5Q31.3) MUTATED    55  72
  DEL PEAK 10(5Q31.3) WILD-TYPE 111 120
  DEL PEAK 10(5Q31.3) MUTATED DEL PEAK 10(5Q31.3) WILD-TYPE 
                          127                           231 
  DEL PEAK 10(5Q31.3) MUTATED DEL PEAK 10(5Q31.3) WILD-TYPE 
                           72                           120 
$`DEL PEAK 10(5Q31.3) MUTATED`
TCGA-D3-A8GI TCGA-EB-A5SH TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GD TCGA-EE-A2MR 
       58.52        54.02        94.98       168.26       340.14       134.40 
TCGA-FS-A1ZF TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q3 TCGA-D3-A1Q8 TCGA-D3-A1Q9 
       15.45        12.99        14.93        16.67        28.08        31.59 
TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JO TCGA-D3-A3C6 
       11.87       113.52        12.10       171.58        66.08        58.06 
TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3MV TCGA-D3-A51N TCGA-D3-A5GL TCGA-D3-A5GN 
       86.93        24.53        45.30        22.62       125.79       135.75 
TCGA-D3-A5GO TCGA-D3-A8GJ TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D9-A148 TCGA-D9-A1JX 
      137.92       241.38       107.15       161.00       151.53         7.10 
TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-DA-A1HV 
       18.12        15.39        18.44         9.90        77.56        76.57 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
       36.03       144.89        20.38       135.02        88.87        53.92 
TCGA-DA-A3F5 TCGA-DA-A95V TCGA-DA-A95Y TCGA-EB-A5KH TCGA-EB-A5UL TCGA-EE-A17X 
      225.96        72.10        14.14        20.35        29.29        29.82 
TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A185 TCGA-EE-A20I TCGA-EE-A29C TCGA-EE-A29E 
       27.22         8.65         4.96        13.55        78.97        63.78 
TCGA-EE-A29G TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29X 
       72.07        56.84        56.42        61.28        25.87        17.92 
TCGA-EE-A2A0 TCGA-EE-A2A2 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GH 
       46.82        59.64        59.28        67.43       173.79       220.24 
TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GM TCGA-EE-A2GR TCGA-EE-A2GT TCGA-EE-A2M6 
       48.72       107.38        75.48        42.77        44.88       129.27 
TCGA-EE-A2M7 TCGA-EE-A2MG TCGA-EE-A2MJ TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MQ 
       28.83       103.20        96.23       167.90       248.65        43.23 
TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AH TCGA-EE-A3J5 TCGA-EE-A3J7 
      122.73        28.77        54.51       138.81        36.95        64.08 
TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A199 TCGA-ER-A19B 
       34.32       201.80       152.81        35.44         9.17        98.40 
TCGA-ER-A19H TCGA-ER-A19Q TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NH TCGA-FR-A44A 
      152.35        50.89        23.34        20.15        41.56       174.21 
TCGA-FR-A69P TCGA-FS-A1YX TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZM TCGA-FS-A1ZQ 
       15.72        48.59        48.85       357.37       101.26       133.55 
TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A4F0 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4FB 
       53.16        49.48        77.82        28.73       174.84        26.73 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A4U3 
        2.04       139.89        10.13        64.44        62.79       121.91 
TCGA-GN-A4U7 TCGA-GN-A8LK TCGA-HR-A2OG TCGA-HR-A2OH TCGA-OD-A75X TCGA-W3-A825 
       10.42        50.10         0.23        65.88       297.90        63.02 
TCGA-W3-A828 TCGA-W3-AA1R TCGA-WE-A8ZM TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AAA4 
      121.08       111.09       101.33        35.80        49.51        24.99 
TCGA-YD-A9TA 
       49.18 

$`DEL PEAK 10(5Q31.3) WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SG TCGA-EE-A184 
       27.65        62.07        46.32        13.87        68.25        68.15 
TCGA-EE-A29L TCGA-EE-A2GO TCGA-EE-A3JD TCGA-ER-A193 TCGA-ER-A198 TCGA-FR-A729 
        2.60       126.81        27.35        31.40        50.76       220.80 
TCGA-FW-A3R5 TCGA-QB-AA9O TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-3N-A9WB TCGA-3N-A9WC 
       36.95        18.05        61.15        21.40        17.03        66.48 
TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1QA 
       16.57       112.04       112.57        71.80       133.25        90.90 
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA 
       95.74        43.43       103.10        65.49        23.77       115.53 
TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JH TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3BZ 
      168.00        86.76        42.08        66.48        59.57       130.72 
TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU 
       46.98       166.52        60.23         9.34       103.59        39.75 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R 
      174.84        55.73        56.35       145.12        32.94        63.81 
TCGA-D3-A51T TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GC 
       26.89       178.32        18.18       125.19        30.84        79.59 
TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GP TCGA-D3-A8GQ 
       23.61        26.43       170.20        89.13       152.75        29.06 
TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D3-A8GV TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A3Z3 
      129.63       117.17       167.70        54.67         3.65        22.29 
TCGA-D9-A6EA TCGA-D9-A6EG TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1IA 
       25.18        22.95       222.51       176.55        35.93        65.92 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-DA-A95W 
       40.60        68.09        33.93        10.49        43.36        37.35 
TCGA-DA-A95X TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5UN TCGA-EB-A5VV 
       73.94        13.02        13.87        10.36        58.92         7.04 
TCGA-EB-A6L9 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20C 
       36.46        33.73        14.70        26.89       133.81       151.27 
TCGA-EE-A20F TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29H TCGA-EE-A29N 
       91.56        63.35        85.08        13.97        64.64        18.61 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A5 
       66.74        14.47       369.93       195.02       115.96        39.29 
TCGA-EE-A2A6 TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GS 
       86.14        54.74        79.66       102.12        13.91        81.21 
TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME 
       94.82        21.67        19.76        61.51        47.28       103.27 
TCGA-EE-A2MF TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MN 
      268.73        16.96       204.66       180.39       216.66        47.54 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AF 
      162.48        71.21        53.26       124.31        64.04        13.81 
TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3JA TCGA-EE-A3JE TCGA-EE-A3JH 
       41.59       172.18       127.20        53.19        51.35       134.33 
TCGA-ER-A197 TCGA-ER-A19A TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F 
       13.94        77.75        48.89        12.59        13.02        26.37 
TCGA-ER-A19G TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P 
      302.07         6.44       131.51        61.05        44.09       162.08 
TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NF 
       49.48         8.88       148.18       105.07        43.82        28.83 
TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K 
       48.99       247.04        93.01        46.98        33.21        12.95 
TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC 
      149.03        92.98        27.85        18.77        38.27        34.82 
TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
       36.26       104.42       216.92       228.59       202.65        20.91 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG 
       28.08         7.79        27.72        53.52        46.45         9.70 
TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZS 
       32.75        47.38        23.93        74.73        11.41       148.80 
TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F9 
       26.56        27.09        27.02        50.14        66.67        34.03 
TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
       54.41        80.68        17.46        55.59        13.51        19.30 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C9 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A26A 
        9.90        19.43        15.78       117.93        96.92        32.48 
TCGA-GN-A26D TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LL TCGA-GN-A9SD 
       48.00        39.35        48.89        22.13        21.37        59.41 
TCGA-LH-A9QB TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 
      368.78         7.23         0.20         0.33         0.69       228.16 
TCGA-W3-AA1O TCGA-W3-AA1Q TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8JZ 
        4.01        69.07        42.08       219.16       105.04        24.03 
TCGA-WE-A8K1 TCGA-WE-A8K6 TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT 
       49.05        17.95        58.98        70.52        63.22        11.80 
TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-XV-AB01 TCGA-YD-A89C TCGA-YG-AA3O TCGA-YG-AA3P 
       12.16        40.41        13.25         6.90        37.94        14.43 
TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       27.58        96.99        15.98 

  DEL PEAK 10(5Q31.3) MUTATED DEL PEAK 10(5Q31.3) WILD-TYPE 
                         0.23                          0.20 
  DEL PEAK 10(5Q31.3) MUTATED DEL PEAK 10(5Q31.3) WILD-TYPE 
                       357.37                        369.93 
  DEL PEAK 10(5Q31.3) MUTATED DEL PEAK 10(5Q31.3) WILD-TYPE 
                        56.84                         48.99 
[1] "0.2 - 357.4 (56.8)" "0.2 - 369.9 (49.0)"
[1] "hr=" "1"  
D30V3, continuous
                               vv
clus                            I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB
  DEL PEAK 10(5Q31.3) MUTATED          6       2      14        5        7
  DEL PEAK 10(5Q31.3) WILD-TYPE        7       5      15       13       21
                               vv
clus                            STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK 10(5Q31.3) MUTATED         10         4         7         8
  DEL PEAK 10(5Q31.3) WILD-TYPE       16        10        12         7
                               vv
clus                            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 10(5Q31.3) MUTATED          14          8         12         15
  DEL PEAK 10(5Q31.3) WILD-TYPE        25          7         23         39
                               vv
clus                            STAGE IV
  DEL PEAK 10(5Q31.3) MUTATED          6
  DEL PEAK 10(5Q31.3) WILD-TYPE       15
D30V4, multiclass
            clus
vv           DEL PEAK 10(5Q31.3) MUTATED DEL PEAK 10(5Q31.3) WILD-TYPE
  I/II NOS                             6                             7
  STAGE 0                              2                             5
  STAGE I                             14                            15
  STAGE IA                             5                            13
  STAGE IB                             7                            21
  STAGE II                            10                            16
  STAGE IIA                            4                            10
  STAGE IIB                            7                            12
  STAGE IIC                            8                             7
  STAGE III                           14                            25
  STAGE IIIA                           8                             7
  STAGE IIIB                          12                            23
  STAGE IIIC                          15                            39
  STAGE IV                             6                            15
[1] 14  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3 T4
  DEL PEAK 10(5Q31.3) MUTATED      20 27 27 31
  DEL PEAK 10(5Q31.3) WILD-TYPE    44 46 54 36
D30V5, multiclass
       clus
vv      DEL PEAK 10(5Q31.3) MUTATED DEL PEAK 10(5Q31.3) WILD-TYPE
  T0+T1                          20                            44
  T2                             27                            46
  T3                             27                            54
  T4                             31                            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  N3
  DEL PEAK 10(5Q31.3) MUTATED    69  26  11  14
  DEL PEAK 10(5Q31.3) WILD-TYPE 108  39  28  31
D30V6, multiclass
    clus
vv   DEL PEAK 10(5Q31.3) MUTATED DEL PEAK 10(5Q31.3) WILD-TYPE
  N0                          69                           108
  N1                          26                            39
  N2                          11                            28
  N3                          14                            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"
D30V7, binary
                               cls
clus                              0   1
  DEL PEAK 10(5Q31.3) MUTATED   115   7
  DEL PEAK 10(5Q31.3) WILD-TYPE 204  15
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(5Q31.3) MUTATED    115    7
  DEL PEAK 10(5Q31.3) WILD-TYPE  204   15
   clus
vv  DEL PEAK 10(5Q31.3) MUTATED DEL PEAK 10(5Q31.3) WILD-TYPE
  0                         115                           204
  1                           7                            15
[1] 2 2
[1] FALSE
D30V8, binary
                               cls
clus                             0  1
  DEL PEAK 10(5Q31.3) MUTATED   49 32
  DEL PEAK 10(5Q31.3) WILD-TYPE 85 58
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(5Q31.3) MUTATED     49   32
  DEL PEAK 10(5Q31.3) WILD-TYPE   85   58
     clus
vv    DEL PEAK 10(5Q31.3) MUTATED DEL PEAK 10(5Q31.3) WILD-TYPE
  NO                           49                            85
  YES                          32                            58
[1] 2 2
[1] FALSE
D30V9, binary
                               cls
clus                              0   1
  DEL PEAK 10(5Q31.3) MUTATED    10 121
  DEL PEAK 10(5Q31.3) WILD-TYPE  37 199
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(5Q31.3) MUTATED     10  121
  DEL PEAK 10(5Q31.3) WILD-TYPE   37  199
     clus
vv    DEL PEAK 10(5Q31.3) MUTATED DEL PEAK 10(5Q31.3) WILD-TYPE
  NO                           10                            37
  YES                         121                           199
[1] 2 2
[1] FALSE
D30V10, continuous
D30V11, binary
                               cls
clus                              0   1
  DEL PEAK 10(5Q31.3) MUTATED    51  80
  DEL PEAK 10(5Q31.3) WILD-TYPE  87 149
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(5Q31.3) MUTATED     51   80
  DEL PEAK 10(5Q31.3) WILD-TYPE   87  149
        clus
vv       DEL PEAK 10(5Q31.3) MUTATED DEL PEAK 10(5Q31.3) WILD-TYPE
  FEMALE                          51                            87
  MALE                            80                           149
[1] 2 2
[1] FALSE
D30V12, binary
                               cls
clus                              0   1
  DEL PEAK 10(5Q31.3) MUTATED   109  22
  DEL PEAK 10(5Q31.3) WILD-TYPE 210  25
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(5Q31.3) MUTATED    109   22
  DEL PEAK 10(5Q31.3) WILD-TYPE  210   25
     clus
vv    DEL PEAK 10(5Q31.3) MUTATED DEL PEAK 10(5Q31.3) WILD-TYPE
  NO                          109                           210
  YES                          22                            25
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 10(5Q31.3) MUTATED       2                         0   127
  DEL PEAK 10(5Q31.3) WILD-TYPE     3                         1   226
D30V13, multiclass
                           clus
vv                          DEL PEAK 10(5Q31.3) MUTATED
  ASIAN                                               2
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                             127
                           clus
vv                          DEL PEAK 10(5Q31.3) WILD-TYPE
  ASIAN                                                 3
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                               226
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V14, binary
                               cls
clus                              0   1
  DEL PEAK 10(5Q31.3) MUTATED     0 127
  DEL PEAK 10(5Q31.3) WILD-TYPE   7 225
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(5Q31.3) MUTATED      0  127
  DEL PEAK 10(5Q31.3) WILD-TYPE    7  225
                        clus
vv                       DEL PEAK 10(5Q31.3) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                         127
                        clus
vv                       DEL PEAK 10(5Q31.3) WILD-TYPE
  HISPANIC OR LATINO                                 7
  NOT HISPANIC OR LATINO                           225
[1] 2 2
[1] FALSE

Clustering(31) Variable = DEL PEAK 11(6Q21) MUTATION ANALYSIS
D31V1, survival
                             sevent
clus2                          0  1
  DEL PEAK 11(6Q21) MUTATED   78 73
  DEL PEAK 11(6Q21) WILD-TYPE 50 51
  DEL PEAK 11(6Q21) MUTATED DEL PEAK 11(6Q21) WILD-TYPE 
                        151                         101 
  DEL PEAK 11(6Q21) MUTATED DEL PEAK 11(6Q21) WILD-TYPE 
                         73                          51 
$`DEL PEAK 11(6Q21) MUTATED`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A8GI TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A20H 
        9.76        62.07        13.41        33.24        31.96       166.75 
TCGA-EE-A2GD TCGA-EE-A2GO TCGA-FW-A3R5 TCGA-WE-AAA3 TCGA-3N-A9WC TCGA-D3-A1Q1 
      269.03        52.90        36.95         7.40        60.46         8.42 
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2JB TCGA-D3-A2JC 
       31.89       110.93        25.64        45.99       168.00        86.30 
TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 
       36.30       171.58        64.83        66.08        43.53        58.06 
TCGA-D3-A3CE TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51J 
       59.70        90.21        23.67       173.85        30.67       144.46 
TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A8GC TCGA-D3-A8GD 
       11.34        42.05        45.70       177.86        78.21        23.61 
TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GP TCGA-D9-A1X3 TCGA-D9-A3Z3 TCGA-D9-A6EC 
       69.53        70.62       135.12        10.78        16.90        69.21 
TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I7 TCGA-DA-A1IA 
       22.85        76.34       138.67        68.68        60.10        64.83 
TCGA-DA-A1IC TCGA-DA-A3F5 TCGA-DA-A95V TCGA-DA-A95W TCGA-DA-A95X TCGA-DA-A95Y 
       58.85       225.11        72.10         0.76        65.03        14.14 
TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17Y TCGA-EE-A181 
       12.30         3.91        52.41        18.21        24.89        20.38 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29G 
        0.00        26.24        75.22        76.14        12.99        44.28 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 
       47.41        47.74        61.12       346.49       185.19       115.43 
TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GL TCGA-EE-A2GN 
       30.02        77.98        26.14        12.95        32.48        93.63 
TCGA-EE-A2GP TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MC TCGA-EE-A2MF 
        0.76        81.99       103.13        15.25        23.77       209.79 
TCGA-EE-A2MK TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB 
       89.26       227.01       143.93        23.51        53.26       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 
       64.04         4.41         6.28        67.89       111.85        45.90 
TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A199 TCGA-ER-A19B 
      168.85        19.86       135.98        34.45         7.82        53.29 
TCGA-ER-A19H TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A2NE TCGA-ER-A2NF 
      150.12        42.51       120.76        49.71        16.87        10.19 
TCGA-ER-A2NG TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A69P 
       28.67        68.52        15.48        32.05        74.47         4.14 
TCGA-FR-A7U8 TCGA-FR-A8YC TCGA-FS-A1YW TCGA-FS-A1Z0 TCGA-FS-A1ZC TCGA-FS-A1ZE 
       26.20        10.06       171.78       195.98       312.07        43.92 
TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT 
        7.82        36.33        78.61       130.95       136.27        35.28 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZZ TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FW-A3TU 
        4.47        23.21         3.06        66.67       173.19        55.59 
TCGA-GF-A4EO TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 
       18.25       117.93        17.06        42.48         7.59       120.53 
TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A693 
       34.49        46.92        85.05       297.01         7.23         0.33 
TCGA-W3-AA1R TCGA-W3-AA21 TCGA-WE-A8ZM TCGA-WE-A8ZQ TCGA-WE-AAA4 TCGA-YG-AA3O 
       79.99        92.84        65.42        62.89        24.99        28.21 
TCGA-Z2-AA3S 
       91.23 

$`DEL PEAK 11(6Q21) WILD-TYPE`
TCGA-D3-A3C8 TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-FR-A729 TCGA-WE-A8K5 
       38.76       134.40        27.35        19.04       216.43        52.73 
TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q3 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       12.99        14.83        15.72        49.35       133.25        19.04 
TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JG TCGA-D3-A3CB 
       76.41        62.60        62.86        15.75       107.61       140.98 
TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A5GU 
       40.01        24.53         9.34        31.76        62.70       124.08 
TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GR TCGA-D9-A3Z1 TCGA-D9-A4Z6 TCGA-DA-A1I2 
      179.97       120.00        36.53        15.02        18.44       150.61 
TCGA-DA-A1I5 TCGA-DA-A3F2 TCGA-DA-A3F8 TCGA-EB-A5KH TCGA-EE-A17X TCGA-EE-A20C 
      110.53        30.44         8.71        16.41        13.15        75.55 
TCGA-EE-A20F TCGA-EE-A29E TCGA-EE-A29P TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK 
       79.20         0.26        27.16       201.60        68.65        10.62 
TCGA-EE-A2GM TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2M8 TCGA-EE-A2MG TCGA-EE-A2MI 
       18.35         0.20        71.31         5.75        94.19       171.85 
TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A3AA TCGA-EE-A3AE TCGA-EE-A3J8 
       63.25       104.78       145.45       124.31        54.51         3.35 
TCGA-ER-A197 TCGA-ER-A19A TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19L 
       10.49         4.54        39.81        11.47       184.60        99.06 
TCGA-ER-A19M TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       59.84        47.18       146.63        73.05        22.36         4.70 
TCGA-ER-A3ES TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A7UA TCGA-FS-A1YY TCGA-FS-A1Z3 
      173.29         4.50       174.21         5.65        49.74         8.35 
TCGA-FS-A1Z4 TCGA-FS-A1ZD TCGA-FS-A1ZY TCGA-FS-A4F0 TCGA-FS-A4F9 TCGA-FS-A4FD 
       27.62        32.78         5.29        30.90        13.28        80.68 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A265 
       11.54        19.30         9.90         1.91        53.29        96.92 
TCGA-GN-A8LK TCGA-GN-A9SD TCGA-RP-A690 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 
       43.23        59.41         0.20       174.12         1.97       120.07 
TCGA-W3-AA1Q TCGA-W3-AA1V TCGA-W3-AA1W TCGA-WE-A8K1 TCGA-WE-A8ZN TCGA-WE-A8ZO 
       44.05         8.09       185.13        47.54        12.69        21.90 
TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-XV-AB01 
       10.95        48.39         1.94        37.32         6.61 

  DEL PEAK 11(6Q21) MUTATED DEL PEAK 11(6Q21) WILD-TYPE 
                        0.0                         0.2 
  DEL PEAK 11(6Q21) MUTATED DEL PEAK 11(6Q21) WILD-TYPE 
                     346.49                      216.43 
  DEL PEAK 11(6Q21) MUTATED DEL PEAK 11(6Q21) WILD-TYPE 
                      52.41                       38.76 
[1] "0.0 - 346.5 (52.4)" "0.2 - 216.4 (38.8)"
[1] "hr=" "1.3"
D31V2, survival
                             sevent
clus2                           0   1
  DEL PEAK 11(6Q21) MUTATED    94 115
  DEL PEAK 11(6Q21) WILD-TYPE  72  77
  DEL PEAK 11(6Q21) MUTATED DEL PEAK 11(6Q21) WILD-TYPE 
                        209                         149 
  DEL PEAK 11(6Q21) MUTATED DEL PEAK 11(6Q21) WILD-TYPE 
                        115                          77 
$`DEL PEAK 11(6Q21) MUTATED`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A3ML TCGA-D3-A8GI TCGA-EB-A5SG TCGA-EE-A180 
       27.65        62.07        13.87        58.52        68.25        94.98 
TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2GO TCGA-FS-A1ZF 
       68.15       168.26         2.60       340.14       126.81        15.45 
TCGA-FW-A3R5 TCGA-QB-AA9O TCGA-WE-AAA3 TCGA-3N-A9WB TCGA-3N-A9WC TCGA-D3-A1Q1 
       36.95        18.05        21.40        17.03        66.48        16.57 
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q9 TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2JB 
      112.04       112.57        31.59        43.43       103.10       168.00 
TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
       86.76        11.87        42.08       171.58        66.48        66.08 
TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV 
       59.57        58.06        60.23       103.59        39.75        45.30 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51N TCGA-D3-A51T TCGA-D3-A5GL 
      174.84        55.73       145.12        22.62        26.89       125.79 
TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GL TCGA-D3-A8GM 
      135.75       178.32        79.59        23.61        89.13       107.15 
TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX 
      161.00       152.75       151.53        54.67         3.65         7.10 
TCGA-D9-A1X3 TCGA-D9-A3Z3 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV 
       18.12        22.29        25.18        77.56        22.95        76.57 
TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I4 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA 
      144.89       222.51        35.93        88.87        53.92        65.92 
TCGA-DA-A1IC TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A95V TCGA-DA-A95W TCGA-DA-A95X 
       68.09        10.49       225.96        72.10        37.35        73.94 
TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A6L9 
       14.14        13.02        13.87        29.29        58.92        36.46 
TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B 
       27.22        33.73        14.70        26.89         4.96       133.81 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29G 
       13.55        63.35        85.08        78.97        13.97        72.07 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T 
       64.64        56.84        66.74        14.47        61.28       369.93 
TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
       25.87       195.02        17.92        46.82       115.96        59.64 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GL TCGA-EE-A2GN 
       39.29        86.14        59.28       173.79        79.66       102.12 
TCGA-EE-A2GP TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MC 
       13.91        94.82        21.67       129.27        28.83        61.51 
TCGA-EE-A2MF TCGA-EE-A2MH TCGA-EE-A2MK TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT 
      268.73        16.96       180.39       248.65       162.48        71.21 
TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG 
       53.26       122.73        64.04        28.77        13.81        41.59 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JH 
      172.18       127.20        64.08        53.19       201.80       134.33 
TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19E TCGA-ER-A19F 
      152.81        35.44         9.17        98.40        13.02        26.37 
TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19T 
      152.35         6.44        44.09       162.08        50.89         8.88 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL 
       20.15        28.83        48.99        93.01        46.98        33.21 
TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A8YC TCGA-FR-A8YD 
       12.95       149.03        15.72        27.85        34.82        36.26 
TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1Z0 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC 
      216.92        48.59       202.65        27.72        48.85       357.37 
TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ 
       46.45         9.70        32.75        47.38       101.26       133.55 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZZ 
       11.41       148.80        53.16        26.56        49.48        27.02 
TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4FB TCGA-FW-A3I3 
       50.14        66.67        28.73       174.84        26.73        17.46 
TCGA-FW-A3TU TCGA-GF-A4EO TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
       55.59        19.43       117.93        64.44        62.79        32.48 
TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LL 
      121.91        39.35        10.42        48.89        22.13        21.37 
TCGA-HR-A2OG TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A693 TCGA-W3-AA1O 
        0.23       368.78       297.90         7.23         0.33         4.01 
TCGA-W3-AA1R TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZQ 
      111.09       105.04        24.03        17.95       101.33        63.22 
TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-AA3S TCGA-Z2-AA3V 
       24.99        37.94        14.43        96.99        15.98 

$`DEL PEAK 11(6Q21) WILD-TYPE`
TCGA-D3-A3C8 TCGA-EB-A5SH TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-ER-A198 
       46.32        54.02       134.40        27.35        31.40        50.76 
TCGA-FR-A729 TCGA-WE-A8K5 TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q3 TCGA-D3-A1Q6 
      220.80        61.15        12.99        14.93        16.67        71.80 
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J8 TCGA-D3-A2J9 
      133.25        28.08        90.90        95.74        65.49        23.77 
TCGA-D3-A2JA TCGA-D3-A2JG TCGA-D3-A2JK TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3CB 
      115.53       113.52        12.10       130.72        46.98       166.52 
TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A51H TCGA-D3-A51K TCGA-D3-A51R 
       86.93        24.53         9.34        56.35        32.94        63.81 
TCGA-D3-A5GO TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GE TCGA-D3-A8GJ 
      137.92        18.18       125.19        30.84        26.43       241.38 
TCGA-D3-A8GK TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D3-A8GV TCGA-D9-A3Z1 
      170.20        29.06       129.63       117.17       167.70        15.39 
TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I5 
       18.44         9.90        36.03        20.38       176.55       135.02 
TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F8 TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5VV 
       40.60        33.93        43.36        10.36        20.35         7.04 
TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29E TCGA-EE-A29N 
       29.82         8.65       151.27        91.56        63.78        18.61 
TCGA-EE-A29P TCGA-EE-A2GC TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
       56.42        67.43       220.24        48.72       107.38        54.74 
TCGA-EE-A2GM TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2M8 TCGA-EE-A2MD 
       75.48        42.77        81.21        44.88        19.76        47.28 
TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MM 
      103.27       103.20       204.66        96.23       216.66       167.90 
TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A3AA TCGA-EE-A3AE TCGA-EE-A3AH TCGA-EE-A3J5 
       47.54        43.23       124.31        54.51       138.81        36.95 
TCGA-EE-A3J8 TCGA-EE-A3JE TCGA-ER-A197 TCGA-ER-A19A TCGA-ER-A19C TCGA-ER-A19D 
       34.32        51.35        13.94        77.75        48.89        12.59 
TCGA-ER-A19G TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 
      302.07       131.51        61.05        49.48       148.18       105.07 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NH TCGA-ER-A3ES TCGA-FR-A3YN TCGA-FR-A44A 
       43.82        23.34        41.56       247.04        92.98       174.21 
TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YE TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1Z4 
       18.77        38.27       104.42       228.59        20.91        28.08 
TCGA-FS-A1Z7 TCGA-FS-A1ZD TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZY TCGA-FS-A4F0 
        7.79        53.52        23.93        74.73        27.09        77.82 
TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
       34.03        54.41        80.68        13.51        19.30         9.90 
TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A26D 
        2.04        15.78       139.89        96.92        10.13        48.00 
TCGA-GN-A8LK TCGA-GN-A9SD TCGA-HR-A2OH TCGA-RP-A690 TCGA-RP-A694 TCGA-W3-A824 
       50.10        59.41        65.88         0.20         0.69       228.16 
TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1Q TCGA-W3-AA1V TCGA-W3-AA1W TCGA-WE-A8K1 
       63.02       121.08        69.07        42.08       219.16        49.05 
TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AA9Y 
       58.98        70.52        11.80        35.80        49.51        12.16 
TCGA-WE-AAA0 TCGA-XV-AB01 TCGA-YD-A89C TCGA-YD-A9TA TCGA-Z2-A8RT 
       40.41        13.25         6.90        49.18        27.58 

  DEL PEAK 11(6Q21) MUTATED DEL PEAK 11(6Q21) WILD-TYPE 
                       0.23                        0.20 
  DEL PEAK 11(6Q21) MUTATED DEL PEAK 11(6Q21) WILD-TYPE 
                     369.93                      302.07 
  DEL PEAK 11(6Q21) MUTATED DEL PEAK 11(6Q21) WILD-TYPE 
                      53.92                       49.51 
[1] "0.2 - 369.9 (53.9)" "0.2 - 302.1 (49.5)"
[1] "hr=" "1"  
D31V3, continuous
                             vv
clus                          I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB
  DEL PEAK 11(6Q21) MUTATED          8       4      16       10       17
  DEL PEAK 11(6Q21) WILD-TYPE        5       3      13        8       11
                             vv
clus                          STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  DEL PEAK 11(6Q21) MUTATED         11         7         9        10        25
  DEL PEAK 11(6Q21) WILD-TYPE       15         7        10         5        14
                             vv
clus                          STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DEL PEAK 11(6Q21) MUTATED            9         20         36        9
  DEL PEAK 11(6Q21) WILD-TYPE          6         15         18       12
D31V4, multiclass
            clus
vv           DEL PEAK 11(6Q21) MUTATED DEL PEAK 11(6Q21) WILD-TYPE
  I/II NOS                           8                           5
  STAGE 0                            4                           3
  STAGE I                           16                          13
  STAGE IA                          10                           8
  STAGE IB                          17                          11
  STAGE II                          11                          15
  STAGE IIA                          7                           7
  STAGE IIB                          9                          10
  STAGE IIC                         10                           5
  STAGE III                         25                          14
  STAGE IIIA                         9                           6
  STAGE IIIB                        20                          15
  STAGE IIIC                        36                          18
  STAGE IV                           9                          12
[1] 14  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          T0+T1 T2 T3 T4
  DEL PEAK 11(6Q21) MUTATED      37 45 41 39
  DEL PEAK 11(6Q21) WILD-TYPE    27 28 40 28
D31V5, multiclass
       clus
vv      DEL PEAK 11(6Q21) MUTATED DEL PEAK 11(6Q21) WILD-TYPE
  T0+T1                        37                          27
  T2                           45                          28
  T3                           41                          40
  T4                           39                          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  N3
  DEL PEAK 11(6Q21) MUTATED   101  41  25  28
  DEL PEAK 11(6Q21) WILD-TYPE  76  24  14  17
D31V6, multiclass
    clus
vv   DEL PEAK 11(6Q21) MUTATED DEL PEAK 11(6Q21) WILD-TYPE
  N0                       101                          76
  N1                        41                          24
  N2                        25                          14
  N3                        28                          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"
D31V7, binary
                             cls
clus                            0   1
  DEL PEAK 11(6Q21) MUTATED   191  10
  DEL PEAK 11(6Q21) WILD-TYPE 128  12
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 11(6Q21) MUTATED    191   10
  DEL PEAK 11(6Q21) WILD-TYPE  128   12
   clus
vv  DEL PEAK 11(6Q21) MUTATED DEL PEAK 11(6Q21) WILD-TYPE
  0                       191                         128
  1                        10                          12
[1] 2 2
[1] FALSE
D31V8, binary
                             cls
clus                           0  1
  DEL PEAK 11(6Q21) MUTATED   70 61
  DEL PEAK 11(6Q21) WILD-TYPE 64 29
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 11(6Q21) MUTATED     70   61
  DEL PEAK 11(6Q21) WILD-TYPE   64   29
     clus
vv    DEL PEAK 11(6Q21) MUTATED DEL PEAK 11(6Q21) WILD-TYPE
  NO                         70                          64
  YES                        61                          29
[1] 2 2
[1] FALSE
D31V9, binary
                             cls
clus                            0   1
  DEL PEAK 11(6Q21) MUTATED    30 184
  DEL PEAK 11(6Q21) WILD-TYPE  17 136
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 11(6Q21) MUTATED     30  184
  DEL PEAK 11(6Q21) WILD-TYPE   17  136
     clus
vv    DEL PEAK 11(6Q21) MUTATED DEL PEAK 11(6Q21) WILD-TYPE
  NO                         30                          17
  YES                       184                         136
[1] 2 2
[1] FALSE
D31V10, continuous
D31V11, binary
                             cls
clus                            0   1
  DEL PEAK 11(6Q21) MUTATED    84 130
  DEL PEAK 11(6Q21) WILD-TYPE  54  99
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 11(6Q21) MUTATED     84  130
  DEL PEAK 11(6Q21) WILD-TYPE   54   99
        clus
vv       DEL PEAK 11(6Q21) MUTATED DEL PEAK 11(6Q21) WILD-TYPE
  FEMALE                        84                          54
  MALE                         130                          99
[1] 2 2
[1] FALSE
D31V12, binary
                             cls
clus                            0   1
  DEL PEAK 11(6Q21) MUTATED   184  30
  DEL PEAK 11(6Q21) WILD-TYPE 135  17
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 11(6Q21) MUTATED    184   30
  DEL PEAK 11(6Q21) WILD-TYPE  135   17
     clus
vv    DEL PEAK 11(6Q21) MUTATED DEL PEAK 11(6Q21) WILD-TYPE
  NO                        184                         135
  YES                        30                          17
[1] 2 2
[1] FALSE
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 11(6Q21) MUTATED       3                         1   205
  DEL PEAK 11(6Q21) WILD-TYPE     2                         0   148
D31V13, multiclass
                           clus
vv                          DEL PEAK 11(6Q21) MUTATED
  ASIAN                                             3
  BLACK OR AFRICAN AMERICAN                         1
  WHITE                                           205
                           clus
vv                          DEL PEAK 11(6Q21) WILD-TYPE
  ASIAN                                               2
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                             148
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V14, binary
                             cls
clus                            0   1
  DEL PEAK 11(6Q21) MUTATED     3 205
  DEL PEAK 11(6Q21) WILD-TYPE   4 147
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 11(6Q21) MUTATED      3  205
  DEL PEAK 11(6Q21) WILD-TYPE    4  147
                        clus
vv                       DEL PEAK 11(6Q21) MUTATED DEL PEAK 11(6Q21) WILD-TYPE
  HISPANIC OR LATINO                             3                           4
  NOT HISPANIC OR LATINO                       205                         147
[1] 2 2
[1] FALSE

Clustering(32) Variable = DEL PEAK 12(6Q26) MUTATION ANALYSIS
D32V1, survival
                             sevent
clus2                          0  1
  DEL PEAK 12(6Q26) MUTATED   79 79
  DEL PEAK 12(6Q26) WILD-TYPE 49 45
  DEL PEAK 12(6Q26) MUTATED DEL PEAK 12(6Q26) WILD-TYPE 
                        158                          94 
  DEL PEAK 12(6Q26) MUTATED DEL PEAK 12(6Q26) WILD-TYPE 
                         79                          45 
$`DEL PEAK 12(6Q26) MUTATED`
TCGA-D3-A2JF TCGA-D3-A8GI TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GD 
       62.07        13.41        33.24        31.96       166.75       269.03 
TCGA-EE-A2GO TCGA-FW-A3R5 TCGA-WE-AAA3 TCGA-3N-A9WC TCGA-D3-A1Q1 TCGA-D3-A1Q4 
       52.90        36.95         7.40        60.46         8.42        31.89 
TCGA-D3-A1Q5 TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JH 
      110.93        25.64        45.99       168.00        86.30        36.30 
TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CE 
      171.58        64.83        66.08        43.53        58.06        59.70 
TCGA-D3-A3CF TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51J 
       24.53        90.21        23.67       173.85        30.67       144.46 
TCGA-D3-A51K TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GU 
       31.76        11.34        42.05        45.70       177.86       124.08 
TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GP TCGA-D3-A8GR 
       78.21        23.61        69.53        70.62       135.12        36.53 
TCGA-D9-A3Z3 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 
       16.90        69.21        22.85        76.34       138.67        68.68 
TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F5 TCGA-DA-A95V TCGA-DA-A95W 
       60.10        64.83        58.85       225.11        72.10         0.76 
TCGA-DA-A95X TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A5UN TCGA-EE-A17Y TCGA-EE-A181 
       65.03        14.14        12.30        52.41        24.89        20.38 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29G 
        0.00        26.24        75.22        76.14        12.99        44.28 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 
       47.41        47.74        61.12       346.49       185.19       115.43 
TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GL TCGA-EE-A2GN 
       30.02        77.98        26.14        12.95        32.48        93.63 
TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MC 
        0.76        71.31        81.99       103.13        15.25        23.77 
TCGA-EE-A2MF TCGA-EE-A2MK TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU 
      209.79        89.26       227.01       143.93        23.51        53.26 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 
      122.73        64.04         4.41         6.28        67.89       111.85 
TCGA-EE-A3J7 TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 
       45.90       168.85        19.86       135.98        34.45        10.49 
TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19N 
        7.82        53.29        11.47       184.60       150.12        42.51 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A2ND TCGA-ER-A2NE 
      120.76        49.71        47.18       146.63         4.70        16.87 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A69P 
       10.19        28.67        15.48        32.05        74.47         4.14 
TCGA-FR-A7U8 TCGA-FR-A8YC TCGA-FS-A1YW TCGA-FS-A1Z0 TCGA-FS-A1ZC TCGA-FS-A1ZD 
       26.20        10.06       171.78       195.98       312.07        32.78 
TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT 
        7.82        36.33        78.61       130.95       136.27        35.28 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F8 TCGA-FW-A3TU 
        4.47        23.21         5.29         3.06       173.19        55.59 
TCGA-GF-A4EO TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 
       18.25       117.93        17.06        42.48         7.59       120.53 
TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-GN-A9SD TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS 
       34.49        46.92        59.41        85.05       297.01         7.23 
TCGA-RP-A693 TCGA-W3-AA1R TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8ZM TCGA-WE-A8ZQ 
        0.33        79.99        92.84        47.54        65.42        62.89 
TCGA-WE-AAA4 TCGA-YG-AA3O 
       24.99        28.21 

$`DEL PEAK 12(6Q26) WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A3C8 TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-FR-A729 
        9.76        38.76       134.40        27.35        19.04       216.43 
TCGA-WE-A8K5 TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q3 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       52.73        12.99        14.83        15.72        49.35       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JG 
       19.04        76.41        62.60        62.86        15.75       107.61 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3MO TCGA-D3-A51R TCGA-D3-A8GJ TCGA-D3-A8GK 
      140.98        40.01         9.34        62.70       179.97       120.00 
TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A4Z6 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A3F2 
       10.78        15.02        18.44       150.61       110.53        30.44 
TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A20C 
        8.71         3.91        16.41        18.21        13.15        75.55 
TCGA-EE-A20F TCGA-EE-A29E TCGA-EE-A29P TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK 
       79.20         0.26        27.16       201.60        68.65        10.62 
TCGA-EE-A2GM TCGA-EE-A2GR TCGA-EE-A2M8 TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ 
       18.35         0.20         5.75        94.19       171.85        63.25 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A3AA TCGA-EE-A3AE TCGA-EE-A3J8 TCGA-ER-A19A 
      104.78       145.45       124.31        54.51         3.35         4.54 
TCGA-ER-A19C TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A3ES 
       39.81        99.06        59.84        73.05        22.36       173.29 
TCGA-ER-A3ET TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A7UA TCGA-FS-A1YY TCGA-FS-A1Z3 
       68.52         4.50       174.21         5.65        49.74         8.35 
TCGA-FS-A1Z4 TCGA-FS-A1ZE TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F9 TCGA-FS-A4FD 
       27.62        43.92        30.90        66.67        13.28        80.68 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A265 
       11.54        19.30         9.90         1.91        53.29        96.92 
TCGA-GN-A8LK TCGA-RP-A690 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1Q 
       43.23         0.20       174.12         1.97       120.07        44.05 
TCGA-W3-AA1V TCGA-W3-AA1W TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-A8ZY 
        8.09       185.13        12.69        21.90        10.95        48.39 
TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-XV-AB01 TCGA-Z2-AA3S 
        1.94        37.32         6.61        91.23 

  DEL PEAK 12(6Q26) MUTATED DEL PEAK 12(6Q26) WILD-TYPE 
                        0.0                         0.2 
  DEL PEAK 12(6Q26) MUTATED DEL PEAK 12(6Q26) WILD-TYPE 
                     346.49                      216.43 
  DEL PEAK 12(6Q26) MUTATED DEL PEAK 12(6Q26) WILD-TYPE 
                     48.725                      39.285 
[1] "0.0 - 346.5 (48.7)" "0.2 - 216.4 (39.3)"
[1] "hr=" "1.2"
D32V2, survival
                             sevent
clus2                           0   1
  DEL PEAK 12(6Q26) MUTATED    96 120
  DEL PEAK 12(6Q26) WILD-TYPE  70  72
  DEL PEAK 12(6Q26) MUTATED DEL PEAK 12(6Q26) WILD-TYPE 
                        216                         142 
  DEL PEAK 12(6Q26) MUTATED DEL PEAK 12(6Q26) WILD-TYPE 
                        120                          72 
$`DEL PEAK 12(6Q26) MUTATED`
TCGA-D3-A2JF TCGA-D3-A3ML TCGA-D3-A8GI TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A184 
       62.07        13.87        58.52        68.25        94.98        68.15 
TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2GO TCGA-FS-A1ZF TCGA-FW-A3R5 
      168.26         2.60       340.14       126.81        15.45        36.95 
TCGA-QB-AA9O TCGA-WE-AAA3 TCGA-3N-A9WB TCGA-3N-A9WC TCGA-D3-A1Q1 TCGA-D3-A1Q4 
       18.05        21.40        17.03        66.48        16.57       112.04 
TCGA-D3-A1Q5 TCGA-D3-A1Q9 TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2JB TCGA-D3-A2JC 
      112.57        31.59        43.43       103.10       168.00        86.76 
TCGA-D3-A2JD TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP 
       11.87        42.08       171.58        66.48        66.08        59.57 
TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV 
       58.06        60.23        24.53       103.59        39.75        45.30 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51T 
      174.84        55.73       145.12        32.94        22.62        26.89 
TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D3-A8GC TCGA-D3-A8GD 
      125.79       135.75       178.32       125.19        79.59        23.61 
TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GR TCGA-D9-A148 
       89.13       107.15       161.00       152.75       129.63       151.53 
TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z3 TCGA-D9-A6EA TCGA-D9-A6EC 
       54.67         3.65         7.10        22.29        25.18        77.56 
TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I4 TCGA-DA-A1I7 
       22.95        76.57       144.89       222.51        35.93        88.87 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A95V 
       53.92        65.92        68.09        10.49       225.96        72.10 
TCGA-DA-A95W TCGA-DA-A95X TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A5UL TCGA-EB-A5UN 
       37.35        73.94        14.14        13.02        29.29        58.92 
TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B 
       27.22        33.73        14.70        26.89         4.96       133.81 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29G 
       13.55        63.35        85.08        78.97        13.97        72.07 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T 
       64.64        56.84        66.74        14.47        61.28       369.93 
TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 
       25.87       195.02        17.92       115.96        59.64        39.29 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GP 
       86.14        59.28       173.79        79.66       102.12        13.91 
TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MC 
       81.21        94.82        21.67       129.27        28.83        61.51 
TCGA-EE-A2MF TCGA-EE-A2MH TCGA-EE-A2MK TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT 
      268.73        16.96       180.39       248.65       162.48        71.21 
TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG 
       53.26       122.73        64.04        28.77        13.81        41.59 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JH 
      172.18       127.20        64.08        53.19       201.80       134.33 
TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19D 
      152.81        35.44        13.94         9.17        98.40        12.59 
TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19N 
       13.02        26.37       302.07       152.35         6.44        44.09 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A2ND 
      162.08        50.89        49.48         8.88       148.18        23.34 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K 
       20.15        28.83        48.99        46.98        33.21        12.95 
TCGA-ER-A42L TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FS-A1YW 
      149.03        15.72        27.85        34.82        36.26       216.92 
TCGA-FS-A1YX TCGA-FS-A1Z0 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD 
       48.59       202.65        27.72        48.85       357.37        53.52 
TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZR 
        9.70        32.75        47.38       101.26       133.55        11.41 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ 
      148.80        53.16        26.56        49.48        27.09        27.02 
TCGA-FS-A4F2 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4FB TCGA-FW-A3I3 TCGA-FW-A3TU 
       50.14        28.73       174.84        26.73        17.46        55.59 
TCGA-GF-A4EO TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 
       19.43       117.93        64.44        62.79        32.48       121.91 
TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LL TCGA-GN-A9SD 
       39.35        10.42        48.89        22.13        21.37        59.41 
TCGA-HR-A2OG TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A693 TCGA-W3-AA1O 
        0.23       368.78       297.90         7.23         0.33         4.01 
TCGA-W3-AA1R TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K6 TCGA-WE-A8ZM 
      111.09       105.04        24.03        49.05        17.95       101.33 
TCGA-WE-A8ZQ TCGA-WE-AAA4 TCGA-YD-A9TA TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-AA3V 
       63.22        24.99        49.18        37.94        14.43        15.98 

$`DEL PEAK 12(6Q26) WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A3C8 TCGA-EB-A5SH TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 
       27.65        46.32        54.02       134.40        27.35        31.40 
TCGA-ER-A198 TCGA-FR-A729 TCGA-WE-A8K5 TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q3 
       50.76       220.80        61.15        12.99        14.93        16.67 
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J8 
       71.80       133.25        28.08        90.90        95.74        65.49 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JG TCGA-D3-A2JK TCGA-D3-A3BZ TCGA-D3-A3C7 
       23.77       115.53       113.52        12.10       130.72        46.98 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3MO TCGA-D3-A51H TCGA-D3-A51R TCGA-D3-A5GO 
      166.52        86.93         9.34        56.35        63.81       137.92 
TCGA-D3-A5GS TCGA-D3-A8GB TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GQ 
       18.18        30.84        26.43       241.38       170.20        29.06 
TCGA-D3-A8GS TCGA-D3-A8GV TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A4Z6 TCGA-D9-A6E9 
      117.17       167.70        18.12        15.39        18.44         9.90 
TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1IB TCGA-DA-A3F2 
       36.03        20.38       176.55       135.02        40.60        33.93 
TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5VV TCGA-EB-A6L9 
       43.36        13.87        10.36        20.35         7.04        36.46 
TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29E TCGA-EE-A29N 
       29.82         8.65       151.27        91.56        63.78        18.61 
TCGA-EE-A29P TCGA-EE-A2A0 TCGA-EE-A2GC TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       56.42        46.82        67.43       220.24        48.72       107.38 
TCGA-EE-A2GK TCGA-EE-A2GM TCGA-EE-A2GR TCGA-EE-A2GT TCGA-EE-A2M8 TCGA-EE-A2MD 
       54.74        75.48        42.77        44.88        19.76        47.28 
TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MM 
      103.27       103.20       204.66        96.23       216.66       167.90 
TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A3AA TCGA-EE-A3AE TCGA-EE-A3AH TCGA-EE-A3J5 
       47.54        43.23       124.31        54.51       138.81        36.95 
TCGA-EE-A3J8 TCGA-EE-A3JE TCGA-ER-A19A TCGA-ER-A19C TCGA-ER-A19L TCGA-ER-A19M 
       34.32        51.35        77.75        48.89       131.51        61.05 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-FR-A3YN 
      105.07        43.82        41.56       247.04        93.01        92.98 
TCGA-FR-A44A TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YE TCGA-FS-A1YY TCGA-FS-A1Z3 
      174.21        18.77        38.27       104.42       228.59        20.91 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZE TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A4F0 
       28.08         7.79        46.45        23.93        74.73        77.82 
TCGA-FS-A4F4 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3TV TCGA-FW-A5DY 
       66.67        34.03        54.41        80.68        13.51        19.30 
TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A266 
        9.90         2.04        15.78       139.89        96.92        10.13 
TCGA-GN-A26D TCGA-GN-A8LK TCGA-HR-A2OH TCGA-RP-A690 TCGA-RP-A694 TCGA-W3-A824 
       48.00        50.10        65.88         0.20         0.69       228.16 
TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1Q TCGA-W3-AA1V TCGA-W3-AA1W TCGA-WE-A8ZN 
       63.02       121.08        69.07        42.08       219.16        58.98 
TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 
       70.52        11.80        35.80        49.51        12.16        40.41 
TCGA-XV-AB01 TCGA-YD-A89C TCGA-Z2-A8RT TCGA-Z2-AA3S 
       13.25         6.90        27.58        96.99 

  DEL PEAK 12(6Q26) MUTATED DEL PEAK 12(6Q26) WILD-TYPE 
                       0.23                        0.20 
  DEL PEAK 12(6Q26) MUTATED DEL PEAK 12(6Q26) WILD-TYPE 
                     369.93                      247.04 
  DEL PEAK 12(6Q26) MUTATED DEL PEAK 12(6Q26) WILD-TYPE 
                      53.72                       49.20 
[1] "0.2 - 369.9 (53.7)" "0.2 - 247.0 (49.2)"
[1] "hr=" "1"  
D32V3, continuous
                             vv
clus                          I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB
  DEL PEAK 12(6Q26) MUTATED          8       5      16       10       20
  DEL PEAK 12(6Q26) WILD-TYPE        5       2      13        8        8
                             vv
clus                          STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  DEL PEAK 12(6Q26) MUTATED         10         7        10         9        25
  DEL PEAK 12(6Q26) WILD-TYPE       16         7         9         6        14
                             vv
clus                          STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DEL PEAK 12(6Q26) MUTATED            8         22         36        9
  DEL PEAK 12(6Q26) WILD-TYPE          7         13         18       12
D32V4, multiclass
            clus
vv           DEL PEAK 12(6Q26) MUTATED DEL PEAK 12(6Q26) WILD-TYPE
  I/II NOS                           8                           5
  STAGE 0                            5                           2
  STAGE I                           16                          13
  STAGE IA                          10                           8
  STAGE IB                          20                           8
  STAGE II                          10                          16
  STAGE IIA                          7                           7
  STAGE IIB                         10                           9
  STAGE IIC                          9                           6
  STAGE III                         25                          14
  STAGE IIIA                         8                           7
  STAGE IIIB                        22                          13
  STAGE IIIC                        36                          18
  STAGE IV                           9                          12
[1] 14  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          T0+T1 T2 T3 T4
  DEL PEAK 12(6Q26) MUTATED      39 48 40 39
  DEL PEAK 12(6Q26) WILD-TYPE    25 25 41 28
D32V5, multiclass
       clus
vv      DEL PEAK 12(6Q26) MUTATED DEL PEAK 12(6Q26) WILD-TYPE
  T0+T1                        39                          25
  T2                           48                          25
  T3                           40                          41
  T4                           39                          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  N3
  DEL PEAK 12(6Q26) MUTATED   104  41  25  28
  DEL PEAK 12(6Q26) WILD-TYPE  73  24  14  17
D32V6, multiclass
    clus
vv   DEL PEAK 12(6Q26) MUTATED DEL PEAK 12(6Q26) WILD-TYPE
  N0                       104                          73
  N1                        41                          24
  N2                        25                          14
  N3                        28                          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"
D32V7, binary
                             cls
clus                            0   1
  DEL PEAK 12(6Q26) MUTATED   196  10
  DEL PEAK 12(6Q26) WILD-TYPE 123  12
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 12(6Q26) MUTATED    196   10
  DEL PEAK 12(6Q26) WILD-TYPE  123   12
   clus
vv  DEL PEAK 12(6Q26) MUTATED DEL PEAK 12(6Q26) WILD-TYPE
  0                       196                         123
  1                        10                          12
[1] 2 2
[1] FALSE
D32V8, binary
                             cls
clus                           0  1
  DEL PEAK 12(6Q26) MUTATED   75 61
  DEL PEAK 12(6Q26) WILD-TYPE 59 29
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 12(6Q26) MUTATED     75   61
  DEL PEAK 12(6Q26) WILD-TYPE   59   29
     clus
vv    DEL PEAK 12(6Q26) MUTATED DEL PEAK 12(6Q26) WILD-TYPE
  NO                         75                          59
  YES                        61                          29
[1] 2 2
[1] FALSE
D32V9, binary
                             cls
clus                            0   1
  DEL PEAK 12(6Q26) MUTATED    31 190
  DEL PEAK 12(6Q26) WILD-TYPE  16 130
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 12(6Q26) MUTATED     31  190
  DEL PEAK 12(6Q26) WILD-TYPE   16  130
     clus
vv    DEL PEAK 12(6Q26) MUTATED DEL PEAK 12(6Q26) WILD-TYPE
  NO                         31                          16
  YES                       190                         130
[1] 2 2
[1] FALSE
D32V10, continuous
D32V11, binary
                             cls
clus                            0   1
  DEL PEAK 12(6Q26) MUTATED    90 131
  DEL PEAK 12(6Q26) WILD-TYPE  48  98
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 12(6Q26) MUTATED     90  131
  DEL PEAK 12(6Q26) WILD-TYPE   48   98
        clus
vv       DEL PEAK 12(6Q26) MUTATED DEL PEAK 12(6Q26) WILD-TYPE
  FEMALE                        90                          48
  MALE                         131                          98
[1] 2 2
[1] FALSE
D32V12, binary
                             cls
clus                            0   1
  DEL PEAK 12(6Q26) MUTATED   194  27
  DEL PEAK 12(6Q26) WILD-TYPE 125  20
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 12(6Q26) MUTATED    194   27
  DEL PEAK 12(6Q26) WILD-TYPE  125   20
     clus
vv    DEL PEAK 12(6Q26) MUTATED DEL PEAK 12(6Q26) WILD-TYPE
  NO                        194                         125
  YES                        27                          20
[1] 2 2
[1] FALSE
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 12(6Q26) MUTATED       1                         1   214
  DEL PEAK 12(6Q26) WILD-TYPE     4                         0   139
D32V13, multiclass
                           clus
vv                          DEL PEAK 12(6Q26) MUTATED
  ASIAN                                             1
  BLACK OR AFRICAN AMERICAN                         1
  WHITE                                           214
                           clus
vv                          DEL PEAK 12(6Q26) WILD-TYPE
  ASIAN                                               4
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                             139
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V14, binary
                             cls
clus                            0   1
  DEL PEAK 12(6Q26) MUTATED     4 212
  DEL PEAK 12(6Q26) WILD-TYPE   3 140
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 12(6Q26) MUTATED      4  212
  DEL PEAK 12(6Q26) WILD-TYPE    3  140
                        clus
vv                       DEL PEAK 12(6Q26) MUTATED DEL PEAK 12(6Q26) WILD-TYPE
  HISPANIC OR LATINO                             4                           3
  NOT HISPANIC OR LATINO                       212                         140
[1] 2 2
[1] FALSE

Clustering(33) Variable = DEL PEAK 13(8P23.3) MUTATION ANALYSIS
D33V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 13(8P23.3) MUTATED    25  36
  DEL PEAK 13(8P23.3) WILD-TYPE 103  88
  DEL PEAK 13(8P23.3) MUTATED DEL PEAK 13(8P23.3) WILD-TYPE 
                           61                           191 
  DEL PEAK 13(8P23.3) MUTATED DEL PEAK 13(8P23.3) WILD-TYPE 
                           36                            88 
$`DEL PEAK 13(8P23.3) MUTATED`
TCGA-D3-A2JE TCGA-FW-A3R5 TCGA-WE-AAA3 TCGA-3N-A9WC TCGA-D3-A1Q1 TCGA-D3-A2J6 
        9.76        36.95         7.40        60.46         8.42        25.64 
TCGA-D3-A2JA TCGA-D3-A2JG TCGA-D3-A2JL TCGA-D3-A2JO TCGA-D3-A3C6 TCGA-D3-A3MO 
       15.75       107.61       171.58        66.08        58.06         9.34 
TCGA-D3-A5GN TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GM TCGA-DA-A1IA TCGA-DA-A95V 
       45.70        78.21        23.61        70.62        64.83        72.10 
TCGA-DA-A95Y TCGA-EB-A6L9 TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A29C TCGA-EE-A29H 
       14.14        18.21        26.24        75.55        76.14        47.41 
TCGA-EE-A29M TCGA-EE-A2A2 TCGA-EE-A2GS TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI 
       47.74        30.02        71.31       209.79        94.19       171.85 
TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC 
      145.45       227.01       143.93        53.26       122.73        64.04 
TCGA-EE-A3J3 TCGA-EE-A3JI TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19C TCGA-ER-A19S 
       67.89       135.98        10.49         7.82        39.81        47.18 
TCGA-ER-A2ND TCGA-ER-A2NF TCGA-ER-A3PL TCGA-FR-A8YC TCGA-FS-A1YY TCGA-FS-A1Z0 
        4.70        10.19        32.05        10.06        49.74       195.98 
TCGA-FS-A1ZC TCGA-FS-A1ZJ TCGA-FS-A1ZT TCGA-FS-A4FD TCGA-GN-A264 TCGA-GN-A265 
      312.07        36.33        35.28        80.68       117.93        96.92 
TCGA-OD-A75X TCGA-QB-A6FS TCGA-W3-AA1R TCGA-W3-AA1V TCGA-WE-A8ZY TCGA-WE-AAA0 
      297.01         7.23        79.99         8.09        48.39        37.32 
TCGA-Z2-AA3S 
       91.23 

$`DEL PEAK 13(8P23.3) WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A8GI TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A20H 
       62.07        38.76        13.41        33.24        31.96       166.75 
TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-FR-A729 
      269.03        52.90       134.40        27.35        19.04       216.43 
TCGA-WE-A8K5 TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
       52.73        12.99        14.83        15.72        31.89       110.93 
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J7 
       49.35       133.25        19.04        76.41        62.60        45.99 
TCGA-D3-A2J8 TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JH TCGA-D3-A2JN TCGA-D3-A2JP 
       62.86       168.00        86.30        36.30        64.83        43.53 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MR TCGA-D3-A3MU 
      140.98        40.01        59.70        24.53        90.21        23.67 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T 
      173.85        30.67       144.46        31.76        62.70        11.34 
TCGA-D3-A5GL TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL 
       42.05       177.86       124.08       179.97       120.00        69.53 
TCGA-D3-A8GP TCGA-D3-A8GR TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 
      135.12        36.53        10.78        15.02        16.90        18.44 
TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 
       69.21        22.85        76.34       138.67        68.68       150.61 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 
      110.53        60.10        58.85        30.44       225.11         8.71 
TCGA-DA-A95W TCGA-DA-A95X TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN 
        0.76        65.03        12.30         3.91        16.41        52.41 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A20F TCGA-EE-A29B 
       13.15        24.89        20.38         0.00        79.20        75.22 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T 
       12.99         0.26        44.28        27.16        61.12       346.49 
TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH 
      185.19       115.43        77.98        26.14        12.95       201.60 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP 
       68.65        10.62        32.48        18.35        93.63         0.76 
TCGA-EE-A2GR TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
        0.20        81.99       103.13        15.25         5.75        23.77 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AD 
       63.25        89.26       104.78        23.51       124.31         4.41 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB 
       54.51         6.28       111.85        45.90         3.35       168.85 
TCGA-EE-A3JH TCGA-ER-A195 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19G 
       19.86        34.45         4.54        53.29        11.47       184.60 
TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
      150.12        99.06        59.84        42.51       120.76        49.71 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A3ES 
      146.63        73.05        22.36        16.87        28.67       173.29 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       68.52        15.48        74.47         4.50       174.21         4.14 
TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FS-A1YW TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZD 
       26.20         5.65       171.78         8.35        27.62        32.78 
TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZU 
       43.92         7.82        78.61       130.95       136.27         4.47 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 
       23.21         5.29         3.06        30.90        66.67       173.19 
TCGA-FS-A4F9 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
       13.28        55.59        11.54        19.30         9.90        18.25 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 
        1.91        53.29        17.06        42.48         7.59       120.53 
TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-GN-A8LK TCGA-GN-A9SD TCGA-LH-A9QB TCGA-RP-A690 
       34.49        46.92        43.23        59.41        85.05         0.20 
TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1Q TCGA-W3-AA1W 
        0.33       174.12         1.97       120.07        44.05       185.13 
TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ 
       92.84        47.54        65.42        12.69        21.90        62.89 
TCGA-WE-A8ZT TCGA-WE-AA9Y TCGA-WE-AAA4 TCGA-XV-AB01 TCGA-YG-AA3O 
       10.95         1.94        24.99         6.61        28.21 

  DEL PEAK 13(8P23.3) MUTATED DEL PEAK 13(8P23.3) WILD-TYPE 
                          4.7                           0.0 
  DEL PEAK 13(8P23.3) MUTATED DEL PEAK 13(8P23.3) WILD-TYPE 
                       312.07                        346.49 
  DEL PEAK 13(8P23.3) MUTATED DEL PEAK 13(8P23.3) WILD-TYPE 
                        53.26                         43.53 
[1] "4.7 - 312.1 (53.3)" "0.0 - 346.5 (43.5)"
[1] "hr=" "1.1"
D33V2, survival
                               sevent
clus2                             0   1
  DEL PEAK 13(8P23.3) MUTATED    35  53
  DEL PEAK 13(8P23.3) WILD-TYPE 131 139
  DEL PEAK 13(8P23.3) MUTATED DEL PEAK 13(8P23.3) WILD-TYPE 
                           88                           270 
  DEL PEAK 13(8P23.3) MUTATED DEL PEAK 13(8P23.3) WILD-TYPE 
                           53                           139 
$`DEL PEAK 13(8P23.3) MUTATED`
TCGA-D3-A2JE TCGA-EE-A29L TCGA-ER-A198 TCGA-FW-A3R5 TCGA-QB-AA9O TCGA-WE-AAA3 
       27.65         2.60        50.76        36.95        18.05        21.40 
TCGA-3N-A9WC TCGA-D3-A1Q1 TCGA-D3-A1Q9 TCGA-D3-A2J6 TCGA-D3-A2JA TCGA-D3-A2JD 
       66.48        16.57        31.59        43.43       115.53        11.87 
TCGA-D3-A2JG TCGA-D3-A2JL TCGA-D3-A2JO TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3MO 
      113.52       171.58        66.08        58.06        46.98         9.34 
TCGA-D3-A51N TCGA-D3-A5GN TCGA-D3-A5GS TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GM 
       22.62       135.75        18.18        79.59        23.61       107.15 
TCGA-D3-A8GV TCGA-D9-A148 TCGA-D9-A1JW TCGA-DA-A1IA TCGA-DA-A3F3 TCGA-DA-A95V 
      167.70       151.53         3.65        65.92        10.49        72.10 
TCGA-DA-A95Y TCGA-EB-A6L9 TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A29C TCGA-EE-A29H 
       14.14        36.46        26.89       151.27        78.97        64.64 
TCGA-EE-A29M TCGA-EE-A29V TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2GI TCGA-EE-A2GS 
       56.84        25.87        59.64        39.29        48.72        81.21 
TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MM TCGA-EE-A2MN 
      268.73       103.20        16.96       204.66       167.90        47.54 
TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AG 
      248.65       162.48        53.26       122.73        64.04        41.59 
TCGA-EE-A3J3 TCGA-EE-A3JI TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19C TCGA-ER-A19E 
      172.18       152.81        13.94         9.17        48.89        13.02 
TCGA-ER-A19J TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A2ND TCGA-ER-A2NF TCGA-ER-A3PL 
        6.44        49.48         8.88        23.34        28.83        33.21 
TCGA-ER-A42K TCGA-FR-A8YC TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1ZA TCGA-FS-A1ZC 
       12.95        34.82       228.59       202.65        27.72       357.37 
TCGA-FS-A1ZJ TCGA-FS-A1ZT TCGA-FS-A4FD TCGA-GN-A264 TCGA-GN-A265 TCGA-OD-A75X 
       47.38        53.16        80.68       117.93        96.92       297.90 
TCGA-QB-A6FS TCGA-W3-AA1R TCGA-W3-AA1V TCGA-WE-A8JZ TCGA-WE-A8K6 TCGA-WE-A8ZY 
        7.23       111.09        42.08        24.03        17.95        49.51 
TCGA-WE-AAA0 TCGA-YD-A9TA TCGA-YG-AA3P TCGA-Z2-AA3S 
       40.41        49.18        14.43        96.99 

$`DEL PEAK 13(8P23.3) WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-D3-A8GI TCGA-EB-A5SG TCGA-EB-A5SH 
       62.07        46.32        13.87        58.52        68.25        54.02 
TCGA-EE-A180 TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR 
       94.98        68.15       168.26       340.14       126.81       134.40 
TCGA-EE-A3JD TCGA-ER-A193 TCGA-FR-A729 TCGA-FS-A1ZF TCGA-WE-A8K5 TCGA-3N-A9WB 
       27.35        31.40       220.80        15.45        61.15        17.03 
TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 
       12.99        14.93        16.67       112.04       112.57        71.80 
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J7 TCGA-D3-A2J8 
      133.25        28.08        90.90        95.74       103.10        65.49 
TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JN 
       23.77       168.00        86.76        42.08        12.10        66.48 
TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF 
       59.57       130.72       166.52        86.93        60.23        24.53 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
      103.59        39.75        45.30       174.84        55.73        56.35 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GO 
      145.12        32.94        63.81        26.89       125.79       137.92 
TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GK 
      178.32       125.19        30.84        26.43       241.38       170.20 
TCGA-D3-A8GL TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS 
       89.13       161.00       152.75        29.06       129.63       117.17 
TCGA-D9-A149 TCGA-D9-A1JX TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 
       54.67         7.10        18.12        15.39        22.29        18.44 
TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW 
        9.90        25.18        77.56        22.95        76.57        36.03 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
      144.89        20.38       222.51       176.55        35.93       135.02 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 
       88.87        53.92        40.60        68.09        33.93       225.96 
TCGA-DA-A3F8 TCGA-DA-A95W TCGA-DA-A95X TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A44R 
       43.36        37.35        73.94        13.02        13.87        10.36 
TCGA-EB-A5KH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EE-A17X TCGA-EE-A17Y 
       20.35        29.29        58.92         7.04        29.82        27.22 
TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F 
        8.65        33.73        14.70         4.96       133.81        91.56 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G 
       13.55        63.35        85.08        13.97        63.78        72.07 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T 
       18.61        56.42        66.74        14.47        61.28       369.93 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A6 TCGA-EE-A2GB 
      195.02        17.92        46.82       115.96        86.14        59.28 
TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       67.43       173.79       220.24       107.38        54.74        79.66 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GT TCGA-EE-A2GU 
       75.48       102.12        13.91        42.77        44.88        94.82 
TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD 
       21.67       129.27        28.83        19.76        61.51        47.28 
TCGA-EE-A2ME TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MQ TCGA-EE-A2MT 
      103.27        96.23       180.39       216.66        43.23        71.21 
TCGA-EE-A3AA TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J4 
      124.31        28.77        54.51        13.81       138.81       127.20 
TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JE 
       36.95        64.08        34.32        53.19       201.80        51.35 
TCGA-EE-A3JH TCGA-ER-A195 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19F 
      134.33        35.44        77.75        98.40        12.59        26.37 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P 
      302.07       152.35       131.51        61.05        44.09       162.08 
TCGA-ER-A19Q TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NG 
       50.89       148.18       105.07        43.82        20.15        48.99 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A42L TCGA-FR-A3YN 
       41.56       247.04        93.01        46.98       149.03        92.98 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YD 
      174.21        15.72        27.85        18.77        38.27        36.26 
TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 
      104.42       216.92        48.59        20.91        28.08         7.79 
TCGA-FS-A1ZB TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZK 
       48.85        53.52        46.45         9.70        32.75        23.93 
TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZU 
      101.26        74.73       133.55        11.41       148.80        26.56 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 
       49.48        27.09        27.02        77.82        50.14        66.67 
TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FW-A3I3 
       28.73       174.84        34.03        26.73        54.41        17.46 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
       55.59        13.51        19.30         9.90        19.43         2.04 
TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
       15.78       139.89        10.13        64.44        62.79        32.48 
TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A4U9 
       48.00       121.91        39.35        10.42        48.89        22.13 
TCGA-GN-A8LK TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OG TCGA-HR-A2OH TCGA-LH-A9QB 
       50.10        21.37        59.41         0.23        65.88       368.78 
TCGA-RP-A690 TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 
        0.20         0.33         0.69       228.16        63.02       121.08 
TCGA-W3-AA1O TCGA-W3-AA1Q TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8ZM 
        4.01        69.07       219.16       105.04        49.05       101.33 
TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-AA9Y 
       58.98        70.52        63.22        11.80        35.80        12.16 
TCGA-WE-AAA4 TCGA-XV-AB01 TCGA-YD-A89C TCGA-YG-AA3O TCGA-Z2-A8RT TCGA-Z2-AA3V 
       24.99        13.25         6.90        37.94        27.58        15.98 

  DEL PEAK 13(8P23.3) MUTATED DEL PEAK 13(8P23.3) WILD-TYPE 
                          2.6                           0.2 
  DEL PEAK 13(8P23.3) MUTATED DEL PEAK 13(8P23.3) WILD-TYPE 
                       357.37                        369.93 
  DEL PEAK 13(8P23.3) MUTATED DEL PEAK 13(8P23.3) WILD-TYPE 
                       49.035                        54.215 
[1] "2.6 - 357.4 (49.0)" "0.2 - 369.9 (54.2)"
[1] "hr=" "1.2"
D33V3, continuous
                               vv
clus                            I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB
  DEL PEAK 13(8P23.3) MUTATED          3       2       9        6        7
  DEL PEAK 13(8P23.3) WILD-TYPE       10       5      20       12       21
                               vv
clus                            STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK 13(8P23.3) MUTATED          3         3         5         2
  DEL PEAK 13(8P23.3) WILD-TYPE       23        11        14        13
                               vv
clus                            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 13(8P23.3) MUTATED           8          2          8         17
  DEL PEAK 13(8P23.3) WILD-TYPE        31         13         27         37
                               vv
clus                            STAGE IV
  DEL PEAK 13(8P23.3) MUTATED          5
  DEL PEAK 13(8P23.3) WILD-TYPE       16
D33V4, multiclass
            clus
vv           DEL PEAK 13(8P23.3) MUTATED DEL PEAK 13(8P23.3) WILD-TYPE
  I/II NOS                             3                            10
  STAGE 0                              2                             5
  STAGE I                              9                            20
  STAGE IA                             6                            12
  STAGE IB                             7                            21
  STAGE II                             3                            23
  STAGE IIA                            3                            11
  STAGE IIB                            5                            14
  STAGE IIC                            2                            13
  STAGE III                            8                            31
  STAGE IIIA                           2                            13
  STAGE IIIB                           8                            27
  STAGE IIIC                          17                            37
  STAGE IV                             5                            16
[1] 14  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3 T4
  DEL PEAK 13(8P23.3) MUTATED      18 20 12 17
  DEL PEAK 13(8P23.3) WILD-TYPE    46 53 69 50
D33V5, multiclass
       clus
vv      DEL PEAK 13(8P23.3) MUTATED DEL PEAK 13(8P23.3) WILD-TYPE
  T0+T1                          18                            46
  T2                             20                            53
  T3                             12                            69
  T4                             17                            50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  DEL PEAK 13(8P23.3) MUTATED    39  12  10  18
  DEL PEAK 13(8P23.3) WILD-TYPE 138  53  29  27
D33V6, multiclass
    clus
vv   DEL PEAK 13(8P23.3) MUTATED DEL PEAK 13(8P23.3) WILD-TYPE
  N0                          39                           138
  N1                          12                            53
  N2                          10                            29
  N3                          18                            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"
D33V7, binary
                               cls
clus                              0   1
  DEL PEAK 13(8P23.3) MUTATED    77   6
  DEL PEAK 13(8P23.3) WILD-TYPE 242  16
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(8P23.3) MUTATED     77    6
  DEL PEAK 13(8P23.3) WILD-TYPE  242   16
   clus
vv  DEL PEAK 13(8P23.3) MUTATED DEL PEAK 13(8P23.3) WILD-TYPE
  0                          77                           242
  1                           6                            16
[1] 2 2
[1] FALSE
D33V8, binary
                               cls
clus                              0   1
  DEL PEAK 13(8P23.3) MUTATED    32  23
  DEL PEAK 13(8P23.3) WILD-TYPE 102  67
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(8P23.3) MUTATED     32   23
  DEL PEAK 13(8P23.3) WILD-TYPE  102   67
     clus
vv    DEL PEAK 13(8P23.3) MUTATED DEL PEAK 13(8P23.3) WILD-TYPE
  NO                           32                           102
  YES                          23                            67
[1] 2 2
[1] FALSE
D33V9, binary
                               cls
clus                              0   1
  DEL PEAK 13(8P23.3) MUTATED    12  77
  DEL PEAK 13(8P23.3) WILD-TYPE  35 243
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(8P23.3) MUTATED     12   77
  DEL PEAK 13(8P23.3) WILD-TYPE   35  243
     clus
vv    DEL PEAK 13(8P23.3) MUTATED DEL PEAK 13(8P23.3) WILD-TYPE
  NO                           12                            35
  YES                          77                           243
[1] 2 2
[1] FALSE
D33V10, continuous
D33V11, binary
                               cls
clus                              0   1
  DEL PEAK 13(8P23.3) MUTATED    31  58
  DEL PEAK 13(8P23.3) WILD-TYPE 107 171
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(8P23.3) MUTATED     31   58
  DEL PEAK 13(8P23.3) WILD-TYPE  107  171
        clus
vv       DEL PEAK 13(8P23.3) MUTATED DEL PEAK 13(8P23.3) WILD-TYPE
  FEMALE                          31                           107
  MALE                            58                           171
[1] 2 2
[1] FALSE
D33V12, binary
                               cls
clus                              0   1
  DEL PEAK 13(8P23.3) MUTATED    79  10
  DEL PEAK 13(8P23.3) WILD-TYPE 240  37
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(8P23.3) MUTATED     79   10
  DEL PEAK 13(8P23.3) WILD-TYPE  240   37
     clus
vv    DEL PEAK 13(8P23.3) MUTATED DEL PEAK 13(8P23.3) WILD-TYPE
  NO                           79                           240
  YES                          10                            37
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 13(8P23.3) MUTATED       1                         0    86
  DEL PEAK 13(8P23.3) WILD-TYPE     4                         1   267
D33V13, multiclass
                           clus
vv                          DEL PEAK 13(8P23.3) MUTATED
  ASIAN                                               1
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                              86
                           clus
vv                          DEL PEAK 13(8P23.3) WILD-TYPE
  ASIAN                                                 4
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                               267
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V14, binary
                               cls
clus                              0   1
  DEL PEAK 13(8P23.3) MUTATED     1  87
  DEL PEAK 13(8P23.3) WILD-TYPE   6 265
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(8P23.3) MUTATED      1   87
  DEL PEAK 13(8P23.3) WILD-TYPE    6  265
                        clus
vv                       DEL PEAK 13(8P23.3) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          87
                        clus
vv                       DEL PEAK 13(8P23.3) WILD-TYPE
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                           265
[1] 2 2
[1] FALSE

Clustering(34) Variable = DEL PEAK 14(9P23) MUTATION ANALYSIS
D34V1, survival
                             sevent
clus2                          0  1
  DEL PEAK 14(9P23) MUTATED   79 90
  DEL PEAK 14(9P23) WILD-TYPE 49 34
  DEL PEAK 14(9P23) MUTATED DEL PEAK 14(9P23) WILD-TYPE 
                        169                          83 
  DEL PEAK 14(9P23) MUTATED DEL PEAK 14(9P23) WILD-TYPE 
                         90                          34 
$`DEL PEAK 14(9P23) MUTATED`
TCGA-D3-A2JF TCGA-D3-A8GI TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GD 
       62.07        13.41        33.24        31.96       166.75       269.03 
TCGA-EE-A2GO TCGA-EE-A2MR TCGA-ER-A193 TCGA-FR-A729 TCGA-FW-A3R5 TCGA-WE-A8K5 
       52.90       134.40        19.04       216.43        36.95        52.73 
TCGA-WE-AAA3 TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 
        7.40        14.83         8.42        31.89       110.93        49.35 
TCGA-D3-A1Q8 TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2JB TCGA-D3-A2JL TCGA-D3-A2JN 
       19.04        25.64        45.99       168.00       171.58        64.83 
TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR 
       43.53        58.06        40.01        24.53         9.34        90.21 
TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51J TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GR 
       23.67       173.85       144.46        11.34        42.05       177.86 
TCGA-D3-A5GU TCGA-D3-A8GC TCGA-D3-A8GL TCGA-D3-A8GP TCGA-D9-A3Z1 TCGA-D9-A3Z3 
      124.08        78.21        69.53       135.12        15.02        16.90 
TCGA-D9-A4Z6 TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 
       18.44        22.85        76.34       138.67        68.68       150.61 
TCGA-DA-A1I5 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A95V TCGA-DA-A95X TCGA-DA-A95Y 
      110.53        64.83        58.85        72.10        65.03        14.14 
TCGA-EB-A44Q TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A182 
        3.91        52.41        13.15        24.89        20.38         0.00 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G 
       75.55        79.20        76.14        12.99         0.26        44.28 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A6 TCGA-EE-A2GB 
       27.16        61.12       346.49       185.19        77.98        26.14 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP 
       12.95       201.60        32.48        18.35        93.63         0.76 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M8 TCGA-EE-A2MF 
        0.20        71.31        81.99       103.13         5.75       209.79 
TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MS 
      171.85        89.26       104.78       145.45       227.01       143.93 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J3 
      124.31       122.73         4.41        54.51         6.28        67.89 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 
       45.90         3.35       168.85        19.86       135.98        34.45 
TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19H 
       10.49         7.82        53.29        39.81        11.47       150.12 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S 
       99.06        59.84        42.51       120.76        49.71        47.18 
TCGA-ER-A19W TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3EV 
      146.63         4.70        16.87        28.67       173.29        15.48 
TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7U8 
       32.05        74.47         4.50       174.21         4.14        26.20 
TCGA-FR-A8YC TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1ZC TCGA-FS-A1ZD 
       10.06       171.78        49.74         8.35       312.07        32.78 
TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A1ZY 
       78.61       130.95       136.27        35.28        23.21         5.29 
TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F9 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-GF-A4EO 
       30.90        66.67        13.28        55.59        11.54        18.25 
TCGA-GF-A6C8 TCGA-GN-A264 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 
        1.91       117.93        42.48         7.59       120.53        34.49 
TCGA-GN-A8LK TCGA-GN-A9SD TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A693 TCGA-W3-A825 
       43.23        59.41       297.01         7.23         0.33         1.97 
TCGA-W3-A828 TCGA-W3-AA1R TCGA-W3-AA1V TCGA-W3-AA21 TCGA-WE-A8ZM TCGA-WE-A8ZN 
      120.07        79.99         8.09        92.84        65.42        12.69 
TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA4 TCGA-YG-AA3O 
       21.90        62.89        48.39         1.94        24.99        28.21 
TCGA-Z2-AA3S 
       91.23 

$`DEL PEAK 14(9P23) WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A3C8 TCGA-EE-A3JD TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q3 
        9.76        38.76        27.35        60.46        12.99        15.72 
TCGA-D3-A1Q7 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JC 
      133.25        76.41        62.60        62.86        15.75        86.30 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JO TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A51F 
      107.61        36.30        66.08       140.98        59.70        30.67 
TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A8GD TCGA-D3-A8GJ TCGA-D3-A8GK 
       31.76        62.70        45.70        23.61       179.97       120.00 
TCGA-D3-A8GM TCGA-D3-A8GR TCGA-D9-A1X3 TCGA-D9-A6EC TCGA-DA-A1I7 TCGA-DA-A3F2 
       70.62        36.53        10.78        69.21        60.10        30.44 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-DA-A95W TCGA-DA-A95Z TCGA-EB-A5KH TCGA-EB-A6L9 
      225.11         8.71         0.76        12.30        16.41        18.21 
TCGA-EE-A183 TCGA-EE-A29B TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A2A1 TCGA-EE-A2A2 
       26.24        75.22        47.41        47.74       115.43        30.02 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2M7 TCGA-EE-A2MC TCGA-EE-A2MG TCGA-EE-A2MJ 
       68.65        10.62        15.25        23.77        94.19        63.25 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AC TCGA-EE-A3J4 TCGA-ER-A19A TCGA-ER-A19G 
       23.51        53.26        64.04       111.85         4.54       184.60 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NF TCGA-ER-A3ET TCGA-FR-A7UA TCGA-FS-A1Z0 
       73.05        22.36        10.19        68.52         5.65       195.98 
TCGA-FS-A1Z4 TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZU TCGA-FS-A1ZZ 
       27.62        43.92         7.82        36.33         4.47         3.06 
TCGA-FS-A4F8 TCGA-FS-A4FD TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GN-A262 TCGA-GN-A265 
      173.19        80.68        19.30         9.90        53.29        96.92 
TCGA-GN-A267 TCGA-GN-A4U8 TCGA-LH-A9QB TCGA-RP-A690 TCGA-W3-A824 TCGA-W3-AA1Q 
       17.06        46.92        85.05         0.20       174.12        44.05 
TCGA-W3-AA1W TCGA-WE-A8K1 TCGA-WE-A8ZT TCGA-WE-AAA0 TCGA-XV-AB01 
      185.13        47.54        10.95        37.32         6.61 

  DEL PEAK 14(9P23) MUTATED DEL PEAK 14(9P23) WILD-TYPE 
                        0.0                         0.2 
  DEL PEAK 14(9P23) MUTATED DEL PEAK 14(9P23) WILD-TYPE 
                     346.49                      225.11 
  DEL PEAK 14(9P23) MUTATED DEL PEAK 14(9P23) WILD-TYPE 
                      48.39                       44.05 
[1] "0.0 - 346.5 (48.4)" "0.2 - 225.1 (44.0)"
[1] "hr=" "1.1"
D34V2, survival
                             sevent
clus2                           0   1
  DEL PEAK 14(9P23) MUTATED   103 138
  DEL PEAK 14(9P23) WILD-TYPE  63  54
  DEL PEAK 14(9P23) MUTATED DEL PEAK 14(9P23) WILD-TYPE 
                        241                         117 
  DEL PEAK 14(9P23) MUTATED DEL PEAK 14(9P23) WILD-TYPE 
                        138                          54 
$`DEL PEAK 14(9P23) MUTATED`
TCGA-D3-A2JF TCGA-D3-A3ML TCGA-D3-A8GI TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A20H 
       62.07        13.87        58.52        68.25        94.98       168.26 
TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR TCGA-ER-A193 TCGA-FR-A729 
        2.60       340.14       126.81       134.40        31.40       220.80 
TCGA-FS-A1ZF TCGA-FW-A3R5 TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-BF-AAP0 TCGA-D3-A1Q1 
       15.45        36.95        61.15        21.40        14.93        16.57 
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q8 TCGA-D3-A2J6 TCGA-D3-A2J7 
      112.04       112.57        71.80        28.08        43.43       103.10 
TCGA-D3-A2JB TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3C6 
      168.00        12.10       171.58        66.48        59.57        58.06 
TCGA-D3-A3C7 TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU 
       46.98        86.93        24.53         9.34       103.59        39.75 
TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51J TCGA-D3-A51N TCGA-D3-A51T TCGA-D3-A5GL 
       45.30       174.84       145.12        22.62        26.89       125.79 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GC 
      137.92       178.32        18.18       125.19        30.84        79.59 
TCGA-D3-A8GL TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GS TCGA-D3-A8GV TCGA-D9-A149 
       89.13       161.00       152.75       117.17       167.70        54.67 
TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EA 
        7.10        15.39        22.29        18.44         9.90        25.18 
TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 
       22.95        76.57        36.03       144.89       222.51       176.55 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F3 
       35.93       135.02        53.92        65.92        68.09        10.49 
TCGA-DA-A95V TCGA-DA-A95X TCGA-DA-A95Y TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5UL 
       72.10        73.94        14.14        13.87        10.36        29.29 
TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A185 
       58.92        29.82        27.22        33.73        14.70         4.96 
TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29C TCGA-EE-A29D 
      133.81       151.27        91.56        13.55        78.97        13.97 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29S 
       63.78        72.07        18.61        56.42        66.74        61.28 
TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A5 
      369.93        25.87       195.02        17.92        46.82        39.29 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
       86.14        59.28        67.43       173.79       220.24        48.72 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
       79.66        75.48       102.12        13.91        42.77        81.21 
TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M8 TCGA-EE-A2MD TCGA-EE-A2MF 
       94.82        21.67       129.27        19.76        47.28       268.73 
TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN 
       16.96       204.66       180.39       216.66       167.90        47.54 
TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE 
      248.65       162.48       124.31       122.73        28.77        54.51 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-EE-A3J8 
       13.81        41.59       138.81       172.18        64.08        34.32 
TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 
       53.19       201.80       134.33       152.81        35.44        13.94 
TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F 
        9.17        98.40        48.89        12.59        13.02        26.37 
TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
      152.35       131.51        61.05        44.09       162.08        50.89 
TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NG 
       49.48         8.88       148.18        23.34        20.15        48.99 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-ER-A42L 
       41.56       247.04        46.98        33.21        12.95       149.03 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A8YC TCGA-FR-A8YE 
       92.98       174.21        15.72        27.85        34.82       104.42 
TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1Z7 TCGA-FS-A1ZA 
      216.92        48.59       228.59        20.91         7.79        27.72 
TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZH TCGA-FS-A1ZM TCGA-FS-A1ZQ 
       48.85       357.37        53.52        32.75       101.26       133.55 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F0 
       11.41       148.80        53.16        49.48        27.09        77.82 
TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC 
       50.14        66.67        28.73        34.03        26.73        54.41 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A264 
       55.59        13.51        19.43         2.04        15.78       117.93 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 
       62.79        32.48        48.00       121.91        39.35        10.42 
TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OG TCGA-HR-A2OH 
       22.13        50.10        21.37        59.41         0.23        65.88 
TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A825 TCGA-W3-A828 
      297.90         7.23         0.33         0.69        63.02       121.08 
TCGA-W3-AA1O TCGA-W3-AA1R TCGA-W3-AA1V TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K6 
        4.01       111.09        42.08       105.04        24.03        17.95 
TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZX TCGA-WE-A8ZY 
      101.33        58.98        70.52        63.22        35.80        49.51 
TCGA-WE-AA9Y TCGA-WE-AAA4 TCGA-YD-A9TA TCGA-YG-AA3O TCGA-Z2-A8RT TCGA-Z2-AA3S 
       12.16        24.99        49.18        37.94        27.58        96.99 
TCGA-Z2-AA3V 
       15.98 

$`DEL PEAK 14(9P23) WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A3C8 TCGA-EB-A5SH TCGA-EE-A184 TCGA-EE-A3JD TCGA-ER-A198 
       27.65        46.32        54.02        68.15        27.35        50.76 
TCGA-QB-AA9O TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q3 TCGA-D3-A1Q7 
       18.05        17.03        66.48        12.99        16.67       133.25 
TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA 
       31.59        90.90        95.74        65.49        23.77       115.53 
TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JO TCGA-D3-A3BZ 
       86.76        11.87       113.52        42.08        66.08       130.72 
TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51K TCGA-D3-A51R 
      166.52        60.23        55.73        56.35        32.94        63.81 
TCGA-D3-A5GN TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GM 
      135.75        23.61        26.43       241.38       170.20       107.15 
TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D9-A148 TCGA-D9-A1JW TCGA-D9-A1X3 TCGA-D9-A6EC 
       29.06       129.63       151.53         3.65        18.12        77.56 
TCGA-DA-A1I0 TCGA-DA-A1I7 TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 
       20.38        88.87        40.60        33.93       225.96        43.36 
TCGA-DA-A95W TCGA-DA-A95Z TCGA-EB-A5KH TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17Z 
       37.35        13.02        20.35         7.04        36.46         8.65 
TCGA-EE-A183 TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29R 
       26.89        63.35        85.08        64.64        56.84        14.47 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GT TCGA-EE-A2M7 
      115.96        59.64       107.38        54.74        44.88        28.83 
TCGA-EE-A2MC TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MJ TCGA-EE-A2MQ TCGA-EE-A2MT 
       61.51       103.27       103.20        96.23        43.23        71.21 
TCGA-EE-A2MU TCGA-EE-A3AC TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3JE TCGA-ER-A19A 
       53.26        64.04       127.20        36.95        51.35        77.75 
TCGA-ER-A19G TCGA-ER-A19J TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NF TCGA-ER-A3ET 
      302.07         6.44       105.07        43.82        28.83        93.01 
TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YD TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1ZE 
       18.77        38.27        36.26       202.65        28.08        46.45 
TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZU TCGA-FS-A1ZZ 
        9.70        47.38        23.93        74.73        26.56        27.02 
TCGA-FS-A4F8 TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GN-A262 
      174.84        80.68        17.46        19.30         9.90       139.89 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A4U8 TCGA-LH-A9QB TCGA-RP-A690 
       96.92        10.13        64.44        48.89       368.78         0.20 
TCGA-W3-A824 TCGA-W3-AA1Q TCGA-W3-AA1W TCGA-WE-A8K1 TCGA-WE-A8ZT TCGA-WE-AAA0 
      228.16        69.07       219.16        49.05        11.80        40.41 
TCGA-XV-AB01 TCGA-YD-A89C TCGA-YG-AA3P 
       13.25         6.90        14.43 

  DEL PEAK 14(9P23) MUTATED DEL PEAK 14(9P23) WILD-TYPE 
                       0.23                        0.20 
  DEL PEAK 14(9P23) MUTATED DEL PEAK 14(9P23) WILD-TYPE 
                     369.93                      368.78 
  DEL PEAK 14(9P23) MUTATED DEL PEAK 14(9P23) WILD-TYPE 
                      53.19                       50.76 
[1] "0.2 - 369.9 (53.2)" "0.2 - 368.8 (50.8)"
[1] "hr=" "1.1"
D34V3, continuous
                             vv
clus                          I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB
  DEL PEAK 14(9P23) MUTATED         12       4      19       11       18
  DEL PEAK 14(9P23) WILD-TYPE        1       3      10        7       10
                             vv
clus                          STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  DEL PEAK 14(9P23) MUTATED         18        10        13        11        28
  DEL PEAK 14(9P23) WILD-TYPE        8         4         6         4        11
                             vv
clus                          STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DEL PEAK 14(9P23) MUTATED            7         26         35       14
  DEL PEAK 14(9P23) WILD-TYPE          8          9         19        7
D34V4, multiclass
            clus
vv           DEL PEAK 14(9P23) MUTATED DEL PEAK 14(9P23) WILD-TYPE
  I/II NOS                          12                           1
  STAGE 0                            4                           3
  STAGE I                           19                          10
  STAGE IA                          11                           7
  STAGE IB                          18                          10
  STAGE II                          18                           8
  STAGE IIA                         10                           4
  STAGE IIB                         13                           6
  STAGE IIC                         11                           4
  STAGE III                         28                          11
  STAGE IIIA                         7                           8
  STAGE IIIB                        26                           9
  STAGE IIIC                        35                          19
  STAGE IV                          14                           7
[1] 14  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          T0+T1 T2 T3 T4
  DEL PEAK 14(9P23) MUTATED      42 53 54 45
  DEL PEAK 14(9P23) WILD-TYPE    22 20 27 22
D34V5, multiclass
       clus
vv      DEL PEAK 14(9P23) MUTATED DEL PEAK 14(9P23) WILD-TYPE
  T0+T1                        42                          22
  T2                           53                          20
  T3                           54                          27
  T4                           45                          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  N3
  DEL PEAK 14(9P23) MUTATED   121  45  25  28
  DEL PEAK 14(9P23) WILD-TYPE  56  20  14  17
D34V6, multiclass
    clus
vv   DEL PEAK 14(9P23) MUTATED DEL PEAK 14(9P23) WILD-TYPE
  N0                       121                          56
  N1                        45                          20
  N2                        25                          14
  N3                        28                          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"
D34V7, binary
                             cls
clus                            0   1
  DEL PEAK 14(9P23) MUTATED   217  14
  DEL PEAK 14(9P23) WILD-TYPE 102   8
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 14(9P23) MUTATED    217   14
  DEL PEAK 14(9P23) WILD-TYPE  102    8
   clus
vv  DEL PEAK 14(9P23) MUTATED DEL PEAK 14(9P23) WILD-TYPE
  0                       217                         102
  1                        14                           8
[1] 2 2
[1] FALSE
D34V8, binary
                             cls
clus                           0  1
  DEL PEAK 14(9P23) MUTATED   92 59
  DEL PEAK 14(9P23) WILD-TYPE 42 31
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 14(9P23) MUTATED     92   59
  DEL PEAK 14(9P23) WILD-TYPE   42   31
     clus
vv    DEL PEAK 14(9P23) MUTATED DEL PEAK 14(9P23) WILD-TYPE
  NO                         92                          42
  YES                        59                          31
[1] 2 2
[1] FALSE
D34V9, binary
                             cls
clus                            0   1
  DEL PEAK 14(9P23) MUTATED    29 220
  DEL PEAK 14(9P23) WILD-TYPE  18 100
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 14(9P23) MUTATED     29  220
  DEL PEAK 14(9P23) WILD-TYPE   18  100
     clus
vv    DEL PEAK 14(9P23) MUTATED DEL PEAK 14(9P23) WILD-TYPE
  NO                         29                          18
  YES                       220                         100
[1] 2 2
[1] FALSE
D34V10, continuous
D34V11, binary
                             cls
clus                            0   1
  DEL PEAK 14(9P23) MUTATED    99 150
  DEL PEAK 14(9P23) WILD-TYPE  39  79
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 14(9P23) MUTATED     99  150
  DEL PEAK 14(9P23) WILD-TYPE   39   79
        clus
vv       DEL PEAK 14(9P23) MUTATED DEL PEAK 14(9P23) WILD-TYPE
  FEMALE                        99                          39
  MALE                         150                          79
[1] 2 2
[1] FALSE
D34V12, binary
                             cls
clus                            0   1
  DEL PEAK 14(9P23) MUTATED   222  27
  DEL PEAK 14(9P23) WILD-TYPE  97  20
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 14(9P23) MUTATED    222   27
  DEL PEAK 14(9P23) WILD-TYPE   97   20
     clus
vv    DEL PEAK 14(9P23) MUTATED DEL PEAK 14(9P23) WILD-TYPE
  NO                        222                          97
  YES                        27                          20
[1] 2 2
[1] FALSE
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 14(9P23) MUTATED       3                         1   238
  DEL PEAK 14(9P23) WILD-TYPE     2                         0   115
D34V13, multiclass
                           clus
vv                          DEL PEAK 14(9P23) MUTATED
  ASIAN                                             3
  BLACK OR AFRICAN AMERICAN                         1
  WHITE                                           238
                           clus
vv                          DEL PEAK 14(9P23) WILD-TYPE
  ASIAN                                               2
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                             115
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V14, binary
                             cls
clus                            0   1
  DEL PEAK 14(9P23) MUTATED     2 241
  DEL PEAK 14(9P23) WILD-TYPE   5 111
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 14(9P23) MUTATED      2  241
  DEL PEAK 14(9P23) WILD-TYPE    5  111
                        clus
vv                       DEL PEAK 14(9P23) MUTATED DEL PEAK 14(9P23) WILD-TYPE
  HISPANIC OR LATINO                             2                           5
  NOT HISPANIC OR LATINO                       241                         111
[1] 2 2
[1] FALSE

Clustering(35) Variable = DEL PEAK 15(9P21.3) MUTATION ANALYSIS
D35V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 15(9P21.3) MUTATED    90 100
  DEL PEAK 15(9P21.3) WILD-TYPE  38  24
  DEL PEAK 15(9P21.3) MUTATED DEL PEAK 15(9P21.3) WILD-TYPE 
                          190                            62 
  DEL PEAK 15(9P21.3) MUTATED DEL PEAK 15(9P21.3) WILD-TYPE 
                          100                            24 
$`DEL PEAK 15(9P21.3) MUTATED`
TCGA-D3-A2JF TCGA-D3-A8GI TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GD 
       62.07        13.41        33.24        31.96       166.75       269.03 
TCGA-EE-A2GO TCGA-EE-A2MR TCGA-ER-A193 TCGA-FR-A729 TCGA-FW-A3R5 TCGA-WE-A8K5 
       52.90       134.40        19.04       216.43        36.95        52.73 
TCGA-WE-AAA3 TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 
        7.40        14.83         8.42        31.89       110.93        49.35 
TCGA-D3-A1Q8 TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JL 
       19.04        25.64        45.99       168.00        86.30       171.58 
TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF 
       64.83        43.53        58.06        40.01        59.70        24.53 
TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51J TCGA-D3-A51R 
        9.34        90.21        23.67       173.85       144.46        62.70 
TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D3-A8GD TCGA-D3-A8GL 
       11.34        42.05       177.86       124.08        23.61        69.53 
TCGA-D3-A8GP TCGA-D3-A8GR TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 
      135.12        36.53        10.78        15.02        16.90        18.44 
TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 
       22.85        76.34       138.67        68.68       150.61       110.53 
TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F5 TCGA-DA-A95V TCGA-DA-A95X 
       60.10        64.83        58.85       225.11        72.10        65.03 
TCGA-DA-A95Y TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y 
       14.14         3.91        16.41        52.41        13.15        24.89 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29D 
       20.38         0.00        75.55        79.20        76.14        12.99 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T 
        0.26        44.28        47.41        27.16        61.12       346.49 
TCGA-EE-A29W TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GL 
      185.19        77.98        26.14        12.95       201.60        32.48 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU 
       18.35        93.63         0.76         0.20        71.31        81.99 
TCGA-EE-A2M6 TCGA-EE-A2M8 TCGA-EE-A2MF TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML 
      103.13         5.75       209.79       171.85        89.26       104.78 
TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC 
      145.45       227.01       143.93       124.31       122.73        64.04 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 
        4.41        54.51         6.28        67.89       111.85        45.90 
TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 
        3.35       168.85        19.86       135.98        34.45        10.49 
TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19H 
        7.82        53.29        39.81        11.47       184.60       150.12 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S 
       99.06        59.84        42.51       120.76        49.71        47.18 
TCGA-ER-A19W TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A3ES 
      146.63        22.36         4.70        16.87        28.67       173.29 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       15.48        32.05        74.47         4.50       174.21         4.14 
TCGA-FR-A7U8 TCGA-FR-A8YC TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
       26.20        10.06       171.78        49.74       195.98         8.35 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM 
      312.07        32.78        43.92         7.82        36.33        78.61 
TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F0 
      130.95       136.27        35.28        23.21         5.29        30.90 
TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-GF-A4EO 
       66.67       173.19        13.28        55.59        11.54        18.25 
TCGA-GF-A6C8 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 
        1.91       117.93        96.92        42.48         7.59       120.53 
TCGA-GN-A4U4 TCGA-GN-A8LK TCGA-GN-A9SD TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS 
       34.49        43.23        59.41        85.05       297.01         7.23 
TCGA-RP-A693 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1R TCGA-W3-AA1V TCGA-W3-AA21 
        0.33         1.97       120.07        79.99         8.09        92.84 
TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZY 
       65.42        12.69        21.90        62.89        10.95        48.39 
TCGA-WE-AA9Y TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-Z2-AA3S 
        1.94        24.99        28.21        91.23 

$`DEL PEAK 15(9P21.3) WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A3C8 TCGA-EE-A3JD TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q3 
        9.76        38.76        27.35        60.46        12.99        15.72 
TCGA-D3-A1Q7 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JG 
      133.25        76.41        62.60        62.86        15.75       107.61 
TCGA-D3-A2JH TCGA-D3-A2JO TCGA-D3-A3CB TCGA-D3-A51F TCGA-D3-A51K TCGA-D3-A5GN 
       36.30        66.08       140.98        30.67        31.76        45.70 
TCGA-D3-A8GC TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GM TCGA-D9-A6EC TCGA-DA-A3F2 
       78.21       179.97       120.00        70.62        69.21        30.44 
TCGA-DA-A3F8 TCGA-DA-A95W TCGA-DA-A95Z TCGA-EB-A6L9 TCGA-EE-A183 TCGA-EE-A29B 
        8.71         0.76        12.30        18.21        26.24        75.22 
TCGA-EE-A29M TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2M7 
       47.74       115.43        30.02        68.65        10.62        15.25 
TCGA-EE-A2MC TCGA-EE-A2MG TCGA-EE-A2MJ TCGA-EE-A2MT TCGA-EE-A2MU TCGA-ER-A19A 
       23.77        94.19        63.25        23.51        53.26         4.54 
TCGA-ER-A1A1 TCGA-ER-A2NF TCGA-ER-A3ET TCGA-FR-A7UA TCGA-FS-A1Z4 TCGA-FS-A1ZU 
       73.05        10.19        68.52         5.65        27.62         4.47 
TCGA-FS-A1ZZ TCGA-FS-A4FD TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GN-A262 TCGA-GN-A267 
        3.06        80.68        19.30         9.90        53.29        17.06 
TCGA-GN-A4U8 TCGA-RP-A690 TCGA-W3-A824 TCGA-W3-AA1Q TCGA-W3-AA1W TCGA-WE-A8K1 
       46.92         0.20       174.12        44.05       185.13        47.54 
TCGA-WE-AAA0 TCGA-XV-AB01 
       37.32         6.61 

  DEL PEAK 15(9P21.3) MUTATED DEL PEAK 15(9P21.3) WILD-TYPE 
                          0.0                           0.2 
  DEL PEAK 15(9P21.3) MUTATED DEL PEAK 15(9P21.3) WILD-TYPE 
                       346.49                        185.13 
  DEL PEAK 15(9P21.3) MUTATED DEL PEAK 15(9P21.3) WILD-TYPE 
                        48.87                         38.04 
[1] "0.0 - 346.5 (48.9)" "0.2 - 185.1 (38.0)"
[1] "hr=" "1"  
D35V2, survival
                               sevent
clus2                             0   1
  DEL PEAK 15(9P21.3) MUTATED   118 152
  DEL PEAK 15(9P21.3) WILD-TYPE  48  40
  DEL PEAK 15(9P21.3) MUTATED DEL PEAK 15(9P21.3) WILD-TYPE 
                          270                            88 
  DEL PEAK 15(9P21.3) MUTATED DEL PEAK 15(9P21.3) WILD-TYPE 
                          152                            40 
$`DEL PEAK 15(9P21.3) MUTATED`
TCGA-D3-A2JF TCGA-D3-A3ML TCGA-D3-A8GI TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A20H 
       62.07        13.87        58.52        68.25        94.98       168.26 
TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR TCGA-ER-A193 TCGA-FR-A729 
        2.60       340.14       126.81       134.40        31.40       220.80 
TCGA-FS-A1ZF TCGA-FW-A3R5 TCGA-QB-AA9O TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-3N-A9WB 
       15.45        36.95        18.05        61.15        21.40        17.03 
TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q8 
       14.93        16.57       112.04       112.57        71.80        28.08 
TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JK TCGA-D3-A2JL 
       43.43       103.10       168.00        86.76        12.10       171.58 
TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CC TCGA-D3-A3CE 
       66.48        59.57        58.06        46.98        86.93        60.23 
TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E 
       24.53         9.34       103.59        39.75        45.30       174.84 
TCGA-D3-A51J TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GO 
      145.12        22.62        63.81        26.89       125.79       137.92 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GD TCGA-D3-A8GE 
      178.32        18.18       125.19        30.84        23.61        26.43 
TCGA-D3-A8GL TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D3-A8GV 
       89.13       161.00       152.75       129.63       117.17       167.70 
TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JX TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 
      151.53        54.67         7.10        18.12        15.39        22.29 
TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY 
       18.44         9.90        22.95        76.57        36.03       144.89 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
      222.51       176.55        35.93       135.02        88.87        53.92 
TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A95V TCGA-DA-A95X 
       65.92        68.09        10.49       225.96        72.10        73.94 
TCGA-DA-A95Y TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5UL TCGA-EB-A5UN 
       14.14        13.87        10.36        20.35        29.29        58.92 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A185 TCGA-EE-A20B 
       29.82        27.22        33.73        14.70         4.96       133.81 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29D 
      151.27        91.56        13.55        63.35        78.97        13.97 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
       63.78        72.07        64.64        18.61        56.42        66.74 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X 
       14.47        61.28       369.93        25.87       195.02        17.92 
TCGA-EE-A2A0 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GE 
       46.82        39.29        86.14        59.28        67.43       173.79 
TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP 
      220.24        48.72        79.66        75.48       102.12        13.91 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M8 
       42.77        81.21        94.82        21.67       129.27        19.76 
TCGA-EE-A2MD TCGA-EE-A2MF TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML 
       47.28       268.73        16.96       204.66       180.39       216.66 
TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A3AA TCGA-EE-A3AB 
      167.90        47.54       248.65       162.48       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH 
       64.04        28.77        54.51        13.81        41.59       138.81 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB 
      172.18       127.20        64.08        34.32        53.19       201.80 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 
       51.35       134.33       152.81        35.44        13.94         9.17 
TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G 
       98.40        48.89        12.59        13.02        26.37       302.07 
TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P 
      152.35         6.44       131.51        61.05        44.09       162.08 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A2NC TCGA-ER-A2ND 
       50.89        49.48         8.88       148.18        43.82        23.34 
TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3EV TCGA-ER-A3PL 
       20.15        48.99        41.56       247.04        46.98        33.21 
TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7U8 
       12.95       149.03        92.98       174.21        15.72        27.85 
TCGA-FR-A7U9 TCGA-FR-A8YC TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
       18.77        34.82       216.92        48.59       228.59       202.65 
TCGA-FS-A1Z3 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD 
       20.91         7.79        27.72        48.85       357.37        53.52 
TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ 
       46.45         9.70        32.75        47.38       101.26       133.55 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F0 
       11.41       148.80        53.16        49.48        27.09        77.82 
TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB 
       50.14        66.67        28.73       174.84        34.03        26.73 
TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-GF-A4EO TCGA-GF-A6C8 
       54.41        17.46        55.59        13.51        19.43         2.04 
TCGA-GF-A6C9 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
       15.78       117.93        96.92        62.79        32.48        48.00 
TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL 
      121.91        39.35        10.42        22.13        50.10        21.37 
TCGA-GN-A9SD TCGA-HR-A2OG TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS 
       59.41         0.23        65.88       368.78       297.90         7.23 
TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1R 
        0.33         0.69        63.02       121.08         4.01       111.09 
TCGA-W3-AA1V TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN 
       42.08       105.04        24.03        17.95       101.33        58.98 
TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AA9Y 
       70.52        63.22        11.80        35.80        49.51        12.16 
TCGA-WE-AAA4 TCGA-YD-A9TA TCGA-YG-AA3O TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       24.99        49.18        37.94        27.58        96.99        15.98 

$`DEL PEAK 15(9P21.3) WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A3C8 TCGA-EB-A5SH TCGA-EE-A184 TCGA-EE-A3JD TCGA-ER-A198 
       27.65        46.32        54.02        68.15        27.35        50.76 
TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q3 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A1QA 
       66.48        12.99        16.67       133.25        31.59        90.90 
TCGA-D3-A1QB TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JD TCGA-D3-A2JG 
       95.74        65.49        23.77       115.53        11.87       113.52 
TCGA-D3-A2JH TCGA-D3-A2JO TCGA-D3-A3BZ TCGA-D3-A3CB TCGA-D3-A51F TCGA-D3-A51H 
       42.08        66.08       130.72       166.52        55.73        56.35 
TCGA-D3-A51K TCGA-D3-A5GN TCGA-D3-A8GC TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GM 
       32.94       135.75        79.59       241.38       170.20       107.15 
TCGA-D3-A8GQ TCGA-D9-A1JW TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1I0 TCGA-DA-A1IB 
       29.06         3.65        25.18        77.56        20.38        40.60 
TCGA-DA-A3F2 TCGA-DA-A3F8 TCGA-DA-A95W TCGA-DA-A95Z TCGA-EB-A5VV TCGA-EB-A6L9 
       33.93        43.36        37.35        13.02         7.04        36.46 
TCGA-EE-A17Z TCGA-EE-A183 TCGA-EE-A29B TCGA-EE-A29M TCGA-EE-A2A1 TCGA-EE-A2A2 
        8.65        26.89        85.08        56.84       115.96        59.64 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GT TCGA-EE-A2M7 TCGA-EE-A2MC TCGA-EE-A2ME 
      107.38        54.74        44.88        28.83        61.51       103.27 
TCGA-EE-A2MG TCGA-EE-A2MJ TCGA-EE-A2MQ TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3J5 
      103.20        96.23        43.23        71.21        53.26        36.95 
TCGA-ER-A19A TCGA-ER-A1A1 TCGA-ER-A2NF TCGA-ER-A3ET TCGA-FR-A7UA TCGA-FR-A8YD 
       77.75       105.07        28.83        93.01        38.27        36.26 
TCGA-FR-A8YE TCGA-FS-A1Z4 TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZU TCGA-FS-A1ZZ 
      104.42        28.08        23.93        74.73        26.56        27.02 
TCGA-FS-A4FD TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GN-A262 TCGA-GN-A266 TCGA-GN-A267 
       80.68        19.30         9.90       139.89        10.13        64.44 
TCGA-GN-A4U8 TCGA-RP-A690 TCGA-W3-A824 TCGA-W3-AA1Q TCGA-W3-AA1W TCGA-WE-A8K1 
       48.89         0.20       228.16        69.07       219.16        49.05 
TCGA-WE-AAA0 TCGA-XV-AB01 TCGA-YD-A89C TCGA-YG-AA3P 
       40.41        13.25         6.90        14.43 

  DEL PEAK 15(9P21.3) MUTATED DEL PEAK 15(9P21.3) WILD-TYPE 
                         0.23                          0.20 
  DEL PEAK 15(9P21.3) MUTATED DEL PEAK 15(9P21.3) WILD-TYPE 
                       369.93                        241.38 
  DEL PEAK 15(9P21.3) MUTATED DEL PEAK 15(9P21.3) WILD-TYPE 
                       53.175                        49.905 
[1] "0.2 - 369.9 (53.2)" "0.2 - 241.4 (49.9)"
[1] "hr=" "1.1"
D35V3, continuous
                               vv
clus                            I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB
  DEL PEAK 15(9P21.3) MUTATED         12       5      22       13       19
  DEL PEAK 15(9P21.3) WILD-TYPE        1       2       7        5        9
                               vv
clus                            STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK 15(9P21.3) MUTATED         19        11        13        12
  DEL PEAK 15(9P21.3) WILD-TYPE        7         3         6         3
                               vv
clus                            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 15(9P21.3) MUTATED          32          8         28         38
  DEL PEAK 15(9P21.3) WILD-TYPE         7          7          7         16
                               vv
clus                            STAGE IV
  DEL PEAK 15(9P21.3) MUTATED         18
  DEL PEAK 15(9P21.3) WILD-TYPE        3
D35V4, multiclass
            clus
vv           DEL PEAK 15(9P21.3) MUTATED DEL PEAK 15(9P21.3) WILD-TYPE
  I/II NOS                            12                             1
  STAGE 0                              5                             2
  STAGE I                             22                             7
  STAGE IA                            13                             5
  STAGE IB                            19                             9
  STAGE II                            19                             7
  STAGE IIA                           11                             3
  STAGE IIB                           13                             6
  STAGE IIC                           12                             3
  STAGE III                           32                             7
  STAGE IIIA                           8                             7
  STAGE IIIB                          28                             7
  STAGE IIIC                          38                            16
  STAGE IV                            18                             3
[1] 14  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3 T4
  DEL PEAK 15(9P21.3) MUTATED      51 55 61 48
  DEL PEAK 15(9P21.3) WILD-TYPE    13 18 20 19
D35V5, multiclass
       clus
vv      DEL PEAK 15(9P21.3) MUTATED DEL PEAK 15(9P21.3) WILD-TYPE
  T0+T1                          51                            13
  T2                             55                            18
  T3                             61                            20
  T4                             48                            19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  DEL PEAK 15(9P21.3) MUTATED   133  51  30  31
  DEL PEAK 15(9P21.3) WILD-TYPE  44  14   9  14
D35V6, multiclass
    clus
vv   DEL PEAK 15(9P21.3) MUTATED DEL PEAK 15(9P21.3) WILD-TYPE
  N0                         133                            44
  N1                          51                            14
  N2                          30                             9
  N3                          31                            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"
D35V7, binary
                               cls
clus                              0   1
  DEL PEAK 15(9P21.3) MUTATED   238  19
  DEL PEAK 15(9P21.3) WILD-TYPE  81   3
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(9P21.3) MUTATED    238   19
  DEL PEAK 15(9P21.3) WILD-TYPE   81    3
   clus
vv  DEL PEAK 15(9P21.3) MUTATED DEL PEAK 15(9P21.3) WILD-TYPE
  0                         238                            81
  1                          19                             3
[1] 2 2
[1] FALSE
D35V8, binary
                               cls
clus                             0  1
  DEL PEAK 15(9P21.3) MUTATED   99 68
  DEL PEAK 15(9P21.3) WILD-TYPE 35 22
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(9P21.3) MUTATED     99   68
  DEL PEAK 15(9P21.3) WILD-TYPE   35   22
     clus
vv    DEL PEAK 15(9P21.3) MUTATED DEL PEAK 15(9P21.3) WILD-TYPE
  NO                           99                            35
  YES                          68                            22
[1] 2 2
[1] FALSE
D35V9, binary
                               cls
clus                              0   1
  DEL PEAK 15(9P21.3) MUTATED    37 241
  DEL PEAK 15(9P21.3) WILD-TYPE  10  79
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(9P21.3) MUTATED     37  241
  DEL PEAK 15(9P21.3) WILD-TYPE   10   79
     clus
vv    DEL PEAK 15(9P21.3) MUTATED DEL PEAK 15(9P21.3) WILD-TYPE
  NO                           37                            10
  YES                         241                            79
[1] 2 2
[1] FALSE
D35V10, continuous
D35V11, binary
                               cls
clus                              0   1
  DEL PEAK 15(9P21.3) MUTATED   113 165
  DEL PEAK 15(9P21.3) WILD-TYPE  25  64
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(9P21.3) MUTATED    113  165
  DEL PEAK 15(9P21.3) WILD-TYPE   25   64
        clus
vv       DEL PEAK 15(9P21.3) MUTATED DEL PEAK 15(9P21.3) WILD-TYPE
  FEMALE                         113                            25
  MALE                           165                            64
[1] 2 2
[1] FALSE
D35V12, binary
                               cls
clus                              0   1
  DEL PEAK 15(9P21.3) MUTATED   249  29
  DEL PEAK 15(9P21.3) WILD-TYPE  70  18
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(9P21.3) MUTATED    249   29
  DEL PEAK 15(9P21.3) WILD-TYPE   70   18
     clus
vv    DEL PEAK 15(9P21.3) MUTATED DEL PEAK 15(9P21.3) WILD-TYPE
  NO                          249                            70
  YES                          29                            18
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 15(9P21.3) MUTATED       4                         1   266
  DEL PEAK 15(9P21.3) WILD-TYPE     1                         0    87
D35V13, multiclass
                           clus
vv                          DEL PEAK 15(9P21.3) MUTATED
  ASIAN                                               4
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                             266
                           clus
vv                          DEL PEAK 15(9P21.3) WILD-TYPE
  ASIAN                                                 1
  BLACK OR AFRICAN AMERICAN                             0
  WHITE                                                87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V14, binary
                               cls
clus                              0   1
  DEL PEAK 15(9P21.3) MUTATED     3 268
  DEL PEAK 15(9P21.3) WILD-TYPE   4  84
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(9P21.3) MUTATED      3  268
  DEL PEAK 15(9P21.3) WILD-TYPE    4   84
                        clus
vv                       DEL PEAK 15(9P21.3) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                         268
                        clus
vv                       DEL PEAK 15(9P21.3) WILD-TYPE
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                            84
[1] 2 2
[1] FALSE

Clustering(36) Variable = DEL PEAK 16(10P15.3) MUTATION ANALYSIS
D36V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 16(10P15.3) MUTATED   67 74
  DEL PEAK 16(10P15.3) WILD-TYPE 61 50
  DEL PEAK 16(10P15.3) MUTATED DEL PEAK 16(10P15.3) WILD-TYPE 
                           141                            111 
  DEL PEAK 16(10P15.3) MUTATED DEL PEAK 16(10P15.3) WILD-TYPE 
                            74                             50 
$`DEL PEAK 16(10P15.3) MUTATED`
TCGA-D3-A8GI TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GO TCGA-FR-A729 TCGA-WE-AAA3 
       13.41        31.96       166.75        52.90       216.43         7.40 
TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
       60.46        12.99        14.83         8.42        31.89       110.93 
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A2J6 TCGA-D3-A2JA TCGA-D3-A2JC 
       49.35       133.25        19.04        25.64        15.75        86.30 
TCGA-D3-A2JG TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3CE TCGA-D3-A3CF 
      107.61        64.83        66.08        43.53        59.70        24.53 
TCGA-D3-A3MO TCGA-D3-A3MU TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51T 
        9.34        23.67        30.67       144.46        31.76        11.34 
TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GJ 
       45.70       177.86       124.08        78.21        23.61       179.97 
TCGA-D3-A8GP TCGA-D3-A8GR TCGA-D9-A1X3 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6EG 
      135.12        36.53        10.78        16.90        18.44        22.85 
TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA 
      138.67        68.68       150.61       110.53        60.10        64.83 
TCGA-DA-A3F5 TCGA-DA-A95V TCGA-DA-A95W TCGA-DA-A95Y TCGA-EE-A181 TCGA-EE-A29G 
      225.11        72.10         0.76        14.14        20.38        44.28 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W 
       47.41        47.74        27.16        61.12       346.49       185.19 
TCGA-EE-A2A2 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GM 
       30.02        26.14        12.95       201.60        68.65        18.35 
TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2M6 TCGA-EE-A2M7 
       93.63         0.76         0.20        71.31       103.13        15.25 
TCGA-EE-A2M8 TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MS 
        5.75        94.19       171.85        89.26       145.45       143.93 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3J3 
       53.26       124.31       122.73         4.41        54.51        67.89 
TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI 
      111.85        45.90         3.35       168.85        19.86       135.98 
TCGA-ER-A199 TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19P 
        7.82        11.47       184.60       150.12        99.06       120.76 
TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NG 
       47.18       146.63        22.36         4.70        16.87        28.67 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A3YN 
      173.29        68.52        15.48        32.05        74.47         4.50 
TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1ZC TCGA-FS-A1ZD 
        4.14        26.20       195.98         8.35       312.07        32.78 
TCGA-FS-A1ZG TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
        7.82        78.61       130.95         4.47        23.21         5.29 
TCGA-FS-A4F4 TCGA-GF-A4EO TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
       66.67        18.25       117.93        17.06        42.48         7.59 
TCGA-GN-A4U3 TCGA-GN-A8LK TCGA-GN-A9SD TCGA-OD-A75X TCGA-RP-A693 TCGA-W3-A824 
      120.53        43.23        59.41       297.01         0.33       174.12 
TCGA-W3-A825 TCGA-W3-AA1V TCGA-W3-AA21 TCGA-WE-A8ZM TCGA-WE-A8ZQ TCGA-WE-A8ZY 
        1.97         8.09        92.84        65.42        62.89        48.39 
TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-Z2-AA3S 
       24.99        28.21        91.23 

$`DEL PEAK 16(10P15.3) WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A2GD TCGA-EE-A2MR 
        9.76        62.07        38.76        33.24       269.03       134.40 
TCGA-EE-A3JD TCGA-ER-A193 TCGA-FW-A3R5 TCGA-WE-A8K5 TCGA-D3-A1Q3 TCGA-D3-A1QA 
       27.35        19.04        36.95        52.73        15.72        76.41 
TCGA-D3-A1QB TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JB TCGA-D3-A2JH TCGA-D3-A2JL 
       62.60        45.99        62.86       168.00        36.30       171.58 
TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3MR TCGA-D3-A51E TCGA-D3-A51R 
       58.06       140.98        40.01        90.21       173.85        62.70 
TCGA-D3-A5GL TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D9-A3Z1 TCGA-D9-A6EC 
       42.05       120.00        69.53        70.62        15.02        69.21 
TCGA-DA-A1HV TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F8 TCGA-DA-A95X TCGA-DA-A95Z 
       76.34        58.85        30.44         8.71        65.03        12.30 
TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
        3.91        16.41        52.41        18.21        13.15        24.89 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29C 
        0.00        26.24        75.55        79.20        75.22        76.14 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A2A1 TCGA-EE-A2A6 TCGA-EE-A2GK TCGA-EE-A2GL 
       12.99         0.26       115.43        77.98        10.62        32.48 
TCGA-EE-A2GU TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MP 
       81.99        23.77       209.79        63.25       104.78       227.01 
TCGA-EE-A2MT TCGA-EE-A3AC TCGA-EE-A3AF TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A19A 
       23.51        64.04         6.28        34.45        10.49         4.54 
TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A1A1 
       53.29        39.81        59.84        42.51        49.71        73.05 
TCGA-ER-A2NF TCGA-FR-A44A TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FS-A1YW TCGA-FS-A1YY 
       10.19       174.21         5.65        10.06       171.78        49.74 
TCGA-FS-A1Z4 TCGA-FS-A1ZE TCGA-FS-A1ZJ TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZZ 
       27.62        43.92        36.33       136.27        35.28         3.06 
TCGA-FS-A4F0 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV 
       30.90       173.19        13.28        80.68        55.59        11.54 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A4U4 
       19.30         9.90         1.91        53.29        96.92        34.49 
TCGA-GN-A4U8 TCGA-LH-A9QB TCGA-QB-A6FS TCGA-RP-A690 TCGA-W3-A828 TCGA-W3-AA1Q 
       46.92        85.05         7.23         0.20       120.07        44.05 
TCGA-W3-AA1R TCGA-W3-AA1W TCGA-WE-A8K1 TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT 
       79.99       185.13        47.54        12.69        21.90        10.95 
TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-XV-AB01 
        1.94        37.32         6.61 

  DEL PEAK 16(10P15.3) MUTATED DEL PEAK 16(10P15.3) WILD-TYPE 
                           0.2                            0.0 
  DEL PEAK 16(10P15.3) MUTATED DEL PEAK 16(10P15.3) WILD-TYPE 
                        346.49                         269.03 
  DEL PEAK 16(10P15.3) MUTATED DEL PEAK 16(10P15.3) WILD-TYPE 
                         47.74                          43.92 
[1] "0.2 - 346.5 (47.7)" "0.0 - 269.0 (43.9)"
[1] "hr=" "1"  
D36V2, survival
                                sevent
clus2                              0   1
  DEL PEAK 16(10P15.3) MUTATED    85 108
  DEL PEAK 16(10P15.3) WILD-TYPE  81  84
  DEL PEAK 16(10P15.3) MUTATED DEL PEAK 16(10P15.3) WILD-TYPE 
                           193                            165 
  DEL PEAK 16(10P15.3) MUTATED DEL PEAK 16(10P15.3) WILD-TYPE 
                           108                             84 
$`DEL PEAK 16(10P15.3) MUTATED`
TCGA-D3-A8GI TCGA-EB-A5SH TCGA-EE-A180 TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A29L 
       58.52        54.02        94.98        68.15       168.26         2.60 
TCGA-EE-A2GO TCGA-FR-A729 TCGA-FS-A1ZF TCGA-WE-AAA3 TCGA-3N-A9WC TCGA-3N-A9WD 
      126.81       220.80        15.45        21.40        66.48        12.99 
TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       14.93        16.57       112.04       112.57        71.80       133.25 
TCGA-D3-A1Q8 TCGA-D3-A2J6 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG 
       28.08        43.43       115.53        86.76        11.87       113.52 
TCGA-D3-A2JK TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C7 TCGA-D3-A3CE 
       12.10        66.48        66.08        59.57        46.98        60.23 
TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51F TCGA-D3-A51J 
       24.53         9.34        39.75        45.30        55.73       145.12 
TCGA-D3-A51K TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GU 
       32.94        26.89       135.75       137.92       178.32       125.19 
TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GJ TCGA-D3-A8GP TCGA-D3-A8GR TCGA-D3-A8GS 
       79.59        23.61       241.38       152.75       129.63       117.17 
TCGA-D9-A1X3 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EG 
       18.12        22.29        18.44         9.90        25.18        22.95 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
       36.03       144.89       222.51       176.55        35.93       135.02 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A3F5 TCGA-DA-A95V TCGA-DA-A95W 
       88.87        53.92        65.92       225.96        72.10        37.35 
TCGA-DA-A95Y TCGA-EB-A44R TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A185 TCGA-EE-A20B 
       14.14        10.36         8.65        33.73         4.96       133.81 
TCGA-EE-A20I TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P 
       13.55        72.07        64.64        56.84        18.61        56.42 
TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A2 
       66.74        61.28       369.93       195.02        17.92        59.64 
TCGA-EE-A2A5 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       39.29        59.28       173.79       220.24        48.72       107.38 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2M6 
       75.48       102.12        13.91        42.77        81.21       129.27 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK 
       28.83        19.76       103.20        16.96       204.66       180.39 
TCGA-EE-A2MM TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AD 
      167.90       162.48        53.26       124.31       122.73        28.77 
TCGA-EE-A3AE TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 
       54.51       138.81       172.18       127.20        36.95        64.08 
TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
       34.32        53.19       201.80        51.35       134.33       152.81 
TCGA-ER-A199 TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L 
        9.17        12.59        13.02       302.07       152.35       131.51 
TCGA-ER-A19P TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
      162.08        49.48       148.18        43.82        23.34        20.15 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL 
       48.99        41.56       247.04        93.01        46.98        33.21 
TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A8YE 
       12.95       149.03        92.98        15.72        27.85       104.42 
TCGA-FS-A1YX TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZC 
       48.59       202.65        20.91         7.79        27.72       357.37 
TCGA-FS-A1ZD TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZR 
       53.52         9.70        32.75       101.26       133.55        11.41 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-GF-A4EO 
       26.56        49.48        27.09        66.67        28.73        19.43 
TCGA-GN-A264 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 
      117.93        10.13        64.44        62.79        32.48       121.91 
TCGA-GN-A4U7 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OG 
       10.42        22.13        50.10        21.37        59.41         0.23 
TCGA-HR-A2OH TCGA-OD-A75X TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 
       65.88       297.90         0.33         0.69       228.16        63.02 
TCGA-W3-AA1V TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8ZM TCGA-WE-A8ZQ TCGA-WE-A8ZX 
       42.08       105.04        24.03       101.33        63.22        35.80 
TCGA-WE-A8ZY TCGA-WE-AAA4 TCGA-YD-A9TA TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-AA3S 
       49.51        24.99        49.18        37.94        14.43        96.99 
TCGA-Z2-AA3V 
       15.98 

$`DEL PEAK 16(10P15.3) WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SG TCGA-EE-A2GD 
       27.65        62.07        46.32        13.87        68.25       340.14 
TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-ER-A198 TCGA-FW-A3R5 TCGA-QB-AA9O 
      134.40        27.35        31.40        50.76        36.95        18.05 
TCGA-WE-A8K5 TCGA-3N-A9WB TCGA-D3-A1Q3 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB 
       61.15        17.03        16.67        31.59        90.90        95.74 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JH TCGA-D3-A2JL 
      103.10        65.49        23.77       168.00        42.08       171.58 
TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3MR TCGA-D3-A51E 
      130.72        58.06       166.52        86.93       103.59       174.84 
TCGA-D3-A51H TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GL TCGA-D3-A5GS TCGA-D3-A8GB 
       56.35        22.62        63.81       125.79        18.18        30.84 
TCGA-D3-A8GE TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GQ 
       26.43       170.20        89.13       107.15       161.00        29.06 
TCGA-D3-A8GV TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 
      167.70       151.53        54.67         3.65         7.10        15.39 
TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1I0 TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       77.56        76.57        20.38        40.60        68.09        33.93 
TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-DA-A95X TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5KH 
       10.49        43.36        73.94        13.02        13.87        20.35 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
       29.29        58.92         7.04        36.46        29.82        27.22 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29A TCGA-EE-A29B 
       14.70        26.89       151.27        91.56        63.35        85.08 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29R TCGA-EE-A29V TCGA-EE-A2A0 
       78.97        13.97        63.78        14.47        25.87        46.82 
TCGA-EE-A2A1 TCGA-EE-A2A6 TCGA-EE-A2GC TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GT 
      115.96        86.14        67.43        54.74        79.66        44.88 
TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF 
       94.82        21.67        61.51        47.28       103.27       268.73 
TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MT 
       96.23       216.66        47.54       248.65        43.23        71.21 
TCGA-EE-A3AC TCGA-EE-A3AF TCGA-EE-A3AG TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A19A 
       64.04        13.81        41.59        35.44        13.94        77.75 
TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19M TCGA-ER-A19N 
       98.40        48.89        26.37         6.44        61.05        44.09 
TCGA-ER-A19Q TCGA-ER-A19T TCGA-ER-A1A1 TCGA-ER-A2NF TCGA-FR-A44A TCGA-FR-A7U9 
       50.89         8.88       105.07        28.83       174.21        18.77 
TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z4 
       38.27        34.82        36.26       216.92       228.59        28.08 
TCGA-FS-A1ZB TCGA-FS-A1ZE TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZS 
       48.85        46.45        47.38        23.93        74.73       148.80 
TCGA-FS-A1ZT TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F8 TCGA-FS-A4F9 
       53.16        27.02        77.82        50.14       174.84        34.03 
TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV 
       26.73        54.41        80.68        17.46        55.59        13.51 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A265 
       19.30         9.90         2.04        15.78       139.89        96.92 
TCGA-GN-A26D TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-LH-A9QB TCGA-QB-A6FS TCGA-RP-A690 
       48.00        39.35        48.89       368.78         7.23         0.20 
TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1W TCGA-WE-A8K1 
      121.08         4.01        69.07       111.09       219.16        49.05 
TCGA-WE-A8K6 TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-AA9Y TCGA-WE-AAA0 
       17.95        58.98        70.52        11.80        12.16        40.41 
TCGA-XV-AB01 TCGA-YD-A89C TCGA-Z2-A8RT 
       13.25         6.90        27.58 

  DEL PEAK 16(10P15.3) MUTATED DEL PEAK 16(10P15.3) WILD-TYPE 
                          0.23                           0.20 
  DEL PEAK 16(10P15.3) MUTATED DEL PEAK 16(10P15.3) WILD-TYPE 
                        369.93                         368.78 
  DEL PEAK 16(10P15.3) MUTATED DEL PEAK 16(10P15.3) WILD-TYPE 
                         55.73                          48.85 
[1] "0.2 - 369.9 (55.7)" "0.2 - 368.8 (48.9)"
[1] "hr=" "1"  
D36V3, continuous
                                vv
clus                             I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB
  DEL PEAK 16(10P15.3) MUTATED          8       4      15       11       16
  DEL PEAK 16(10P15.3) WILD-TYPE        5       3      14        7       12
                                vv
clus                             STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK 16(10P15.3) MUTATED         15         6         7         8
  DEL PEAK 16(10P15.3) WILD-TYPE       11         8        12         7
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 16(10P15.3) MUTATED          25         11         17         31
  DEL PEAK 16(10P15.3) WILD-TYPE        14          4         18         23
                                vv
clus                             STAGE IV
  DEL PEAK 16(10P15.3) MUTATED          9
  DEL PEAK 16(10P15.3) WILD-TYPE       12
D36V4, multiclass
            clus
vv           DEL PEAK 16(10P15.3) MUTATED DEL PEAK 16(10P15.3) WILD-TYPE
  I/II NOS                              8                              5
  STAGE 0                               4                              3
  STAGE I                              15                             14
  STAGE IA                             11                              7
  STAGE IB                             16                             12
  STAGE II                             15                             11
  STAGE IIA                             6                              8
  STAGE IIB                             7                             12
  STAGE IIC                             8                              7
  STAGE III                            25                             14
  STAGE IIIA                           11                              4
  STAGE IIIB                           17                             18
  STAGE IIIC                           31                             23
  STAGE IV                              9                             12
[1] 14  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  DEL PEAK 16(10P15.3) MUTATED      37 41 35 46
  DEL PEAK 16(10P15.3) WILD-TYPE    27 32 46 21
D36V5, multiclass
       clus
vv      DEL PEAK 16(10P15.3) MUTATED DEL PEAK 16(10P15.3) WILD-TYPE
  T0+T1                           37                             27
  T2                              41                             32
  T3                              35                             46
  T4                              46                             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 N3
  DEL PEAK 16(10P15.3) MUTATED   97 39 22 21
  DEL PEAK 16(10P15.3) WILD-TYPE 80 26 17 24
D36V6, multiclass
    clus
vv   DEL PEAK 16(10P15.3) MUTATED DEL PEAK 16(10P15.3) WILD-TYPE
  N0                           97                             80
  N1                           39                             26
  N2                           22                             17
  N3                           21                             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"
D36V7, binary
                                cls
clus                               0   1
  DEL PEAK 16(10P15.3) MUTATED   176   9
  DEL PEAK 16(10P15.3) WILD-TYPE 143  13
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 16(10P15.3) MUTATED    176    9
  DEL PEAK 16(10P15.3) WILD-TYPE  143   13
   clus
vv  DEL PEAK 16(10P15.3) MUTATED DEL PEAK 16(10P15.3) WILD-TYPE
  0                          176                            143
  1                            9                             13
[1] 2 2
[1] FALSE
D36V8, binary
                                cls
clus                              0  1
  DEL PEAK 16(10P15.3) MUTATED   70 52
  DEL PEAK 16(10P15.3) WILD-TYPE 64 38
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 16(10P15.3) MUTATED     70   52
  DEL PEAK 16(10P15.3) WILD-TYPE   64   38
     clus
vv    DEL PEAK 16(10P15.3) MUTATED DEL PEAK 16(10P15.3) WILD-TYPE
  NO                            70                             64
  YES                           52                             38
[1] 2 2
[1] FALSE
D36V9, binary
                                cls
clus                               0   1
  DEL PEAK 16(10P15.3) MUTATED    23 176
  DEL PEAK 16(10P15.3) WILD-TYPE  24 144
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 16(10P15.3) MUTATED     23  176
  DEL PEAK 16(10P15.3) WILD-TYPE   24  144
     clus
vv    DEL PEAK 16(10P15.3) MUTATED DEL PEAK 16(10P15.3) WILD-TYPE
  NO                            23                             24
  YES                          176                            144
[1] 2 2
[1] FALSE
D36V10, continuous
D36V11, binary
                                cls
clus                               0   1
  DEL PEAK 16(10P15.3) MUTATED    81 118
  DEL PEAK 16(10P15.3) WILD-TYPE  57 111
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 16(10P15.3) MUTATED     81  118
  DEL PEAK 16(10P15.3) WILD-TYPE   57  111
        clus
vv       DEL PEAK 16(10P15.3) MUTATED DEL PEAK 16(10P15.3) WILD-TYPE
  FEMALE                           81                             57
  MALE                            118                            111
[1] 2 2
[1] FALSE
D36V12, binary
                                cls
clus                               0   1
  DEL PEAK 16(10P15.3) MUTATED   174  25
  DEL PEAK 16(10P15.3) WILD-TYPE 145  22
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 16(10P15.3) MUTATED    174   25
  DEL PEAK 16(10P15.3) WILD-TYPE  145   22
     clus
vv    DEL PEAK 16(10P15.3) MUTATED DEL PEAK 16(10P15.3) WILD-TYPE
  NO                           174                            145
  YES                           25                             22
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 16(10P15.3) MUTATED       1                         0   192
  DEL PEAK 16(10P15.3) WILD-TYPE     4                         1   161
D36V13, multiclass
                           clus
vv                          DEL PEAK 16(10P15.3) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                              192
                           clus
vv                          DEL PEAK 16(10P15.3) WILD-TYPE
  ASIAN                                                  4
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                161
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V14, binary
                                cls
clus                               0   1
  DEL PEAK 16(10P15.3) MUTATED     4 190
  DEL PEAK 16(10P15.3) WILD-TYPE   3 162
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 16(10P15.3) MUTATED      4  190
  DEL PEAK 16(10P15.3) WILD-TYPE    3  162
                        clus
vv                       DEL PEAK 16(10P15.3) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                          190
                        clus
vv                       DEL PEAK 16(10P15.3) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            162
[1] 2 2
[1] FALSE

Clustering(37) Variable = DEL PEAK 17(10Q21.1) MUTATION ANALYSIS
D37V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 17(10Q21.1) MUTATED   75 76
  DEL PEAK 17(10Q21.1) WILD-TYPE 53 48
  DEL PEAK 17(10Q21.1) MUTATED DEL PEAK 17(10Q21.1) WILD-TYPE 
                           151                            101 
  DEL PEAK 17(10Q21.1) MUTATED DEL PEAK 17(10Q21.1) WILD-TYPE 
                            76                             48 
$`DEL PEAK 17(10Q21.1) MUTATED`
TCGA-D3-A8GI TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GD TCGA-EE-A2GO TCGA-ER-A193 
       13.41        31.96       166.75       269.03        52.90        19.04 
TCGA-FR-A729 TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q4 
      216.43        52.73         7.40        12.99        14.83        31.89 
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A2JA TCGA-D3-A2JC 
      110.93        49.35       133.25        19.04        15.75        86.30 
TCGA-D3-A2JG TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 
      107.61       171.58        64.83        66.08        43.53        58.06 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51F 
       59.70        24.53         9.34        90.21        23.67        30.67 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GU 
      144.46        31.76        11.34        45.70       177.86       124.08 
TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GM TCGA-D3-A8GP TCGA-D9-A1X3 TCGA-D9-A3Z3 
       78.21        23.61        70.62       135.12        10.78        16.90 
TCGA-D9-A4Z6 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 
       18.44        69.21        22.85        68.68       150.61       110.53 
TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-DA-A95V TCGA-DA-A95W 
       60.10        64.83       225.11         8.71        72.10         0.76 
TCGA-DA-A95Y TCGA-EB-A5UN TCGA-EE-A181 TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29H 
       14.14        52.41        20.38        12.99        44.28        47.41 
TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A2 
       47.74        27.16        61.12       346.49       185.19        30.02 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GM 
       77.98        26.14        12.95       201.60        68.65        18.35 
TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 
       93.63         0.76         0.20        71.31        81.99       103.13 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MK TCGA-EE-A2MM 
       15.25         5.75       209.79        94.19        89.26       145.45 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
       53.26       124.31       122.73         4.41        54.51         6.28 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH 
       67.89       111.85        45.90         3.35       168.85        19.86 
TCGA-EE-A3JI TCGA-ER-A199 TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19H TCGA-ER-A19L 
      135.98         7.82        39.81        11.47       150.12        99.06 
TCGA-ER-A19P TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NG 
      120.76        47.18       146.63        22.36        16.87        28.67 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       15.48        32.05        74.47         4.50       174.21         4.14 
TCGA-FR-A7U8 TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1ZC TCGA-FS-A1ZD 
       26.20        49.74       195.98         8.35       312.07        32.78 
TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
       36.33        78.61       130.95         4.47        23.21         5.29 
TCGA-FS-A4F4 TCGA-FW-A3TV TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 
       66.67        11.54        18.25         1.91        53.29       117.93 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U8 TCGA-GN-A8LK 
       17.06        42.48         7.59       120.53        46.92        43.23 
TCGA-GN-A9SD TCGA-OD-A75X TCGA-RP-A693 TCGA-W3-A825 TCGA-W3-AA21 TCGA-WE-A8ZM 
       59.41       297.01         0.33         1.97        92.84        65.42 
TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA4 TCGA-YG-AA3O 
       62.89        10.95        48.39         1.94        24.99        28.21 
TCGA-Z2-AA3S 
       91.23 

$`DEL PEAK 17(10Q21.1) WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A2MR TCGA-EE-A3JD 
        9.76        62.07        38.76        33.24       134.40        27.35 
TCGA-FW-A3R5 TCGA-3N-A9WC TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1QA TCGA-D3-A1QB 
       36.95        60.46         8.42        15.72        76.41        62.60 
TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JB TCGA-D3-A2JH TCGA-D3-A3CB 
       25.64        45.99        62.86       168.00        36.30       140.98 
TCGA-D3-A3CC TCGA-D3-A51E TCGA-D3-A51R TCGA-D3-A5GL TCGA-D3-A8GJ TCGA-D3-A8GK 
       40.01       173.85        62.70        42.05       179.97       120.00 
TCGA-D3-A8GL TCGA-D3-A8GR TCGA-D9-A3Z1 TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1IC 
       69.53        36.53        15.02        76.34       138.67        58.85 
TCGA-DA-A3F2 TCGA-DA-A95X TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A6L9 
       30.44        65.03        12.30         3.91        16.41        18.21 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A20F 
       13.15        24.89         0.00        26.24        75.55        79.20 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A2A1 TCGA-EE-A2GK TCGA-EE-A2GL 
       75.22        76.14         0.26       115.43        10.62        32.48 
TCGA-EE-A2MC TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MP TCGA-EE-A2MS 
       23.77       171.85        63.25       104.78       227.01       143.93 
TCGA-EE-A2MT TCGA-EE-A3AC TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A19A TCGA-ER-A19B 
       23.51        64.04        34.45        10.49         4.54        53.29 
TCGA-ER-A19G TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A1A1 TCGA-ER-A2ND 
      184.60        59.84        42.51        49.71        73.05         4.70 
TCGA-ER-A2NF TCGA-ER-A3ES TCGA-ER-A3ET TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FS-A1YW 
       10.19       173.29        68.52         5.65        10.06       171.78 
TCGA-FS-A1Z4 TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZZ 
       27.62        43.92         7.82       136.27        35.28         3.06 
TCGA-FS-A4F0 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A5DY 
       30.90       173.19        13.28        80.68        55.59        19.30 
TCGA-GF-A3OT TCGA-GN-A265 TCGA-GN-A4U4 TCGA-LH-A9QB TCGA-QB-A6FS TCGA-RP-A690 
        9.90        96.92        34.49        85.05         7.23         0.20 
TCGA-W3-A824 TCGA-W3-A828 TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1V TCGA-W3-AA1W 
      174.12       120.07        44.05        79.99         8.09       185.13 
TCGA-WE-A8K1 TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-AAA0 TCGA-XV-AB01 
       47.54        12.69        21.90        37.32         6.61 

  DEL PEAK 17(10Q21.1) MUTATED DEL PEAK 17(10Q21.1) WILD-TYPE 
                           0.2                            0.0 
  DEL PEAK 17(10Q21.1) MUTATED DEL PEAK 17(10Q21.1) WILD-TYPE 
                        346.49                         227.01 
  DEL PEAK 17(10Q21.1) MUTATED DEL PEAK 17(10Q21.1) WILD-TYPE 
                         47.74                          42.51 
[1] "0.2 - 346.5 (47.7)" "0.0 - 227.0 (42.5)"
[1] "hr=" "1"  
D37V2, survival
                                sevent
clus2                              0   1
  DEL PEAK 17(10Q21.1) MUTATED   100 110
  DEL PEAK 17(10Q21.1) WILD-TYPE  66  82
  DEL PEAK 17(10Q21.1) MUTATED DEL PEAK 17(10Q21.1) WILD-TYPE 
                           210                            148 
  DEL PEAK 17(10Q21.1) MUTATED DEL PEAK 17(10Q21.1) WILD-TYPE 
                           110                             82 
$`DEL PEAK 17(10Q21.1) MUTATED`
TCGA-D3-A8GI TCGA-EB-A5SH TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD 
       58.52        54.02        94.98       168.26         2.60       340.14 
TCGA-EE-A2GO TCGA-ER-A193 TCGA-FR-A729 TCGA-FS-A1ZF TCGA-WE-A8K5 TCGA-WE-AAA3 
      126.81        31.40       220.80        15.45        61.15        21.40 
TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       12.99        14.93       112.04       112.57        71.80       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG 
       28.08        31.59       115.53        86.76        11.87       113.52 
TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 
       12.10       171.58        66.48        66.08        59.57        58.06 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV 
       60.23        24.53         9.34       103.59        39.75        45.30 
TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO 
       55.73       145.12        32.94        26.89       135.75       137.92 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GM 
      178.32        18.18       125.19        79.59        23.61       107.15 
TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GS TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1X3 
      161.00       152.75       117.17       151.53        54.67        18.12 
TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG 
       22.29        18.44         9.90        25.18        77.56        22.95 
TCGA-DA-A1HW TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 
       36.03       222.51       176.55        35.93       135.02        88.87 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-DA-A95V TCGA-DA-A95W 
       53.92        65.92       225.96        43.36        72.10        37.35 
TCGA-DA-A95Y TCGA-EB-A44R TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17Z TCGA-EE-A181 
       14.14        10.36        29.29        58.92         8.65        33.73 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20I TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29H 
        4.96       133.81        13.55        13.97        72.07        64.64 
TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A29X 
       56.84        56.42        66.74       369.93       195.02        17.92 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GE 
       59.64        39.29        86.14        59.28        67.43       173.79 
TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP 
      220.24        48.72       107.38        75.48       102.12        13.91 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
       42.77        81.21        94.82       129.27        28.83        19.76 
TCGA-EE-A2MD TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MK TCGA-EE-A2MM 
       47.28       268.73       103.20        16.96       180.39       167.90 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
       53.26       124.31       122.73        28.77        54.51        13.81 
TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 
      138.81       172.18       127.20        36.95        64.08        34.32 
TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A199 
       53.19       201.80        51.35       134.33       152.81         9.17 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19P 
       48.89        12.59        13.02       152.35       131.51       162.08 
TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NG 
       49.48         8.88       148.18        43.82        20.15        48.99 
TCGA-ER-A2NH TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A3YN 
       41.56        46.98        33.21        12.95       149.03        92.98 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A8YE TCGA-FS-A1YX TCGA-FS-A1YY 
      174.21        15.72        27.85       104.42        48.59       228.59 
TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZC TCGA-FS-A1ZD 
      202.65        20.91         7.79        27.72       357.37        53.52 
TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZU 
       32.75        47.38       101.26       133.55        11.41        26.56 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4FB TCGA-FW-A3TV 
       49.48        27.09        66.67        28.73        26.73        13.51 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A266 
       19.43         2.04        15.78       139.89       117.93        10.13 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U7 TCGA-GN-A4U8 
       64.44        62.79        32.48       121.91        10.42        48.89 
TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A9SD TCGA-HR-A2OG TCGA-HR-A2OH TCGA-OD-A75X 
       22.13        50.10        59.41         0.23        65.88       297.90 
TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A825 TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K6 
        0.33         0.69        63.02       105.04        24.03        17.95 
TCGA-WE-A8ZM TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AA9Y 
      101.33        63.22        11.80        35.80        49.51        12.16 
TCGA-WE-AAA4 TCGA-YD-A9TA TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-AA3S TCGA-Z2-AA3V 
       24.99        49.18        37.94        14.43        96.99        15.98 

$`DEL PEAK 17(10Q21.1) WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SG TCGA-EE-A184 
       27.65        62.07        46.32        13.87        68.25        68.15 
TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A198 TCGA-FW-A3R5 TCGA-QB-AA9O TCGA-3N-A9WB 
      134.40        27.35        50.76        36.95        18.05        17.03 
TCGA-3N-A9WC TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 
       66.48        16.57        16.67        90.90        95.74        43.43 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JH TCGA-D3-A3BZ 
      103.10        65.49        23.77       168.00        42.08       130.72 
TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A51E TCGA-D3-A51H TCGA-D3-A51N 
       46.98       166.52        86.93       174.84        56.35        22.62 
TCGA-D3-A51R TCGA-D3-A5GL TCGA-D3-A8GB TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GK 
       63.81       125.79        30.84        26.43       241.38       170.20 
TCGA-D3-A8GL TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GV TCGA-D9-A1JW TCGA-D9-A1JX 
       89.13        29.06       129.63       167.70         3.65         7.10 
TCGA-D9-A3Z1 TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1IB TCGA-DA-A1IC 
       15.39        76.57       144.89        20.38        40.60        68.09 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A95X TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5KH 
       33.93        10.49        73.94        13.02        13.87        20.35 
TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A182 TCGA-EE-A183 
        7.04        36.46        29.82        27.22        14.70        26.89 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E 
      151.27        91.56        63.35        85.08        78.97        63.78 
TCGA-EE-A29N TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A2A0 TCGA-EE-A2A1 
       18.61        14.47        61.28        25.87        46.82       115.96 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2MC TCGA-EE-A2ME 
       54.74        79.66        44.88        21.67        61.51       103.27 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ 
      204.66        96.23       216.66        47.54       248.65        43.23 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AC TCGA-EE-A3AG TCGA-ER-A195 TCGA-ER-A197 
      162.48        71.21        64.04        41.59        35.44        13.94 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19J TCGA-ER-A19M 
       77.75        98.40        26.37       302.07         6.44        61.05 
TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A1A1 TCGA-ER-A2ND TCGA-ER-A2NF TCGA-ER-A3ES 
       44.09        50.89       105.07        23.34        28.83       247.04 
TCGA-ER-A3ET TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FS-A1YW 
       93.01        18.77        38.27        34.82        36.26       216.92 
TCGA-FS-A1Z4 TCGA-FS-A1ZB TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZK TCGA-FS-A1ZP 
       28.08        48.85        46.45         9.70        23.93        74.73 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F8 
      148.80        53.16        27.02        77.82        50.14       174.84 
TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A5DY 
       34.03        54.41        80.68        17.46        55.59        19.30 
TCGA-GF-A3OT TCGA-GN-A265 TCGA-GN-A26D TCGA-GN-A4U4 TCGA-GN-A8LL TCGA-LH-A9QB 
        9.90        96.92        48.00        39.35        21.37       368.78 
TCGA-QB-A6FS TCGA-RP-A690 TCGA-W3-A824 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1Q 
        7.23         0.20       228.16       121.08         4.01        69.07 
TCGA-W3-AA1R TCGA-W3-AA1V TCGA-W3-AA1W TCGA-WE-A8K1 TCGA-WE-A8ZN TCGA-WE-A8ZO 
      111.09        42.08       219.16        49.05        58.98        70.52 
TCGA-WE-AAA0 TCGA-XV-AB01 TCGA-YD-A89C TCGA-Z2-A8RT 
       40.41        13.25         6.90        27.58 

  DEL PEAK 17(10Q21.1) MUTATED DEL PEAK 17(10Q21.1) WILD-TYPE 
                          0.23                           0.20 
  DEL PEAK 17(10Q21.1) MUTATED DEL PEAK 17(10Q21.1) WILD-TYPE 
                        369.93                         368.78 
  DEL PEAK 17(10Q21.1) MUTATED DEL PEAK 17(10Q21.1) WILD-TYPE 
                         53.97                          48.95 
[1] "0.2 - 369.9 (54.0)" "0.2 - 368.8 (49.0)"
[1] "hr=" "1.1"
D37V3, continuous
                                vv
clus                             I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB
  DEL PEAK 17(10Q21.1) MUTATED          9       3      17       13       16
  DEL PEAK 17(10Q21.1) WILD-TYPE        4       4      12        5       12
                                vv
clus                             STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK 17(10Q21.1) MUTATED         14         5        10         8
  DEL PEAK 17(10Q21.1) WILD-TYPE       12         9         9         7
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 17(10Q21.1) MUTATED          26         11         22         31
  DEL PEAK 17(10Q21.1) WILD-TYPE        13          4         13         23
                                vv
clus                             STAGE IV
  DEL PEAK 17(10Q21.1) MUTATED         13
  DEL PEAK 17(10Q21.1) WILD-TYPE        8
D37V4, multiclass
            clus
vv           DEL PEAK 17(10Q21.1) MUTATED DEL PEAK 17(10Q21.1) WILD-TYPE
  I/II NOS                              9                              4
  STAGE 0                               3                              4
  STAGE I                              17                             12
  STAGE IA                             13                              5
  STAGE IB                             16                             12
  STAGE II                             14                             12
  STAGE IIA                             5                              9
  STAGE IIB                            10                              9
  STAGE IIC                             8                              7
  STAGE III                            26                             13
  STAGE IIIA                           11                              4
  STAGE IIIB                           22                             13
  STAGE IIIC                           31                             23
  STAGE IV                             13                              8
[1] 14  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  DEL PEAK 17(10Q21.1) MUTATED      40 45 39 47
  DEL PEAK 17(10Q21.1) WILD-TYPE    24 28 42 20
D37V5, multiclass
       clus
vv      DEL PEAK 17(10Q21.1) MUTATED DEL PEAK 17(10Q21.1) WILD-TYPE
  T0+T1                           40                             24
  T2                              45                             28
  T3                              39                             42
  T4                              47                             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  N3
  DEL PEAK 17(10Q21.1) MUTATED   100  45  24  24
  DEL PEAK 17(10Q21.1) WILD-TYPE  77  20  15  21
D37V6, multiclass
    clus
vv   DEL PEAK 17(10Q21.1) MUTATED DEL PEAK 17(10Q21.1) WILD-TYPE
  N0                          100                             77
  N1                           45                             20
  N2                           24                             15
  N3                           24                             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"
D37V7, binary
                                cls
clus                               0   1
  DEL PEAK 17(10Q21.1) MUTATED   186  14
  DEL PEAK 17(10Q21.1) WILD-TYPE 133   8
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 17(10Q21.1) MUTATED    186   14
  DEL PEAK 17(10Q21.1) WILD-TYPE  133    8
   clus
vv  DEL PEAK 17(10Q21.1) MUTATED DEL PEAK 17(10Q21.1) WILD-TYPE
  0                          186                            133
  1                           14                              8
[1] 2 2
[1] FALSE
D37V8, binary
                                cls
clus                              0  1
  DEL PEAK 17(10Q21.1) MUTATED   79 56
  DEL PEAK 17(10Q21.1) WILD-TYPE 55 34
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 17(10Q21.1) MUTATED     79   56
  DEL PEAK 17(10Q21.1) WILD-TYPE   55   34
     clus
vv    DEL PEAK 17(10Q21.1) MUTATED DEL PEAK 17(10Q21.1) WILD-TYPE
  NO                            79                             55
  YES                           56                             34
[1] 2 2
[1] FALSE
D37V9, binary
                                cls
clus                               0   1
  DEL PEAK 17(10Q21.1) MUTATED    26 191
  DEL PEAK 17(10Q21.1) WILD-TYPE  21 129
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 17(10Q21.1) MUTATED     26  191
  DEL PEAK 17(10Q21.1) WILD-TYPE   21  129
     clus
vv    DEL PEAK 17(10Q21.1) MUTATED DEL PEAK 17(10Q21.1) WILD-TYPE
  NO                            26                             21
  YES                          191                            129
[1] 2 2
[1] FALSE
D37V10, continuous
D37V11, binary
                                cls
clus                               0   1
  DEL PEAK 17(10Q21.1) MUTATED    90 127
  DEL PEAK 17(10Q21.1) WILD-TYPE  48 102
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 17(10Q21.1) MUTATED     90  127
  DEL PEAK 17(10Q21.1) WILD-TYPE   48  102
        clus
vv       DEL PEAK 17(10Q21.1) MUTATED DEL PEAK 17(10Q21.1) WILD-TYPE
  FEMALE                           90                             48
  MALE                            127                            102
[1] 2 2
[1] FALSE
D37V12, binary
                                cls
clus                               0   1
  DEL PEAK 17(10Q21.1) MUTATED   186  31
  DEL PEAK 17(10Q21.1) WILD-TYPE 133  16
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 17(10Q21.1) MUTATED    186   31
  DEL PEAK 17(10Q21.1) WILD-TYPE  133   16
     clus
vv    DEL PEAK 17(10Q21.1) MUTATED DEL PEAK 17(10Q21.1) WILD-TYPE
  NO                           186                            133
  YES                           31                             16
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 17(10Q21.1) MUTATED       1                         0   210
  DEL PEAK 17(10Q21.1) WILD-TYPE     4                         1   143
D37V13, multiclass
                           clus
vv                          DEL PEAK 17(10Q21.1) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                              210
                           clus
vv                          DEL PEAK 17(10Q21.1) WILD-TYPE
  ASIAN                                                  4
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                143
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V14, binary
                                cls
clus                               0   1
  DEL PEAK 17(10Q21.1) MUTATED     4 208
  DEL PEAK 17(10Q21.1) WILD-TYPE   3 144
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 17(10Q21.1) MUTATED      4  208
  DEL PEAK 17(10Q21.1) WILD-TYPE    3  144
                        clus
vv                       DEL PEAK 17(10Q21.1) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                          208
                        clus
vv                       DEL PEAK 17(10Q21.1) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            144
[1] 2 2
[1] FALSE

Clustering(38) Variable = DEL PEAK 18(10Q23.31) MUTATION ANALYSIS
D38V1, survival
                                 sevent
clus2                              0  1
  DEL PEAK 18(10Q23.31) MUTATED   80 78
  DEL PEAK 18(10Q23.31) WILD-TYPE 48 46
  DEL PEAK 18(10Q23.31) MUTATED DEL PEAK 18(10Q23.31) WILD-TYPE 
                            158                              94 
  DEL PEAK 18(10Q23.31) MUTATED DEL PEAK 18(10Q23.31) WILD-TYPE 
                             78                              46 
$`DEL PEAK 18(10Q23.31) MUTATED`
TCGA-D3-A8GI TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GD TCGA-EE-A2GO TCGA-ER-A193 
       13.41        31.96       166.75       269.03        52.90        19.04 
TCGA-FR-A729 TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 
      216.43        52.73         7.40        60.46        12.99        14.83 
TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
        8.42        31.89       110.93        49.35       133.25        19.04 
TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
       15.75        86.30       107.61       171.58        64.83        66.08 
TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO 
       43.53        58.06        40.01        59.70        24.53         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51T 
       90.21        23.67        30.67       144.46        31.76        11.34 
TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GM 
       45.70       177.86       124.08        78.21        23.61        70.62 
TCGA-D3-A8GP TCGA-D9-A1X3 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6EC TCGA-D9-A6EG 
      135.12        10.78        16.90        18.44        69.21        22.85 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A3F5 
       68.68       150.61       110.53        60.10        64.83       225.11 
TCGA-DA-A3F8 TCGA-DA-A95V TCGA-DA-A95W TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A5UN 
        8.71        72.10         0.76        14.14        12.30        52.41 
TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A20F TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29H 
       24.89        20.38        79.20        12.99        44.28        47.41 
TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A2 
       47.74        27.16        61.12       346.49       185.19        30.02 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GM 
       77.98        26.14        12.95       201.60        68.65        18.35 
TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 
       93.63         0.76         0.20        71.31        81.99       103.13 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MK 
       15.25         5.75       209.79        94.19       171.85        89.26 
TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AD 
      145.45       227.01        53.26       124.31       122.73         4.41 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J8 TCGA-EE-A3JB 
       54.51         6.28        67.89       111.85         3.35       168.85 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A199 TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19H 
       19.86       135.98         7.82        39.81        11.47       150.12 
TCGA-ER-A19L TCGA-ER-A19P TCGA-ER-A19S TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NG 
       99.06       120.76        47.18        22.36        16.87        28.67 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       15.48        32.05        74.47         4.50       174.21         4.14 
TCGA-FR-A7U8 TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1ZC TCGA-FS-A1ZD 
       26.20        49.74       195.98         8.35       312.07        32.78 
TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
       36.33        78.61       130.95         4.47        23.21         5.29 
TCGA-FS-A4F4 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 
       66.67        55.59        11.54        18.25         1.91        53.29 
TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U8 TCGA-GN-A8LK 
      117.93        17.06         7.59       120.53        46.92        43.23 
TCGA-GN-A9SD TCGA-OD-A75X TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-AA21 
       59.41       297.01         0.33       174.12         1.97        92.84 
TCGA-WE-A8ZM TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA4 
       65.42        62.89        10.95        48.39         1.94        24.99 
TCGA-YG-AA3O TCGA-Z2-AA3S 
       28.21        91.23 

$`DEL PEAK 18(10Q23.31) WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A2MR TCGA-EE-A3JD 
        9.76        62.07        38.76        33.24       134.40        27.35 
TCGA-FW-A3R5 TCGA-D3-A1Q3 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       36.95        15.72        76.41        62.60        25.64        45.99 
TCGA-D3-A2J8 TCGA-D3-A2JB TCGA-D3-A2JH TCGA-D3-A3CB TCGA-D3-A51E TCGA-D3-A51R 
       62.86       168.00        36.30       140.98       173.85        62.70 
TCGA-D3-A5GL TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GR TCGA-D9-A3Z1 
       42.05       179.97       120.00        69.53        36.53        15.02 
TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A95X TCGA-EB-A44Q 
       76.34       138.67        58.85        30.44        65.03         3.91 
TCGA-EB-A5KH TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20C 
       16.41        18.21        13.15         0.00        26.24        75.55 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A2A1 TCGA-EE-A2GK TCGA-EE-A2GL 
       75.22        76.14         0.26       115.43        10.62        32.48 
TCGA-EE-A2MC TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AC 
       23.77        63.25       104.78       143.93        23.51        64.04 
TCGA-EE-A3J7 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19G 
       45.90        34.45        10.49         4.54        53.29       184.60 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2ND 
       59.84        42.51        49.71       146.63        73.05         4.70 
TCGA-ER-A2NF TCGA-ER-A3ES TCGA-ER-A3ET TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FS-A1YW 
       10.19       173.29        68.52         5.65        10.06       171.78 
TCGA-FS-A1Z4 TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZZ 
       27.62        43.92         7.82       136.27        35.28         3.06 
TCGA-FS-A4F0 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A5DY TCGA-GF-A3OT 
       30.90       173.19        13.28        80.68        19.30         9.90 
TCGA-GN-A265 TCGA-GN-A268 TCGA-GN-A4U4 TCGA-LH-A9QB TCGA-QB-A6FS TCGA-RP-A690 
       96.92        42.48        34.49        85.05         7.23         0.20 
TCGA-W3-A828 TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1V TCGA-W3-AA1W TCGA-WE-A8K1 
      120.07        44.05        79.99         8.09       185.13        47.54 
TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-AAA0 TCGA-XV-AB01 
       12.69        21.90        37.32         6.61 

  DEL PEAK 18(10Q23.31) MUTATED DEL PEAK 18(10Q23.31) WILD-TYPE 
                            0.2                             0.0 
  DEL PEAK 18(10Q23.31) MUTATED DEL PEAK 18(10Q23.31) WILD-TYPE 
                         346.49                          185.13 
  DEL PEAK 18(10Q23.31) MUTATED DEL PEAK 18(10Q23.31) WILD-TYPE 
                         48.870                          42.495 
[1] "0.2 - 346.5 (48.9)" "0.0 - 185.1 (42.5)"
[1] "hr=" "1.2"
D38V2, survival
                                 sevent
clus2                               0   1
  DEL PEAK 18(10Q23.31) MUTATED   107 116
  DEL PEAK 18(10Q23.31) WILD-TYPE  59  76
  DEL PEAK 18(10Q23.31) MUTATED DEL PEAK 18(10Q23.31) WILD-TYPE 
                            223                             135 
  DEL PEAK 18(10Q23.31) MUTATED DEL PEAK 18(10Q23.31) WILD-TYPE 
                            116                              76 
$`DEL PEAK 18(10Q23.31) MUTATED`
TCGA-D3-A8GI TCGA-EB-A5SH TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD 
       58.52        54.02        94.98       168.26         2.60       340.14 
TCGA-EE-A2GO TCGA-ER-A193 TCGA-FR-A729 TCGA-FS-A1ZF TCGA-WE-A8K5 TCGA-WE-AAA3 
      126.81        31.40       220.80        15.45        61.15        21.40 
TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
       66.48        12.99        14.93        16.57       112.04       112.57 
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A2JA TCGA-D3-A2JC 
       71.80       133.25        28.08        31.59       115.53        86.76 
TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
       11.87       113.52        12.10       171.58        66.48        66.08 
TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF 
       59.57        58.06        46.98        86.93        60.23        24.53 
TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51F TCGA-D3-A51J 
        9.34       103.59        39.75        45.30        55.73       145.12 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR 
       32.94        22.62        26.89       135.75       137.92       178.32 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GM 
       18.18       125.19        30.84        79.59        23.61       107.15 
TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GS TCGA-D3-A8GV TCGA-D9-A148 TCGA-D9-A149 
      161.00       152.75       117.17       167.70       151.53        54.67 
TCGA-D9-A1JX TCGA-D9-A1X3 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EA 
        7.10        18.12        22.29        18.44         9.90        25.18 
TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HW TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 
       77.56        22.95        36.03       222.51       176.55        35.93 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A3F5 TCGA-DA-A3F8 
      135.02        88.87        53.92        65.92       225.96        43.36 
TCGA-DA-A95V TCGA-DA-A95W TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44R TCGA-EB-A5UL 
       72.10        37.35        14.14        13.02        10.36        29.29 
TCGA-EB-A5UN TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A185 TCGA-EE-A20B 
       58.92        27.22         8.65        33.73         4.96       133.81 
TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M 
       91.56        13.55        13.97        72.07        64.64        56.84 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 
       56.42        66.74       369.93       195.02        17.92        46.82 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GE 
       59.64        39.29        86.14        59.28        67.43       173.79 
TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP 
      220.24        48.72       107.38        75.48       102.12        13.91 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
       42.77        81.21        94.82       129.27        28.83        19.76 
TCGA-EE-A2MD TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK 
       47.28       268.73       103.20        16.96       204.66       180.39 
TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AD 
      167.90       248.65        53.26       124.31       122.73        28.77 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 
       54.51        13.81        41.59       138.81       172.18       127.20 
TCGA-EE-A3J5 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JE TCGA-EE-A3JH 
       36.95        34.32        53.19       201.80        51.35       134.33 
TCGA-EE-A3JI TCGA-ER-A199 TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19H 
      152.81         9.17        48.89        12.59        13.02       152.35 
TCGA-ER-A19L TCGA-ER-A19P TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A2NC TCGA-ER-A2NE 
      131.51       162.08        49.48         8.88        43.82        20.15 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-ER-A42L 
       48.99        41.56        46.98        33.21        12.95       149.03 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A8YE TCGA-FS-A1YY 
       92.98       174.21        15.72        27.85       104.42       228.59 
TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZC TCGA-FS-A1ZD 
      202.65        20.91         7.79        27.72       357.37        53.52 
TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZU 
       32.75        47.38       101.26       133.55        11.41        26.56 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4FB TCGA-FW-A3I3 
       49.48        27.09        66.67        28.73        26.73        17.46 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 
       55.59        13.51        19.43         2.04       139.89       117.93 
TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U7 TCGA-GN-A4U8 
       10.13        64.44        32.48       121.91        10.42        48.89 
TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A9SD TCGA-HR-A2OG TCGA-HR-A2OH TCGA-OD-A75X 
       22.13        50.10        59.41         0.23        65.88       297.90 
TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-AA21 TCGA-WE-A8JZ 
        0.33         0.69       228.16        63.02       105.04        24.03 
TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-A8ZY 
       17.95       101.33        63.22        11.80        35.80        49.51 
TCGA-WE-AA9Y TCGA-WE-AAA4 TCGA-YD-A9TA TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-AA3S 
       12.16        24.99        49.18        37.94        14.43        96.99 
TCGA-Z2-AA3V 
       15.98 

$`DEL PEAK 18(10Q23.31) WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SG TCGA-EE-A184 
       27.65        62.07        46.32        13.87        68.25        68.15 
TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A198 TCGA-FW-A3R5 TCGA-QB-AA9O TCGA-3N-A9WB 
      134.40        27.35        50.76        36.95        18.05        17.03 
TCGA-D3-A1Q3 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 
       16.67        90.90        95.74        43.43       103.10        65.49 
TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JH TCGA-D3-A3BZ TCGA-D3-A3CB TCGA-D3-A51E 
       23.77       168.00        42.08       130.72       166.52       174.84 
TCGA-D3-A51H TCGA-D3-A51R TCGA-D3-A5GL TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GK 
       56.35        63.81       125.79        26.43       241.38       170.20 
TCGA-D3-A8GL TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D9-A1JW TCGA-D9-A3Z1 TCGA-DA-A1HV 
       89.13        29.06       129.63         3.65        15.39        76.57 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
      144.89        20.38        40.60        68.09        33.93        10.49 
TCGA-DA-A95X TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X 
       73.94        13.87        20.35         7.04        36.46        29.82 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C 
       14.70        26.89       151.27        63.35        85.08        78.97 
TCGA-EE-A29E TCGA-EE-A29N TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A2A1 
       63.78        18.61        14.47        61.28        25.87       115.96 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2MC TCGA-EE-A2ME 
       54.74        79.66        44.88        21.67        61.51       103.27 
TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A2MT 
       96.23       216.66        47.54        43.23       162.48        71.21 
TCGA-EE-A3AC TCGA-EE-A3J7 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A19A TCGA-ER-A19B 
       64.04        64.08        35.44        13.94        77.75        98.40 
TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19J TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19Q 
       26.37       302.07         6.44        61.05        44.09        50.89 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2ND TCGA-ER-A2NF TCGA-ER-A3ES TCGA-ER-A3ET 
      148.18       105.07        23.34        28.83       247.04        93.01 
TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FS-A1YW TCGA-FS-A1YX 
       18.77        38.27        34.82        36.26       216.92        48.59 
TCGA-FS-A1Z4 TCGA-FS-A1ZB TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZK TCGA-FS-A1ZP 
       28.08        48.85        46.45         9.70        23.93        74.73 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F8 
      148.80        53.16        27.02        77.82        50.14       174.84 
TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C9 
       34.03        54.41        80.68        19.30         9.90        15.78 
TCGA-GN-A265 TCGA-GN-A268 TCGA-GN-A26D TCGA-GN-A4U4 TCGA-GN-A8LL TCGA-LH-A9QB 
       96.92        62.79        48.00        39.35        21.37       368.78 
TCGA-QB-A6FS TCGA-RP-A690 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1Q TCGA-W3-AA1R 
        7.23         0.20       121.08         4.01        69.07       111.09 
TCGA-W3-AA1V TCGA-W3-AA1W TCGA-WE-A8K1 TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-AAA0 
       42.08       219.16        49.05        58.98        70.52        40.41 
TCGA-XV-AB01 TCGA-YD-A89C TCGA-Z2-A8RT 
       13.25         6.90        27.58 

  DEL PEAK 18(10Q23.31) MUTATED DEL PEAK 18(10Q23.31) WILD-TYPE 
                           0.23                            0.20 
  DEL PEAK 18(10Q23.31) MUTATED DEL PEAK 18(10Q23.31) WILD-TYPE 
                         369.93                          368.78 
  DEL PEAK 18(10Q23.31) MUTATED DEL PEAK 18(10Q23.31) WILD-TYPE 
                          53.52                           50.14 
[1] "0.2 - 369.9 (53.5)" "0.2 - 368.8 (50.1)"
[1] "hr=" "1.2"
D38V3, continuous
                                 vv
clus                              I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB
  DEL PEAK 18(10Q23.31) MUTATED          9       3      18       13       16
  DEL PEAK 18(10Q23.31) WILD-TYPE        4       4      11        5       12
                                 vv
clus                              STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK 18(10Q23.31) MUTATED         14         7        10         9
  DEL PEAK 18(10Q23.31) WILD-TYPE       12         7         9         6
                                 vv
clus                              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 18(10Q23.31) MUTATED          28         11         23         32
  DEL PEAK 18(10Q23.31) WILD-TYPE        11          4         12         22
                                 vv
clus                              STAGE IV
  DEL PEAK 18(10Q23.31) MUTATED         17
  DEL PEAK 18(10Q23.31) WILD-TYPE        4
D38V4, multiclass
            clus
vv           DEL PEAK 18(10Q23.31) MUTATED DEL PEAK 18(10Q23.31) WILD-TYPE
  I/II NOS                               9                               4
  STAGE 0                                3                               4
  STAGE I                               18                              11
  STAGE IA                              13                               5
  STAGE IB                              16                              12
  STAGE II                              14                              12
  STAGE IIA                              7                               7
  STAGE IIB                             10                               9
  STAGE IIC                              9                               6
  STAGE III                             28                              11
  STAGE IIIA                            11                               4
  STAGE IIIB                            23                              12
  STAGE IIIC                            32                              22
  STAGE IV                              17                               4
[1] 14  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              T0+T1 T2 T3 T4
  DEL PEAK 18(10Q23.31) MUTATED      45 46 42 48
  DEL PEAK 18(10Q23.31) WILD-TYPE    19 27 39 19
D38V5, multiclass
       clus
vv      DEL PEAK 18(10Q23.31) MUTATED DEL PEAK 18(10Q23.31) WILD-TYPE
  T0+T1                            45                              19
  T2                               46                              27
  T3                               42                              39
  T4                               48                              19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               N0  N1  N2  N3
  DEL PEAK 18(10Q23.31) MUTATED   105  48  25  26
  DEL PEAK 18(10Q23.31) WILD-TYPE  72  17  14  19
D38V6, multiclass
    clus
vv   DEL PEAK 18(10Q23.31) MUTATED DEL PEAK 18(10Q23.31) WILD-TYPE
  N0                           105                              72
  N1                            48                              17
  N2                            25                              14
  N3                            26                              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"
D38V7, binary
                                 cls
clus                                0   1
  DEL PEAK 18(10Q23.31) MUTATED   196  18
  DEL PEAK 18(10Q23.31) WILD-TYPE 123   4
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 18(10Q23.31) MUTATED    196   18
  DEL PEAK 18(10Q23.31) WILD-TYPE  123    4
   clus
vv  DEL PEAK 18(10Q23.31) MUTATED DEL PEAK 18(10Q23.31) WILD-TYPE
  0                           196                             123
  1                            18                               4
[1] 2 2
[1] FALSE
D38V8, binary
                                 cls
clus                               0  1
  DEL PEAK 18(10Q23.31) MUTATED   80 58
  DEL PEAK 18(10Q23.31) WILD-TYPE 54 32
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 18(10Q23.31) MUTATED     80   58
  DEL PEAK 18(10Q23.31) WILD-TYPE   54   32
     clus
vv    DEL PEAK 18(10Q23.31) MUTATED DEL PEAK 18(10Q23.31) WILD-TYPE
  NO                             80                              54
  YES                            58                              32
[1] 2 2
[1] FALSE
D38V9, binary
                                 cls
clus                                0   1
  DEL PEAK 18(10Q23.31) MUTATED    30 200
  DEL PEAK 18(10Q23.31) WILD-TYPE  17 120
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 18(10Q23.31) MUTATED     30  200
  DEL PEAK 18(10Q23.31) WILD-TYPE   17  120
     clus
vv    DEL PEAK 18(10Q23.31) MUTATED DEL PEAK 18(10Q23.31) WILD-TYPE
  NO                             30                              17
  YES                           200                             120
[1] 2 2
[1] FALSE
D38V10, continuous
D38V11, binary
                                 cls
clus                                0   1
  DEL PEAK 18(10Q23.31) MUTATED    95 135
  DEL PEAK 18(10Q23.31) WILD-TYPE  43  94
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 18(10Q23.31) MUTATED     95  135
  DEL PEAK 18(10Q23.31) WILD-TYPE   43   94
        clus
vv       DEL PEAK 18(10Q23.31) MUTATED DEL PEAK 18(10Q23.31) WILD-TYPE
  FEMALE                            95                              43
  MALE                             135                              94
[1] 2 2
[1] FALSE
D38V12, binary
                                 cls
clus                                0   1
  DEL PEAK 18(10Q23.31) MUTATED   199  31
  DEL PEAK 18(10Q23.31) WILD-TYPE 120  16
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 18(10Q23.31) MUTATED    199   31
  DEL PEAK 18(10Q23.31) WILD-TYPE  120   16
     clus
vv    DEL PEAK 18(10Q23.31) MUTATED DEL PEAK 18(10Q23.31) WILD-TYPE
  NO                            199                             120
  YES                            31                              16
[1] 2 2
[1] FALSE
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 18(10Q23.31) MUTATED       2                         0   222
  DEL PEAK 18(10Q23.31) WILD-TYPE     3                         1   131
D38V13, multiclass
                           clus
vv                          DEL PEAK 18(10Q23.31) MUTATED
  ASIAN                                                 2
  BLACK OR AFRICAN AMERICAN                             0
  WHITE                                               222
                           clus
vv                          DEL PEAK 18(10Q23.31) WILD-TYPE
  ASIAN                                                   3
  BLACK OR AFRICAN AMERICAN                               1
  WHITE                                                 131
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V14, binary
                                 cls
clus                                0   1
  DEL PEAK 18(10Q23.31) MUTATED     4 220
  DEL PEAK 18(10Q23.31) WILD-TYPE   3 132
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 18(10Q23.31) MUTATED      4  220
  DEL PEAK 18(10Q23.31) WILD-TYPE    3  132
                        clus
vv                       DEL PEAK 18(10Q23.31) MUTATED
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           220
                        clus
vv                       DEL PEAK 18(10Q23.31) WILD-TYPE
  HISPANIC OR LATINO                                   3
  NOT HISPANIC OR LATINO                             132
[1] 2 2
[1] FALSE

Clustering(39) Variable = DEL PEAK 19(10Q26.3) MUTATION ANALYSIS
D39V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 19(10Q26.3) MUTATED   83 81
  DEL PEAK 19(10Q26.3) WILD-TYPE 45 43
  DEL PEAK 19(10Q26.3) MUTATED DEL PEAK 19(10Q26.3) WILD-TYPE 
                           164                             88 
  DEL PEAK 19(10Q26.3) MUTATED DEL PEAK 19(10Q26.3) WILD-TYPE 
                            81                             43 
$`DEL PEAK 19(10Q26.3) MUTATED`
TCGA-D3-A8GI TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GD TCGA-EE-A2GO TCGA-ER-A193 
       13.41        31.96       166.75       269.03        52.90        19.04 
TCGA-FR-A729 TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 
      216.43        52.73         7.40        60.46        12.99        14.83 
TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
        8.42        31.89       110.93        49.35       133.25        19.04 
TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JP 
       15.75        86.30       107.61       171.58        64.83        43.53 
TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR 
       58.06        40.01        59.70        24.53         9.34        90.21 
TCGA-D3-A3MU TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51T TCGA-D3-A5GN 
       23.67        30.67       144.46        31.76        11.34        45.70 
TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GJ TCGA-D3-A8GM 
      177.86       124.08        78.21        23.61       179.97        70.62 
TCGA-D3-A8GP TCGA-D9-A1X3 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6EC TCGA-D9-A6EG 
      135.12        10.78        16.90        18.44        69.21        22.85 
TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA 
      138.67        68.68       150.61       110.53        60.10        64.83 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-DA-A95V TCGA-DA-A95W TCGA-DA-A95Y TCGA-DA-A95Z 
      225.11         8.71        72.10         0.76        14.14        12.30 
TCGA-EB-A5UN TCGA-EE-A181 TCGA-EE-A20F TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29H 
       52.41        20.38        79.20        12.99        44.28        47.41 
TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A2 
       47.74        27.16        61.12       346.49       185.19        30.02 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GM 
       77.98        26.14        12.95       201.60        68.65        18.35 
TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 
       93.63         0.76         0.20        71.31        81.99       103.13 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MK 
       15.25         5.75       209.79        94.19       171.85        89.26 
TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AD 
      145.45       227.01        53.26       124.31       122.73         4.41 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 
       54.51         6.28        67.89       111.85        45.90         3.35 
TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A199 TCGA-ER-A19B 
      168.85        19.86       135.98        34.45         7.82        53.29 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19P TCGA-ER-A19S 
       39.81        11.47       150.12        99.06       120.76        47.18 
TCGA-ER-A19W TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ET 
      146.63        22.36        16.87        10.19        28.67        68.52 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       15.48        32.05        74.47         4.50       174.21         4.14 
TCGA-FR-A7U8 TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1ZC TCGA-FS-A1ZJ 
       26.20        49.74       195.98         8.35       312.07        36.33 
TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F4 
       78.61       130.95         4.47        23.21         5.29        66.67 
TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A4EO TCGA-GF-A6C8 
       80.68        55.59        11.54        19.30        18.25         1.91 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U8 TCGA-GN-A8LK 
       53.29       117.93         7.59       120.53        46.92        43.23 
TCGA-GN-A9SD TCGA-OD-A75X TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-AA21 
       59.41       297.01         0.33       174.12         1.97        92.84 
TCGA-WE-A8ZM TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA4 
       65.42        62.89        10.95        48.39         1.94        24.99 
TCGA-YG-AA3O TCGA-Z2-AA3S 
       28.21        91.23 

$`DEL PEAK 19(10Q26.3) WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A2MR TCGA-EE-A3JD 
        9.76        62.07        38.76        33.24       134.40        27.35 
TCGA-FW-A3R5 TCGA-D3-A1Q3 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       36.95        15.72        76.41        62.60        25.64        45.99 
TCGA-D3-A2J8 TCGA-D3-A2JB TCGA-D3-A2JH TCGA-D3-A2JO TCGA-D3-A3CB TCGA-D3-A51E 
       62.86       168.00        36.30        66.08       140.98       173.85 
TCGA-D3-A51R TCGA-D3-A5GL TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GR TCGA-D9-A3Z1 
       62.70        42.05       120.00        69.53        36.53        15.02 
TCGA-DA-A1HV TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A95X TCGA-EB-A44Q TCGA-EB-A5KH 
       76.34        58.85        30.44        65.03         3.91        16.41 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20C 
       18.21        13.15        24.89         0.00        26.24        75.55 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A2A1 TCGA-EE-A2GK TCGA-EE-A2GL 
       75.22        76.14         0.26       115.43        10.62        32.48 
TCGA-EE-A2MC TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AC 
       23.77        63.25       104.78       143.93        23.51        64.04 
TCGA-ER-A197 TCGA-ER-A19A TCGA-ER-A19G TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19Q 
       10.49         4.54       184.60        59.84        42.51        49.71 
TCGA-ER-A1A1 TCGA-ER-A2ND TCGA-ER-A3ES TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FS-A1YW 
       73.05         4.70       173.29         5.65        10.06       171.78 
TCGA-FS-A1Z4 TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZS TCGA-FS-A1ZT 
       27.62        32.78        43.92         7.82       136.27        35.28 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-GF-A3OT TCGA-GN-A265 
        3.06        30.90       173.19        13.28         9.90        96.92 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A4U4 TCGA-LH-A9QB TCGA-QB-A6FS TCGA-RP-A690 
       17.06        42.48        34.49        85.05         7.23         0.20 
TCGA-W3-A828 TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1V TCGA-W3-AA1W TCGA-WE-A8K1 
      120.07        44.05        79.99         8.09       185.13        47.54 
TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-AAA0 TCGA-XV-AB01 
       12.69        21.90        37.32         6.61 

  DEL PEAK 19(10Q26.3) MUTATED DEL PEAK 19(10Q26.3) WILD-TYPE 
                           0.2                            0.0 
  DEL PEAK 19(10Q26.3) MUTATED DEL PEAK 19(10Q26.3) WILD-TYPE 
                        346.49                         185.13 
  DEL PEAK 19(10Q26.3) MUTATED DEL PEAK 19(10Q26.3) WILD-TYPE 
                        51.075                         38.040 
[1] "0.2 - 346.5 (51.1)" "0.0 - 185.1 (38.0)"
[1] "hr=" "1.3"
D39V2, survival
                                sevent
clus2                              0   1
  DEL PEAK 19(10Q26.3) MUTATED   108 120
  DEL PEAK 19(10Q26.3) WILD-TYPE  58  72
  DEL PEAK 19(10Q26.3) MUTATED DEL PEAK 19(10Q26.3) WILD-TYPE 
                           228                            130 
  DEL PEAK 19(10Q26.3) MUTATED DEL PEAK 19(10Q26.3) WILD-TYPE 
                           120                             72 
$`DEL PEAK 19(10Q26.3) MUTATED`
TCGA-D3-A8GI TCGA-EB-A5SH TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GD TCGA-EE-A2GO 
       58.52        54.02        94.98       168.26       340.14       126.81 
TCGA-ER-A193 TCGA-FR-A729 TCGA-FS-A1ZF TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-3N-A9WC 
       31.40       220.80        15.45        61.15        21.40        66.48 
TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 
       12.99        14.93        16.57       112.04       112.57        71.80 
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JD 
      133.25        28.08        31.59       115.53        86.76        11.87 
TCGA-D3-A2JG TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3C6 
      113.52        12.10       171.58        66.48        59.57        58.06 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU 
       86.93        60.23        24.53         9.34       103.59        39.75 
TCGA-D3-A3MV TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51T 
       45.30        55.73       145.12        32.94        22.62        26.89 
TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB 
      135.75       137.92       178.32        18.18       125.19        30.84 
TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GJ TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GP 
       79.59        23.61       241.38       107.15       161.00       152.75 
TCGA-D3-A8GS TCGA-D3-A8GV TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1X3 TCGA-D9-A3Z3 
      117.17       167.70       151.53        54.67        18.12        22.29 
TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HW 
       18.44         9.90        25.18        77.56        22.95        36.03 
TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 
      144.89       222.51       176.55        35.93       135.02        88.87 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-DA-A95V TCGA-DA-A95W 
       53.92        65.92       225.96        43.36        72.10        37.35 
TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44R TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17Z 
       14.14        13.02        10.36        29.29        58.92         8.65 
TCGA-EE-A181 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29D 
       33.73         4.96       133.81        91.56        13.55        13.97 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T 
       72.07        64.64        56.84        56.42        66.74       369.93 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
      195.02        17.92        46.82        59.64        39.29        86.14 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       59.28        67.43       173.79       220.24        48.72       107.38 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU 
       75.48       102.12        13.91        42.77        81.21        94.82 
TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MD TCGA-EE-A2ME 
       21.67       129.27        28.83        19.76        47.28       103.27 
TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2MM 
      268.73       103.20        16.96       204.66       180.39       167.90 
TCGA-EE-A2MP TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE 
      248.65        53.26       124.31       122.73        28.77        54.51 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 
       13.81        41.59       138.81       172.18       127.20        36.95 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JE TCGA-EE-A3JH 
       64.08        34.32        53.19       201.80        51.35       134.33 
TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D 
      152.81        35.44         9.17        98.40        48.89        12.59 
TCGA-ER-A19E TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19P TCGA-ER-A19S TCGA-ER-A19T 
       13.02       152.35       131.51       162.08        49.48         8.88 
TCGA-ER-A19W TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH 
      148.18        43.82        20.15        28.83        48.99        41.56 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A3YN 
       93.01        46.98        33.21        12.95       149.03        92.98 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A8YE TCGA-FS-A1YX TCGA-FS-A1YY 
      174.21        15.72        27.85       104.42        48.59       228.59 
TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZC TCGA-FS-A1ZH 
      202.65        20.91         7.79        27.72       357.37        32.75 
TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZU TCGA-FS-A1ZW 
       47.38       101.26       133.55        11.41        26.56        49.48 
TCGA-FS-A1ZY TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4FB TCGA-FS-A4FD TCGA-FW-A3TU 
       27.09        66.67        28.73        26.73        80.68        55.59 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 
       13.51        19.30        19.43         2.04       139.89       117.93 
TCGA-GN-A266 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A4U9 
       10.13        32.48       121.91        10.42        48.89        22.13 
TCGA-GN-A8LK TCGA-GN-A9SD TCGA-HR-A2OG TCGA-HR-A2OH TCGA-OD-A75X TCGA-RP-A693 
       50.10        59.41         0.23        65.88       297.90         0.33 
TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K6 
        0.69       228.16        63.02       105.04        24.03        17.95 
TCGA-WE-A8ZM TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AA9Y 
      101.33        63.22        11.80        35.80        49.51        12.16 
TCGA-WE-AAA4 TCGA-YD-A9TA TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-AA3S TCGA-Z2-AA3V 
       24.99        49.18        37.94        14.43        96.99        15.98 

$`DEL PEAK 19(10Q26.3) WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SG TCGA-EE-A184 
       27.65        62.07        46.32        13.87        68.25        68.15 
TCGA-EE-A29L TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A198 TCGA-FW-A3R5 TCGA-QB-AA9O 
        2.60       134.40        27.35        50.76        36.95        18.05 
TCGA-3N-A9WB TCGA-D3-A1Q3 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       17.03        16.67        90.90        95.74        43.43       103.10 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JH TCGA-D3-A2JO TCGA-D3-A3BZ 
       65.49        23.77       168.00        42.08        66.08       130.72 
TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A51E TCGA-D3-A51H TCGA-D3-A51R TCGA-D3-A5GL 
       46.98       166.52       174.84        56.35        63.81       125.79 
TCGA-D3-A8GE TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D9-A1JW 
       26.43       170.20        89.13        29.06       129.63         3.65 
TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-DA-A1HV TCGA-DA-A1I0 TCGA-DA-A1IB TCGA-DA-A1IC 
        7.10        15.39        76.57        20.38        40.60        68.09 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A95X TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5VV 
       33.93        10.49        73.94        13.87        20.35         7.04 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20C 
       36.46        29.82        27.22        14.70        26.89       151.27 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29N TCGA-EE-A29R 
       63.35        85.08        78.97        63.78        18.61        14.47 
TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A2A1 TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GT 
       61.28        25.87       115.96        54.74        79.66        44.88 
TCGA-EE-A2MC TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MS 
       61.51        96.23       216.66        47.54        43.23       162.48 
TCGA-EE-A2MT TCGA-EE-A3AC TCGA-ER-A197 TCGA-ER-A19A TCGA-ER-A19F TCGA-ER-A19G 
       71.21        64.04        13.94        77.75        26.37       302.07 
TCGA-ER-A19J TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A1A1 TCGA-ER-A2ND 
        6.44        61.05        44.09        50.89       105.07        23.34 
TCGA-ER-A3ES TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FS-A1YW 
      247.04        18.77        38.27        34.82        36.26       216.92 
TCGA-FS-A1Z4 TCGA-FS-A1ZB TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZK 
       28.08        48.85        53.52        46.45         9.70        23.93 
TCGA-FS-A1ZP TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 
       74.73       148.80        53.16        27.02        77.82        50.14 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-GF-A3OT TCGA-GF-A6C9 
      174.84        34.03        54.41        17.46         9.90        15.78 
TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26D TCGA-GN-A4U4 TCGA-GN-A8LL 
       96.92        64.44        62.79        48.00        39.35        21.37 
TCGA-LH-A9QB TCGA-QB-A6FS TCGA-RP-A690 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1Q 
      368.78         7.23         0.20       121.08         4.01        69.07 
TCGA-W3-AA1R TCGA-W3-AA1V TCGA-W3-AA1W TCGA-WE-A8K1 TCGA-WE-A8ZN TCGA-WE-A8ZO 
      111.09        42.08       219.16        49.05        58.98        70.52 
TCGA-WE-AAA0 TCGA-XV-AB01 TCGA-YD-A89C TCGA-Z2-A8RT 
       40.41        13.25         6.90        27.58 

  DEL PEAK 19(10Q26.3) MUTATED DEL PEAK 19(10Q26.3) WILD-TYPE 
                          0.23                           0.20 
  DEL PEAK 19(10Q26.3) MUTATED DEL PEAK 19(10Q26.3) WILD-TYPE 
                        369.93                         368.78 
  DEL PEAK 19(10Q26.3) MUTATED DEL PEAK 19(10Q26.3) WILD-TYPE 
                        54.590                         48.425 
[1] "0.2 - 369.9 (54.6)" "0.2 - 368.8 (48.4)"
[1] "hr=" "1.2"
D39V3, continuous
                                vv
clus                             I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB
  DEL PEAK 19(10Q26.3) MUTATED         10       3      22       13       16
  DEL PEAK 19(10Q26.3) WILD-TYPE        3       4       7        5       12
                                vv
clus                             STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK 19(10Q26.3) MUTATED         15         6        10         9
  DEL PEAK 19(10Q26.3) WILD-TYPE       11         8         9         6
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 19(10Q26.3) MUTATED          29         11         23         31
  DEL PEAK 19(10Q26.3) WILD-TYPE        10          4         12         23
                                vv
clus                             STAGE IV
  DEL PEAK 19(10Q26.3) MUTATED         16
  DEL PEAK 19(10Q26.3) WILD-TYPE        5
D39V4, multiclass
            clus
vv           DEL PEAK 19(10Q26.3) MUTATED DEL PEAK 19(10Q26.3) WILD-TYPE
  I/II NOS                             10                              3
  STAGE 0                               3                              4
  STAGE I                              22                              7
  STAGE IA                             13                              5
  STAGE IB                             16                             12
  STAGE II                             15                             11
  STAGE IIA                             6                              8
  STAGE IIB                            10                              9
  STAGE IIC                             9                              6
  STAGE III                            29                             10
  STAGE IIIA                           11                              4
  STAGE IIIB                           23                             12
  STAGE IIIC                           31                             23
  STAGE IV                             16                              5
[1] 14  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  DEL PEAK 19(10Q26.3) MUTATED      44 51 45 46
  DEL PEAK 19(10Q26.3) WILD-TYPE    20 22 36 21
D39V5, multiclass
       clus
vv      DEL PEAK 19(10Q26.3) MUTATED DEL PEAK 19(10Q26.3) WILD-TYPE
  T0+T1                           44                             20
  T2                              51                             22
  T3                              45                             36
  T4                              46                             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  N3
  DEL PEAK 19(10Q26.3) MUTATED   111  48  25  26
  DEL PEAK 19(10Q26.3) WILD-TYPE  66  17  14  19
D39V6, multiclass
    clus
vv   DEL PEAK 19(10Q26.3) MUTATED DEL PEAK 19(10Q26.3) WILD-TYPE
  N0                          111                             66
  N1                           48                             17
  N2                           25                             14
  N3                           26                             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"
D39V7, binary
                                cls
clus                               0   1
  DEL PEAK 19(10Q26.3) MUTATED   201  17
  DEL PEAK 19(10Q26.3) WILD-TYPE 118   5
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(10Q26.3) MUTATED    201   17
  DEL PEAK 19(10Q26.3) WILD-TYPE  118    5
   clus
vv  DEL PEAK 19(10Q26.3) MUTATED DEL PEAK 19(10Q26.3) WILD-TYPE
  0                          201                            118
  1                           17                              5
[1] 2 2
[1] FALSE
D39V8, binary
                                cls
clus                              0  1
  DEL PEAK 19(10Q26.3) MUTATED   82 57
  DEL PEAK 19(10Q26.3) WILD-TYPE 52 33
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(10Q26.3) MUTATED     82   57
  DEL PEAK 19(10Q26.3) WILD-TYPE   52   33
     clus
vv    DEL PEAK 19(10Q26.3) MUTATED DEL PEAK 19(10Q26.3) WILD-TYPE
  NO                            82                             52
  YES                           57                             33
[1] 2 2
[1] FALSE
D39V9, binary
                                cls
clus                               0   1
  DEL PEAK 19(10Q26.3) MUTATED    28 208
  DEL PEAK 19(10Q26.3) WILD-TYPE  19 112
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(10Q26.3) MUTATED     28  208
  DEL PEAK 19(10Q26.3) WILD-TYPE   19  112
     clus
vv    DEL PEAK 19(10Q26.3) MUTATED DEL PEAK 19(10Q26.3) WILD-TYPE
  NO                            28                             19
  YES                          208                            112
[1] 2 2
[1] FALSE
D39V10, continuous
D39V11, binary
                                cls
clus                               0   1
  DEL PEAK 19(10Q26.3) MUTATED    96 140
  DEL PEAK 19(10Q26.3) WILD-TYPE  42  89
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(10Q26.3) MUTATED     96  140
  DEL PEAK 19(10Q26.3) WILD-TYPE   42   89
        clus
vv       DEL PEAK 19(10Q26.3) MUTATED DEL PEAK 19(10Q26.3) WILD-TYPE
  FEMALE                           96                             42
  MALE                            140                             89
[1] 2 2
[1] FALSE
D39V12, binary
                                cls
clus                               0   1
  DEL PEAK 19(10Q26.3) MUTATED   205  31
  DEL PEAK 19(10Q26.3) WILD-TYPE 114  16
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(10Q26.3) MUTATED    205   31
  DEL PEAK 19(10Q26.3) WILD-TYPE  114   16
     clus
vv    DEL PEAK 19(10Q26.3) MUTATED DEL PEAK 19(10Q26.3) WILD-TYPE
  NO                           205                            114
  YES                           31                             16
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 19(10Q26.3) MUTATED       1                         0   229
  DEL PEAK 19(10Q26.3) WILD-TYPE     4                         1   124
D39V13, multiclass
                           clus
vv                          DEL PEAK 19(10Q26.3) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                              229
                           clus
vv                          DEL PEAK 19(10Q26.3) WILD-TYPE
  ASIAN                                                  4
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                124
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V14, binary
                                cls
clus                               0   1
  DEL PEAK 19(10Q26.3) MUTATED     4 227
  DEL PEAK 19(10Q26.3) WILD-TYPE   3 125
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(10Q26.3) MUTATED      4  227
  DEL PEAK 19(10Q26.3) WILD-TYPE    3  125
                        clus
vv                       DEL PEAK 19(10Q26.3) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                          227
                        clus
vv                       DEL PEAK 19(10Q26.3) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            125
[1] 2 2
[1] FALSE

Clustering(40) Variable = DEL PEAK 20(11P15.5) MUTATION ANALYSIS
D40V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 20(11P15.5) MUTATED   40 36
  DEL PEAK 20(11P15.5) WILD-TYPE 88 88
  DEL PEAK 20(11P15.5) MUTATED DEL PEAK 20(11P15.5) WILD-TYPE 
                            76                            176 
  DEL PEAK 20(11P15.5) MUTATED DEL PEAK 20(11P15.5) WILD-TYPE 
                            36                             88 
$`DEL PEAK 20(11P15.5) MUTATED`
TCGA-D3-A8GI TCGA-EB-A5SG TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-3N-A9WC TCGA-D3-A1Q1 
       13.41        33.24        52.73         7.40        60.46         8.42 
TCGA-D3-A1Q5 TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A3C6 
      110.93        25.64        45.99       171.58        64.83        58.06 
TCGA-D3-A3CC TCGA-D3-A3MO TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GU 
       40.01         9.34        11.34        45.70       177.86       124.08 
TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GM TCGA-D3-A8GP TCGA-D9-A3Z3 TCGA-D9-A4Z6 
       78.21        23.61        70.62       135.12        16.90        18.44 
TCGA-DA-A1HV TCGA-DA-A1I1 TCGA-DA-A1I5 TCGA-DA-A3F5 TCGA-DA-A95V TCGA-EE-A182 
       76.34        68.68       110.53       225.11        72.10         0.00 
TCGA-EE-A20C TCGA-EE-A29C TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A2A2 
       75.55        76.14        47.74        27.16        61.12        30.02 
TCGA-EE-A2GE TCGA-EE-A2GM TCGA-EE-A2M6 TCGA-EE-A2MJ TCGA-EE-A2MP TCGA-EE-A2MS 
       12.95        18.35       103.13        63.25       227.01       143.93 
TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AE TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JH 
       53.26       122.73        54.51        45.90         3.35        19.86 
TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19L TCGA-ER-A19S 
       10.49         7.82        39.81        11.47        99.06        47.18 
TCGA-ER-A2ND TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A42L TCGA-FR-A3YN 
        4.70       173.29        68.52        15.48        74.47         4.50 
TCGA-FR-A69P TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZW TCGA-FS-A4F8 TCGA-FS-A4F9 
        4.14        36.33        78.61        23.21       173.19        13.28 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A9SD TCGA-W3-AA1R 
       53.29       117.93        17.06         7.59        59.41        79.99 
TCGA-WE-A8ZM TCGA-WE-A8ZO TCGA-WE-A8ZY TCGA-WE-AAA4 
       65.42        21.90        48.39        24.99 

$`DEL PEAK 20(11P15.5) WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GD 
        9.76        62.07        38.76        31.96       166.75       269.03 
TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-FR-A729 TCGA-FW-A3R5 
       52.90       134.40        27.35        19.04       216.43        36.95 
TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       12.99        14.83        15.72        31.89        49.35       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB 
       19.04        76.41        62.60        62.86        15.75       168.00 
TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3CB 
       86.30       107.61        36.30        66.08        43.53       140.98 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F 
       59.70        24.53        90.21        23.67       173.85        30.67 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A5GL TCGA-D3-A8GJ TCGA-D3-A8GK 
      144.46        31.76        62.70        42.05       179.97       120.00 
TCGA-D3-A8GL TCGA-D3-A8GR TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A6EC TCGA-D9-A6EG 
       69.53        36.53        10.78        15.02        69.21        22.85 
TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 
      138.67       150.61        60.10        64.83        58.85        30.44 
TCGA-DA-A3F8 TCGA-DA-A95W TCGA-DA-A95X TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q 
        8.71         0.76        65.03        14.14        12.30         3.91 
TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A181 
       16.41        52.41        18.21        13.15        24.89        20.38 
TCGA-EE-A183 TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G 
       26.24        79.20        75.22        12.99         0.26        44.28 
TCGA-EE-A29H TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A6 TCGA-EE-A2GB 
       47.41       346.49       185.19       115.43        77.98        26.14 
TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GP 
      201.60        68.65        10.62        32.48        93.63         0.76 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
        0.20        71.31        81.99        15.25         5.75        23.77 
TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
      209.79        94.19       171.85        89.26       104.78       145.45 
TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3J3 
       23.51       124.31        64.04         4.41         6.28        67.89 
TCGA-EE-A3J4 TCGA-EE-A3JB TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A19A TCGA-ER-A19B 
      111.85       168.85       135.98        34.45         4.54        53.29 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
      184.60       150.12        59.84        42.51       120.76        49.71 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
      146.63        73.05        22.36        16.87        10.19        28.67 
TCGA-ER-A3PL TCGA-FR-A44A TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FS-A1YW 
       32.05       174.21        26.20         5.65        10.06       171.78 
TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD 
       49.74       195.98         8.35        27.62       312.07        32.78 
TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU 
       43.92         7.82       130.95       136.27        35.28         4.47 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4FD TCGA-FW-A3TU 
        5.29         3.06        30.90        66.67        80.68        55.59 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A265 
       11.54        19.30         9.90        18.25         1.91        96.92 
TCGA-GN-A268 TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-GN-A8LK TCGA-LH-A9QB 
       42.48       120.53        34.49        46.92        43.23        85.05 
TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A825 
      297.01         7.23         0.20         0.33       174.12         1.97 
TCGA-W3-A828 TCGA-W3-AA1Q TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 
      120.07        44.05         8.09       185.13        92.84        47.54 
TCGA-WE-A8ZN TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-XV-AB01 
       12.69        62.89        10.95         1.94        37.32         6.61 
TCGA-YG-AA3O TCGA-Z2-AA3S 
       28.21        91.23 

  DEL PEAK 20(11P15.5) MUTATED DEL PEAK 20(11P15.5) WILD-TYPE 
                           0.0                            0.2 
  DEL PEAK 20(11P15.5) MUTATED DEL PEAK 20(11P15.5) WILD-TYPE 
                        227.01                         346.49 
  DEL PEAK 20(11P15.5) MUTATED DEL PEAK 20(11P15.5) WILD-TYPE 
                        48.065                         43.985 
[1] "0.0 - 227.0 (48.1)" "0.2 - 346.5 (44.0)"
[1] "hr=" "1.1"
D40V2, survival
                                sevent
clus2                              0   1
  DEL PEAK 20(11P15.5) MUTATED    51  61
  DEL PEAK 20(11P15.5) WILD-TYPE 115 131
  DEL PEAK 20(11P15.5) MUTATED DEL PEAK 20(11P15.5) WILD-TYPE 
                           112                            246 
  DEL PEAK 20(11P15.5) MUTATED DEL PEAK 20(11P15.5) WILD-TYPE 
                            61                            131 
$`DEL PEAK 20(11P15.5) MUTATED`
TCGA-D3-A8GI TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A29L TCGA-ER-A198 TCGA-FS-A1ZF 
       58.52        68.25        54.02         2.60        50.76        15.45 
TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-3N-A9WC TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A2J6 
       61.15        21.40        66.48        16.57       112.57        43.43 
TCGA-D3-A2J7 TCGA-D3-A2JD TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A3C6 TCGA-D3-A3C7 
      103.10        11.87       171.58        66.48        58.06        46.98 
TCGA-D3-A3CC TCGA-D3-A3MO TCGA-D3-A3MV TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GR 
       86.93         9.34        45.30        26.89       135.75       178.32 
TCGA-D3-A5GU TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GP 
      125.19        79.59        23.61       107.15       161.00       152.75 
TCGA-D9-A149 TCGA-D9-A1JX TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6EA TCGA-DA-A1HV 
       54.67         7.10        22.29        18.44        25.18        76.57 
TCGA-DA-A1HW TCGA-DA-A1I1 TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A3F5 TCGA-DA-A95V 
       36.03       222.51       135.02        53.92       225.96        72.10 
TCGA-EB-A44R TCGA-EB-A5UL TCGA-EE-A182 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20I 
       10.36        29.29        14.70       133.81       151.27        13.55 
TCGA-EE-A29C TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
       78.97        56.84        18.61        56.42        66.74        14.47 
TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2GE TCGA-EE-A2GM 
       25.87        17.92        59.64        39.29       173.79        75.48 
TCGA-EE-A2M6 TCGA-EE-A2MJ TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MU 
      129.27        96.23        47.54       248.65       162.48        53.26 
TCGA-EE-A3AB TCGA-EE-A3AE TCGA-EE-A3AG TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 
      122.73        54.51        41.59        36.95        64.08        34.32 
TCGA-EE-A3JH TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19L 
      134.33        13.94         9.17        48.89        12.59       131.51 
TCGA-ER-A19S TCGA-ER-A2ND TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A42K 
       49.48        23.34       247.04        93.01        46.98        12.95 
TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A69P TCGA-FS-A1ZA TCGA-FS-A1ZH TCGA-FS-A1ZJ 
      149.03        92.98        15.72        27.72        32.75        47.38 
TCGA-FS-A1ZM TCGA-FS-A1ZW TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB 
      101.26        49.48        28.73       174.84        34.03        26.73 
TCGA-FW-A3I3 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A4U7 
       17.46       139.89       117.93        64.44        32.48        10.42 
TCGA-GN-A4U9 TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OH TCGA-W3-AA1R TCGA-WE-A8ZM 
       22.13        21.37        59.41        65.88       111.09       101.33 
TCGA-WE-A8ZO TCGA-WE-A8ZY TCGA-WE-AAA4 TCGA-Z2-A8RT 
       70.52        49.51        24.99        27.58 

$`DEL PEAK 20(11P15.5) WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EE-A180 TCGA-EE-A184 
       27.65        62.07        46.32        13.87        94.98        68.15 
TCGA-EE-A20H TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 
      168.26       340.14       126.81       134.40        27.35        31.40 
TCGA-FR-A729 TCGA-FW-A3R5 TCGA-QB-AA9O TCGA-3N-A9WB TCGA-3N-A9WD TCGA-BF-AAP0 
      220.80        36.95        18.05        17.03        12.99        14.93 
TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 
       16.67       112.04        71.80       133.25        28.08        31.59 
TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB 
       90.90        95.74        65.49        23.77       115.53       168.00 
TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JO TCGA-D3-A2JP 
       86.76       113.52        42.08        12.10        66.08        59.57 
TCGA-D3-A3BZ TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MR TCGA-D3-A3MU 
      130.72       166.52        60.23        24.53       103.59        39.75 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
      174.84        55.73        56.35       145.12        32.94        22.62 
TCGA-D3-A51R TCGA-D3-A5GL TCGA-D3-A5GO TCGA-D3-A5GS TCGA-D3-A8GB TCGA-D3-A8GE 
       63.81       125.79       137.92        18.18        30.84        26.43 
TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS 
      241.38       170.20        89.13        29.06       129.63       117.17 
TCGA-D3-A8GV TCGA-D9-A148 TCGA-D9-A1JW TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A6E9 
      167.70       151.53         3.65        18.12        15.39         9.90 
TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 
       77.56        22.95       144.89        20.38       176.55        35.93 
TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
       88.87        65.92        40.60        68.09        33.93        10.49 
TCGA-DA-A3F8 TCGA-DA-A95W TCGA-DA-A95X TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q 
       43.36        37.35        73.94        14.14        13.02        13.87 
TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
       20.35        58.92         7.04        36.46        29.82        27.22 
TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20F TCGA-EE-A29A 
        8.65        33.73        26.89         4.96        91.56        63.35 
TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29S 
       85.08        13.97        63.78        72.07        64.64        61.28 
TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A6 TCGA-EE-A2GB 
      369.93       195.02        46.82       115.96        86.14        59.28 
TCGA-EE-A2GC TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       67.43       220.24        48.72       107.38        54.74        79.66 
TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU 
      102.12        13.91        42.77        81.21        44.88        94.82 
TCGA-EE-A2M5 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME 
       21.67        28.83        19.76        61.51        47.28       103.27 
TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML 
      268.73       103.20        16.96       204.66       180.39       216.66 
TCGA-EE-A2MM TCGA-EE-A2MQ TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AD 
      167.90        43.23        71.21       124.31        64.04        28.77 
TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3JA TCGA-EE-A3JB 
       13.81       138.81       172.18       127.20        53.19       201.80 
TCGA-EE-A3JE TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19E 
       51.35       152.81        35.44        77.75        98.40        13.02 
TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19M TCGA-ER-A19N 
       26.37       302.07       152.35         6.44        61.05        44.09 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
      162.08        50.89         8.88       148.18       105.07        43.82 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3PL TCGA-FR-A44A 
       20.15        28.83        48.99        41.56        33.21       174.21 
TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE 
       27.85        18.77        38.27        34.82        36.26       104.42 
TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 
      216.92        48.59       228.59       202.65        20.91        28.08 
TCGA-FS-A1Z7 TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG 
        7.79        48.85       357.37        53.52        46.45         9.70 
TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT 
       23.93        74.73       133.55        11.41       148.80        53.16 
TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 
       26.56        27.09        27.02        77.82        50.14        66.67 
TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
       54.41        80.68        55.59        13.51        19.30         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A268 
       19.43         2.04        15.78        96.92        10.13        62.79 
TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-GN-A8LK TCGA-HR-A2OG 
       48.00       121.91        39.35        48.89        50.10         0.23 
TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 TCGA-RP-A694 
      368.78       297.90         7.23         0.20         0.33         0.69 
TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1Q TCGA-W3-AA1V 
      228.16        63.02       121.08         4.01        69.07        42.08 
TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K6 TCGA-WE-A8ZN 
      219.16       105.04        24.03        49.05        17.95        58.98 
TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-XV-AB01 
       63.22        11.80        35.80        12.16        40.41        13.25 
TCGA-YD-A89C TCGA-YD-A9TA TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-AA3S TCGA-Z2-AA3V 
        6.90        49.18        37.94        14.43        96.99        15.98 

  DEL PEAK 20(11P15.5) MUTATED DEL PEAK 20(11P15.5) WILD-TYPE 
                           2.6                            0.2 
  DEL PEAK 20(11P15.5) MUTATED DEL PEAK 20(11P15.5) WILD-TYPE 
                        248.65                         369.93 
  DEL PEAK 20(11P15.5) MUTATED DEL PEAK 20(11P15.5) WILD-TYPE 
                        53.970                         50.515 
[1] "2.6 - 248.7 (54.0)" "0.2 - 369.9 (50.5)"
[1] "hr=" "1.1"
D40V3, continuous
                                vv
clus                             I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB
  DEL PEAK 20(11P15.5) MUTATED          5       1      10        4       10
  DEL PEAK 20(11P15.5) WILD-TYPE        8       6      19       14       18
                                vv
clus                             STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK 20(11P15.5) MUTATED          4         2         4         7
  DEL PEAK 20(11P15.5) WILD-TYPE       22        12        15         8
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 20(11P15.5) MUTATED          15          4         11         22
  DEL PEAK 20(11P15.5) WILD-TYPE        24         11         24         32
                                vv
clus                             STAGE IV
  DEL PEAK 20(11P15.5) MUTATED          6
  DEL PEAK 20(11P15.5) WILD-TYPE       15
D40V4, multiclass
            clus
vv           DEL PEAK 20(11P15.5) MUTATED DEL PEAK 20(11P15.5) WILD-TYPE
  I/II NOS                              5                              8
  STAGE 0                               1                              6
  STAGE I                              10                             19
  STAGE IA                              4                             14
  STAGE IB                             10                             18
  STAGE II                              4                             22
  STAGE IIA                             2                             12
  STAGE IIB                             4                             15
  STAGE IIC                             7                              8
  STAGE III                            15                             24
  STAGE IIIA                            4                             11
  STAGE IIIB                           11                             24
  STAGE IIIC                           22                             32
  STAGE IV                              6                             15
[1] 14  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  DEL PEAK 20(11P15.5) MUTATED      20 25 19 26
  DEL PEAK 20(11P15.5) WILD-TYPE    44 48 62 41
D40V5, multiclass
       clus
vv      DEL PEAK 20(11P15.5) MUTATED DEL PEAK 20(11P15.5) WILD-TYPE
  T0+T1                           20                             44
  T2                              25                             48
  T3                              19                             62
  T4                              26                             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  N3
  DEL PEAK 20(11P15.5) MUTATED    48  25  13  14
  DEL PEAK 20(11P15.5) WILD-TYPE 129  40  26  31
D40V6, multiclass
    clus
vv   DEL PEAK 20(11P15.5) MUTATED DEL PEAK 20(11P15.5) WILD-TYPE
  N0                           48                            129
  N1                           25                             40
  N2                           13                             26
  N3                           14                             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"
D40V7, binary
                                cls
clus                               0   1
  DEL PEAK 20(11P15.5) MUTATED   100   6
  DEL PEAK 20(11P15.5) WILD-TYPE 219  16
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(11P15.5) MUTATED    100    6
  DEL PEAK 20(11P15.5) WILD-TYPE  219   16
   clus
vv  DEL PEAK 20(11P15.5) MUTATED DEL PEAK 20(11P15.5) WILD-TYPE
  0                          100                            219
  1                            6                             16
[1] 2 2
[1] FALSE
D40V8, binary
                                cls
clus                              0  1
  DEL PEAK 20(11P15.5) MUTATED   39 36
  DEL PEAK 20(11P15.5) WILD-TYPE 95 54
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(11P15.5) MUTATED     39   36
  DEL PEAK 20(11P15.5) WILD-TYPE   95   54
     clus
vv    DEL PEAK 20(11P15.5) MUTATED DEL PEAK 20(11P15.5) WILD-TYPE
  NO                            39                             95
  YES                           36                             54
[1] 2 2
[1] FALSE
D40V9, binary
                                cls
clus                               0   1
  DEL PEAK 20(11P15.5) MUTATED    11 103
  DEL PEAK 20(11P15.5) WILD-TYPE  36 217
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(11P15.5) MUTATED     11  103
  DEL PEAK 20(11P15.5) WILD-TYPE   36  217
     clus
vv    DEL PEAK 20(11P15.5) MUTATED DEL PEAK 20(11P15.5) WILD-TYPE
  NO                            11                             36
  YES                          103                            217
[1] 2 2
[1] FALSE
D40V10, continuous
D40V11, binary
                                cls
clus                               0   1
  DEL PEAK 20(11P15.5) MUTATED    58  56
  DEL PEAK 20(11P15.5) WILD-TYPE  80 173
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(11P15.5) MUTATED     58   56
  DEL PEAK 20(11P15.5) WILD-TYPE   80  173
        clus
vv       DEL PEAK 20(11P15.5) MUTATED DEL PEAK 20(11P15.5) WILD-TYPE
  FEMALE                           58                             80
  MALE                             56                            173
[1] 2 2
[1] FALSE
D40V12, binary
                                cls
clus                               0   1
  DEL PEAK 20(11P15.5) MUTATED   103  11
  DEL PEAK 20(11P15.5) WILD-TYPE 216  36
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(11P15.5) MUTATED    103   11
  DEL PEAK 20(11P15.5) WILD-TYPE  216   36
     clus
vv    DEL PEAK 20(11P15.5) MUTATED DEL PEAK 20(11P15.5) WILD-TYPE
  NO                           103                            216
  YES                           11                             36
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 20(11P15.5) MUTATED       1                         0   111
  DEL PEAK 20(11P15.5) WILD-TYPE     4                         1   242
D40V13, multiclass
                           clus
vv                          DEL PEAK 20(11P15.5) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                              111
                           clus
vv                          DEL PEAK 20(11P15.5) WILD-TYPE
  ASIAN                                                  4
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                242
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V14, binary
                                cls
clus                               0   1
  DEL PEAK 20(11P15.5) MUTATED     0 113
  DEL PEAK 20(11P15.5) WILD-TYPE   7 239
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(11P15.5) MUTATED      0  113
  DEL PEAK 20(11P15.5) WILD-TYPE    7  239
                        clus
vv                       DEL PEAK 20(11P15.5) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                          113
                        clus
vv                       DEL PEAK 20(11P15.5) WILD-TYPE
  HISPANIC OR LATINO                                  7
  NOT HISPANIC OR LATINO                            239
[1] 2 2
[1] FALSE

Clustering(41) Variable = DEL PEAK 21(11Q23.3) MUTATION ANALYSIS
D41V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 21(11Q23.3) MUTATED   69 72
  DEL PEAK 21(11Q23.3) WILD-TYPE 59 52
  DEL PEAK 21(11Q23.3) MUTATED DEL PEAK 21(11Q23.3) WILD-TYPE 
                           141                            111 
  DEL PEAK 21(11Q23.3) MUTATED DEL PEAK 21(11Q23.3) WILD-TYPE 
                            72                             52 
$`DEL PEAK 21(11Q23.3) MUTATED`
TCGA-D3-A2JF TCGA-D3-A8GI TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A20H TCGA-ER-A193 
       62.07        13.41        33.24        31.96       166.75        19.04 
TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-3N-A9WC TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q5 
       52.73         7.40        60.46        14.83         8.42       110.93 
TCGA-D3-A1Q7 TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2JB TCGA-D3-A2JC 
      133.25        62.60        25.64        45.99       168.00        86.30 
TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3CF 
      171.58        64.83        66.08        58.06        40.01        24.53 
TCGA-D3-A3MO TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GU 
        9.34        23.67       173.85        45.70       177.86       124.08 
TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GJ TCGA-D3-A8GM TCGA-D3-A8GP TCGA-D3-A8GR 
       78.21        23.61       179.97        70.62       135.12        36.53 
TCGA-D9-A3Z3 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1I1 TCGA-DA-A1I5 
       16.90        69.21        22.85        76.34        68.68       110.53 
TCGA-DA-A1IA TCGA-DA-A3F5 TCGA-DA-A95V TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q 
       64.83       225.11        72.10        14.14        12.30         3.91 
TCGA-EE-A17Y TCGA-EE-A182 TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29H 
       24.89         0.00        79.20        76.14        12.99        47.41 
TCGA-EE-A29M TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A2A2 TCGA-EE-A2GB TCGA-EE-A2GE 
       47.74        61.12       346.49        30.02        26.14        12.95 
TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GM TCGA-EE-A2GR TCGA-EE-A2GU TCGA-EE-A2M6 
      201.60        68.65        18.35         0.20        81.99       103.13 
TCGA-EE-A2MC TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MS 
       23.77        63.25       104.78       145.45       227.01       143.93 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3J7 
       23.51        53.26       122.73         4.41        54.51        45.90 
TCGA-EE-A3J8 TCGA-EE-A3JH TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19C TCGA-ER-A19D 
        3.35        19.86        10.49         7.82        39.81        11.47 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W 
       99.06        59.84        42.51        49.71        47.18       146.63 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET 
        4.70        16.87        10.19        28.67       173.29        68.52 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       15.48        32.05        74.47         4.50       174.21         4.14 
TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1ZE TCGA-FS-A1ZJ 
       26.20         5.65       195.98         8.35        43.92        36.33 
TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
       78.61       130.95        35.28         4.47        23.21         5.29 
TCGA-FS-A1ZZ TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-GN-A262 
        3.06        66.67       173.19        80.68        55.59        53.29 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 
      117.93        96.92        17.06        42.48         7.59       120.53 
TCGA-GN-A8LK TCGA-GN-A9SD TCGA-LH-A9QB TCGA-QB-A6FS TCGA-W3-AA1R TCGA-W3-AA1V 
       43.23        59.41        85.05         7.23        79.99         8.09 
TCGA-WE-A8K1 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZY TCGA-WE-AA9Y 
       47.54        65.42        12.69        21.90        48.39         1.94 
TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-YG-AA3O 
       37.32        24.99        28.21 

$`DEL PEAK 21(11Q23.3) WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A3C8 TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD 
        9.76        38.76       269.03        52.90       134.40        27.35 
TCGA-FR-A729 TCGA-FW-A3R5 TCGA-3N-A9WD TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q6 
      216.43        36.95        12.99        15.72        31.89        49.35 
TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JG TCGA-D3-A2JH 
       19.04        76.41        62.86        15.75       107.61        36.30 
TCGA-D3-A2JP TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3MR TCGA-D3-A51F TCGA-D3-A51J 
       43.53       140.98        59.70        90.21        30.67       144.46 
TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A8GK TCGA-D3-A8GL 
       31.76        62.70        11.34        42.05       120.00        69.53 
TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A4Z6 TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A1I7 
       10.78        15.02        18.44       138.67       150.61        60.10 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F8 TCGA-DA-A95W TCGA-DA-A95X TCGA-EB-A5KH 
       58.85        30.44         8.71         0.76        65.03        16.41 
TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A20C 
       52.41        18.21        13.15        20.38        26.24        75.55 
TCGA-EE-A29B TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29P TCGA-EE-A29W TCGA-EE-A2A1 
       75.22         0.26        44.28        27.16       185.19       115.43 
TCGA-EE-A2A6 TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GS 
       77.98        10.62        32.48        93.63         0.76        71.31 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MK 
       15.25         5.75       209.79        94.19       171.85        89.26 
TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3JB 
      124.31        64.04         6.28        67.89       111.85       168.85 
TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19G TCGA-ER-A19H 
      135.98        34.45         4.54        53.29       184.60       150.12 
TCGA-ER-A19P TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-FR-A8YC TCGA-FS-A1YW TCGA-FS-A1YY 
      120.76        73.05        22.36        10.06       171.78        49.74 
TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZG TCGA-FS-A1ZS TCGA-FS-A4F0 
       27.62       312.07        32.78         7.82       136.27        30.90 
TCGA-FS-A4F9 TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
       13.28        11.54        19.30         9.90        18.25         1.91 
TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-OD-A75X TCGA-RP-A690 TCGA-RP-A693 TCGA-W3-A824 
       34.49        46.92       297.01         0.20         0.33       174.12 
TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1Q TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8ZQ 
        1.97       120.07        44.05       185.13        92.84        62.89 
TCGA-WE-A8ZT TCGA-XV-AB01 TCGA-Z2-AA3S 
       10.95         6.61        91.23 

  DEL PEAK 21(11Q23.3) MUTATED DEL PEAK 21(11Q23.3) WILD-TYPE 
                           0.0                            0.2 
  DEL PEAK 21(11Q23.3) MUTATED DEL PEAK 21(11Q23.3) WILD-TYPE 
                        346.49                         312.07 
  DEL PEAK 21(11Q23.3) MUTATED DEL PEAK 21(11Q23.3) WILD-TYPE 
                         47.18                          44.28 
[1] "0.0 - 346.5 (47.2)" "0.2 - 312.1 (44.3)"
[1] "hr=" "1.2"
D41V2, survival
                                sevent
clus2                              0   1
  DEL PEAK 21(11Q23.3) MUTATED    91 110
  DEL PEAK 21(11Q23.3) WILD-TYPE  75  82
  DEL PEAK 21(11Q23.3) MUTATED DEL PEAK 21(11Q23.3) WILD-TYPE 
                           201                            157 
  DEL PEAK 21(11Q23.3) MUTATED DEL PEAK 21(11Q23.3) WILD-TYPE 
                           110                             82 
$`DEL PEAK 21(11Q23.3) MUTATED`
TCGA-D3-A2JF TCGA-D3-A3ML TCGA-D3-A8GI TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A180 
       62.07        13.87        58.52        68.25        54.02        94.98 
TCGA-EE-A20H TCGA-EE-A29L TCGA-ER-A193 TCGA-FS-A1ZF TCGA-QB-AA9O TCGA-WE-A8K5 
      168.26         2.60        31.40        15.45        18.05        61.15 
TCGA-WE-AAA3 TCGA-3N-A9WC TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q7 
       21.40        66.48        14.93        16.57       112.57       133.25 
TCGA-D3-A1Q9 TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2JB TCGA-D3-A2JC 
       31.59        95.74        43.43       103.10       168.00        86.76 
TCGA-D3-A2JD TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A3C6 TCGA-D3-A3C7 
       11.87       171.58        66.48        66.08        58.06        46.98 
TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E 
       86.93        24.53         9.34        39.75        45.30       174.84 
TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GC 
      135.75       178.32        18.18       125.19        30.84        79.59 
TCGA-D3-A8GD TCGA-D3-A8GJ TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GQ 
       23.61       241.38       107.15       161.00       152.75        29.06 
TCGA-D3-A8GR TCGA-D3-A8GV TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JX TCGA-D9-A3Z3 
      129.63       167.70       151.53        54.67         7.10        22.29 
TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW 
        9.90        25.18        77.56        22.95        76.57        36.03 
TCGA-DA-A1I1 TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A3F3 TCGA-DA-A3F5 
      222.51       135.02        53.92        65.92        10.49       225.96 
TCGA-DA-A95V TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5UL 
       72.10        14.14        13.02        13.87        10.36        29.29 
TCGA-EE-A17Y TCGA-EE-A182 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29A 
       27.22        14.70       133.81        91.56        13.55        63.35 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29Q 
       78.97        13.97        64.64        56.84        18.61        66.74 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A2A2 TCGA-EE-A2A5 
       14.47        61.28       369.93        25.87        59.64        39.29 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       59.28        67.43       173.79       220.24        48.72       107.38 
TCGA-EE-A2GM TCGA-EE-A2GR TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2MC TCGA-EE-A2MD 
       75.48        42.77        94.82       129.27        61.51        47.28 
TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MS 
       96.23       216.66       167.90        47.54       248.65       162.48 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AG 
       71.21        53.26       122.73        28.77        54.51        41.59 
TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JH TCGA-ER-A197 
       36.95        64.08        34.32        53.19       134.33        13.94 
TCGA-ER-A199 TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19L TCGA-ER-A19M 
        9.17        48.89        12.59        26.37       131.51        61.05 
TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A2ND 
       44.09        50.89        49.48         8.88       148.18        23.34 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
       20.15        28.83        48.99        41.56       247.04        93.01 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       46.98        33.21       149.03        92.98       174.21        15.72 
TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z7 TCGA-FS-A1ZA 
       27.85        38.27       202.65        20.91         7.79        27.72 
TCGA-FS-A1ZB TCGA-FS-A1ZE TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ 
       48.85        46.45        32.75        47.38       101.26       133.55 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F4 
       53.16        26.56        49.48        27.09        27.02        66.67 
TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-GN-A262 
       28.73       174.84        80.68        17.46        55.59       139.89 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
      117.93        96.92        10.13        64.44        62.79        32.48 
TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U7 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL 
       48.00       121.91        10.42        22.13        50.10        21.37 
TCGA-GN-A9SD TCGA-HR-A2OH TCGA-LH-A9QB TCGA-QB-A6FS TCGA-RP-A694 TCGA-W3-AA1R 
       59.41        65.88       368.78         7.23         0.69       111.09 
TCGA-W3-AA1V TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO 
       42.08        24.03        49.05       101.33        58.98        70.52 
TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-YD-A9TA TCGA-YG-AA3O 
       49.51        12.16        40.41        24.99        49.18        37.94 
TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3V 
       14.43        27.58        15.98 

$`DEL PEAK 21(11Q23.3) WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A3C8 TCGA-EE-A184 TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR 
       27.65        46.32        68.15       340.14       126.81       134.40 
TCGA-EE-A3JD TCGA-ER-A198 TCGA-FR-A729 TCGA-FW-A3R5 TCGA-3N-A9WB TCGA-3N-A9WD 
       27.35        50.76       220.80        36.95        17.03        12.99 
TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q6 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A2J8 
       16.67       112.04        71.80        28.08        90.90        65.49 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JP 
       23.77       115.53       113.52        42.08        12.10        59.57 
TCGA-D3-A3BZ TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3MR TCGA-D3-A51F TCGA-D3-A51H 
      130.72       166.52        60.23       103.59        55.73        56.35 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL 
      145.12        32.94        22.62        63.81        26.89       125.79 
TCGA-D3-A5GO TCGA-D3-A8GE TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GS TCGA-D9-A1JW 
      137.92        26.43       170.20        89.13       117.17         3.65 
TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A4Z6 TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 
       18.12        15.39        18.44       144.89        20.38       176.55 
TCGA-DA-A1I4 TCGA-DA-A1I7 TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F8 
       35.93        88.87        40.60        68.09        33.93        43.36 
TCGA-DA-A95W TCGA-DA-A95X TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 
       37.35        73.94        20.35        58.92         7.04        36.46 
TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20C 
       29.82         8.65        33.73        26.89         4.96       151.27 
TCGA-EE-A29B TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29P TCGA-EE-A29W TCGA-EE-A29X 
       85.08        63.78        72.07        56.42       195.02        17.92 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A6 TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN 
       46.82       115.96        86.14        54.74        79.66       102.12 
TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2M7 TCGA-EE-A2M8 
       13.91        81.21        44.88        21.67        28.83        19.76 
TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK 
      103.27       268.73       103.20        16.96       204.66       180.39 
TCGA-EE-A2MQ TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J3 
       43.23       124.31        64.04        13.81       138.81       172.18 
TCGA-EE-A3J4 TCGA-EE-A3JB TCGA-EE-A3JE TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A19A 
      127.20       201.80        51.35       152.81        35.44        77.75 
TCGA-ER-A19B TCGA-ER-A19E TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19P 
       98.40        13.02       302.07       152.35         6.44       162.08 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A42K TCGA-FR-A7U9 TCGA-FR-A8YC TCGA-FR-A8YD 
      105.07        43.82        12.95        18.77        34.82        36.26 
TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z4 TCGA-FS-A1ZC 
      104.42       216.92        48.59       228.59        28.08       357.37 
TCGA-FS-A1ZD TCGA-FS-A1ZG TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZS 
       53.52         9.70        23.93        74.73        11.41       148.80 
TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FW-A3TV 
       77.82        50.14        34.03        26.73        54.41        13.51 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A4U4 
       19.30         9.90        19.43         2.04        15.78        39.35 
TCGA-GN-A4U8 TCGA-HR-A2OG TCGA-OD-A75X TCGA-RP-A690 TCGA-RP-A693 TCGA-W3-A824 
       48.89         0.23       297.90         0.20         0.33       228.16 
TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1Q TCGA-W3-AA1W TCGA-W3-AA21 
       63.02       121.08         4.01        69.07       219.16       105.04 
TCGA-WE-A8K6 TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-XV-AB01 TCGA-YD-A89C 
       17.95        63.22        11.80        35.80        13.25         6.90 
TCGA-Z2-AA3S 
       96.99 

  DEL PEAK 21(11Q23.3) MUTATED DEL PEAK 21(11Q23.3) WILD-TYPE 
                          0.69                           0.20 
  DEL PEAK 21(11Q23.3) MUTATED DEL PEAK 21(11Q23.3) WILD-TYPE 
                        369.93                         357.37 
  DEL PEAK 21(11Q23.3) MUTATED DEL PEAK 21(11Q23.3) WILD-TYPE 
                         50.89                          53.52 
[1] "0.7 - 369.9 (50.9)" "0.2 - 357.4 (53.5)"
[1] "hr=" "1.1"
D41V3, continuous
                                vv
clus                             I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB
  DEL PEAK 21(11Q23.3) MUTATED          7       3      15       12       15
  DEL PEAK 21(11Q23.3) WILD-TYPE        6       4      14        6       13
                                vv
clus                             STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK 21(11Q23.3) MUTATED         13         3        11        10
  DEL PEAK 21(11Q23.3) WILD-TYPE       13        11         8         5
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 21(11Q23.3) MUTATED          20         10         20         31
  DEL PEAK 21(11Q23.3) WILD-TYPE        19          5         15         23
                                vv
clus                             STAGE IV
  DEL PEAK 21(11Q23.3) MUTATED         13
  DEL PEAK 21(11Q23.3) WILD-TYPE        8
D41V4, multiclass
            clus
vv           DEL PEAK 21(11Q23.3) MUTATED DEL PEAK 21(11Q23.3) WILD-TYPE
  I/II NOS                              7                              6
  STAGE 0                               3                              4
  STAGE I                              15                             14
  STAGE IA                             12                              6
  STAGE IB                             15                             13
  STAGE II                             13                             13
  STAGE IIA                             3                             11
  STAGE IIB                            11                              8
  STAGE IIC                            10                              5
  STAGE III                            20                             19
  STAGE IIIA                           10                              5
  STAGE IIIB                           20                             15
  STAGE IIIC                           31                             23
  STAGE IV                             13                              8
[1] 14  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  DEL PEAK 21(11Q23.3) MUTATED      37 36 46 38
  DEL PEAK 21(11Q23.3) WILD-TYPE    27 37 35 29
D41V5, multiclass
       clus
vv      DEL PEAK 21(11Q23.3) MUTATED DEL PEAK 21(11Q23.3) WILD-TYPE
  T0+T1                           37                             27
  T2                              36                             37
  T3                              46                             35
  T4                              38                             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 N3
  DEL PEAK 21(11Q23.3) MUTATED   94 38 19 26
  DEL PEAK 21(11Q23.3) WILD-TYPE 83 27 20 19
D41V6, multiclass
    clus
vv   DEL PEAK 21(11Q23.3) MUTATED DEL PEAK 21(11Q23.3) WILD-TYPE
  N0                           94                             83
  N1                           38                             27
  N2                           19                             20
  N3                           26                             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"
D41V7, binary
                                cls
clus                               0   1
  DEL PEAK 21(11Q23.3) MUTATED   171  14
  DEL PEAK 21(11Q23.3) WILD-TYPE 148   8
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(11Q23.3) MUTATED    171   14
  DEL PEAK 21(11Q23.3) WILD-TYPE  148    8
   clus
vv  DEL PEAK 21(11Q23.3) MUTATED DEL PEAK 21(11Q23.3) WILD-TYPE
  0                          171                            148
  1                           14                              8
[1] 2 2
[1] FALSE
D41V8, binary
                                cls
clus                              0  1
  DEL PEAK 21(11Q23.3) MUTATED   79 54
  DEL PEAK 21(11Q23.3) WILD-TYPE 55 36
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(11Q23.3) MUTATED     79   54
  DEL PEAK 21(11Q23.3) WILD-TYPE   55   36
     clus
vv    DEL PEAK 21(11Q23.3) MUTATED DEL PEAK 21(11Q23.3) WILD-TYPE
  NO                            79                             55
  YES                           54                             36
[1] 2 2
[1] FALSE
D41V9, binary
                                cls
clus                               0   1
  DEL PEAK 21(11Q23.3) MUTATED    24 180
  DEL PEAK 21(11Q23.3) WILD-TYPE  23 140
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(11Q23.3) MUTATED     24  180
  DEL PEAK 21(11Q23.3) WILD-TYPE   23  140
     clus
vv    DEL PEAK 21(11Q23.3) MUTATED DEL PEAK 21(11Q23.3) WILD-TYPE
  NO                            24                             23
  YES                          180                            140
[1] 2 2
[1] FALSE
D41V10, continuous
D41V11, binary
                                cls
clus                               0   1
  DEL PEAK 21(11Q23.3) MUTATED    84 120
  DEL PEAK 21(11Q23.3) WILD-TYPE  54 109
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(11Q23.3) MUTATED     84  120
  DEL PEAK 21(11Q23.3) WILD-TYPE   54  109
        clus
vv       DEL PEAK 21(11Q23.3) MUTATED DEL PEAK 21(11Q23.3) WILD-TYPE
  FEMALE                           84                             54
  MALE                            120                            109
[1] 2 2
[1] FALSE
D41V12, binary
                                cls
clus                               0   1
  DEL PEAK 21(11Q23.3) MUTATED   178  26
  DEL PEAK 21(11Q23.3) WILD-TYPE 141  21
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(11Q23.3) MUTATED    178   26
  DEL PEAK 21(11Q23.3) WILD-TYPE  141   21
     clus
vv    DEL PEAK 21(11Q23.3) MUTATED DEL PEAK 21(11Q23.3) WILD-TYPE
  NO                           178                            141
  YES                           26                             21
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 21(11Q23.3) MUTATED       3                         1   194
  DEL PEAK 21(11Q23.3) WILD-TYPE     2                         0   159
D41V13, multiclass
                           clus
vv                          DEL PEAK 21(11Q23.3) MUTATED
  ASIAN                                                3
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                              194
                           clus
vv                          DEL PEAK 21(11Q23.3) WILD-TYPE
  ASIAN                                                  2
  BLACK OR AFRICAN AMERICAN                              0
  WHITE                                                159
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V14, binary
                                cls
clus                               0   1
  DEL PEAK 21(11Q23.3) MUTATED     3 196
  DEL PEAK 21(11Q23.3) WILD-TYPE   4 156
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(11Q23.3) MUTATED      3  196
  DEL PEAK 21(11Q23.3) WILD-TYPE    4  156
                        clus
vv                       DEL PEAK 21(11Q23.3) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                          196
                        clus
vv                       DEL PEAK 21(11Q23.3) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            156
[1] 2 2
[1] FALSE

Clustering(42) Variable = DEL PEAK 22(12Q23.3) MUTATION ANALYSIS
D42V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 22(12Q23.3) MUTATED   30 31
  DEL PEAK 22(12Q23.3) WILD-TYPE 98 93
  DEL PEAK 22(12Q23.3) MUTATED DEL PEAK 22(12Q23.3) WILD-TYPE 
                            61                            191 
  DEL PEAK 22(12Q23.3) MUTATED DEL PEAK 22(12Q23.3) WILD-TYPE 
                            31                             93 
$`DEL PEAK 22(12Q23.3) MUTATED`
TCGA-D3-A8GI TCGA-ER-A193 TCGA-FW-A3R5 TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A2J7 
       13.41        19.04        36.95        12.99         8.42        45.99 
TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A51J TCGA-D3-A5GR 
      171.58        64.83        58.06        40.01       144.46       177.86 
TCGA-D3-A8GC TCGA-D3-A8GL TCGA-D9-A1X3 TCGA-D9-A6EC TCGA-DA-A1I1 TCGA-DA-A95X 
       78.21        69.53        10.78        69.21        68.68        65.03 
TCGA-EE-A20C TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29Q TCGA-EE-A2A2 TCGA-EE-A2GH 
       75.55        12.99        44.28        61.12        30.02       201.60 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GU TCGA-EE-A2MG TCGA-EE-A2MK TCGA-EE-A2MP 
        0.76         0.20        81.99        94.19        89.26       227.01 
TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3J3 
      143.93        53.26       124.31         4.41        54.51        67.89 
TCGA-EE-A3J7 TCGA-EE-A3JI TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19S TCGA-ER-A2ND 
       45.90       135.98        10.49         7.82        47.18         4.70 
TCGA-ER-A2NE TCGA-ER-A3PL TCGA-FR-A44A TCGA-FS-A1Z4 TCGA-FS-A1ZM TCGA-FS-A1ZQ 
       16.87        32.05       174.21        27.62        78.61       130.95 
TCGA-FS-A1ZT TCGA-FS-A4F9 TCGA-FW-A3TU TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A4U3 
       35.28        13.28        55.59        17.06        42.48       120.53 
TCGA-LH-A9QB TCGA-OD-A75X TCGA-RP-A693 TCGA-W3-AA1R TCGA-W3-AA1V TCGA-WE-A8ZM 
       85.05       297.01         0.33        79.99         8.09        65.42 
TCGA-WE-A8ZQ 
       62.89 

$`DEL PEAK 22(12Q23.3) WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A20H 
        9.76        62.07        38.76        33.24        31.96       166.75 
TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-FR-A729 TCGA-WE-A8K5 
      269.03        52.90       134.40        27.35       216.43        52.73 
TCGA-WE-AAA3 TCGA-3N-A9WC TCGA-BF-AAP0 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
        7.40        60.46        14.83        15.72        31.89       110.93 
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 
       49.35       133.25        19.04        76.41        62.60        25.64 
TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A2JH 
       62.86        15.75       168.00        86.30       107.61        36.30 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO 
       66.08        43.53       140.98        59.70        24.53         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51K TCGA-D3-A51R 
       90.21        23.67       173.85        30.67        31.76        62.70 
TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GU TCGA-D3-A8GD TCGA-D3-A8GJ 
       11.34        42.05        45.70       124.08        23.61       179.97 
TCGA-D3-A8GK TCGA-D3-A8GM TCGA-D3-A8GP TCGA-D3-A8GR TCGA-D9-A3Z1 TCGA-D9-A3Z3 
      120.00        70.62       135.12        36.53        15.02        16.90 
TCGA-D9-A4Z6 TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A1I5 
       18.44        22.85        76.34       138.67       150.61       110.53 
TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 
       60.10        64.83        58.85        30.44       225.11         8.71 
TCGA-DA-A95V TCGA-DA-A95W TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5KH 
       72.10         0.76        14.14        12.30         3.91        16.41 
TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A182 
       52.41        18.21        13.15        24.89        20.38         0.00 
TCGA-EE-A183 TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H 
       26.24        79.20        75.22        76.14         0.26        47.41 
TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A6 
       47.74        27.16       346.49       185.19       115.43        77.98 
TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
       26.14        12.95        68.65        10.62        32.48        18.35 
TCGA-EE-A2GN TCGA-EE-A2GS TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
       93.63        71.31       103.13        15.25         5.75        23.77 
TCGA-EE-A2MF TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MT 
      209.79       171.85        63.25       104.78       145.45        23.51 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AF TCGA-EE-A3J4 TCGA-EE-A3J8 TCGA-EE-A3JB 
      122.73        64.04         6.28       111.85         3.35       168.85 
TCGA-EE-A3JH TCGA-ER-A195 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D 
       19.86        34.45         4.54        53.29        39.81        11.47 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P 
      184.60       150.12        99.06        59.84        42.51       120.76 
TCGA-ER-A19Q TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NF TCGA-ER-A2NG 
       49.71       146.63        73.05        22.36        10.19        28.67 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A69P 
      173.29        68.52        15.48        74.47         4.50         4.14 
TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 
       26.20         5.65        10.06       171.78        49.74       195.98 
TCGA-FS-A1Z3 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ 
        8.35       312.07        32.78        43.92         7.82        36.33 
TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 
      136.27         4.47        23.21         5.29         3.06        30.90 
TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4FD TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
       66.67       173.19        80.68        11.54        19.30         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A26A 
       18.25         1.91        53.29       117.93        96.92         7.59 
TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-GN-A8LK TCGA-GN-A9SD TCGA-QB-A6FS TCGA-RP-A690 
       34.49        46.92        43.23        59.41         7.23         0.20 
TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1Q TCGA-W3-AA1W TCGA-W3-AA21 
      174.12         1.97       120.07        44.05       185.13        92.84 
TCGA-WE-A8K1 TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y 
       47.54        12.69        21.90        10.95        48.39         1.94 
TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-XV-AB01 TCGA-YG-AA3O TCGA-Z2-AA3S 
       37.32        24.99         6.61        28.21        91.23 

  DEL PEAK 22(12Q23.3) MUTATED DEL PEAK 22(12Q23.3) WILD-TYPE 
                           0.2                            0.0 
  DEL PEAK 22(12Q23.3) MUTATED DEL PEAK 22(12Q23.3) WILD-TYPE 
                        297.01                         346.49 
  DEL PEAK 22(12Q23.3) MUTATED DEL PEAK 22(12Q23.3) WILD-TYPE 
                         55.59                          43.53 
[1] "0.2 - 297.0 (55.6)" "0.0 - 346.5 (43.5)"
[1] "hr=" "1"  
D42V2, survival
                                sevent
clus2                              0   1
  DEL PEAK 22(12Q23.3) MUTATED    44  45
  DEL PEAK 22(12Q23.3) WILD-TYPE 122 147
  DEL PEAK 22(12Q23.3) MUTATED DEL PEAK 22(12Q23.3) WILD-TYPE 
                            89                            269 
  DEL PEAK 22(12Q23.3) MUTATED DEL PEAK 22(12Q23.3) WILD-TYPE 
                            45                            147 
$`DEL PEAK 22(12Q23.3) MUTATED`
TCGA-D3-A8GI TCGA-EB-A5SH TCGA-ER-A193 TCGA-FW-A3R5 TCGA-3N-A9WD TCGA-D3-A1Q1 
       58.52        54.02        31.40        36.95        12.99        16.57 
TCGA-D3-A2J7 TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3MV 
      103.10       171.58        66.48        58.06        86.93        45.30 
TCGA-D3-A51J TCGA-D3-A51N TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A8GC TCGA-D3-A8GL 
      145.12        22.62       137.92       178.32        79.59        89.13 
TCGA-D3-A8GN TCGA-D9-A148 TCGA-D9-A1X3 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1I1 
      161.00       151.53        18.12        25.18        77.56       222.51 
TCGA-DA-A95X TCGA-EB-A5UL TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A29D TCGA-EE-A29G 
       73.94        29.29       133.81       151.27        13.97        72.07 
TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29X TCGA-EE-A2A2 TCGA-EE-A2GH TCGA-EE-A2GP 
       66.74        61.28        17.92        59.64       220.24        13.91 
TCGA-EE-A2GR TCGA-EE-A2GU TCGA-EE-A2MG TCGA-EE-A2MK TCGA-EE-A2MP TCGA-EE-A2MS 
       42.77        94.82       103.20       180.39       248.65       162.48 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3J3 TCGA-EE-A3J7 
       53.26       124.31        28.77        54.51       172.18        64.08 
TCGA-EE-A3JA TCGA-EE-A3JE TCGA-EE-A3JI TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19E 
       53.19        51.35       152.81        13.94         9.17        13.02 
TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A3PL TCGA-ER-A42K 
       49.48         8.88        23.34        20.15        33.21        12.95 
TCGA-FR-A44A TCGA-FS-A1YX TCGA-FS-A1Z4 TCGA-FS-A1ZA TCGA-FS-A1ZH TCGA-FS-A1ZM 
      174.21        48.59        28.08        27.72        32.75       101.26 
TCGA-FS-A1ZQ TCGA-FS-A1ZT TCGA-FS-A4F2 TCGA-FS-A4F5 TCGA-FS-A4F9 TCGA-FS-A4FB 
      133.55        53.16        50.14        28.73        34.03        26.73 
TCGA-FW-A3TU TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A4U3 TCGA-GN-A8LL TCGA-HR-A2OH 
       55.59        64.44        62.79       121.91        21.37        65.88 
TCGA-LH-A9QB TCGA-OD-A75X TCGA-RP-A693 TCGA-W3-AA1R TCGA-W3-AA1V TCGA-WE-A8JZ 
      368.78       297.90         0.33       111.09        42.08        24.03 
TCGA-WE-A8ZM TCGA-WE-A8ZQ TCGA-WE-A8ZX TCGA-YD-A9TA TCGA-Z2-A8RT 
      101.33        63.22        35.80        49.18        27.58 

$`DEL PEAK 22(12Q23.3) WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SG TCGA-EE-A180 
       27.65        62.07        46.32        13.87        68.25        94.98 
TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR 
       68.15       168.26         2.60       340.14       126.81       134.40 
TCGA-EE-A3JD TCGA-ER-A198 TCGA-FR-A729 TCGA-FS-A1ZF TCGA-QB-AA9O TCGA-WE-A8K5 
       27.35        50.76       220.80        15.45        18.05        61.15 
TCGA-WE-AAA3 TCGA-3N-A9WB TCGA-3N-A9WC TCGA-BF-AAP0 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
       21.40        17.03        66.48        14.93        16.67       112.04 
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA 
      112.57        71.80       133.25        28.08        31.59        90.90 
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB 
       95.74        43.43        65.49        23.77       115.53       168.00 
TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JO 
       86.76        11.87       113.52        42.08        12.10        66.08 
TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3CF 
       59.57       130.72        46.98       166.52        60.23        24.53 
TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
        9.34       103.59        39.75       174.84        55.73        56.35 
TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GS 
       32.94        63.81        26.89       125.79       135.75        18.18 
TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GK 
      125.19        30.84        23.61        26.43       241.38       170.20 
TCGA-D3-A8GM TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D3-A8GV 
      107.15       152.75        29.06       129.63       117.17       167.70 
TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 
       54.67         3.65         7.10        15.39        22.29        18.44 
TCGA-D9-A6E9 TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 
        9.90        22.95        76.57        36.03       144.89        20.38 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA 
      176.55        35.93       135.02        88.87        53.92        65.92 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 
       40.60        68.09        33.93        10.49       225.96        43.36 
TCGA-DA-A95V TCGA-DA-A95W TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A44R 
       72.10        37.35        14.14        13.02        13.87        10.36 
TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
       20.35        58.92         7.04        36.46        29.82        27.22 
TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20F 
        8.65        33.73        14.70        26.89         4.96        91.56 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H 
       13.55        63.35        85.08        78.97        63.78        64.64 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A29T TCGA-EE-A29V 
       56.84        18.61        56.42        14.47       369.93        25.87 
TCGA-EE-A29W TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
      195.02        46.82       115.96        39.29        86.14        59.28 
TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       67.43       173.79        48.72       107.38        54.74        79.66 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2M6 
       75.48       102.12        81.21        44.88        21.67       129.27 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF 
       28.83        19.76        61.51        47.28       103.27       268.73 
TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN 
       16.96       204.66        96.23       216.66       167.90        47.54 
TCGA-EE-A2MQ TCGA-EE-A2MT TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AF TCGA-EE-A3AG 
       43.23        71.21       122.73        64.04        13.81        41.59 
TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH 
      138.81       127.20        36.95        34.32       201.80       134.33 
TCGA-ER-A195 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19F 
       35.44        77.75        98.40        48.89        12.59        26.37 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
      302.07       152.35         6.44       131.51        61.05        44.09 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NF 
      162.08        50.89       148.18       105.07        43.82        28.83 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A42L 
       48.99        41.56       247.04        93.01        46.98       149.03 
TCGA-FR-A3YN TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC 
       92.98        15.72        27.85        18.77        38.27        34.82 
TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
       36.26       104.42       216.92       228.59       202.65        20.91 
TCGA-FS-A1Z7 TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG 
        7.79        48.85       357.37        53.52        46.45         9.70 
TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZU 
       47.38        23.93        74.73        11.41       148.80        26.56 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 
       49.48        27.09        27.02        77.82        66.67       174.84 
TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
       54.41        80.68        17.46        13.51        19.30         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
       19.43         2.04        15.78       139.89       117.93        96.92 
TCGA-GN-A266 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 
       10.13        32.48        48.00        39.35        10.42        48.89 
TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A9SD TCGA-HR-A2OG TCGA-QB-A6FS TCGA-RP-A690 
       22.13        50.10        59.41         0.23         7.23         0.20 
TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1Q 
        0.69       228.16        63.02       121.08         4.01        69.07 
TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K6 TCGA-WE-A8ZN TCGA-WE-A8ZO 
      219.16       105.04        49.05        17.95        58.98        70.52 
TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-XV-AB01 
       11.80        49.51        12.16        40.41        24.99        13.25 
TCGA-YD-A89C TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-AA3S TCGA-Z2-AA3V 
        6.90        37.94        14.43        96.99        15.98 

  DEL PEAK 22(12Q23.3) MUTATED DEL PEAK 22(12Q23.3) WILD-TYPE 
                          0.33                           0.20 
  DEL PEAK 22(12Q23.3) MUTATED DEL PEAK 22(12Q23.3) WILD-TYPE 
                        368.78                         369.93 
  DEL PEAK 22(12Q23.3) MUTATED DEL PEAK 22(12Q23.3) WILD-TYPE 
                         55.59                          49.05 
[1] "0.3 - 368.8 (55.6)" "0.2 - 369.9 (49.0)"
[1] "hr=" "1.2"
D42V3, continuous
                                vv
clus                             I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB
  DEL PEAK 22(12Q23.3) MUTATED          4       2       7        4        7
  DEL PEAK 22(12Q23.3) WILD-TYPE        9       5      22       14       21
                                vv
clus                             STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK 22(12Q23.3) MUTATED          7         2         4         3
  DEL PEAK 22(12Q23.3) WILD-TYPE       19        12        15        12
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 22(12Q23.3) MUTATED          14          4         10         10
  DEL PEAK 22(12Q23.3) WILD-TYPE        25         11         25         44
                                vv
clus                             STAGE IV
  DEL PEAK 22(12Q23.3) MUTATED          5
  DEL PEAK 22(12Q23.3) WILD-TYPE       16
D42V4, multiclass
            clus
vv           DEL PEAK 22(12Q23.3) MUTATED DEL PEAK 22(12Q23.3) WILD-TYPE
  I/II NOS                              4                              9
  STAGE 0                               2                              5
  STAGE I                               7                             22
  STAGE IA                              4                             14
  STAGE IB                              7                             21
  STAGE II                              7                             19
  STAGE IIA                             2                             12
  STAGE IIB                             4                             15
  STAGE IIC                             3                             12
  STAGE III                            14                             25
  STAGE IIIA                            4                             11
  STAGE IIIB                           10                             25
  STAGE IIIC                           10                             44
  STAGE IV                              5                             16
[1] 14  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  DEL PEAK 22(12Q23.3) MUTATED      14 19 18 21
  DEL PEAK 22(12Q23.3) WILD-TYPE    50 54 63 46
D42V5, multiclass
       clus
vv      DEL PEAK 22(12Q23.3) MUTATED DEL PEAK 22(12Q23.3) WILD-TYPE
  T0+T1                           14                             50
  T2                              19                             54
  T3                              18                             63
  T4                              21                             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  N3
  DEL PEAK 22(12Q23.3) MUTATED    42  21  10  10
  DEL PEAK 22(12Q23.3) WILD-TYPE 135  44  29  35
D42V6, multiclass
    clus
vv   DEL PEAK 22(12Q23.3) MUTATED DEL PEAK 22(12Q23.3) WILD-TYPE
  N0                           42                            135
  N1                           21                             44
  N2                           10                             29
  N3                           10                             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"
D42V7, binary
                                cls
clus                               0   1
  DEL PEAK 22(12Q23.3) MUTATED    79   6
  DEL PEAK 22(12Q23.3) WILD-TYPE 240  16
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 22(12Q23.3) MUTATED     79    6
  DEL PEAK 22(12Q23.3) WILD-TYPE  240   16
   clus
vv  DEL PEAK 22(12Q23.3) MUTATED DEL PEAK 22(12Q23.3) WILD-TYPE
  0                           79                            240
  1                            6                             16
[1] 2 2
[1] FALSE
D42V8, binary
                                cls
clus                               0   1
  DEL PEAK 22(12Q23.3) MUTATED    33  23
  DEL PEAK 22(12Q23.3) WILD-TYPE 101  67
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 22(12Q23.3) MUTATED     33   23
  DEL PEAK 22(12Q23.3) WILD-TYPE  101   67
     clus
vv    DEL PEAK 22(12Q23.3) MUTATED DEL PEAK 22(12Q23.3) WILD-TYPE
  NO                            33                            101
  YES                           23                             67
[1] 2 2
[1] FALSE
D42V9, binary
                                cls
clus                               0   1
  DEL PEAK 22(12Q23.3) MUTATED    11  81
  DEL PEAK 22(12Q23.3) WILD-TYPE  36 239
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 22(12Q23.3) MUTATED     11   81
  DEL PEAK 22(12Q23.3) WILD-TYPE   36  239
     clus
vv    DEL PEAK 22(12Q23.3) MUTATED DEL PEAK 22(12Q23.3) WILD-TYPE
  NO                            11                             36
  YES                           81                            239
[1] 2 2
[1] FALSE
D42V10, continuous
D42V11, binary
                                cls
clus                               0   1
  DEL PEAK 22(12Q23.3) MUTATED    38  54
  DEL PEAK 22(12Q23.3) WILD-TYPE 100 175
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 22(12Q23.3) MUTATED     38   54
  DEL PEAK 22(12Q23.3) WILD-TYPE  100  175
        clus
vv       DEL PEAK 22(12Q23.3) MUTATED DEL PEAK 22(12Q23.3) WILD-TYPE
  FEMALE                           38                            100
  MALE                             54                            175
[1] 2 2
[1] FALSE
D42V12, binary
                                cls
clus                               0   1
  DEL PEAK 22(12Q23.3) MUTATED    79  13
  DEL PEAK 22(12Q23.3) WILD-TYPE 240  34
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 22(12Q23.3) MUTATED     79   13
  DEL PEAK 22(12Q23.3) WILD-TYPE  240   34
     clus
vv    DEL PEAK 22(12Q23.3) MUTATED DEL PEAK 22(12Q23.3) WILD-TYPE
  NO                            79                            240
  YES                           13                             34
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 22(12Q23.3) MUTATED       0                         0    89
  DEL PEAK 22(12Q23.3) WILD-TYPE     5                         1   264
D42V13, multiclass
                           clus
vv                          DEL PEAK 22(12Q23.3) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                               89
                           clus
vv                          DEL PEAK 22(12Q23.3) WILD-TYPE
  ASIAN                                                  5
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                264
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V14, binary
                                cls
clus                               0   1
  DEL PEAK 22(12Q23.3) MUTATED     0  90
  DEL PEAK 22(12Q23.3) WILD-TYPE   7 262
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 22(12Q23.3) MUTATED      0   90
  DEL PEAK 22(12Q23.3) WILD-TYPE    7  262
                        clus
vv                       DEL PEAK 22(12Q23.3) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           90
                        clus
vv                       DEL PEAK 22(12Q23.3) WILD-TYPE
  HISPANIC OR LATINO                                  7
  NOT HISPANIC OR LATINO                            262
[1] 2 2
[1] FALSE

Clustering(43) Variable = DEL PEAK 23(13Q34) MUTATION ANALYSIS
D43V1, survival
                              sevent
clus2                            0   1
  DEL PEAK 23(13Q34) MUTATED    33  23
  DEL PEAK 23(13Q34) WILD-TYPE  95 101
  DEL PEAK 23(13Q34) MUTATED DEL PEAK 23(13Q34) WILD-TYPE 
                          56                          196 
  DEL PEAK 23(13Q34) MUTATED DEL PEAK 23(13Q34) WILD-TYPE 
                          23                          101 
$`DEL PEAK 23(13Q34) MUTATED`
TCGA-EE-A2MR TCGA-ER-A193 TCGA-BF-AAP0 TCGA-D3-A1Q8 TCGA-D3-A2J7 TCGA-D3-A2J8 
      134.40        19.04        14.83        19.04        45.99        62.86 
TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JL TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A5GL 
       15.75        86.30       171.58        90.21        23.67        42.05 
TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A8GK TCGA-D3-A8GR TCGA-D9-A3Z3 TCGA-DA-A1HV 
       45.70       177.86       120.00        36.53        16.90        76.34 
TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1IC TCGA-DA-A95V TCGA-DA-A95X TCGA-EB-A5UN 
      150.61       110.53        58.85        72.10        65.03        52.41 
TCGA-EE-A181 TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A2A6 
       20.38        12.99         0.26        61.12       346.49        77.98 
TCGA-EE-A2GE TCGA-EE-A2GJ TCGA-EE-A2GM TCGA-EE-A2MG TCGA-EE-A2MS TCGA-EE-A2MU 
       12.95        68.65        18.35        94.19       143.93        53.26 
TCGA-EE-A3AB TCGA-EE-A3AE TCGA-EE-A3JB TCGA-EE-A3JH TCGA-ER-A19Q TCGA-ER-A2NG 
      122.73        54.51       168.85        19.86        49.71        28.67 
TCGA-FR-A3YN TCGA-FS-A1ZJ TCGA-FS-A4F4 TCGA-FS-A4F9 TCGA-GN-A8LK TCGA-GN-A9SD 
        4.50        36.33        66.67        13.28        43.23        59.41 
TCGA-RP-A693 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1V TCGA-WE-A8ZM TCGA-WE-A8ZQ 
        0.33         1.97       120.07         8.09        65.42        62.89 
TCGA-WE-A8ZY TCGA-YG-AA3O 
       48.39        28.21 

$`DEL PEAK 23(13Q34) WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A8GI TCGA-EB-A5SG TCGA-EE-A180 
        9.76        62.07        38.76        13.41        33.24        31.96 
TCGA-EE-A20H TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A3JD TCGA-FR-A729 TCGA-FW-A3R5 
      166.75       269.03        52.90        27.35       216.43        36.95 
TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q3 
       52.73         7.40        60.46        12.99         8.42        15.72 
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1QA TCGA-D3-A1QB 
       31.89       110.93        49.35       133.25        76.41        62.60 
TCGA-D3-A2J6 TCGA-D3-A2JB TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JN TCGA-D3-A2JO 
       25.64       168.00       107.61        36.30        64.83        66.08 
TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF 
       43.53        58.06       140.98        40.01        59.70        24.53 
TCGA-D3-A3MO TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R 
        9.34       173.85        30.67       144.46        31.76        62.70 
TCGA-D3-A51T TCGA-D3-A5GU TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GJ TCGA-D3-A8GL 
       11.34       124.08        78.21        23.61       179.97        69.53 
TCGA-D3-A8GM TCGA-D3-A8GP TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A4Z6 TCGA-D9-A6EC 
       70.62       135.12        10.78        15.02        18.44        69.21 
TCGA-D9-A6EG TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A3F2 
       22.85       138.67        68.68        60.10        64.83        30.44 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-DA-A95W TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q 
      225.11         8.71         0.76        14.14        12.30         3.91 
TCGA-EB-A5KH TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A182 TCGA-EE-A183 
       16.41        18.21        13.15        24.89         0.00        26.24 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29G TCGA-EE-A29H 
       75.55        79.20        75.22        76.14        44.28        47.41 
TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2GB 
       47.74        27.16       185.19       115.43        30.02        26.14 
TCGA-EE-A2GH TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR 
      201.60        10.62        32.48        93.63         0.76         0.20 
TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
       71.31        81.99       103.13        15.25         5.75        23.77 
TCGA-EE-A2MF TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
      209.79       171.85        63.25        89.26       104.78       145.45 
TCGA-EE-A2MP TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF 
      227.01        23.51       124.31        64.04         4.41         6.28 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JI TCGA-ER-A195 
       67.89       111.85        45.90         3.35       135.98        34.45 
TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D 
       10.49         7.82         4.54        53.29        39.81        11.47 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P 
      184.60       150.12        99.06        59.84        42.51       120.76 
TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
       47.18       146.63        73.05        22.36         4.70        16.87 
TCGA-ER-A2NF TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42L 
       10.19       173.29        68.52        15.48        32.05        74.47 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FS-A1YW 
      174.21         4.14        26.20         5.65        10.06       171.78 
TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD 
       49.74       195.98         8.35        27.62       312.07        32.78 
TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT 
       43.92         7.82        78.61       130.95       136.27        35.28 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F8 
        4.47        23.21         5.29         3.06        30.90       173.19 
TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
       80.68        55.59        11.54        19.30         9.90        18.25 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 
        1.91        53.29       117.93        96.92        17.06        42.48 
TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-LH-A9QB TCGA-OD-A75X 
        7.59       120.53        34.49        46.92        85.05       297.01 
TCGA-QB-A6FS TCGA-RP-A690 TCGA-W3-A824 TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1W 
        7.23         0.20       174.12        44.05        79.99       185.13 
TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-AA9Y 
       92.84        47.54        12.69        21.90        10.95         1.94 
TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-XV-AB01 TCGA-Z2-AA3S 
       37.32        24.99         6.61        91.23 

  DEL PEAK 23(13Q34) MUTATED DEL PEAK 23(13Q34) WILD-TYPE 
                        0.26                         0.00 
  DEL PEAK 23(13Q34) MUTATED DEL PEAK 23(13Q34) WILD-TYPE 
                      346.49                       312.07 
  DEL PEAK 23(13Q34) MUTATED DEL PEAK 23(13Q34) WILD-TYPE 
                      52.835                       43.985 
[1] "0.3 - 346.5 (52.8)" "0.0 - 312.1 (44.0)"
[1] "hr=" "1.3"
D43V2, survival
                              sevent
clus2                            0   1
  DEL PEAK 23(13Q34) MUTATED    42  43
  DEL PEAK 23(13Q34) WILD-TYPE 124 149
  DEL PEAK 23(13Q34) MUTATED DEL PEAK 23(13Q34) WILD-TYPE 
                          85                          273 
  DEL PEAK 23(13Q34) MUTATED DEL PEAK 23(13Q34) WILD-TYPE 
                          43                          149 
$`DEL PEAK 23(13Q34) MUTATED`
TCGA-EE-A184 TCGA-EE-A2MR TCGA-ER-A193 TCGA-BF-AAP0 TCGA-D3-A1Q8 TCGA-D3-A1Q9 
       68.15       134.40        31.40        14.93        28.08        31.59 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JL TCGA-D3-A3C7 
      103.10        65.49       115.53        86.76       171.58        46.98 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A8GB 
      103.59        39.75       125.79       135.75       178.32        30.84 
TCGA-D3-A8GK TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D3-A8GV TCGA-D9-A148 TCGA-D9-A149 
      170.20       129.63       117.17       167.70       151.53        54.67 
TCGA-D9-A3Z3 TCGA-D9-A6EA TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I2 TCGA-DA-A1I4 
       22.29        25.18        76.57        36.03       176.55        35.93 
TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A1IC TCGA-DA-A95V TCGA-DA-A95X TCGA-EB-A5UL 
      135.02        53.92        68.09        72.10        73.94        29.29 
TCGA-EB-A5UN TCGA-EE-A181 TCGA-EE-A20I TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29N 
       58.92        33.73        13.55        13.97        63.78        18.61 
TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A2A6 TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GJ 
       66.74       369.93        86.14       173.79        48.72       107.38 
TCGA-EE-A2GM TCGA-EE-A2M5 TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MS TCGA-EE-A2MU 
       75.48        21.67       103.20        16.96       162.48        53.26 
TCGA-EE-A3AB TCGA-EE-A3AE TCGA-EE-A3AH TCGA-EE-A3J5 TCGA-EE-A3JB TCGA-EE-A3JH 
      122.73        54.51       138.81        36.95       201.80       134.33 
TCGA-ER-A19Q TCGA-ER-A19T TCGA-ER-A2NG TCGA-FR-A3YN TCGA-FR-A7U9 TCGA-FS-A1ZA 
       50.89         8.88        48.99        92.98        18.77        27.72 
TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A4F4 TCGA-FS-A4F9 TCGA-GN-A266 TCGA-GN-A26D 
       32.75        47.38        66.67        34.03        10.13        48.00 
TCGA-GN-A4U7 TCGA-GN-A8LK TCGA-GN-A9SD TCGA-RP-A693 TCGA-W3-A825 TCGA-W3-A828 
       10.42        50.10        59.41         0.33        63.02       121.08 
TCGA-W3-AA1V TCGA-WE-A8ZM TCGA-WE-A8ZQ TCGA-WE-A8ZY TCGA-YD-A9TA TCGA-YG-AA3O 
       42.08       101.33        63.22        49.51        49.18        37.94 
TCGA-YG-AA3P 
       14.43 

$`DEL PEAK 23(13Q34) WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-D3-A8GI TCGA-EB-A5SG 
       27.65        62.07        46.32        13.87        58.52        68.25 
TCGA-EB-A5SH TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2GO 
       54.02        94.98       168.26         2.60       340.14       126.81 
TCGA-EE-A3JD TCGA-ER-A198 TCGA-FR-A729 TCGA-FS-A1ZF TCGA-FW-A3R5 TCGA-QB-AA9O 
       27.35        50.76       220.80        15.45        36.95        18.05 
TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 
       61.15        21.40        17.03        66.48        12.99        16.57 
TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1QA 
       16.67       112.04       112.57        71.80       133.25        90.90 
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JD TCGA-D3-A2JG 
       95.74        43.43        23.77       168.00        11.87       113.52 
TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ 
       42.08        12.10        66.48        66.08        59.57       130.72 
TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO 
       58.06       166.52        86.93        60.23        24.53         9.34 
TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K 
       45.30       174.84        55.73        56.35       145.12        32.94 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GO TCGA-D3-A5GS TCGA-D3-A5GU 
       22.62        63.81        26.89       137.92        18.18       125.19 
TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GL TCGA-D3-A8GM 
       79.59        23.61        26.43       241.38        89.13       107.15 
TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A1X3 
      161.00       152.75        29.06         3.65         7.10        18.12 
TCGA-D9-A3Z1 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HY 
       15.39        18.44         9.90        77.56        22.95       144.89 
TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A3F2 
       20.38       222.51        88.87        65.92        40.60        33.93 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-DA-A95W TCGA-DA-A95Y TCGA-DA-A95Z 
       10.49       225.96        43.36        37.35        14.14        13.02 
TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X 
       13.87        10.36        20.35         7.04        36.46        29.82 
TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B 
       27.22         8.65        14.70        26.89         4.96       133.81 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29G 
      151.27        91.56        63.35        85.08        78.97        72.07 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V 
       64.64        56.84        56.42        14.47        61.28        25.87 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 
      195.02        17.92        46.82       115.96        59.64        39.29 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GH TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN 
       59.28        67.43       220.24        54.74        79.66       102.12 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M6 
       13.91        42.77        81.21        44.88        94.82       129.27 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF 
       28.83        19.76        61.51        47.28       103.27       268.73 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN 
      204.66        96.23       180.39       216.66       167.90        47.54 
TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AD 
      248.65        43.23        71.21       124.31        64.04        28.77 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 
       13.81        41.59       172.18       127.20        64.08        34.32 
TCGA-EE-A3JA TCGA-EE-A3JE TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 
       53.19        51.35       152.81        35.44        13.94         9.17 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F 
       77.75        98.40        48.89        12.59        13.02        26.37 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
      302.07       152.35         6.44       131.51        61.05        44.09 
TCGA-ER-A19P TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
      162.08        49.48       148.18       105.07        43.82        23.34 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       20.15        28.83        41.56       247.04        93.01        46.98 
TCGA-ER-A3PL TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7U8 
       33.21        12.95       149.03       174.21        15.72        27.85 
TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YX 
       38.27        34.82        36.26       104.42       216.92        48.59 
TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZB 
      228.59       202.65        20.91        28.08         7.79        48.85 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZK TCGA-FS-A1ZM 
      357.37        53.52        46.45         9.70        23.93       101.26 
TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU 
       74.73       133.55        11.41       148.80        53.16        26.56 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F5 
       49.48        27.09        27.02        77.82        50.14        28.73 
TCGA-FS-A4F8 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU 
      174.84        26.73        54.41        80.68        17.46        55.59 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 
       13.51        19.30         9.90        19.43         2.04        15.78 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
      139.89       117.93        96.92        64.44        62.79        32.48 
TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LL TCGA-HR-A2OG 
      121.91        39.35        48.89        22.13        21.37         0.23 
TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A694 
       65.88       368.78       297.90         7.23         0.20         0.69 
TCGA-W3-A824 TCGA-W3-AA1O TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1W TCGA-W3-AA21 
      228.16         4.01        69.07       111.09       219.16       105.04 
TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K6 TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT 
       24.03        49.05        17.95        58.98        70.52        11.80 
TCGA-WE-A8ZX TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-XV-AB01 TCGA-YD-A89C 
       35.80        12.16        40.41        24.99        13.25         6.90 
TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       27.58        96.99        15.98 

  DEL PEAK 23(13Q34) MUTATED DEL PEAK 23(13Q34) WILD-TYPE 
                        0.33                         0.20 
  DEL PEAK 23(13Q34) MUTATED DEL PEAK 23(13Q34) WILD-TYPE 
                      369.93                       368.78 
  DEL PEAK 23(13Q34) MUTATED DEL PEAK 23(13Q34) WILD-TYPE 
                       58.92                        49.48 
[1] "0.3 - 369.9 (58.9)" "0.2 - 368.8 (49.5)"
[1] "hr=" "1.2"
D43V3, continuous
                              vv
clus                           I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB
  DEL PEAK 23(13Q34) MUTATED          3       1       7        6        7
  DEL PEAK 23(13Q34) WILD-TYPE       10       6      22       12       21
                              vv
clus                           STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  DEL PEAK 23(13Q34) MUTATED          7         3         3         5        10
  DEL PEAK 23(13Q34) WILD-TYPE       19        11        16        10        29
                              vv
clus                           STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DEL PEAK 23(13Q34) MUTATED            2          9          8        7
  DEL PEAK 23(13Q34) WILD-TYPE         13         26         46       14
D43V4, multiclass
            clus
vv           DEL PEAK 23(13Q34) MUTATED DEL PEAK 23(13Q34) WILD-TYPE
  I/II NOS                            3                           10
  STAGE 0                             1                            6
  STAGE I                             7                           22
  STAGE IA                            6                           12
  STAGE IB                            7                           21
  STAGE II                            7                           19
  STAGE IIA                           3                           11
  STAGE IIB                           3                           16
  STAGE IIC                           5                           10
  STAGE III                          10                           29
  STAGE IIIA                          2                           13
  STAGE IIIB                          9                           26
  STAGE IIIC                          8                           46
  STAGE IV                            7                           14
[1] 14  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           T0+T1 T2 T3 T4
  DEL PEAK 23(13Q34) MUTATED      18 13 24 15
  DEL PEAK 23(13Q34) WILD-TYPE    46 60 57 52
D43V5, multiclass
       clus
vv      DEL PEAK 23(13Q34) MUTATED DEL PEAK 23(13Q34) WILD-TYPE
  T0+T1                         18                           46
  T2                            13                           60
  T3                            24                           57
  T4                            15                           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  N3
  DEL PEAK 23(13Q34) MUTATED    42  15  10   8
  DEL PEAK 23(13Q34) WILD-TYPE 135  50  29  37
D43V6, multiclass
    clus
vv   DEL PEAK 23(13Q34) MUTATED DEL PEAK 23(13Q34) WILD-TYPE
  N0                         42                          135
  N1                         15                           50
  N2                         10                           29
  N3                          8                           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"
D43V7, binary
                              cls
clus                             0   1
  DEL PEAK 23(13Q34) MUTATED    71   8
  DEL PEAK 23(13Q34) WILD-TYPE 248  14
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 23(13Q34) MUTATED     71    8
  DEL PEAK 23(13Q34) WILD-TYPE  248   14
   clus
vv  DEL PEAK 23(13Q34) MUTATED DEL PEAK 23(13Q34) WILD-TYPE
  0                         71                          248
  1                          8                           14
[1] 2 2
[1] FALSE
D43V8, binary
                              cls
clus                            0  1
  DEL PEAK 23(13Q34) MUTATED   40 18
  DEL PEAK 23(13Q34) WILD-TYPE 94 72
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 23(13Q34) MUTATED     40   18
  DEL PEAK 23(13Q34) WILD-TYPE   94   72
     clus
vv    DEL PEAK 23(13Q34) MUTATED DEL PEAK 23(13Q34) WILD-TYPE
  NO                          40                           94
  YES                         18                           72
[1] 2 2
[1] FALSE
D43V9, binary
                              cls
clus                             0   1
  DEL PEAK 23(13Q34) MUTATED     8  77
  DEL PEAK 23(13Q34) WILD-TYPE  39 243
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 23(13Q34) MUTATED      8   77
  DEL PEAK 23(13Q34) WILD-TYPE   39  243
     clus
vv    DEL PEAK 23(13Q34) MUTATED DEL PEAK 23(13Q34) WILD-TYPE
  NO                           8                           39
  YES                         77                          243
[1] 2 2
[1] FALSE
D43V10, continuous
D43V11, binary
                              cls
clus                             0   1
  DEL PEAK 23(13Q34) MUTATED    31  54
  DEL PEAK 23(13Q34) WILD-TYPE 107 175
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 23(13Q34) MUTATED     31   54
  DEL PEAK 23(13Q34) WILD-TYPE  107  175
        clus
vv       DEL PEAK 23(13Q34) MUTATED DEL PEAK 23(13Q34) WILD-TYPE
  FEMALE                         31                          107
  MALE                           54                          175
[1] 2 2
[1] FALSE
D43V12, binary
                              cls
clus                             0   1
  DEL PEAK 23(13Q34) MUTATED    74  11
  DEL PEAK 23(13Q34) WILD-TYPE 245  36
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 23(13Q34) MUTATED     74   11
  DEL PEAK 23(13Q34) WILD-TYPE  245   36
     clus
vv    DEL PEAK 23(13Q34) MUTATED DEL PEAK 23(13Q34) WILD-TYPE
  NO                          74                          245
  YES                         11                           36
[1] 2 2
[1] FALSE
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 23(13Q34) MUTATED       0                         0    82
  DEL PEAK 23(13Q34) WILD-TYPE     5                         1   271
D43V13, multiclass
                           clus
vv                          DEL PEAK 23(13Q34) MUTATED
  ASIAN                                              0
  BLACK OR AFRICAN AMERICAN                          0
  WHITE                                             82
                           clus
vv                          DEL PEAK 23(13Q34) WILD-TYPE
  ASIAN                                                5
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                              271
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V14, binary
                              cls
clus                             0   1
  DEL PEAK 23(13Q34) MUTATED     2  82
  DEL PEAK 23(13Q34) WILD-TYPE   5 270
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 23(13Q34) MUTATED      2   82
  DEL PEAK 23(13Q34) WILD-TYPE    5  270
                        clus
vv                       DEL PEAK 23(13Q34) MUTATED
  HISPANIC OR LATINO                              2
  NOT HISPANIC OR LATINO                         82
                        clus
vv                       DEL PEAK 23(13Q34) WILD-TYPE
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                          270
[1] 2 2
[1] FALSE

Clustering(44) Variable = DEL PEAK 24(14Q23.3) MUTATION ANALYSIS
D44V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 24(14Q23.3) MUTATED   39 40
  DEL PEAK 24(14Q23.3) WILD-TYPE 89 84
  DEL PEAK 24(14Q23.3) MUTATED DEL PEAK 24(14Q23.3) WILD-TYPE 
                            79                            173 
  DEL PEAK 24(14Q23.3) MUTATED DEL PEAK 24(14Q23.3) WILD-TYPE 
                            40                             84 
$`DEL PEAK 24(14Q23.3) MUTATED`
TCGA-D3-A2JF TCGA-D3-A8GI TCGA-3N-A9WC TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A2J6 
       62.07        13.41        60.46         8.42        31.89        25.64 
TCGA-D3-A2JA TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3CC TCGA-D3-A3CE 
       15.75        64.83        66.08        43.53        40.01        59.70 
TCGA-D3-A3MR TCGA-D3-A51J TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A8GC TCGA-DA-A1HV 
       90.21       144.46        45.70       177.86        78.21        76.34 
TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I5 TCGA-DA-A3F5 TCGA-EE-A17Y TCGA-EE-A181 
      138.67        68.68       110.53       225.11        24.89        20.38 
TCGA-EE-A29C TCGA-EE-A29G TCGA-EE-A29P TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GE 
       76.14        44.28        27.16        30.02        77.98        12.95 
TCGA-EE-A2GH TCGA-EE-A2GP TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
      201.60         0.76        81.99       103.13        15.25         5.75 
TCGA-EE-A2MG TCGA-EE-A2MK TCGA-EE-A2MS TCGA-EE-A3AA TCGA-EE-A3J3 TCGA-EE-A3J7 
       94.19        89.26       143.93       124.31        67.89        45.90 
TCGA-EE-A3JB TCGA-EE-A3JI TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19G 
      168.85       135.98        10.49         7.82        53.29       184.60 
TCGA-ER-A19H TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A2ND TCGA-ER-A3PL TCGA-FR-A44A 
      150.12        47.18       146.63         4.70        32.05       174.21 
TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZE TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZT 
       27.62       312.07        43.92        78.61       130.95        35.28 
TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FW-A3TU TCGA-GF-A4EO TCGA-GF-A6C8 
       66.67       173.19        13.28        55.59        18.25         1.91 
TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-LH-A9QB 
      117.93        17.06        42.48         7.59       120.53        85.05 
TCGA-OD-A75X TCGA-W3-A825 TCGA-W3-AA1R TCGA-W3-AA1V TCGA-WE-A8ZM TCGA-WE-A8ZY 
      297.01         1.97        79.99         8.09        65.42        48.39 
TCGA-YG-AA3O 
       28.21 

$`DEL PEAK 24(14Q23.3) WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GD 
        9.76        38.76        33.24        31.96       166.75       269.03 
TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-FR-A729 TCGA-FW-A3R5 
       52.90       134.40        27.35        19.04       216.43        36.95 
TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q3 TCGA-D3-A1Q5 
       52.73         7.40        12.99        14.83        15.72       110.93 
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J7 
       49.35       133.25        19.04        76.41        62.60        45.99 
TCGA-D3-A2J8 TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL 
       62.86       168.00        86.30       107.61        36.30       171.58 
TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MU TCGA-D3-A51E 
       58.06       140.98        24.53         9.34        23.67       173.85 
TCGA-D3-A51F TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GU 
       30.67        31.76        62.70        11.34        42.05       124.08 
TCGA-D3-A8GD TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GP 
       23.61       179.97       120.00        69.53        70.62       135.12 
TCGA-D3-A8GR TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6EC 
       36.53        10.78        15.02        16.90        18.44        69.21 
TCGA-D9-A6EG TCGA-DA-A1I2 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 
       22.85       150.61        60.10        64.83        58.85        30.44 
TCGA-DA-A3F8 TCGA-DA-A95V TCGA-DA-A95W TCGA-DA-A95X TCGA-DA-A95Y TCGA-DA-A95Z 
        8.71        72.10         0.76        65.03        14.14        12.30 
TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A182 
        3.91        16.41        52.41        18.21        13.15         0.00 
TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29E 
       26.24        75.55        79.20        75.22        12.99         0.26 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 
       47.41        47.74        61.12       346.49       185.19       115.43 
TCGA-EE-A2GB TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
       26.14        68.65        10.62        32.48        18.35        93.63 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MI TCGA-EE-A2MJ 
        0.20        71.31        23.77       209.79       171.85        63.25 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB 
      104.78       145.45       227.01        23.51        53.26       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J4 TCGA-EE-A3J8 
       64.04         4.41        54.51         6.28       111.85         3.35 
TCGA-EE-A3JH TCGA-ER-A195 TCGA-ER-A19A TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19L 
       19.86        34.45         4.54        39.81        11.47        99.06 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A1A1 TCGA-ER-A2NC 
       59.84        42.51       120.76        49.71        73.05        22.36 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       16.87        10.19        28.67       173.29        68.52        15.48 
TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FR-A8YC 
       74.47         4.50         4.14        26.20         5.65        10.06 
TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1ZD TCGA-FS-A1ZG 
      171.78        49.74       195.98         8.35        32.78         7.82 
TCGA-FS-A1ZJ TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ 
       36.33       136.27         4.47        23.21         5.29         3.06 
TCGA-FS-A4F0 TCGA-FS-A4FD TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GN-A262 
       30.90        80.68        11.54        19.30         9.90        53.29 
TCGA-GN-A265 TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-GN-A8LK TCGA-GN-A9SD TCGA-QB-A6FS 
       96.92        34.49        46.92        43.23        59.41         7.23 
TCGA-RP-A690 TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A828 TCGA-W3-AA1Q TCGA-W3-AA1W 
        0.20         0.33       174.12       120.07        44.05       185.13 
TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT 
       92.84        47.54        12.69        21.90        62.89        10.95 
TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-XV-AB01 TCGA-Z2-AA3S 
        1.94        37.32        24.99         6.61        91.23 

  DEL PEAK 24(14Q23.3) MUTATED DEL PEAK 24(14Q23.3) WILD-TYPE 
                          0.76                           0.00 
  DEL PEAK 24(14Q23.3) MUTATED DEL PEAK 24(14Q23.3) WILD-TYPE 
                        312.07                         346.49 
  DEL PEAK 24(14Q23.3) MUTATED DEL PEAK 24(14Q23.3) WILD-TYPE 
                         60.46                          39.81 
[1] "0.8 - 312.1 (60.5)" "0.0 - 346.5 (39.8)"
[1] "hr=" "1.2"
D44V2, survival
                                sevent
clus2                              0   1
  DEL PEAK 24(14Q23.3) MUTATED    53  65
  DEL PEAK 24(14Q23.3) WILD-TYPE 113 127
  DEL PEAK 24(14Q23.3) MUTATED DEL PEAK 24(14Q23.3) WILD-TYPE 
                           118                            240 
  DEL PEAK 24(14Q23.3) MUTATED DEL PEAK 24(14Q23.3) WILD-TYPE 
                            65                            127 
$`DEL PEAK 24(14Q23.3) MUTATED`
TCGA-D3-A2JF TCGA-D3-A8GI TCGA-3N-A9WC TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A2J6 
       62.07        58.52        66.48        16.57       112.04        43.43 
TCGA-D3-A2JA TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3CC TCGA-D3-A3CE 
      115.53        66.48        66.08        59.57        86.93        60.23 
TCGA-D3-A3MR TCGA-D3-A3MV TCGA-D3-A51J TCGA-D3-A51N TCGA-D3-A5GN TCGA-D3-A5GO 
      103.59        45.30       145.12        22.62       135.75       137.92 
TCGA-D3-A5GR TCGA-D3-A8GC TCGA-D3-A8GN TCGA-D3-A8GS TCGA-D9-A149 TCGA-D9-A6EA 
      178.32        79.59       161.00       117.17        54.67        25.18 
TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A3F5 
       76.57       144.89       222.51       135.02        53.92       225.96 
TCGA-EB-A44R TCGA-EB-A5UL TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A29C TCGA-EE-A29G 
       10.36        29.29        27.22        33.73        78.97        72.07 
TCGA-EE-A29P TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
       56.42        25.87        17.92        59.64        39.29        86.14 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GP TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 
      173.79       220.24        13.91        94.82       129.27        28.83 
TCGA-EE-A2M8 TCGA-EE-A2MD TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MK TCGA-EE-A2MN 
       19.76        47.28       103.20        16.96       180.39        47.54 
TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A3AA TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J5 
       43.23       162.48       124.31       138.81       172.18        36.95 
TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JE TCGA-EE-A3JI TCGA-ER-A197 
       64.08        53.19       201.80        51.35       152.81        13.94 
TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19E TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19S 
        9.17        98.40        13.02       302.07       152.35        49.48 
TCGA-ER-A19W TCGA-ER-A2ND TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A44A TCGA-FS-A1YX 
      148.18        23.34        33.21        12.95       174.21        48.59 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZC TCGA-FS-A1ZE TCGA-FS-A1ZH 
       28.08         7.79        27.72       357.37        46.45        32.75 
TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZT TCGA-FS-A4F2 TCGA-FS-A4F4 
      101.26       133.55        11.41        53.16        50.14        66.67 
TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FW-A3TU TCGA-GF-A4EO TCGA-GF-A6C8 
       28.73       174.84        34.03        55.59        19.43         2.04 
TCGA-GF-A6C9 TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 
       15.78       117.93        64.44        62.79        32.48       121.91 
TCGA-GN-A4U7 TCGA-GN-A4U9 TCGA-GN-A8LL TCGA-HR-A2OG TCGA-LH-A9QB TCGA-OD-A75X 
       10.42        22.13        21.37         0.23       368.78       297.90 
TCGA-W3-A825 TCGA-W3-AA1R TCGA-W3-AA1V TCGA-WE-A8JZ TCGA-WE-A8ZM TCGA-WE-A8ZX 
       63.02       111.09        42.08        24.03       101.33        35.80 
TCGA-WE-A8ZY TCGA-YD-A9TA TCGA-YG-AA3O TCGA-Z2-A8RT 
       49.51        49.18        37.94        27.58 

$`DEL PEAK 24(14Q23.3) WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A180 
       27.65        46.32        13.87        68.25        54.02        94.98 
TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR 
       68.15       168.26         2.60       340.14       126.81       134.40 
TCGA-EE-A3JD TCGA-ER-A193 TCGA-ER-A198 TCGA-FR-A729 TCGA-FS-A1ZF TCGA-FW-A3R5 
       27.35        31.40        50.76       220.80        15.45        36.95 
TCGA-QB-AA9O TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-3N-A9WB TCGA-3N-A9WD TCGA-BF-AAP0 
       18.05        61.15        21.40        17.03        12.99        14.93 
TCGA-D3-A1Q3 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 
       16.67       112.57        71.80       133.25        28.08        31.59 
TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JB 
       90.90        95.74       103.10        65.49        23.77       168.00 
TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL 
       86.76        11.87       113.52        42.08        12.10       171.58 
TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CF TCGA-D3-A3MO 
      130.72        58.06        46.98       166.52        24.53         9.34 
TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51K TCGA-D3-A51R 
       39.75       174.84        55.73        56.35        32.94        63.81 
TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GD 
       26.89       125.79        18.18       125.19        30.84        23.61 
TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GP 
       26.43       241.38       170.20        89.13       107.15       152.75 
TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GV TCGA-D9-A148 TCGA-D9-A1JW TCGA-D9-A1JX 
       29.06       129.63       167.70       151.53         3.65         7.10 
TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EC 
       18.12        15.39        22.29        18.44         9.90        77.56 
TCGA-D9-A6EG TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I7 
       22.95        36.03        20.38       176.55        35.93        88.87 
TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 
       65.92        40.60        68.09        33.93        10.49        43.36 
TCGA-DA-A95V TCGA-DA-A95W TCGA-DA-A95X TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q 
       72.10        37.35        73.94        14.14        13.02        13.87 
TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Z 
       20.35        58.92         7.04        36.46        29.82         8.65 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F 
       14.70        26.89         4.96       133.81       151.27        91.56 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H 
       13.55        63.35        85.08        13.97        63.78        64.64 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T 
       56.84        18.61        66.74        14.47        61.28       369.93 
TCGA-EE-A29W TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GI 
      195.02        46.82       115.96        59.28        67.43        48.72 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GR 
      107.38        54.74        79.66        75.48       102.12        42.77 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2MC TCGA-EE-A2ME TCGA-EE-A2MF 
       81.21        44.88        21.67        61.51       103.27       268.73 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MT 
      204.66        96.23       216.66       167.90       248.65        71.21 
TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
       53.26       122.73        64.04        28.77        54.51        13.81 
TCGA-EE-A3AG TCGA-EE-A3J4 TCGA-EE-A3J8 TCGA-EE-A3JH TCGA-ER-A195 TCGA-ER-A19A 
       41.59       127.20        34.32       134.33        35.44        77.75 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
       48.89        12.59        26.37         6.44       131.51        61.05 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19T TCGA-ER-A1A1 TCGA-ER-A2NC 
       44.09       162.08        50.89         8.88       105.07        43.82 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
       20.15        28.83        48.99        41.56       247.04        93.01 
TCGA-ER-A3EV TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A7U9 
       46.98       149.03        92.98        15.72        27.85        18.77 
TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YY 
       38.27        34.82        36.26       104.42       216.92       228.59 
TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1ZB TCGA-FS-A1ZD TCGA-FS-A1ZG TCGA-FS-A1ZJ 
      202.65        20.91        48.85        53.52         9.70        47.38 
TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
       23.93        74.73       148.80        26.56        49.48        27.09 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 
       27.02        77.82        26.73        54.41        80.68        17.46 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A266 
       13.51        19.30         9.90       139.89        96.92        10.13 
TCGA-GN-A26D TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-GN-A8LK TCGA-GN-A9SD TCGA-HR-A2OH 
       48.00        39.35        48.89        50.10        59.41        65.88 
TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A828 
        7.23         0.20         0.33         0.69       228.16       121.08 
TCGA-W3-AA1O TCGA-W3-AA1Q TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K6 
        4.01        69.07       219.16       105.04        49.05        17.95 
TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-AA9Y TCGA-WE-AAA0 
       58.98        70.52        63.22        11.80        12.16        40.41 
TCGA-WE-AAA4 TCGA-XV-AB01 TCGA-YD-A89C TCGA-YG-AA3P TCGA-Z2-AA3S TCGA-Z2-AA3V 
       24.99        13.25         6.90        14.43        96.99        15.98 

  DEL PEAK 24(14Q23.3) MUTATED DEL PEAK 24(14Q23.3) WILD-TYPE 
                          0.23                           0.20 
  DEL PEAK 24(14Q23.3) MUTATED DEL PEAK 24(14Q23.3) WILD-TYPE 
                        368.78                         369.93 
  DEL PEAK 24(14Q23.3) MUTATED DEL PEAK 24(14Q23.3) WILD-TYPE 
                         57.47                          48.94 
[1] "0.2 - 368.8 (57.5)" "0.2 - 369.9 (48.9)"
[1] "hr=" "1.1"
D44V3, continuous
                                vv
clus                             I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB
  DEL PEAK 24(14Q23.3) MUTATED          5       0      13        4        7
  DEL PEAK 24(14Q23.3) WILD-TYPE        8       7      16       14       21
                                vv
clus                             STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK 24(14Q23.3) MUTATED         12         2         4         6
  DEL PEAK 24(14Q23.3) WILD-TYPE       14        12        15         9
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 24(14Q23.3) MUTATED          17          5         12         16
  DEL PEAK 24(14Q23.3) WILD-TYPE        22         10         23         38
                                vv
clus                             STAGE IV
  DEL PEAK 24(14Q23.3) MUTATED          4
  DEL PEAK 24(14Q23.3) WILD-TYPE       17
D44V4, multiclass
            clus
vv           DEL PEAK 24(14Q23.3) MUTATED DEL PEAK 24(14Q23.3) WILD-TYPE
  I/II NOS                              5                              8
  STAGE 0                               0                              7
  STAGE I                              13                             16
  STAGE IA                              4                             14
  STAGE IB                              7                             21
  STAGE II                             12                             14
  STAGE IIA                             2                             12
  STAGE IIB                             4                             15
  STAGE IIC                             6                              9
  STAGE III                            17                             22
  STAGE IIIA                            5                             10
  STAGE IIIB                           12                             23
  STAGE IIIC                           16                             38
  STAGE IV                              4                             17
[1] 14  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  DEL PEAK 24(14Q23.3) MUTATED      24 26 24 23
  DEL PEAK 24(14Q23.3) WILD-TYPE    40 47 57 44
D44V5, multiclass
       clus
vv      DEL PEAK 24(14Q23.3) MUTATED DEL PEAK 24(14Q23.3) WILD-TYPE
  T0+T1                           24                             40
  T2                              26                             47
  T3                              24                             57
  T4                              23                             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  N3
  DEL PEAK 24(14Q23.3) MUTATED    56  27  10  13
  DEL PEAK 24(14Q23.3) WILD-TYPE 121  38  29  32
D44V6, multiclass
    clus
vv   DEL PEAK 24(14Q23.3) MUTATED DEL PEAK 24(14Q23.3) WILD-TYPE
  N0                           56                            121
  N1                           27                             38
  N2                           10                             29
  N3                           13                             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"
D44V7, binary
                                cls
clus                               0   1
  DEL PEAK 24(14Q23.3) MUTATED   107   4
  DEL PEAK 24(14Q23.3) WILD-TYPE 212  18
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(14Q23.3) MUTATED    107    4
  DEL PEAK 24(14Q23.3) WILD-TYPE  212   18
   clus
vv  DEL PEAK 24(14Q23.3) MUTATED DEL PEAK 24(14Q23.3) WILD-TYPE
  0                          107                            212
  1                            4                             18
[1] 2 2
[1] FALSE
D44V8, binary
                                cls
clus                              0  1
  DEL PEAK 24(14Q23.3) MUTATED   41 32
  DEL PEAK 24(14Q23.3) WILD-TYPE 93 58
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(14Q23.3) MUTATED     41   32
  DEL PEAK 24(14Q23.3) WILD-TYPE   93   58
     clus
vv    DEL PEAK 24(14Q23.3) MUTATED DEL PEAK 24(14Q23.3) WILD-TYPE
  NO                            41                             93
  YES                           32                             58
[1] 2 2
[1] FALSE
D44V9, binary
                                cls
clus                               0   1
  DEL PEAK 24(14Q23.3) MUTATED    15 105
  DEL PEAK 24(14Q23.3) WILD-TYPE  32 215
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(14Q23.3) MUTATED     15  105
  DEL PEAK 24(14Q23.3) WILD-TYPE   32  215
     clus
vv    DEL PEAK 24(14Q23.3) MUTATED DEL PEAK 24(14Q23.3) WILD-TYPE
  NO                            15                             32
  YES                          105                            215
[1] 2 2
[1] FALSE
D44V10, continuous
D44V11, binary
                                cls
clus                               0   1
  DEL PEAK 24(14Q23.3) MUTATED    50  70
  DEL PEAK 24(14Q23.3) WILD-TYPE  88 159
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(14Q23.3) MUTATED     50   70
  DEL PEAK 24(14Q23.3) WILD-TYPE   88  159
        clus
vv       DEL PEAK 24(14Q23.3) MUTATED DEL PEAK 24(14Q23.3) WILD-TYPE
  FEMALE                           50                             88
  MALE                             70                            159
[1] 2 2
[1] FALSE
D44V12, binary
                                cls
clus                               0   1
  DEL PEAK 24(14Q23.3) MUTATED   107  13
  DEL PEAK 24(14Q23.3) WILD-TYPE 212  34
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(14Q23.3) MUTATED    107   13
  DEL PEAK 24(14Q23.3) WILD-TYPE  212   34
     clus
vv    DEL PEAK 24(14Q23.3) MUTATED DEL PEAK 24(14Q23.3) WILD-TYPE
  NO                           107                            212
  YES                           13                             34
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 24(14Q23.3) MUTATED       2                         0   115
  DEL PEAK 24(14Q23.3) WILD-TYPE     3                         1   238
D44V13, multiclass
                           clus
vv                          DEL PEAK 24(14Q23.3) MUTATED
  ASIAN                                                2
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                              115
                           clus
vv                          DEL PEAK 24(14Q23.3) WILD-TYPE
  ASIAN                                                  3
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                238
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V14, binary
                                cls
clus                               0   1
  DEL PEAK 24(14Q23.3) MUTATED     2 114
  DEL PEAK 24(14Q23.3) WILD-TYPE   5 238
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(14Q23.3) MUTATED      2  114
  DEL PEAK 24(14Q23.3) WILD-TYPE    5  238
                        clus
vv                       DEL PEAK 24(14Q23.3) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                          114
                        clus
vv                       DEL PEAK 24(14Q23.3) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                            238
[1] 2 2
[1] FALSE

Clustering(45) Variable = DEL PEAK 25(14Q32.31) MUTATION ANALYSIS
D45V1, survival
                                 sevent
clus2                              0  1
  DEL PEAK 25(14Q32.31) MUTATED   40 41
  DEL PEAK 25(14Q32.31) WILD-TYPE 88 83
  DEL PEAK 25(14Q32.31) MUTATED DEL PEAK 25(14Q32.31) WILD-TYPE 
                             81                             171 
  DEL PEAK 25(14Q32.31) MUTATED DEL PEAK 25(14Q32.31) WILD-TYPE 
                             41                              83 
$`DEL PEAK 25(14Q32.31) MUTATED`
TCGA-D3-A2JF TCGA-D3-A8GI TCGA-3N-A9WC TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
       62.07        13.41        60.46         8.42        31.89       110.93 
TCGA-D3-A2J6 TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3CC TCGA-D3-A3CE 
       25.64        64.83        66.08        43.53        40.01        59.70 
TCGA-D3-A3MR TCGA-D3-A51J TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A8GC TCGA-DA-A1HV 
       90.21       144.46        45.70       177.86        78.21        76.34 
TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I5 TCGA-DA-A3F5 TCGA-DA-A95V TCGA-EE-A17Y 
      138.67        68.68       110.53       225.11        72.10        24.89 
TCGA-EE-A181 TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A2A2 TCGA-EE-A2A6 
       20.38        76.14         0.26        44.28        30.02        77.98 
TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GJ TCGA-EE-A2GP TCGA-EE-A2GU TCGA-EE-A2M6 
       26.14        12.95        68.65         0.76        81.99       103.13 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MG TCGA-EE-A2MK TCGA-EE-A2MS 
       15.25         5.75        23.77        94.19        89.26       143.93 
TCGA-EE-A3AA TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-EE-A3JB TCGA-EE-A3JI TCGA-ER-A197 
      124.31        67.89        45.90       168.85       135.98        10.49 
TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19S TCGA-ER-A2ND 
        7.82        53.29       184.60       150.12        47.18         4.70 
TCGA-ER-A2NE TCGA-ER-A3PL TCGA-FR-A44A TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZE 
       16.87        32.05       174.21        27.62       312.07        43.92 
TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZT TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FW-A3TU 
       78.61       130.95        35.28       173.19        13.28        55.59 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
       18.25         1.91       117.93        17.06        42.48         7.59 
TCGA-GN-A4U3 TCGA-GN-A8LK TCGA-LH-A9QB TCGA-OD-A75X TCGA-RP-A693 TCGA-W3-AA1V 
      120.53        43.23        85.05       297.01         0.33         8.09 
TCGA-WE-A8ZM TCGA-WE-A8ZY TCGA-YG-AA3O 
       65.42        48.39        28.21 

$`DEL PEAK 25(14Q32.31) WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GD 
        9.76        38.76        33.24        31.96       166.75       269.03 
TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-FR-A729 TCGA-FW-A3R5 
       52.90       134.40        27.35        19.04       216.43        36.95 
TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q3 TCGA-D3-A1Q6 
       52.73         7.40        12.99        14.83        15.72        49.35 
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J7 TCGA-D3-A2J8 
      133.25        19.04        76.41        62.60        45.99        62.86 
TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL 
       15.75       168.00        86.30       107.61        36.30       171.58 
TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MU TCGA-D3-A51E 
       58.06       140.98        24.53         9.34        23.67       173.85 
TCGA-D3-A51F TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GU 
       30.67        31.76        62.70        11.34        42.05       124.08 
TCGA-D3-A8GD TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GP 
       23.61       179.97       120.00        69.53        70.62       135.12 
TCGA-D3-A8GR TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6EC 
       36.53        10.78        15.02        16.90        18.44        69.21 
TCGA-D9-A6EG TCGA-DA-A1I2 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 
       22.85       150.61        60.10        64.83        58.85        30.44 
TCGA-DA-A3F8 TCGA-DA-A95W TCGA-DA-A95X TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q 
        8.71         0.76        65.03        14.14        12.30         3.91 
TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A182 TCGA-EE-A183 
       16.41        52.41        18.21        13.15         0.00        26.24 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29H TCGA-EE-A29M 
       75.55        79.20        75.22        12.99        47.41        47.74 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2GH 
       27.16        61.12       346.49       185.19       115.43       201.60 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GR TCGA-EE-A2GS 
       10.62        32.48        18.35        93.63         0.20        71.31 
TCGA-EE-A2MF TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP 
      209.79       171.85        63.25       104.78       145.45       227.01 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
       23.51        53.26       122.73        64.04         4.41        54.51 
TCGA-EE-A3AF TCGA-EE-A3J4 TCGA-EE-A3J8 TCGA-EE-A3JH TCGA-ER-A195 TCGA-ER-A19A 
        6.28       111.85         3.35        19.86        34.45         4.54 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P 
       39.81        11.47        99.06        59.84        42.51       120.76 
TCGA-ER-A19Q TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NF TCGA-ER-A2NG 
       49.71       146.63        73.05        22.36        10.19        28.67 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A69P 
      173.29        68.52        15.48        74.47         4.50         4.14 
TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 
       26.20         5.65        10.06       171.78        49.74       195.98 
TCGA-FS-A1Z3 TCGA-FS-A1ZD TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZS TCGA-FS-A1ZU 
        8.35        32.78         7.82        36.33       136.27         4.47 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4FD 
       23.21         5.29         3.06        30.90        66.67        80.68 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A4U4 
       11.54        19.30         9.90        53.29        96.92        34.49 
TCGA-GN-A4U8 TCGA-GN-A9SD TCGA-QB-A6FS TCGA-RP-A690 TCGA-W3-A824 TCGA-W3-A825 
       46.92        59.41         7.23         0.20       174.12         1.97 
TCGA-W3-A828 TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 
      120.07        44.05        79.99       185.13        92.84        47.54 
TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-AA9Y TCGA-WE-AAA0 
       12.69        21.90        62.89        10.95         1.94        37.32 
TCGA-WE-AAA4 TCGA-XV-AB01 TCGA-Z2-AA3S 
       24.99         6.61        91.23 

  DEL PEAK 25(14Q32.31) MUTATED DEL PEAK 25(14Q32.31) WILD-TYPE 
                           0.26                            0.00 
  DEL PEAK 25(14Q32.31) MUTATED DEL PEAK 25(14Q32.31) WILD-TYPE 
                         312.07                          346.49 
  DEL PEAK 25(14Q32.31) MUTATED DEL PEAK 25(14Q32.31) WILD-TYPE 
                          55.59                           42.05 
[1] "0.3 - 312.1 (55.6)" "0.0 - 346.5 (42.0)"
[1] "hr=" "1.1"
D45V2, survival
                                 sevent
clus2                               0   1
  DEL PEAK 25(14Q32.31) MUTATED    53  61
  DEL PEAK 25(14Q32.31) WILD-TYPE 113 131
  DEL PEAK 25(14Q32.31) MUTATED DEL PEAK 25(14Q32.31) WILD-TYPE 
                            114                             244 
  DEL PEAK 25(14Q32.31) MUTATED DEL PEAK 25(14Q32.31) WILD-TYPE 
                             61                             131 
$`DEL PEAK 25(14Q32.31) MUTATED`
TCGA-D3-A2JF TCGA-D3-A8GI TCGA-3N-A9WC TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
       62.07        58.52        66.48        16.57       112.04       112.57 
TCGA-D3-A2J6 TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3CC TCGA-D3-A3CE 
       43.43        66.48        66.08        59.57        86.93        60.23 
TCGA-D3-A3MR TCGA-D3-A3MV TCGA-D3-A51J TCGA-D3-A51N TCGA-D3-A5GN TCGA-D3-A5GO 
      103.59        45.30       145.12        22.62       135.75       137.92 
TCGA-D3-A5GR TCGA-D3-A8GC TCGA-D3-A8GN TCGA-D9-A149 TCGA-D9-A6EA TCGA-DA-A1HV 
      178.32        79.59       161.00        54.67        25.18        76.57 
TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A3F5 TCGA-DA-A95V 
      144.89       222.51       135.02        53.92       225.96        72.10 
TCGA-EB-A44R TCGA-EB-A5UL TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A29C TCGA-EE-A29E 
       10.36        29.29        27.22        33.73        78.97        63.78 
TCGA-EE-A29G TCGA-EE-A29V TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
       72.07        25.87        59.64        39.29        86.14        59.28 
TCGA-EE-A2GE TCGA-EE-A2GJ TCGA-EE-A2GP TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 
      173.79       107.38        13.91        94.82       129.27        28.83 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MK 
       19.76        61.51        47.28       103.20        16.96       180.39 
TCGA-EE-A2MN TCGA-EE-A2MS TCGA-EE-A3AA TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J5 
       47.54       162.48       124.31       138.81       172.18        36.95 
TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JE TCGA-EE-A3JI TCGA-ER-A197 
       64.08        53.19       201.80        51.35       152.81        13.94 
TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19E TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19S 
        9.17        98.40        13.02       302.07       152.35        49.48 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A44A TCGA-FS-A1YX 
       23.34        20.15        33.21        12.95       174.21        48.59 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZC TCGA-FS-A1ZE TCGA-FS-A1ZH 
       28.08         7.79        27.72       357.37        46.45        32.75 
TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZT TCGA-FS-A4F2 TCGA-FS-A4F5 
      101.26       133.55        11.41        53.16        50.14        28.73 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FW-A3TU TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 
      174.84        34.03        55.59        19.43         2.04        15.78 
TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U9 
      117.93        64.44        62.79        32.48       121.91        22.13 
TCGA-GN-A8LK TCGA-HR-A2OG TCGA-LH-A9QB TCGA-OD-A75X TCGA-RP-A693 TCGA-W3-AA1V 
       50.10         0.23       368.78       297.90         0.33        42.08 
TCGA-WE-A8JZ TCGA-WE-A8ZM TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-YG-AA3O TCGA-Z2-A8RT 
       24.03       101.33        35.80        49.51        37.94        27.58 

$`DEL PEAK 25(14Q32.31) WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A180 
       27.65        46.32        13.87        68.25        54.02        94.98 
TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR 
       68.15       168.26         2.60       340.14       126.81       134.40 
TCGA-EE-A3JD TCGA-ER-A193 TCGA-ER-A198 TCGA-FR-A729 TCGA-FS-A1ZF TCGA-FW-A3R5 
       27.35        31.40        50.76       220.80        15.45        36.95 
TCGA-QB-AA9O TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-3N-A9WB TCGA-3N-A9WD TCGA-BF-AAP0 
       18.05        61.15        21.40        17.03        12.99        14.93 
TCGA-D3-A1Q3 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA 
       16.67        71.80       133.25        28.08        31.59        90.90 
TCGA-D3-A1QB TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB 
       95.74       103.10        65.49        23.77       115.53       168.00 
TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL 
       86.76        11.87       113.52        42.08        12.10       171.58 
TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CF TCGA-D3-A3MO 
      130.72        58.06        46.98       166.52        24.53         9.34 
TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51K TCGA-D3-A51R 
       39.75       174.84        55.73        56.35        32.94        63.81 
TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GD 
       26.89       125.79        18.18       125.19        30.84        23.61 
TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GP 
       26.43       241.38       170.20        89.13       107.15       152.75 
TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D3-A8GV TCGA-D9-A148 TCGA-D9-A1JW 
       29.06       129.63       117.17       167.70       151.53         3.65 
TCGA-D9-A1JX TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 
        7.10        18.12        15.39        22.29        18.44         9.90 
TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 
       77.56        22.95        36.03        20.38       176.55        35.93 
TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
       88.87        65.92        40.60        68.09        33.93        10.49 
TCGA-DA-A3F8 TCGA-DA-A95W TCGA-DA-A95X TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q 
       43.36        37.35        73.94        14.14        13.02        13.87 
TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Z 
       20.35        58.92         7.04        36.46        29.82         8.65 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F 
       14.70        26.89         4.96       133.81       151.27        91.56 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29H TCGA-EE-A29M 
       13.55        63.35        85.08        13.97        64.64        56.84 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T 
       18.61        56.42        66.74        14.47        61.28       369.93 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2GC TCGA-EE-A2GH 
      195.02        17.92        46.82       115.96        67.43       220.24 
TCGA-EE-A2GI TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GR 
       48.72        54.74        79.66        75.48       102.12        42.77 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MI 
       81.21        44.88        21.67       103.27       268.73       204.66 
TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MT 
       96.23       216.66       167.90       248.65        43.23        71.21 
TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
       53.26       122.73        64.04        28.77        54.51        13.81 
TCGA-EE-A3AG TCGA-EE-A3J4 TCGA-EE-A3J8 TCGA-EE-A3JH TCGA-ER-A195 TCGA-ER-A19A 
       41.59       127.20        34.32       134.33        35.44        77.75 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
       48.89        12.59        26.37         6.44       131.51        61.05 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 
       44.09       162.08        50.89         8.88       148.18       105.07 
TCGA-ER-A2NC TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
       43.82        28.83        48.99        41.56       247.04        93.01 
TCGA-ER-A3EV TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A7U9 
       46.98       149.03        92.98        15.72        27.85        18.77 
TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YY 
       38.27        34.82        36.26       104.42       216.92       228.59 
TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1ZB TCGA-FS-A1ZD TCGA-FS-A1ZG TCGA-FS-A1ZJ 
      202.65        20.91        48.85        53.52         9.70        47.38 
TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
       23.93        74.73       148.80        26.56        49.48        27.09 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD 
       27.02        77.82        66.67        26.73        54.41        80.68 
TCGA-FW-A3I3 TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GN-A262 TCGA-GN-A265 
       17.46        13.51        19.30         9.90       139.89        96.92 
TCGA-GN-A266 TCGA-GN-A26D TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A8LL 
       10.13        48.00        39.35        10.42        48.89        21.37 
TCGA-GN-A9SD TCGA-HR-A2OH TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A694 TCGA-W3-A824 
       59.41        65.88         7.23         0.20         0.69       228.16 
TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1W 
       63.02       121.08         4.01        69.07       111.09       219.16 
TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K6 TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ 
      105.04        49.05        17.95        58.98        70.52        63.22 
TCGA-WE-A8ZT TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-XV-AB01 TCGA-YD-A89C 
       11.80        12.16        40.41        24.99        13.25         6.90 
TCGA-YD-A9TA TCGA-YG-AA3P TCGA-Z2-AA3S TCGA-Z2-AA3V 
       49.18        14.43        96.99        15.98 

  DEL PEAK 25(14Q32.31) MUTATED DEL PEAK 25(14Q32.31) WILD-TYPE 
                           0.23                            0.20 
  DEL PEAK 25(14Q32.31) MUTATED DEL PEAK 25(14Q32.31) WILD-TYPE 
                         368.78                          369.93 
  DEL PEAK 25(14Q32.31) MUTATED DEL PEAK 25(14Q32.31) WILD-TYPE 
                          58.90                           48.94 
[1] "0.2 - 368.8 (58.9)" "0.2 - 369.9 (48.9)"
[1] "hr=" "1.2"
D45V3, continuous
                                 vv
clus                              I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB
  DEL PEAK 25(14Q32.31) MUTATED          7       1      12        5        7
  DEL PEAK 25(14Q32.31) WILD-TYPE        6       6      17       13       21
                                 vv
clus                              STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK 25(14Q32.31) MUTATED          9         2         4         5
  DEL PEAK 25(14Q32.31) WILD-TYPE       17        12        15        10
                                 vv
clus                              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 25(14Q32.31) MUTATED          17          3         14         15
  DEL PEAK 25(14Q32.31) WILD-TYPE        22         12         21         39
                                 vv
clus                              STAGE IV
  DEL PEAK 25(14Q32.31) MUTATED          5
  DEL PEAK 25(14Q32.31) WILD-TYPE       16
D45V4, multiclass
            clus
vv           DEL PEAK 25(14Q32.31) MUTATED DEL PEAK 25(14Q32.31) WILD-TYPE
  I/II NOS                               7                               6
  STAGE 0                                1                               6
  STAGE I                               12                              17
  STAGE IA                               5                              13
  STAGE IB                               7                              21
  STAGE II                               9                              17
  STAGE IIA                              2                              12
  STAGE IIB                              4                              15
  STAGE IIC                              5                              10
  STAGE III                             17                              22
  STAGE IIIA                             3                              12
  STAGE IIIB                            14                              21
  STAGE IIIC                            15                              39
  STAGE IV                               5                              16
[1] 14  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              T0+T1 T2 T3 T4
  DEL PEAK 25(14Q32.31) MUTATED      25 24 21 22
  DEL PEAK 25(14Q32.31) WILD-TYPE    39 49 60 45
D45V5, multiclass
       clus
vv      DEL PEAK 25(14Q32.31) MUTATED DEL PEAK 25(14Q32.31) WILD-TYPE
  T0+T1                            25                              39
  T2                               24                              49
  T3                               21                              60
  T4                               22                              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  N3
  DEL PEAK 25(14Q32.31) MUTATED    55  28   9  12
  DEL PEAK 25(14Q32.31) WILD-TYPE 122  37  30  33
D45V6, multiclass
    clus
vv   DEL PEAK 25(14Q32.31) MUTATED DEL PEAK 25(14Q32.31) WILD-TYPE
  N0                            55                             122
  N1                            28                              37
  N2                             9                              30
  N3                            12                              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"
D45V7, binary
                                 cls
clus                                0   1
  DEL PEAK 25(14Q32.31) MUTATED   103   5
  DEL PEAK 25(14Q32.31) WILD-TYPE 216  17
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 25(14Q32.31) MUTATED    103    5
  DEL PEAK 25(14Q32.31) WILD-TYPE  216   17
   clus
vv  DEL PEAK 25(14Q32.31) MUTATED DEL PEAK 25(14Q32.31) WILD-TYPE
  0                           103                             216
  1                             5                              17
[1] 2 2
[1] FALSE
D45V8, binary
                                 cls
clus                               0  1
  DEL PEAK 25(14Q32.31) MUTATED   40 31
  DEL PEAK 25(14Q32.31) WILD-TYPE 94 59
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 25(14Q32.31) MUTATED     40   31
  DEL PEAK 25(14Q32.31) WILD-TYPE   94   59
     clus
vv    DEL PEAK 25(14Q32.31) MUTATED DEL PEAK 25(14Q32.31) WILD-TYPE
  NO                             40                              94
  YES                            31                              59
[1] 2 2
[1] FALSE
D45V9, binary
                                 cls
clus                                0   1
  DEL PEAK 25(14Q32.31) MUTATED    16 101
  DEL PEAK 25(14Q32.31) WILD-TYPE  31 219
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 25(14Q32.31) MUTATED     16  101
  DEL PEAK 25(14Q32.31) WILD-TYPE   31  219
     clus
vv    DEL PEAK 25(14Q32.31) MUTATED DEL PEAK 25(14Q32.31) WILD-TYPE
  NO                             16                              31
  YES                           101                             219
[1] 2 2
[1] FALSE
D45V10, continuous
D45V11, binary
                                 cls
clus                                0   1
  DEL PEAK 25(14Q32.31) MUTATED    45  72
  DEL PEAK 25(14Q32.31) WILD-TYPE  93 157
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 25(14Q32.31) MUTATED     45   72
  DEL PEAK 25(14Q32.31) WILD-TYPE   93  157
        clus
vv       DEL PEAK 25(14Q32.31) MUTATED DEL PEAK 25(14Q32.31) WILD-TYPE
  FEMALE                            45                              93
  MALE                              72                             157
[1] 2 2
[1] FALSE
D45V12, binary
                                 cls
clus                                0   1
  DEL PEAK 25(14Q32.31) MUTATED   102  15
  DEL PEAK 25(14Q32.31) WILD-TYPE 217  32
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 25(14Q32.31) MUTATED    102   15
  DEL PEAK 25(14Q32.31) WILD-TYPE  217   32
     clus
vv    DEL PEAK 25(14Q32.31) MUTATED DEL PEAK 25(14Q32.31) WILD-TYPE
  NO                            102                             217
  YES                            15                              32
[1] 2 2
[1] FALSE
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 25(14Q32.31) MUTATED       2                         0   112
  DEL PEAK 25(14Q32.31) WILD-TYPE     3                         1   241
D45V13, multiclass
                           clus
vv                          DEL PEAK 25(14Q32.31) MUTATED
  ASIAN                                                 2
  BLACK OR AFRICAN AMERICAN                             0
  WHITE                                               112
                           clus
vv                          DEL PEAK 25(14Q32.31) WILD-TYPE
  ASIAN                                                   3
  BLACK OR AFRICAN AMERICAN                               1
  WHITE                                                 241
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V14, binary
                                 cls
clus                                0   1
  DEL PEAK 25(14Q32.31) MUTATED     2 112
  DEL PEAK 25(14Q32.31) WILD-TYPE   5 240
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 25(14Q32.31) MUTATED      2  112
  DEL PEAK 25(14Q32.31) WILD-TYPE    5  240
                        clus
vv                       DEL PEAK 25(14Q32.31) MUTATED
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                           112
                        clus
vv                       DEL PEAK 25(14Q32.31) WILD-TYPE
  HISPANIC OR LATINO                                   5
  NOT HISPANIC OR LATINO                             240
[1] 2 2
[1] FALSE

Clustering(46) Variable = DEL PEAK 26(15Q13.3) MUTATION ANALYSIS
D46V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 26(15Q13.3) MUTATED    20  33
  DEL PEAK 26(15Q13.3) WILD-TYPE 108  91
  DEL PEAK 26(15Q13.3) MUTATED DEL PEAK 26(15Q13.3) WILD-TYPE 
                            53                            199 
  DEL PEAK 26(15Q13.3) MUTATED DEL PEAK 26(15Q13.3) WILD-TYPE 
                            33                             91 
$`DEL PEAK 26(15Q13.3) MUTATED`
TCGA-EE-A180 TCGA-ER-A193 TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1QB TCGA-D3-A2J7 
       31.96        19.04        12.99         8.42        62.60        45.99 
TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3MU TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A8GC 
       58.06        40.01        23.67        62.70        45.70        78.21 
TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A95Z TCGA-EB-A5KH 
       69.21        76.34       138.67        68.68        12.30        16.41 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A2GH TCGA-EE-A2GP TCGA-EE-A2MC TCGA-EE-A2MF 
       27.16        61.12       201.60         0.76        23.77       209.79 
TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB 
      171.85        89.26       145.45        23.51        53.26       122.73 
TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19W TCGA-ER-A2NE 
       67.89        45.90        10.49         7.82       146.63        16.87 
TCGA-ER-A3EV TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZM 
       15.48       195.98        27.62        43.92         7.82        78.61 
TCGA-FS-A4F8 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV TCGA-GN-A264 TCGA-GN-A267 
      173.19        80.68        55.59        11.54       117.93        17.06 
TCGA-GN-A8LK TCGA-OD-A75X TCGA-W3-AA1R TCGA-W3-AA1V TCGA-WE-A8ZQ 
       43.23       297.01        79.99         8.09        62.89 

$`DEL PEAK 26(15Q13.3) WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A8GI TCGA-EB-A5SG TCGA-EE-A20H 
        9.76        62.07        38.76        13.41        33.24       166.75 
TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-FR-A729 TCGA-FW-A3R5 
      269.03        52.90       134.40        27.35       216.43        36.95 
TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-3N-A9WC TCGA-BF-AAP0 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
       52.73         7.40        60.46        14.83        15.72        31.89 
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A2J6 
      110.93        49.35       133.25        19.04        76.41        25.64 
TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A2JH 
       62.86        15.75       168.00        86.30       107.61        36.30 
TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3CB TCGA-D3-A3CE 
      171.58        64.83        66.08        43.53       140.98        59.70 
TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51J 
       24.53         9.34        90.21       173.85        30.67       144.46 
TCGA-D3-A51K TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D3-A8GD 
       31.76        11.34        42.05       177.86       124.08        23.61 
TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GP TCGA-D3-A8GR 
      179.97       120.00        69.53        70.62       135.12        36.53 
TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6EG TCGA-DA-A1I2 
       10.78        15.02        16.90        18.44        22.85       150.61 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 
      110.53        60.10        64.83        58.85        30.44       225.11 
TCGA-DA-A3F8 TCGA-DA-A95V TCGA-DA-A95W TCGA-DA-A95X TCGA-DA-A95Y TCGA-EB-A44Q 
        8.71        72.10         0.76        65.03        14.14         3.91 
TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A182 
       52.41        18.21        13.15        24.89        20.38         0.00 
TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D 
       26.24        75.55        79.20        75.22        76.14        12.99 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29T TCGA-EE-A29W 
        0.26        44.28        47.41        47.74       346.49       185.19 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GJ 
      115.43        30.02        77.98        26.14        12.95        68.65 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GR TCGA-EE-A2GS 
       10.62        32.48        18.35        93.63         0.20        71.31 
TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MG TCGA-EE-A2MJ 
       81.99       103.13        15.25         5.75        94.19        63.25 
TCGA-EE-A2ML TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AD 
      104.78       227.01       143.93       124.31        64.04         4.41 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J4 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH 
       54.51         6.28       111.85         3.35       168.85        19.86 
TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D 
      135.98        34.45         4.54        53.29        39.81        11.47 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P 
      184.60       150.12        99.06        59.84        42.51       120.76 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NF 
       49.71        47.18        73.05        22.36         4.70        10.19 
TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A3YN 
       28.67       173.29        68.52        32.05        74.47         4.50 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FS-A1YW 
      174.21         4.14        26.20         5.65        10.06       171.78 
TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZJ TCGA-FS-A1ZQ 
       49.74         8.35       312.07        32.78        36.33       130.95 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ 
      136.27        35.28         4.47        23.21         5.29         3.06 
TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F9 TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
       30.90        66.67        13.28        19.30         9.90        18.25 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 
        1.91        53.29        96.92        42.48         7.59       120.53 
TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-GN-A9SD TCGA-LH-A9QB TCGA-QB-A6FS TCGA-RP-A690 
       34.49        46.92        59.41        85.05         7.23         0.20 
TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1Q TCGA-W3-AA1W 
        0.33       174.12         1.97       120.07        44.05       185.13 
TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT 
       92.84        47.54        65.42        12.69        21.90        10.95 
TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-XV-AB01 TCGA-YG-AA3O 
       48.39         1.94        37.32        24.99         6.61        28.21 
TCGA-Z2-AA3S 
       91.23 

  DEL PEAK 26(15Q13.3) MUTATED DEL PEAK 26(15Q13.3) WILD-TYPE 
                          0.76                           0.00 
  DEL PEAK 26(15Q13.3) MUTATED DEL PEAK 26(15Q13.3) WILD-TYPE 
                        297.01                         346.49 
  DEL PEAK 26(15Q13.3) MUTATED DEL PEAK 26(15Q13.3) WILD-TYPE 
                         53.26                          44.28 
[1] "0.8 - 297.0 (53.3)" "0.0 - 346.5 (44.3)"
[1] "hr=" "1.3"
D46V2, survival
                                sevent
clus2                              0   1
  DEL PEAK 26(15Q13.3) MUTATED    28  54
  DEL PEAK 26(15Q13.3) WILD-TYPE 138 138
  DEL PEAK 26(15Q13.3) MUTATED DEL PEAK 26(15Q13.3) WILD-TYPE 
                            82                            276 
  DEL PEAK 26(15Q13.3) MUTATED DEL PEAK 26(15Q13.3) WILD-TYPE 
                            54                            138 
$`DEL PEAK 26(15Q13.3) MUTATED`
TCGA-D3-A3ML TCGA-EB-A5SH TCGA-EE-A180 TCGA-EE-A29L TCGA-ER-A193 TCGA-3N-A9WD 
       13.87        54.02        94.98         2.60        31.40        12.99 
TCGA-D3-A1Q1 TCGA-D3-A1QB TCGA-D3-A2J7 TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3MU 
       16.57        95.74       103.10        58.06        86.93        39.75 
TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A8GC TCGA-D3-A8GN TCGA-D9-A148 
       63.81       135.75       137.92        79.59       161.00       151.53 
TCGA-D9-A1JX TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I1 
        7.10        77.56        76.57        36.03       144.89       222.51 
TCGA-DA-A1I8 TCGA-DA-A95Z TCGA-EB-A44R TCGA-EB-A5KH TCGA-EE-A17Z TCGA-EE-A29P 
       53.92        13.02        10.36        20.35         8.65        56.42 
TCGA-EE-A29Q TCGA-EE-A2A5 TCGA-EE-A2GH TCGA-EE-A2GP TCGA-EE-A2M5 TCGA-EE-A2MC 
       66.74        39.29       220.24        13.91        21.67        61.51 
TCGA-EE-A2MD TCGA-EE-A2MF TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2MM 
       47.28       268.73        16.96       204.66       180.39       167.90 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-EE-A3JA 
       71.21        53.26       122.73       172.18        64.08        53.19 
TCGA-EE-A3JE TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A2NE 
       51.35        13.94         9.17         8.88       148.18        20.15 
TCGA-ER-A3EV TCGA-FS-A1YX TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1ZE TCGA-FS-A1ZG 
       46.98        48.59       202.65        28.08        46.45         9.70 
TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A4F8 TCGA-FS-A4FB TCGA-FS-A4FD TCGA-FW-A3I3 
       23.93       101.26       174.84        26.73        80.68        17.46 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-GN-A264 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A26D 
       55.59        13.51       117.93        10.13        64.44        48.00 
TCGA-GN-A4U7 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL TCGA-OD-A75X TCGA-RP-A694 
       10.42        22.13        50.10        21.37       297.90         0.69 
TCGA-W3-AA1R TCGA-W3-AA1V TCGA-WE-A8JZ TCGA-WE-A8ZQ 
      111.09        42.08        24.03        63.22 

$`DEL PEAK 26(15Q13.3) WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A8GI TCGA-EB-A5SG TCGA-EE-A184 
       27.65        62.07        46.32        58.52        68.25        68.15 
TCGA-EE-A20H TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A198 
      168.26       340.14       126.81       134.40        27.35        50.76 
TCGA-FR-A729 TCGA-FS-A1ZF TCGA-FW-A3R5 TCGA-QB-AA9O TCGA-WE-A8K5 TCGA-WE-AAA3 
      220.80        15.45        36.95        18.05        61.15        21.40 
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-BF-AAP0 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
       17.03        66.48        14.93        16.67       112.04       112.57 
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A2J6 
       71.80       133.25        28.08        31.59        90.90        43.43 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
       65.49        23.77       115.53       168.00        86.76        11.87 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
      113.52        42.08        12.10       171.58        66.48        66.08 
TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3CF 
       59.57       130.72        46.98       166.52        60.23        24.53 
TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
        9.34       103.59        45.30       174.84        55.73        56.35 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GR 
      145.12        32.94        22.62        26.89       125.79       178.32 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GJ 
       18.18       125.19        30.84        23.61        26.43       241.38 
TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR 
      170.20        89.13       107.15       152.75        29.06       129.63 
TCGA-D3-A8GS TCGA-D3-A8GV TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1X3 TCGA-D9-A3Z1 
      117.17       167.70        54.67         3.65        18.12        15.39 
TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EG TCGA-DA-A1I0 
       22.29        18.44         9.90        25.18        22.95        20.38 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IB 
      176.55        35.93       135.02        88.87        65.92        40.60 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-DA-A95V 
       68.09        33.93        10.49       225.96        43.36        72.10 
TCGA-DA-A95W TCGA-DA-A95X TCGA-DA-A95Y TCGA-EB-A44Q TCGA-EB-A5UL TCGA-EB-A5UN 
       37.35        73.94        14.14        13.87        29.29        58.92 
TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A182 
        7.04        36.46        29.82        27.22        33.73        14.70 
TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I 
       26.89         4.96       133.81       151.27        91.56        13.55 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G 
       63.35        85.08        78.97        13.97        63.78        72.07 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T 
       64.64        56.84        18.61        14.47        61.28       369.93 
TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
       25.87       195.02        17.92        46.82       115.96        59.64 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GJ 
       86.14        59.28        67.43       173.79        48.72       107.38 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GR TCGA-EE-A2GS 
       54.74        79.66        75.48       102.12        42.77        81.21 
TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2ME 
       44.88        94.82       129.27        28.83        19.76       103.27 
TCGA-EE-A2MG TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ 
      103.20        96.23       216.66        47.54       248.65        43.23 
TCGA-EE-A2MS TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
      162.48       124.31        64.04        28.77        54.51        13.81 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J8 TCGA-EE-A3JB 
       41.59       138.81       127.20        36.95        34.32       201.80 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C 
      134.33       152.81        35.44        77.75        98.40        48.89 
TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J 
       12.59        13.02        26.37       302.07       152.35         6.44 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S 
      131.51        61.05        44.09       162.08        50.89        49.48 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH 
      105.07        43.82        23.34        28.83        48.99        41.56 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3PL TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A3YN 
      247.04        93.01        33.21        12.95       149.03        92.98 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC 
      174.21        15.72        27.85        18.77        38.27        34.82 
TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1Z7 
       36.26       104.42       216.92       228.59        20.91         7.79 
TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZH TCGA-FS-A1ZJ 
       27.72        48.85       357.37        53.52        32.75        47.38 
TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU 
       74.73       133.55        11.41       148.80        53.16        26.56 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 
       49.48        27.09        27.02        77.82        50.14        66.67 
TCGA-FS-A4F5 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
       28.73        34.03        54.41        19.30         9.90        19.43 
TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A268 TCGA-GN-A26A 
        2.04        15.78       139.89        96.92        62.79        32.48 
TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-GN-A9SD TCGA-HR-A2OG TCGA-HR-A2OH 
      121.91        39.35        48.89        59.41         0.23        65.88 
TCGA-LH-A9QB TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A825 
      368.78         7.23         0.20         0.33       228.16        63.02 
TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1Q TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 
      121.08         4.01        69.07       219.16       105.04        49.05 
TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-A8ZX 
       17.95       101.33        58.98        70.52        11.80        35.80 
TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-XV-AB01 TCGA-YD-A89C 
       49.51        12.16        40.41        24.99        13.25         6.90 
TCGA-YD-A9TA TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       49.18        37.94        14.43        27.58        96.99        15.98 

  DEL PEAK 26(15Q13.3) MUTATED DEL PEAK 26(15Q13.3) WILD-TYPE 
                          0.69                           0.20 
  DEL PEAK 26(15Q13.3) MUTATED DEL PEAK 26(15Q13.3) WILD-TYPE 
                        297.90                         369.93 
  DEL PEAK 26(15Q13.3) MUTATED DEL PEAK 26(15Q13.3) WILD-TYPE 
                        53.225                         50.825 
[1] "0.7 - 297.9 (53.2)" "0.2 - 369.9 (50.8)"
[1] "hr=" "1.4"
D46V3, continuous
                                vv
clus                             I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB
  DEL PEAK 26(15Q13.3) MUTATED          1       2      10        2        6
  DEL PEAK 26(15Q13.3) WILD-TYPE       12       5      19       16       22
                                vv
clus                             STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK 26(15Q13.3) MUTATED          5         2         4         6
  DEL PEAK 26(15Q13.3) WILD-TYPE       21        12        15         9
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 26(15Q13.3) MUTATED          12          5          8          9
  DEL PEAK 26(15Q13.3) WILD-TYPE        27         10         27         45
                                vv
clus                             STAGE IV
  DEL PEAK 26(15Q13.3) MUTATED          5
  DEL PEAK 26(15Q13.3) WILD-TYPE       16
D46V4, multiclass
            clus
vv           DEL PEAK 26(15Q13.3) MUTATED DEL PEAK 26(15Q13.3) WILD-TYPE
  I/II NOS                              1                             12
  STAGE 0                               2                              5
  STAGE I                              10                             19
  STAGE IA                              2                             16
  STAGE IB                              6                             22
  STAGE II                              5                             21
  STAGE IIA                             2                             12
  STAGE IIB                             4                             15
  STAGE IIC                             6                              9
  STAGE III                            12                             27
  STAGE IIIA                            5                             10
  STAGE IIIB                            8                             27
  STAGE IIIC                            9                             45
  STAGE IV                              5                             16
[1] 14  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  DEL PEAK 26(15Q13.3) MUTATED      14 19 12 23
  DEL PEAK 26(15Q13.3) WILD-TYPE    50 54 69 44
D46V5, multiclass
       clus
vv      DEL PEAK 26(15Q13.3) MUTATED DEL PEAK 26(15Q13.3) WILD-TYPE
  T0+T1                           14                             50
  T2                              19                             54
  T3                              12                             69
  T4                              23                             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  N3
  DEL PEAK 26(15Q13.3) MUTATED    43  12  10   9
  DEL PEAK 26(15Q13.3) WILD-TYPE 134  53  29  36
D46V6, multiclass
    clus
vv   DEL PEAK 26(15Q13.3) MUTATED DEL PEAK 26(15Q13.3) WILD-TYPE
  N0                           43                            134
  N1                           12                             53
  N2                           10                             29
  N3                            9                             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"
D46V7, binary
                                cls
clus                               0   1
  DEL PEAK 26(15Q13.3) MUTATED    72   6
  DEL PEAK 26(15Q13.3) WILD-TYPE 247  16
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(15Q13.3) MUTATED     72    6
  DEL PEAK 26(15Q13.3) WILD-TYPE  247   16
   clus
vv  DEL PEAK 26(15Q13.3) MUTATED DEL PEAK 26(15Q13.3) WILD-TYPE
  0                           72                            247
  1                            6                             16
[1] 2 2
[1] FALSE
D46V8, binary
                                cls
clus                               0   1
  DEL PEAK 26(15Q13.3) MUTATED    32  20
  DEL PEAK 26(15Q13.3) WILD-TYPE 102  70
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(15Q13.3) MUTATED     32   20
  DEL PEAK 26(15Q13.3) WILD-TYPE  102   70
     clus
vv    DEL PEAK 26(15Q13.3) MUTATED DEL PEAK 26(15Q13.3) WILD-TYPE
  NO                            32                            102
  YES                           20                             70
[1] 2 2
[1] FALSE
D46V9, binary
                                cls
clus                               0   1
  DEL PEAK 26(15Q13.3) MUTATED    10  74
  DEL PEAK 26(15Q13.3) WILD-TYPE  37 246
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(15Q13.3) MUTATED     10   74
  DEL PEAK 26(15Q13.3) WILD-TYPE   37  246
     clus
vv    DEL PEAK 26(15Q13.3) MUTATED DEL PEAK 26(15Q13.3) WILD-TYPE
  NO                            10                             37
  YES                           74                            246
[1] 2 2
[1] FALSE
D46V10, continuous
D46V11, binary
                                cls
clus                               0   1
  DEL PEAK 26(15Q13.3) MUTATED    29  55
  DEL PEAK 26(15Q13.3) WILD-TYPE 109 174
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(15Q13.3) MUTATED     29   55
  DEL PEAK 26(15Q13.3) WILD-TYPE  109  174
        clus
vv       DEL PEAK 26(15Q13.3) MUTATED DEL PEAK 26(15Q13.3) WILD-TYPE
  FEMALE                           29                            109
  MALE                             55                            174
[1] 2 2
[1] FALSE
D46V12, binary
                                cls
clus                               0   1
  DEL PEAK 26(15Q13.3) MUTATED    76   8
  DEL PEAK 26(15Q13.3) WILD-TYPE 243  39
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(15Q13.3) MUTATED     76    8
  DEL PEAK 26(15Q13.3) WILD-TYPE  243   39
     clus
vv    DEL PEAK 26(15Q13.3) MUTATED DEL PEAK 26(15Q13.3) WILD-TYPE
  NO                            76                            243
  YES                            8                             39
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 26(15Q13.3) MUTATED       2                         0    80
  DEL PEAK 26(15Q13.3) WILD-TYPE     3                         1   273
D46V13, multiclass
                           clus
vv                          DEL PEAK 26(15Q13.3) MUTATED
  ASIAN                                                2
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                               80
                           clus
vv                          DEL PEAK 26(15Q13.3) WILD-TYPE
  ASIAN                                                  3
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                273
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V14, binary
                                cls
clus                               0   1
  DEL PEAK 26(15Q13.3) MUTATED     0  83
  DEL PEAK 26(15Q13.3) WILD-TYPE   7 269
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(15Q13.3) MUTATED      0   83
  DEL PEAK 26(15Q13.3) WILD-TYPE    7  269
                        clus
vv                       DEL PEAK 26(15Q13.3) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           83
                        clus
vv                       DEL PEAK 26(15Q13.3) WILD-TYPE
  HISPANIC OR LATINO                                  7
  NOT HISPANIC OR LATINO                            269
[1] 2 2
[1] FALSE

Clustering(47) Variable = DEL PEAK 27(15Q21.1) MUTATION ANALYSIS
D47V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 27(15Q21.1) MUTATED    24  36
  DEL PEAK 27(15Q21.1) WILD-TYPE 104  88
  DEL PEAK 27(15Q21.1) MUTATED DEL PEAK 27(15Q21.1) WILD-TYPE 
                            60                            192 
  DEL PEAK 27(15Q21.1) MUTATED DEL PEAK 27(15Q21.1) WILD-TYPE 
                            36                             88 
$`DEL PEAK 27(15Q21.1) MUTATED`
TCGA-D3-A2JE TCGA-EE-A180 TCGA-ER-A193 TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1QB 
        9.76        31.96        19.04        12.99         8.42        62.60 
TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3MU TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A5GN 
       58.06        40.01        23.67        31.76        62.70        45.70 
TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1I1 TCGA-DA-A1IA 
       78.21        23.61        69.21        76.34        68.68        64.83 
TCGA-DA-A95V TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EE-A181 TCGA-EE-A183 
       72.10        12.30         3.91        16.41        20.38        26.24 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A2GH TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MI 
       27.16        61.12       201.60        23.77       209.79       171.85 
TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3J3 TCGA-EE-A3J7 
       89.26       145.45        53.26       122.73        67.89        45.90 
TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19C TCGA-ER-A19G TCGA-ER-A19W TCGA-ER-A3ET 
       10.49         7.82        39.81       184.60       146.63        68.52 
TCGA-ER-A3EV TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1ZG TCGA-FS-A1ZM TCGA-FS-A1ZT 
       15.48       195.98        27.62         7.82        78.61        35.28 
TCGA-FS-A4F8 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV TCGA-GN-A264 TCGA-GN-A267 
      173.19        80.68        55.59        11.54       117.93        17.06 
TCGA-GN-A26A TCGA-GN-A8LK TCGA-OD-A75X TCGA-W3-AA1R TCGA-W3-AA1V TCGA-WE-A8ZQ 
        7.59        43.23       297.01        79.99         8.09        62.89 

$`DEL PEAK 27(15Q21.1) WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A8GI TCGA-EB-A5SG TCGA-EE-A20H TCGA-EE-A2GD 
       62.07        38.76        13.41        33.24       166.75       269.03 
TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-FR-A729 TCGA-FW-A3R5 TCGA-WE-A8K5 
       52.90       134.40        27.35       216.43        36.95        52.73 
TCGA-WE-AAA3 TCGA-3N-A9WC TCGA-BF-AAP0 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
        7.40        60.46        14.83        15.72        31.89       110.93 
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A2J6 TCGA-D3-A2J7 
       49.35       133.25        19.04        76.41        25.64        45.99 
TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A2JH 
       62.86        15.75       168.00        86.30       107.61        36.30 
TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3CB TCGA-D3-A3CE 
      171.58        64.83        66.08        43.53       140.98        59.70 
TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51J 
       24.53         9.34        90.21       173.85        30.67       144.46 
TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D3-A8GJ TCGA-D3-A8GK 
       11.34        42.05       177.86       124.08       179.97       120.00 
TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GP TCGA-D3-A8GR TCGA-D9-A1X3 TCGA-D9-A3Z1 
       69.53        70.62       135.12        36.53        10.78        15.02 
TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6EG TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A1I5 
       16.90        18.44        22.85       138.67       150.61       110.53 
TCGA-DA-A1I7 TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-DA-A95W 
       60.10        58.85        30.44       225.11         8.71         0.76 
TCGA-DA-A95X TCGA-DA-A95Y TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
       65.03        14.14        52.41        18.21        13.15        24.89 
TCGA-EE-A182 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D 
        0.00        75.55        79.20        75.22        76.14        12.99 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29T TCGA-EE-A29W 
        0.26        44.28        47.41        47.74       346.49       185.19 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GJ 
      115.43        30.02        77.98        26.14        12.95        68.65 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR 
       10.62        32.48        18.35        93.63         0.76         0.20 
TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MG 
       71.31        81.99       103.13        15.25         5.75        94.19 
TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AA 
       63.25       104.78       227.01       143.93        23.51       124.31 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J4 TCGA-EE-A3J8 
       64.04         4.41        54.51         6.28       111.85         3.35 
TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A19A TCGA-ER-A19B 
      168.85        19.86       135.98        34.45         4.54        53.29 
TCGA-ER-A19D TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P 
       11.47       150.12        99.06        59.84        42.51       120.76 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
       49.71        47.18        73.05        22.36         4.70        16.87 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A3YN 
       10.19        28.67       173.29        32.05        74.47         4.50 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FS-A1YW 
      174.21         4.14        26.20         5.65        10.06       171.78 
TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZJ 
       49.74         8.35       312.07        32.78        43.92        36.33 
TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ 
      130.95       136.27         4.47        23.21         5.29         3.06 
TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F9 TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
       30.90        66.67        13.28        19.30         9.90        18.25 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A268 TCGA-GN-A4U3 TCGA-GN-A4U4 
        1.91        53.29        96.92        42.48       120.53        34.49 
TCGA-GN-A4U8 TCGA-GN-A9SD TCGA-LH-A9QB TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 
       46.92        59.41        85.05         7.23         0.20         0.33 
TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1Q TCGA-W3-AA1W TCGA-W3-AA21 
      174.12         1.97       120.07        44.05       185.13        92.84 
TCGA-WE-A8K1 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-A8ZY 
       47.54        65.42        12.69        21.90        10.95        48.39 
TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-XV-AB01 TCGA-YG-AA3O TCGA-Z2-AA3S 
        1.94        37.32        24.99         6.61        28.21        91.23 

  DEL PEAK 27(15Q21.1) MUTATED DEL PEAK 27(15Q21.1) WILD-TYPE 
                          3.91                           0.00 
  DEL PEAK 27(15Q21.1) MUTATED DEL PEAK 27(15Q21.1) WILD-TYPE 
                        297.01                         346.49 
  DEL PEAK 27(15Q21.1) MUTATED DEL PEAK 27(15Q21.1) WILD-TYPE 
                        49.580                         46.455 
[1] "3.9 - 297.0 (49.6)" "0.0 - 346.5 (46.5)"
[1] "hr=" "1.3"
D47V2, survival
                                sevent
clus2                              0   1
  DEL PEAK 27(15Q21.1) MUTATED    31  57
  DEL PEAK 27(15Q21.1) WILD-TYPE 135 135
  DEL PEAK 27(15Q21.1) MUTATED DEL PEAK 27(15Q21.1) WILD-TYPE 
                            88                            270 
  DEL PEAK 27(15Q21.1) MUTATED DEL PEAK 27(15Q21.1) WILD-TYPE 
                            57                            135 
$`DEL PEAK 27(15Q21.1) MUTATED`
TCGA-D3-A2JE TCGA-D3-A3ML TCGA-EB-A5SH TCGA-EE-A180 TCGA-EE-A29L TCGA-ER-A193 
       27.65        13.87        54.02        94.98         2.60        31.40 
TCGA-ER-A198 TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1QB TCGA-D3-A3C6 TCGA-D3-A3CC 
       50.76        12.99        16.57        95.74        58.06        86.93 
TCGA-D3-A3MU TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A8GC 
       39.75        32.94        63.81       135.75       137.92        79.59 
TCGA-D3-A8GD TCGA-D3-A8GN TCGA-D9-A148 TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW 
       23.61       161.00       151.53        77.56        76.57        36.03 
TCGA-DA-A1I1 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A95V TCGA-DA-A95Z TCGA-EB-A44Q 
      222.51        53.92        65.92        72.10        13.02        13.87 
TCGA-EB-A44R TCGA-EB-A5KH TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A29P 
       10.36        20.35         8.65        33.73        26.89        56.42 
TCGA-EE-A29Q TCGA-EE-A2A5 TCGA-EE-A2GH TCGA-EE-A2M5 TCGA-EE-A2MC TCGA-EE-A2MD 
       66.74        39.29       220.24        21.67        61.51        47.28 
TCGA-EE-A2MF TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MU 
      268.73        16.96       204.66       180.39       167.90        53.26 
TCGA-EE-A3AB TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-EE-A3JE TCGA-ER-A197 
      122.73       172.18        64.08        53.19        51.35        13.94 
TCGA-ER-A199 TCGA-ER-A19C TCGA-ER-A19G TCGA-ER-A19J TCGA-ER-A19T TCGA-ER-A19W 
        9.17        48.89       302.07         6.44         8.88       148.18 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-FR-A8YD TCGA-FS-A1YX TCGA-FS-A1Z0 TCGA-FS-A1Z4 
       93.01        46.98        36.26        48.59       202.65        28.08 
TCGA-FS-A1ZG TCGA-FS-A1ZM TCGA-FS-A1ZT TCGA-FS-A4F8 TCGA-FS-A4FD TCGA-FW-A3TU 
        9.70       101.26        53.16       174.84        80.68        55.59 
TCGA-FW-A3TV TCGA-GN-A264 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A26D 
       13.51       117.93        10.13        64.44        32.48        48.00 
TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL TCGA-HR-A2OH TCGA-OD-A75X TCGA-RP-A694 
       22.13        50.10        21.37        65.88       297.90         0.69 
TCGA-W3-AA1R TCGA-W3-AA1V TCGA-WE-A8JZ TCGA-WE-A8ZQ 
      111.09        42.08        24.03        63.22 

$`DEL PEAK 27(15Q21.1) WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A8GI TCGA-EB-A5SG TCGA-EE-A184 TCGA-EE-A20H 
       62.07        46.32        58.52        68.25        68.15       168.26 
TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-FR-A729 TCGA-FS-A1ZF 
      340.14       126.81       134.40        27.35       220.80        15.45 
TCGA-FW-A3R5 TCGA-QB-AA9O TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-3N-A9WB TCGA-3N-A9WC 
       36.95        18.05        61.15        21.40        17.03        66.48 
TCGA-BF-AAP0 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       14.93        16.67       112.04       112.57        71.80       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 
       28.08        31.59        90.90        43.43       103.10        65.49 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG 
       23.77       115.53       168.00        86.76        11.87       113.52 
TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP 
       42.08        12.10       171.58        66.48        66.08        59.57 
TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO 
      130.72        46.98       166.52        60.23        24.53         9.34 
TCGA-D3-A3MR TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
      103.59        45.30       174.84        55.73        56.35       145.12 
TCGA-D3-A51N TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU 
       22.62        26.89       125.79       178.32        18.18       125.19 
TCGA-D3-A8GB TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM 
       30.84        26.43       241.38       170.20        89.13       107.15 
TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D3-A8GV TCGA-D9-A149 
      152.75        29.06       129.63       117.17       167.70        54.67 
TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 
        3.65         7.10        18.12        15.39        22.29        18.44 
TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EG TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 
        9.90        25.18        22.95       144.89        20.38       176.55 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       35.93       135.02        88.87        40.60        68.09        33.93 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-DA-A95W TCGA-DA-A95X TCGA-DA-A95Y 
       10.49       225.96        43.36        37.35        73.94        14.14 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
       29.29        58.92         7.04        36.46        29.82        27.22 
TCGA-EE-A182 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I 
       14.70         4.96       133.81       151.27        91.56        13.55 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G 
       63.35        85.08        78.97        13.97        63.78        72.07 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T 
       64.64        56.84        18.61        14.47        61.28       369.93 
TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
       25.87       195.02        17.92        46.82       115.96        59.64 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GJ 
       86.14        59.28        67.43       173.79        48.72       107.38 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR 
       54.74        79.66        75.48       102.12        13.91        42.77 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
       81.21        44.88        94.82       129.27        28.83        19.76 
TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MP 
      103.27       103.20        96.23       216.66        47.54       248.65 
TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AD 
       43.23       162.48        71.21       124.31        64.04        28.77 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J5 
       54.51        13.81        41.59       138.81       127.20        36.95 
TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A19A 
       34.32       201.80       134.33       152.81        35.44        77.75 
TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19H TCGA-ER-A19L 
       98.40        12.59        13.02        26.37       152.35       131.51 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A1A1 
       61.05        44.09       162.08        50.89        49.48       105.07 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH 
       43.82        23.34        20.15        28.83        48.99        41.56 
TCGA-ER-A3ES TCGA-ER-A3PL TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A 
      247.04        33.21        12.95       149.03        92.98       174.21 
TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YE 
       15.72        27.85        18.77        38.27        34.82       104.42 
TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB 
      216.92       228.59        20.91         7.79        27.72        48.85 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK 
      357.37        53.52        46.45        32.75        47.38        23.93 
TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZW 
       74.73       133.55        11.41       148.80        26.56        49.48 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 
       27.09        27.02        77.82        50.14        66.67        28.73 
TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-FW-A5DY TCGA-GF-A3OT 
       34.03        26.73        54.41        17.46        19.30         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A268 
       19.43         2.04        15.78       139.89        96.92        62.79 
TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A9SD TCGA-HR-A2OG 
      121.91        39.35        10.42        48.89        59.41         0.23 
TCGA-LH-A9QB TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A825 
      368.78         7.23         0.20         0.33       228.16        63.02 
TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1Q TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 
      121.08         4.01        69.07       219.16       105.04        49.05 
TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-A8ZX 
       17.95       101.33        58.98        70.52        11.80        35.80 
TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-XV-AB01 TCGA-YD-A89C 
       49.51        12.16        40.41        24.99        13.25         6.90 
TCGA-YD-A9TA TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       49.18        37.94        14.43        27.58        96.99        15.98 

  DEL PEAK 27(15Q21.1) MUTATED DEL PEAK 27(15Q21.1) WILD-TYPE 
                          0.69                           0.20 
  DEL PEAK 27(15Q21.1) MUTATED DEL PEAK 27(15Q21.1) WILD-TYPE 
                        302.07                         369.93 
  DEL PEAK 27(15Q21.1) MUTATED DEL PEAK 27(15Q21.1) WILD-TYPE 
                        53.175                         50.515 
[1] "0.7 - 302.1 (53.2)" "0.2 - 369.9 (50.5)"
[1] "hr=" "1.3"
D47V3, continuous
                                vv
clus                             I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB
  DEL PEAK 27(15Q21.1) MUTATED          2       2      11        2        5
  DEL PEAK 27(15Q21.1) WILD-TYPE       11       5      18       16       23
                                vv
clus                             STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK 27(15Q21.1) MUTATED          5         2         4         7
  DEL PEAK 27(15Q21.1) WILD-TYPE       21        12        15         8
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 27(15Q21.1) MUTATED          11          7         10         10
  DEL PEAK 27(15Q21.1) WILD-TYPE        28          8         25         44
                                vv
clus                             STAGE IV
  DEL PEAK 27(15Q21.1) MUTATED          5
  DEL PEAK 27(15Q21.1) WILD-TYPE       16
D47V4, multiclass
            clus
vv           DEL PEAK 27(15Q21.1) MUTATED DEL PEAK 27(15Q21.1) WILD-TYPE
  I/II NOS                              2                             11
  STAGE 0                               2                              5
  STAGE I                              11                             18
  STAGE IA                              2                             16
  STAGE IB                              5                             23
  STAGE II                              5                             21
  STAGE IIA                             2                             12
  STAGE IIB                             4                             15
  STAGE IIC                             7                              8
  STAGE III                            11                             28
  STAGE IIIA                            7                              8
  STAGE IIIB                           10                             25
  STAGE IIIC                           10                             44
  STAGE IV                              5                             16
[1] 14  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  DEL PEAK 27(15Q21.1) MUTATED      14 18 15 23
  DEL PEAK 27(15Q21.1) WILD-TYPE    50 55 66 44
D47V5, multiclass
       clus
vv      DEL PEAK 27(15Q21.1) MUTATED DEL PEAK 27(15Q21.1) WILD-TYPE
  T0+T1                           14                             50
  T2                              18                             55
  T3                              15                             66
  T4                              23                             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  N3
  DEL PEAK 27(15Q21.1) MUTATED    44  12  12  12
  DEL PEAK 27(15Q21.1) WILD-TYPE 133  53  27  33
D47V6, multiclass
    clus
vv   DEL PEAK 27(15Q21.1) MUTATED DEL PEAK 27(15Q21.1) WILD-TYPE
  N0                           44                            133
  N1                           12                             53
  N2                           12                             27
  N3                           12                             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"
D47V7, binary
                                cls
clus                               0   1
  DEL PEAK 27(15Q21.1) MUTATED    78   6
  DEL PEAK 27(15Q21.1) WILD-TYPE 241  16
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(15Q21.1) MUTATED     78    6
  DEL PEAK 27(15Q21.1) WILD-TYPE  241   16
   clus
vv  DEL PEAK 27(15Q21.1) MUTATED DEL PEAK 27(15Q21.1) WILD-TYPE
  0                           78                            241
  1                            6                             16
[1] 2 2
[1] FALSE
D47V8, binary
                                cls
clus                               0   1
  DEL PEAK 27(15Q21.1) MUTATED    33  22
  DEL PEAK 27(15Q21.1) WILD-TYPE 101  68
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(15Q21.1) MUTATED     33   22
  DEL PEAK 27(15Q21.1) WILD-TYPE  101   68
     clus
vv    DEL PEAK 27(15Q21.1) MUTATED DEL PEAK 27(15Q21.1) WILD-TYPE
  NO                            33                            101
  YES                           22                             68
[1] 2 2
[1] FALSE
D47V9, binary
                                cls
clus                               0   1
  DEL PEAK 27(15Q21.1) MUTATED    10  81
  DEL PEAK 27(15Q21.1) WILD-TYPE  37 239
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(15Q21.1) MUTATED     10   81
  DEL PEAK 27(15Q21.1) WILD-TYPE   37  239
     clus
vv    DEL PEAK 27(15Q21.1) MUTATED DEL PEAK 27(15Q21.1) WILD-TYPE
  NO                            10                             37
  YES                           81                            239
[1] 2 2
[1] FALSE
D47V10, continuous
D47V11, binary
                                cls
clus                               0   1
  DEL PEAK 27(15Q21.1) MUTATED    37  54
  DEL PEAK 27(15Q21.1) WILD-TYPE 101 175
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(15Q21.1) MUTATED     37   54
  DEL PEAK 27(15Q21.1) WILD-TYPE  101  175
        clus
vv       DEL PEAK 27(15Q21.1) MUTATED DEL PEAK 27(15Q21.1) WILD-TYPE
  FEMALE                           37                            101
  MALE                             54                            175
[1] 2 2
[1] FALSE
D47V12, binary
                                cls
clus                               0   1
  DEL PEAK 27(15Q21.1) MUTATED    83   8
  DEL PEAK 27(15Q21.1) WILD-TYPE 236  39
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(15Q21.1) MUTATED     83    8
  DEL PEAK 27(15Q21.1) WILD-TYPE  236   39
     clus
vv    DEL PEAK 27(15Q21.1) MUTATED DEL PEAK 27(15Q21.1) WILD-TYPE
  NO                            83                            236
  YES                            8                             39
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 27(15Q21.1) MUTATED       3                         0    85
  DEL PEAK 27(15Q21.1) WILD-TYPE     2                         1   268
D47V13, multiclass
                           clus
vv                          DEL PEAK 27(15Q21.1) MUTATED
  ASIAN                                                3
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                               85
                           clus
vv                          DEL PEAK 27(15Q21.1) WILD-TYPE
  ASIAN                                                  2
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                268
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V14, binary
                                cls
clus                               0   1
  DEL PEAK 27(15Q21.1) MUTATED     1  88
  DEL PEAK 27(15Q21.1) WILD-TYPE   6 264
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(15Q21.1) MUTATED      1   88
  DEL PEAK 27(15Q21.1) WILD-TYPE    6  264
                        clus
vv                       DEL PEAK 27(15Q21.1) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           88
                        clus
vv                       DEL PEAK 27(15Q21.1) WILD-TYPE
  HISPANIC OR LATINO                                  6
  NOT HISPANIC OR LATINO                            264
[1] 2 2
[1] FALSE

Clustering(48) Variable = DEL PEAK 28(16P13.3) MUTATION ANALYSIS
D48V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 28(16P13.3) MUTATED    22  18
  DEL PEAK 28(16P13.3) WILD-TYPE 106 106
  DEL PEAK 28(16P13.3) MUTATED DEL PEAK 28(16P13.3) WILD-TYPE 
                            40                            212 
  DEL PEAK 28(16P13.3) MUTATED DEL PEAK 28(16P13.3) WILD-TYPE 
                            18                            106 
$`DEL PEAK 28(16P13.3) MUTATED`
TCGA-EE-A180 TCGA-EE-A2GO TCGA-ER-A193 TCGA-FW-A3R5 TCGA-WE-A8K5 TCGA-D3-A1Q4 
       31.96        52.90        19.04        36.95        52.73        31.89 
TCGA-D3-A1Q5 TCGA-D3-A1QA TCGA-D3-A2JB TCGA-D3-A2JL TCGA-D3-A2JO TCGA-D3-A3CC 
      110.93        76.41       168.00       171.58        66.08        40.01 
TCGA-D3-A51K TCGA-D3-A8GD TCGA-D3-A8GM TCGA-D9-A6EC TCGA-DA-A1I2 TCGA-DA-A95X 
       31.76        23.61        70.62        69.21       150.61        65.03 
TCGA-EE-A181 TCGA-EE-A29D TCGA-EE-A29M TCGA-EE-A29W TCGA-EE-A2GU TCGA-EE-A2M6 
       20.38        12.99        47.74       185.19        81.99       103.13 
TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3JI TCGA-ER-A197 
       89.26       145.45        53.26       122.73       135.98        10.49 
TCGA-FS-A1Z0 TCGA-FS-A1ZD TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FW-A3TU 
      195.98        32.78        35.28         4.47        23.21        55.59 
TCGA-GN-A262 TCGA-GN-A267 TCGA-GN-A4U3 TCGA-OD-A75X 
       53.29        17.06       120.53       297.01 

$`DEL PEAK 28(16P13.3) WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A8GI TCGA-EB-A5SG TCGA-EE-A20H 
        9.76        62.07        38.76        13.41        33.24       166.75 
TCGA-EE-A2GD TCGA-EE-A2MR TCGA-EE-A3JD TCGA-FR-A729 TCGA-WE-AAA3 TCGA-3N-A9WC 
      269.03       134.40        27.35       216.43         7.40        60.46 
TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       12.99        14.83         8.42        15.72        49.35       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA 
       19.04        62.60        25.64        45.99        62.86        15.75 
TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3C6 
       86.30       107.61        36.30        64.83        43.53        58.06 
TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU 
      140.98        59.70        24.53         9.34        90.21        23.67 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL 
      173.85        30.67       144.46        62.70        11.34        42.05 
TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D3-A8GC TCGA-D3-A8GJ TCGA-D3-A8GK 
       45.70       177.86       124.08        78.21       179.97       120.00 
TCGA-D3-A8GL TCGA-D3-A8GP TCGA-D3-A8GR TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       69.53       135.12        36.53        10.78        15.02        16.90 
TCGA-D9-A4Z6 TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I5 
       18.44        22.85        76.34       138.67        68.68       110.53 
TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 
       60.10        64.83        58.85        30.44       225.11         8.71 
TCGA-DA-A95V TCGA-DA-A95W TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5KH 
       72.10         0.76        14.14        12.30         3.91        16.41 
TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A182 TCGA-EE-A183 
       52.41        18.21        13.15        24.89         0.00        26.24 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G 
       75.55        79.20        75.22        76.14         0.26        44.28 
TCGA-EE-A29H TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A2A1 TCGA-EE-A2A2 
       47.41        27.16        61.12       346.49       115.43        30.02 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK 
       77.98        26.14        12.95       201.60        68.65        10.62 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
       32.48        18.35        93.63         0.76         0.20        71.31 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI 
       15.25         5.75        23.77       209.79        94.19       171.85 
TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AA 
       63.25       104.78       227.01       143.93        23.51       124.31 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 
       64.04         4.41        54.51         6.28        67.89       111.85 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH TCGA-ER-A195 TCGA-ER-A199 
       45.90         3.35       168.85        19.86        34.45         7.82 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19H 
        4.54        53.29        39.81        11.47       184.60       150.12 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S 
       99.06        59.84        42.51       120.76        49.71        47.18 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF 
      146.63        73.05        22.36         4.70        16.87        10.19 
TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42L 
       28.67       173.29        68.52        15.48        32.05        74.47 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FR-A8YC 
        4.50       174.21         4.14        26.20         5.65        10.06 
TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZE 
      171.78        49.74         8.35        27.62       312.07        43.92 
TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZY 
        7.82        36.33        78.61       130.95       136.27         5.29 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FD 
        3.06        30.90        66.67       173.19        13.28        80.68 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A264 
       11.54        19.30         9.90        18.25         1.91       117.93 
TCGA-GN-A265 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-GN-A8LK 
       96.92        42.48         7.59        34.49        46.92        43.23 
TCGA-GN-A9SD TCGA-LH-A9QB TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 TCGA-W3-A824 
       59.41        85.05         7.23         0.20         0.33       174.12 
TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1V TCGA-W3-AA1W 
        1.97       120.07        44.05        79.99         8.09       185.13 
TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ 
       92.84        47.54        65.42        12.69        21.90        62.89 
TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-XV-AB01 
       10.95        48.39         1.94        37.32        24.99         6.61 
TCGA-YG-AA3O TCGA-Z2-AA3S 
       28.21        91.23 

  DEL PEAK 28(16P13.3) MUTATED DEL PEAK 28(16P13.3) WILD-TYPE 
                          4.47                           0.00 
  DEL PEAK 28(16P13.3) MUTATED DEL PEAK 28(16P13.3) WILD-TYPE 
                        297.01                         346.49 
  DEL PEAK 28(16P13.3) MUTATED DEL PEAK 28(16P13.3) WILD-TYPE 
                        54.440                         43.985 
[1] "4.5 - 297.0 (54.4)" "0.0 - 346.5 (44.0)"
[1] "hr=" "1.4"
D48V2, survival
                                sevent
clus2                              0   1
  DEL PEAK 28(16P13.3) MUTATED    28  32
  DEL PEAK 28(16P13.3) WILD-TYPE 138 160
  DEL PEAK 28(16P13.3) MUTATED DEL PEAK 28(16P13.3) WILD-TYPE 
                            60                            298 
  DEL PEAK 28(16P13.3) MUTATED DEL PEAK 28(16P13.3) WILD-TYPE 
                            32                            160 
$`DEL PEAK 28(16P13.3) MUTATED`
TCGA-EE-A180 TCGA-EE-A29L TCGA-EE-A2GO TCGA-ER-A193 TCGA-FW-A3R5 TCGA-WE-A8K5 
       94.98         2.60       126.81        31.40        36.95        61.15 
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A2JB TCGA-D3-A2JL 
      112.04       112.57        31.59        90.90       168.00       171.58 
TCGA-D3-A2JO TCGA-D3-A3BZ TCGA-D3-A3CC TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A8GD 
       66.08       130.72        86.93        32.94        22.62        23.61 
TCGA-D3-A8GM TCGA-D9-A6EC TCGA-DA-A1HW TCGA-DA-A1I2 TCGA-DA-A95X TCGA-EB-A44R 
      107.15        77.56        36.03       176.55        73.94        10.36 
TCGA-EB-A5UL TCGA-EE-A181 TCGA-EE-A20I TCGA-EE-A29D TCGA-EE-A29M TCGA-EE-A29W 
       29.29        33.73        13.55        13.97        56.84       195.02 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2GC TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 
       17.92        46.82        67.43        94.82        21.67       129.27 
TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MQ TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3J5 
      180.39       167.90        43.23        53.26       122.73        36.95 
TCGA-EE-A3JA TCGA-EE-A3JI TCGA-ER-A197 TCGA-ER-A19E TCGA-ER-A19T TCGA-FS-A1Z0 
       53.19       152.81        13.94        13.02         8.88       202.65 
TCGA-FS-A1ZD TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FW-A3TU TCGA-GN-A262 
       53.52        53.16        26.56        49.48        55.59       139.89 
TCGA-GN-A267 TCGA-GN-A26D TCGA-GN-A4U3 TCGA-OD-A75X TCGA-YG-AA3P TCGA-Z2-A8RT 
       64.44        48.00       121.91       297.90        14.43        27.58 

$`DEL PEAK 28(16P13.3) WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-D3-A8GI TCGA-EB-A5SG 
       27.65        62.07        46.32        13.87        58.52        68.25 
TCGA-EB-A5SH TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A2GD TCGA-EE-A2MR TCGA-EE-A3JD 
       54.02        68.15       168.26       340.14       134.40        27.35 
TCGA-ER-A198 TCGA-FR-A729 TCGA-FS-A1ZF TCGA-QB-AA9O TCGA-WE-AAA3 TCGA-3N-A9WB 
       50.76       220.80        15.45        18.05        21.40        17.03 
TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q6 
       66.48        12.99        14.93        16.57        16.67        71.80 
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 
      133.25        28.08        95.74        43.43       103.10        65.49 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH 
       23.77       115.53        86.76        11.87       113.52        42.08 
TCGA-D3-A2JK TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CB 
       12.10        66.48        59.57        58.06        46.98       166.52 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV 
       60.23        24.53         9.34       103.59        39.75        45.30 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51R TCGA-D3-A51T 
      174.84        55.73        56.35       145.12        63.81        26.89 
TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU 
      125.79       135.75       137.92       178.32        18.18       125.19 
TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL 
       30.84        79.59        26.43       241.38       170.20        89.13 
TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D3-A8GV 
      161.00       152.75        29.06       129.63       117.17       167.70 
TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A1X3 TCGA-D9-A3Z1 
      151.53        54.67         3.65         7.10        18.12        15.39 
TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EG TCGA-DA-A1HV 
       22.29        18.44         9.90        25.18        22.95        76.57 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 
      144.89        20.38       222.51        35.93       135.02        88.87 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
       53.92        65.92        40.60        68.09        33.93        10.49 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-DA-A95V TCGA-DA-A95W TCGA-DA-A95Y TCGA-DA-A95Z 
      225.96        43.36        72.10        37.35        14.14        13.02 
TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X 
       13.87        20.35        58.92         7.04        36.46        29.82 
TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B 
       27.22         8.65        14.70        26.89         4.96       133.81 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E 
      151.27        91.56        63.35        85.08        78.97        63.78 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
       72.07        64.64        18.61        56.42        66.74        14.47 
TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 
       61.28       369.93        25.87       115.96        59.64        39.29 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       86.14        59.28       173.79       220.24        48.72       107.38 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR 
       54.74        79.66        75.48       102.12        13.91        42.77 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD 
       81.21        44.88        28.83        19.76        61.51        47.28 
TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ 
      103.27       268.73       103.20        16.96       204.66        96.23 
TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AA 
      216.66        47.54       248.65       162.48        71.21       124.31 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH 
       64.04        28.77        54.51        13.81        41.59       138.81 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JE 
      172.18       127.20        64.08        34.32       201.80        51.35 
TCGA-EE-A3JH TCGA-ER-A195 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C 
      134.33        35.44         9.17        77.75        98.40        48.89 
TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L 
       12.59        26.37       302.07       152.35         6.44       131.51 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W 
       61.05        44.09       162.08        50.89        49.48       148.18 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
      105.07        43.82        23.34        20.15        28.83        48.99 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K 
       41.56       247.04        93.01        46.98        33.21        12.95 
TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A7U9 
      149.03        92.98       174.21        15.72        27.85        18.77 
TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YX 
       38.27        34.82        36.26       104.42       216.92        48.59 
TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB 
      228.59        20.91        28.08         7.79        27.72        48.85 
TCGA-FS-A1ZC TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK 
      357.37        46.45         9.70        32.75        47.38        23.93 
TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZY 
      101.26        74.73       133.55        11.41       148.80        27.09 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 
       27.02        77.82        50.14        66.67        28.73       174.84 
TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TV 
       34.03        26.73        54.41        80.68        17.46        13.51 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A264 
       19.30         9.90        19.43         2.04        15.78       117.93 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U4 TCGA-GN-A4U7 
       96.92        10.13        62.79        32.48        39.35        10.42 
TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OG 
       48.89        22.13        50.10        21.37        59.41         0.23 
TCGA-HR-A2OH TCGA-LH-A9QB TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 TCGA-RP-A694 
       65.88       368.78         7.23         0.20         0.33         0.69 
TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1Q TCGA-W3-AA1R 
      228.16        63.02       121.08         4.01        69.07       111.09 
TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K6 
       42.08       219.16       105.04        24.03        49.05        17.95 
TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX 
      101.33        58.98        70.52        63.22        11.80        35.80 
TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-XV-AB01 TCGA-YD-A89C 
       49.51        12.16        40.41        24.99        13.25         6.90 
TCGA-YD-A9TA TCGA-YG-AA3O TCGA-Z2-AA3S TCGA-Z2-AA3V 
       49.18        37.94        96.99        15.98 

  DEL PEAK 28(16P13.3) MUTATED DEL PEAK 28(16P13.3) WILD-TYPE 
                           2.6                            0.2 
  DEL PEAK 28(16P13.3) MUTATED DEL PEAK 28(16P13.3) WILD-TYPE 
                        297.90                         369.93 
  DEL PEAK 28(16P13.3) MUTATED DEL PEAK 28(16P13.3) WILD-TYPE 
                        54.555                         50.120 
[1] "2.6 - 297.9 (54.6)" "0.2 - 369.9 (50.1)"
[1] "hr=" "1.1"
D48V3, continuous
                                vv
clus                             I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB
  DEL PEAK 28(16P13.3) MUTATED          3       2       4        3        6
  DEL PEAK 28(16P13.3) WILD-TYPE       10       5      25       15       22
                                vv
clus                             STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK 28(16P13.3) MUTATED          2         2         6         3
  DEL PEAK 28(16P13.3) WILD-TYPE       24        12        13        12
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 28(16P13.3) MUTATED           9          3          6          5
  DEL PEAK 28(16P13.3) WILD-TYPE        30         12         29         49
                                vv
clus                             STAGE IV
  DEL PEAK 28(16P13.3) MUTATED          5
  DEL PEAK 28(16P13.3) WILD-TYPE       16
D48V4, multiclass
            clus
vv           DEL PEAK 28(16P13.3) MUTATED DEL PEAK 28(16P13.3) WILD-TYPE
  I/II NOS                              3                             10
  STAGE 0                               2                              5
  STAGE I                               4                             25
  STAGE IA                              3                             15
  STAGE IB                              6                             22
  STAGE II                              2                             24
  STAGE IIA                             2                             12
  STAGE IIB                             6                             13
  STAGE IIC                             3                             12
  STAGE III                             9                             30
  STAGE IIIA                            3                             12
  STAGE IIIB                            6                             29
  STAGE IIIC                            5                             49
  STAGE IV                              5                             16
[1] 14  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  DEL PEAK 28(16P13.3) MUTATED       7 15 11 15
  DEL PEAK 28(16P13.3) WILD-TYPE    57 58 70 52
D48V5, multiclass
       clus
vv      DEL PEAK 28(16P13.3) MUTATED DEL PEAK 28(16P13.3) WILD-TYPE
  T0+T1                            7                             57
  T2                              15                             58
  T3                              11                             70
  T4                              15                             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  N3
  DEL PEAK 28(16P13.3) MUTATED    34  11   7   6
  DEL PEAK 28(16P13.3) WILD-TYPE 143  54  32  39
D48V6, multiclass
    clus
vv   DEL PEAK 28(16P13.3) MUTATED DEL PEAK 28(16P13.3) WILD-TYPE
  N0                           34                            143
  N1                           11                             54
  N2                            7                             32
  N3                            6                             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"
D48V7, binary
                                cls
clus                               0   1
  DEL PEAK 28(16P13.3) MUTATED    54   5
  DEL PEAK 28(16P13.3) WILD-TYPE 265  17
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 28(16P13.3) MUTATED     54    5
  DEL PEAK 28(16P13.3) WILD-TYPE  265   17
   clus
vv  DEL PEAK 28(16P13.3) MUTATED DEL PEAK 28(16P13.3) WILD-TYPE
  0                           54                            265
  1                            5                             17
[1] 2 2
[1] FALSE
D48V8, binary
                                cls
clus                               0   1
  DEL PEAK 28(16P13.3) MUTATED    27  17
  DEL PEAK 28(16P13.3) WILD-TYPE 107  73
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 28(16P13.3) MUTATED     27   17
  DEL PEAK 28(16P13.3) WILD-TYPE  107   73
     clus
vv    DEL PEAK 28(16P13.3) MUTATED DEL PEAK 28(16P13.3) WILD-TYPE
  NO                            27                            107
  YES                           17                             73
[1] 2 2
[1] FALSE
D48V9, binary
                                cls
clus                               0   1
  DEL PEAK 28(16P13.3) MUTATED     2  60
  DEL PEAK 28(16P13.3) WILD-TYPE  45 260
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 28(16P13.3) MUTATED      2   60
  DEL PEAK 28(16P13.3) WILD-TYPE   45  260
     clus
vv    DEL PEAK 28(16P13.3) MUTATED DEL PEAK 28(16P13.3) WILD-TYPE
  NO                             2                             45
  YES                           60                            260
[1] 2 2
[1] FALSE
D48V10, continuous
D48V11, binary
                                cls
clus                               0   1
  DEL PEAK 28(16P13.3) MUTATED    27  35
  DEL PEAK 28(16P13.3) WILD-TYPE 111 194
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 28(16P13.3) MUTATED     27   35
  DEL PEAK 28(16P13.3) WILD-TYPE  111  194
        clus
vv       DEL PEAK 28(16P13.3) MUTATED DEL PEAK 28(16P13.3) WILD-TYPE
  FEMALE                           27                            111
  MALE                             35                            194
[1] 2 2
[1] FALSE
D48V12, binary
                                cls
clus                               0   1
  DEL PEAK 28(16P13.3) MUTATED    54   8
  DEL PEAK 28(16P13.3) WILD-TYPE 265  39
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 28(16P13.3) MUTATED     54    8
  DEL PEAK 28(16P13.3) WILD-TYPE  265   39
     clus
vv    DEL PEAK 28(16P13.3) MUTATED DEL PEAK 28(16P13.3) WILD-TYPE
  NO                            54                            265
  YES                            8                             39
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 28(16P13.3) MUTATED       1                         1    59
  DEL PEAK 28(16P13.3) WILD-TYPE     4                         0   294
D48V13, multiclass
                           clus
vv                          DEL PEAK 28(16P13.3) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                               59
                           clus
vv                          DEL PEAK 28(16P13.3) WILD-TYPE
  ASIAN                                                  4
  BLACK OR AFRICAN AMERICAN                              0
  WHITE                                                294
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V14, binary
                                cls
clus                               0   1
  DEL PEAK 28(16P13.3) MUTATED     3  59
  DEL PEAK 28(16P13.3) WILD-TYPE   4 293
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 28(16P13.3) MUTATED      3   59
  DEL PEAK 28(16P13.3) WILD-TYPE    4  293
                        clus
vv                       DEL PEAK 28(16P13.3) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           59
                        clus
vv                       DEL PEAK 28(16P13.3) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            293
[1] 2 2
[1] FALSE

Clustering(49) Variable = DEL PEAK 29(16Q12.1) MUTATION ANALYSIS
D49V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 29(16Q12.1) MUTATED   38 37
  DEL PEAK 29(16Q12.1) WILD-TYPE 90 87
  DEL PEAK 29(16Q12.1) MUTATED DEL PEAK 29(16Q12.1) WILD-TYPE 
                            75                            177 
  DEL PEAK 29(16Q12.1) MUTATED DEL PEAK 29(16Q12.1) WILD-TYPE 
                            37                             87 
$`DEL PEAK 29(16Q12.1) MUTATED`
TCGA-D3-A2JF TCGA-D3-A8GI TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A2GO TCGA-ER-A193 
       62.07        13.41        33.24        31.96        52.90        19.04 
TCGA-FW-A3R5 TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 
       36.95        52.73         7.40        31.89       110.93       133.25 
TCGA-D3-A1QA TCGA-D3-A2J6 TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JL TCGA-D3-A2JN 
       76.41        25.64       168.00        86.30       171.58        64.83 
TCGA-D3-A2JO TCGA-D3-A3CC TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GM TCGA-D9-A3Z3 
       66.08        40.01        78.21        23.61        70.62        16.90 
TCGA-D9-A6EC TCGA-DA-A1I2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-DA-A95V TCGA-DA-A95X 
       69.21       150.61       225.11         8.71        72.10        65.03 
TCGA-EE-A181 TCGA-EE-A20C TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29M 
       20.38        75.55        75.22        76.14        12.99        47.74 
TCGA-EE-A29P TCGA-EE-A29W TCGA-EE-A2GH TCGA-EE-A2GP TCGA-EE-A2MJ TCGA-EE-A2MK 
       27.16       185.19       201.60         0.76        63.25        89.26 
TCGA-EE-A2MM TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AE TCGA-EE-A3AF 
      145.45       143.93        53.26       122.73        54.51         6.28 
TCGA-EE-A3J4 TCGA-EE-A3JI TCGA-ER-A197 TCGA-ER-A19B TCGA-ER-A19N TCGA-ER-A19W 
      111.85       135.98        10.49        53.29        42.51       146.63 
TCGA-ER-A42L TCGA-FS-A1Z0 TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A4F4 
       74.47       195.98        35.28         4.47        23.21        66.67 
TCGA-FW-A3TU TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A267 
       55.59        18.25         1.91        53.29       117.93        17.06 
TCGA-GN-A4U3 TCGA-GN-A8LK TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-W3-AA1R 
      120.53        43.23        85.05       297.01         7.23        79.99 
TCGA-WE-A8ZQ TCGA-YG-AA3O TCGA-Z2-AA3S 
       62.89        28.21        91.23 

$`DEL PEAK 29(16Q12.1) WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A3C8 TCGA-EE-A20H TCGA-EE-A2GD TCGA-EE-A2MR TCGA-EE-A3JD 
        9.76        38.76       166.75       269.03       134.40        27.35 
TCGA-FR-A729 TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 
      216.43        60.46        12.99        14.83         8.42        15.72 
TCGA-D3-A1Q6 TCGA-D3-A1Q8 TCGA-D3-A1QB TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA 
       49.35        19.04        62.60        45.99        62.86        15.75 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CE 
      107.61        36.30        43.53        58.06       140.98        59.70 
TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F 
       24.53         9.34        90.21        23.67       173.85        30.67 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN 
      144.46        31.76        62.70        11.34        42.05        45.70 
TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GP 
      177.86       124.08       179.97       120.00        69.53       135.12 
TCGA-D3-A8GR TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A4Z6 TCGA-D9-A6EG TCGA-DA-A1HV 
       36.53        10.78        15.02        18.44        22.85        76.34 
TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC 
      138.67        68.68       110.53        60.10        64.83        58.85 
TCGA-DA-A3F2 TCGA-DA-A95W TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5KH 
       30.44         0.76        14.14        12.30         3.91        16.41 
TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A182 TCGA-EE-A183 
       52.41        18.21        13.15        24.89         0.00        26.24 
TCGA-EE-A20F TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29Q TCGA-EE-A29T 
       79.20         0.26        44.28        47.41        61.12       346.49 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GJ 
      115.43        30.02        77.98        26.14        12.95        68.65 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GR TCGA-EE-A2GS 
       10.62        32.48        18.35        93.63         0.20        71.31 
TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MF 
       81.99       103.13        15.25         5.75        23.77       209.79 
TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2ML TCGA-EE-A2MP TCGA-EE-A2MT TCGA-EE-A3AA 
       94.19       171.85       104.78       227.01        23.51       124.31 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB 
       64.04         4.41        67.89        45.90         3.35       168.85 
TCGA-EE-A3JH TCGA-ER-A195 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19C TCGA-ER-A19D 
       19.86        34.45         7.82         4.54        39.81        11.47 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19P TCGA-ER-A19Q 
      184.60       150.12        99.06        59.84       120.76        49.71 
TCGA-ER-A19S TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF 
       47.18        73.05        22.36         4.70        16.87        10.19 
TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN 
       28.67       173.29        68.52        15.48        32.05         4.50 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FS-A1YW 
      174.21         4.14        26.20         5.65        10.06       171.78 
TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE 
       49.74         8.35        27.62       312.07        32.78        43.92 
TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZY 
        7.82        36.33        78.61       130.95       136.27         5.29 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TV 
        3.06        30.90       173.19        13.28        80.68        11.54 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GN-A265 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U4 
       19.30         9.90        96.92        42.48         7.59        34.49 
TCGA-GN-A4U8 TCGA-GN-A9SD TCGA-RP-A690 TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A825 
       46.92        59.41         0.20         0.33       174.12         1.97 
TCGA-W3-A828 TCGA-W3-AA1Q TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 
      120.07        44.05         8.09       185.13        92.84        47.54 
TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y 
       65.42        12.69        21.90        10.95        48.39         1.94 
TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-XV-AB01 
       37.32        24.99         6.61 

  DEL PEAK 29(16Q12.1) MUTATED DEL PEAK 29(16Q12.1) WILD-TYPE 
                          0.76                           0.00 
  DEL PEAK 29(16Q12.1) MUTATED DEL PEAK 29(16Q12.1) WILD-TYPE 
                        297.01                         346.49 
  DEL PEAK 29(16Q12.1) MUTATED DEL PEAK 29(16Q12.1) WILD-TYPE 
                         62.89                          39.81 
[1] "0.8 - 297.0 (62.9)" "0.0 - 346.5 (39.8)"
[1] "hr=" "1.2"
D49V2, survival
                                sevent
clus2                              0   1
  DEL PEAK 29(16Q12.1) MUTATED    50  64
  DEL PEAK 29(16Q12.1) WILD-TYPE 116 128
  DEL PEAK 29(16Q12.1) MUTATED DEL PEAK 29(16Q12.1) WILD-TYPE 
                           114                            244 
  DEL PEAK 29(16Q12.1) MUTATED DEL PEAK 29(16Q12.1) WILD-TYPE 
                            64                            128 
$`DEL PEAK 29(16Q12.1) MUTATED`
TCGA-D3-A2JF TCGA-D3-A8GI TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A29L TCGA-EE-A2GO 
       62.07        58.52        68.25        94.98         2.60       126.81 
TCGA-ER-A193 TCGA-FS-A1ZF TCGA-FW-A3R5 TCGA-QB-AA9O TCGA-WE-A8K5 TCGA-WE-AAA3 
       31.40        15.45        36.95        18.05        61.15        21.40 
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1QA TCGA-D3-A2J6 TCGA-D3-A2JB 
      112.04       112.57       133.25        90.90        43.43       168.00 
TCGA-D3-A2JC TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A3BZ TCGA-D3-A3CC 
       86.76       171.58        66.48        66.08       130.72        86.93 
TCGA-D3-A51N TCGA-D3-A5GS TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GM TCGA-D9-A148 
       22.62        18.18        79.59        23.61       107.15       151.53 
TCGA-D9-A149 TCGA-D9-A3Z3 TCGA-D9-A6EC TCGA-DA-A1HW TCGA-DA-A1I2 TCGA-DA-A1I4 
       54.67        22.29        77.56        36.03       176.55        35.93 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-DA-A95V TCGA-DA-A95X TCGA-EB-A44R TCGA-EB-A5UL 
      225.96        43.36        72.10        73.94        10.36        29.29 
TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20I TCGA-EE-A29B 
        8.65        33.73         4.96       151.27        13.55        85.08 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29W 
       78.97        13.97        56.84        18.61        56.42       195.02 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A5 TCGA-EE-A2GC TCGA-EE-A2GH TCGA-EE-A2GP 
       17.92        46.82        39.29        67.43       220.24        13.91 
TCGA-EE-A2M5 TCGA-EE-A2MD TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MN 
       21.67        47.28        96.23       180.39       167.90        47.54 
TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AE TCGA-EE-A3AF 
       43.23       162.48        53.26       122.73        54.51        13.81 
TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3JA TCGA-EE-A3JI TCGA-ER-A197 TCGA-ER-A19B 
      127.20        36.95        53.19       152.81        13.94        98.40 
TCGA-ER-A19E TCGA-ER-A19N TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A42L TCGA-FS-A1Z0 
       13.02        44.09         8.88       148.18       149.03       202.65 
TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZP TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW 
       27.72        48.85        74.73        53.16        26.56        49.48 
TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-GF-A4EO TCGA-GF-A6C8 
       50.14        66.67        17.46        55.59        19.43         2.04 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A8LK 
      139.89       117.93        64.44        48.00       121.91        50.10 
TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-W3-AA1O TCGA-W3-AA1R TCGA-WE-A8JZ 
      368.78       297.90         7.23         4.01       111.09        24.03 
TCGA-WE-A8ZQ TCGA-WE-A8ZX TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-AA3S TCGA-Z2-AA3V 
       63.22        35.80        37.94        14.43        96.99        15.98 

$`DEL PEAK 29(16Q12.1) WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SH TCGA-EE-A184 TCGA-EE-A20H 
       27.65        46.32        13.87        54.02        68.15       168.26 
TCGA-EE-A2GD TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A198 TCGA-FR-A729 TCGA-3N-A9WB 
      340.14       134.40        27.35        50.76       220.80        17.03 
TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q6 
       66.48        12.99        14.93        16.57        16.67        71.80 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QB TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 
       28.08        31.59        95.74       103.10        65.49        23.77 
TCGA-D3-A2JA TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JP 
      115.53        11.87       113.52        42.08        12.10        59.57 
TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO 
       58.06        46.98       166.52        60.23        24.53         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
      103.59        39.75        45.30       174.84        55.73        56.35 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN 
      145.12        32.94        63.81        26.89       125.79       135.75 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GE TCGA-D3-A8GJ 
      137.92       178.32       125.19        30.84        26.43       241.38 
TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR 
      170.20        89.13       161.00       152.75        29.06       129.63 
TCGA-D3-A8GS TCGA-D3-A8GV TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A1X3 TCGA-D9-A3Z1 
      117.17       167.70         3.65         7.10        18.12        15.39 
TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY 
       18.44         9.90        25.18        22.95        76.57       144.89 
TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA 
       20.38       222.51       135.02        88.87        53.92        65.92 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A95W TCGA-DA-A95Y 
       40.60        68.09        33.93        10.49        37.35        14.14 
TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 
       13.02        13.87        20.35        58.92         7.04        36.46 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20F 
       29.82        27.22        14.70        26.89       133.81        91.56 
TCGA-EE-A29A TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29Q TCGA-EE-A29R 
       63.35        63.78        72.07        64.64        66.74        14.47 
TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 
       61.28       369.93        25.87       115.96        59.64        86.14 
TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       59.28       173.79        48.72       107.38        54.74        79.66 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU 
       75.48       102.12        42.77        81.21        44.88        94.82 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2ME TCGA-EE-A2MF 
      129.27        28.83        19.76        61.51       103.27       268.73 
TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2ML TCGA-EE-A2MP TCGA-EE-A2MT 
      103.20        16.96       204.66       216.66       248.65        71.21 
TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 
      124.31        64.04        28.77        41.59       138.81       172.18 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A195 
       64.08        34.32       201.80        51.35       134.33        35.44 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19G 
        9.17        77.75        48.89        12.59        26.37       302.07 
TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19P TCGA-ER-A19Q 
      152.35         6.44       131.51        61.05       162.08        50.89 
TCGA-ER-A19S TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF 
       49.48       105.07        43.82        23.34        20.15        28.83 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL 
       48.99        41.56       247.04        93.01        46.98        33.21 
TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A7U9 
       12.95        92.98       174.21        15.72        27.85        18.77 
TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YX 
       38.27        34.82        36.26       104.42       216.92        48.59 
TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZC TCGA-FS-A1ZD 
      228.59        20.91        28.08         7.79       357.37        53.52 
TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM 
       46.45         9.70        32.75        47.38        23.93       101.26 
TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 
      133.55        11.41       148.80        27.09        27.02        77.82 
TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD 
       28.73       174.84        34.03        26.73        54.41        80.68 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C9 TCGA-GN-A265 TCGA-GN-A266 
       13.51        19.30         9.90        15.78        96.92        10.13 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A4U9 
       62.79        32.48        39.35        10.42        48.89        22.13 
TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OG TCGA-HR-A2OH TCGA-RP-A690 TCGA-RP-A693 
       21.37        59.41         0.23        65.88         0.20         0.33 
TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1Q TCGA-W3-AA1V 
        0.69       228.16        63.02       121.08        69.07        42.08 
TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN 
      219.16       105.04        49.05        17.95       101.33        58.98 
TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 
       70.52        11.80        49.51        12.16        40.41        24.99 
TCGA-XV-AB01 TCGA-YD-A89C TCGA-YD-A9TA TCGA-Z2-A8RT 
       13.25         6.90        49.18        27.58 

  DEL PEAK 29(16Q12.1) MUTATED DEL PEAK 29(16Q12.1) WILD-TYPE 
                          2.04                           0.20 
  DEL PEAK 29(16Q12.1) MUTATED DEL PEAK 29(16Q12.1) WILD-TYPE 
                        368.78                         369.93 
  DEL PEAK 29(16Q12.1) MUTATED DEL PEAK 29(16Q12.1) WILD-TYPE 
                        54.590                         49.495 
[1] "2.0 - 368.8 (54.6)" "0.2 - 369.9 (49.5)"
[1] "hr=" "1"  
D49V3, continuous
                                vv
clus                             I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB
  DEL PEAK 29(16Q12.1) MUTATED          4       3       6        7       10
  DEL PEAK 29(16Q12.1) WILD-TYPE        9       4      23       11       18
                                vv
clus                             STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK 29(16Q12.1) MUTATED         10         2         9         7
  DEL PEAK 29(16Q12.1) WILD-TYPE       16        12        10         8
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 29(16Q12.1) MUTATED          13          3         10         13
  DEL PEAK 29(16Q12.1) WILD-TYPE        26         12         25         41
                                vv
clus                             STAGE IV
  DEL PEAK 29(16Q12.1) MUTATED          7
  DEL PEAK 29(16Q12.1) WILD-TYPE       14
D49V4, multiclass
            clus
vv           DEL PEAK 29(16Q12.1) MUTATED DEL PEAK 29(16Q12.1) WILD-TYPE
  I/II NOS                              4                              9
  STAGE 0                               3                              4
  STAGE I                               6                             23
  STAGE IA                              7                             11
  STAGE IB                             10                             18
  STAGE II                             10                             16
  STAGE IIA                             2                             12
  STAGE IIB                             9                             10
  STAGE IIC                             7                              8
  STAGE III                            13                             26
  STAGE IIIA                            3                             12
  STAGE IIIB                           10                             25
  STAGE IIIC                           13                             41
  STAGE IV                              7                             14
[1] 14  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  DEL PEAK 29(16Q12.1) MUTATED      19 19 24 25
  DEL PEAK 29(16Q12.1) WILD-TYPE    45 54 57 42
D49V5, multiclass
       clus
vv      DEL PEAK 29(16Q12.1) MUTATED DEL PEAK 29(16Q12.1) WILD-TYPE
  T0+T1                           19                             45
  T2                              19                             54
  T3                              24                             57
  T4                              25                             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  N3
  DEL PEAK 29(16Q12.1) MUTATED    62  18  11  13
  DEL PEAK 29(16Q12.1) WILD-TYPE 115  47  28  32
D49V6, multiclass
    clus
vv   DEL PEAK 29(16Q12.1) MUTATED DEL PEAK 29(16Q12.1) WILD-TYPE
  N0                           62                            115
  N1                           18                             47
  N2                           11                             28
  N3                           13                             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"
D49V7, binary
                                cls
clus                               0   1
  DEL PEAK 29(16Q12.1) MUTATED    97   8
  DEL PEAK 29(16Q12.1) WILD-TYPE 222  14
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(16Q12.1) MUTATED     97    8
  DEL PEAK 29(16Q12.1) WILD-TYPE  222   14
   clus
vv  DEL PEAK 29(16Q12.1) MUTATED DEL PEAK 29(16Q12.1) WILD-TYPE
  0                           97                            222
  1                            8                             14
[1] 2 2
[1] FALSE
D49V8, binary
                                cls
clus                              0  1
  DEL PEAK 29(16Q12.1) MUTATED   49 30
  DEL PEAK 29(16Q12.1) WILD-TYPE 85 60
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(16Q12.1) MUTATED     49   30
  DEL PEAK 29(16Q12.1) WILD-TYPE   85   60
     clus
vv    DEL PEAK 29(16Q12.1) MUTATED DEL PEAK 29(16Q12.1) WILD-TYPE
  NO                            49                             85
  YES                           30                             60
[1] 2 2
[1] FALSE
D49V9, binary
                                cls
clus                               0   1
  DEL PEAK 29(16Q12.1) MUTATED    13 104
  DEL PEAK 29(16Q12.1) WILD-TYPE  34 216
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(16Q12.1) MUTATED     13  104
  DEL PEAK 29(16Q12.1) WILD-TYPE   34  216
     clus
vv    DEL PEAK 29(16Q12.1) MUTATED DEL PEAK 29(16Q12.1) WILD-TYPE
  NO                            13                             34
  YES                          104                            216
[1] 2 2
[1] FALSE
D49V10, continuous
D49V11, binary
                                cls
clus                               0   1
  DEL PEAK 29(16Q12.1) MUTATED    47  70
  DEL PEAK 29(16Q12.1) WILD-TYPE  91 159
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(16Q12.1) MUTATED     47   70
  DEL PEAK 29(16Q12.1) WILD-TYPE   91  159
        clus
vv       DEL PEAK 29(16Q12.1) MUTATED DEL PEAK 29(16Q12.1) WILD-TYPE
  FEMALE                           47                             91
  MALE                             70                            159
[1] 2 2
[1] FALSE
D49V12, binary
                                cls
clus                               0   1
  DEL PEAK 29(16Q12.1) MUTATED   101  16
  DEL PEAK 29(16Q12.1) WILD-TYPE 218  31
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(16Q12.1) MUTATED    101   16
  DEL PEAK 29(16Q12.1) WILD-TYPE  218   31
     clus
vv    DEL PEAK 29(16Q12.1) MUTATED DEL PEAK 29(16Q12.1) WILD-TYPE
  NO                           101                            218
  YES                           16                             31
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 29(16Q12.1) MUTATED       1                         1   111
  DEL PEAK 29(16Q12.1) WILD-TYPE     4                         0   242
D49V13, multiclass
                           clus
vv                          DEL PEAK 29(16Q12.1) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                              111
                           clus
vv                          DEL PEAK 29(16Q12.1) WILD-TYPE
  ASIAN                                                  4
  BLACK OR AFRICAN AMERICAN                              0
  WHITE                                                242
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V14, binary
                                cls
clus                               0   1
  DEL PEAK 29(16Q12.1) MUTATED     3 112
  DEL PEAK 29(16Q12.1) WILD-TYPE   4 240
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(16Q12.1) MUTATED      3  112
  DEL PEAK 29(16Q12.1) WILD-TYPE    4  240
                        clus
vv                       DEL PEAK 29(16Q12.1) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                          112
                        clus
vv                       DEL PEAK 29(16Q12.1) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            240
[1] 2 2
[1] FALSE

Clustering(50) Variable = DEL PEAK 30(16Q23.1) MUTATION ANALYSIS
D50V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 30(16Q23.1) MUTATED   40 41
  DEL PEAK 30(16Q23.1) WILD-TYPE 88 83
  DEL PEAK 30(16Q23.1) MUTATED DEL PEAK 30(16Q23.1) WILD-TYPE 
                            81                            171 
  DEL PEAK 30(16Q23.1) MUTATED DEL PEAK 30(16Q23.1) WILD-TYPE 
                            41                             83 
$`DEL PEAK 30(16Q23.1) MUTATED`
TCGA-D3-A2JF TCGA-D3-A8GI TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A2GO TCGA-ER-A193 
       62.07        13.41        33.24        31.96        52.90        19.04 
TCGA-FW-A3R5 TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 
       36.95        52.73         7.40        31.89       110.93       133.25 
TCGA-D3-A1QA TCGA-D3-A2J6 TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JL TCGA-D3-A2JN 
       76.41        25.64       168.00        86.30       171.58        64.83 
TCGA-D3-A2JO TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A8GD TCGA-D3-A8GM TCGA-D9-A3Z3 
       66.08        40.01        59.70        23.61        70.62        16.90 
TCGA-D9-A6EC TCGA-DA-A1I2 TCGA-DA-A3F8 TCGA-DA-A95V TCGA-DA-A95X TCGA-EE-A181 
       69.21       150.61         8.71        72.10        65.03        20.38 
TCGA-EE-A20C TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P 
       75.55        75.22        12.99        47.41        47.74        27.16 
TCGA-EE-A29W TCGA-EE-A2GH TCGA-EE-A2GP TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ 
      185.19       201.60         0.76        94.19       171.85        63.25 
TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AE TCGA-EE-A3AF 
       89.26       145.45        53.26       122.73        54.51         6.28 
TCGA-EE-A3J4 TCGA-EE-A3JI TCGA-ER-A197 TCGA-ER-A19B TCGA-ER-A19N TCGA-ER-A19Q 
      111.85       135.98        10.49        53.29        42.51        49.71 
TCGA-ER-A19W TCGA-ER-A2ND TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A7U8 TCGA-FR-A8YC 
      146.63         4.70        32.05        74.47        26.20        10.06 
TCGA-FS-A1Z0 TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A4F4 TCGA-FW-A3TU 
      195.98        35.28         4.47        23.21        66.67        55.59 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 
       18.25         1.91        53.29       117.93        17.06        42.48 
TCGA-GN-A4U3 TCGA-GN-A8LK TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A693 
      120.53        43.23        85.05       297.01         7.23         0.33 
TCGA-W3-AA1R TCGA-WE-A8ZQ TCGA-YG-AA3O 
       79.99        62.89        28.21 

$`DEL PEAK 30(16Q23.1) WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A3C8 TCGA-EE-A20H TCGA-EE-A2GD TCGA-EE-A2MR TCGA-EE-A3JD 
        9.76        38.76       166.75       269.03       134.40        27.35 
TCGA-FR-A729 TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 
      216.43        60.46        12.99        14.83         8.42        15.72 
TCGA-D3-A1Q6 TCGA-D3-A1Q8 TCGA-D3-A1QB TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA 
       49.35        19.04        62.60        45.99        62.86        15.75 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CF 
      107.61        36.30        43.53        58.06       140.98        24.53 
TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51J 
        9.34        90.21        23.67       173.85        30.67       144.46 
TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR 
       31.76        62.70        11.34        42.05        45.70       177.86 
TCGA-D3-A5GU TCGA-D3-A8GC TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GP 
      124.08        78.21       179.97       120.00        69.53       135.12 
TCGA-D3-A8GR TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A4Z6 TCGA-D9-A6EG TCGA-DA-A1HV 
       36.53        10.78        15.02        18.44        22.85        76.34 
TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC 
      138.67        68.68       110.53        60.10        64.83        58.85 
TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A95W TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q 
       30.44       225.11         0.76        14.14        12.30         3.91 
TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A182 
       16.41        52.41        18.21        13.15        24.89         0.00 
TCGA-EE-A183 TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29Q 
       26.24        79.20        76.14         0.26        44.28        61.12 
TCGA-EE-A29T TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE 
      346.49       115.43        30.02        77.98        26.14        12.95 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GR 
       68.65        10.62        32.48        18.35        93.63         0.20 
TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
       71.31        81.99       103.13        15.25         5.75        23.77 
TCGA-EE-A2MF TCGA-EE-A2ML TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AA 
      209.79       104.78       227.01       143.93        23.51       124.31 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB 
       64.04         4.41        67.89        45.90         3.35       168.85 
TCGA-EE-A3JH TCGA-ER-A195 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19C TCGA-ER-A19D 
       19.86        34.45         7.82         4.54        39.81        11.47 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19P TCGA-ER-A19S 
      184.60       150.12        99.06        59.84       120.76        47.18 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES 
       73.05        22.36        16.87        10.19        28.67       173.29 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7UA 
       68.52        15.48         4.50       174.21         4.14         5.65 
TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD 
      171.78        49.74         8.35        27.62       312.07        32.78 
TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS 
       43.92         7.82        36.33        78.61       130.95       136.27 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FD 
        5.29         3.06        30.90       173.19        13.28        80.68 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GN-A265 TCGA-GN-A26A TCGA-GN-A4U4 
       11.54        19.30         9.90        96.92         7.59        34.49 
TCGA-GN-A4U8 TCGA-GN-A9SD TCGA-RP-A690 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 
       46.92        59.41         0.20       174.12         1.97       120.07 
TCGA-W3-AA1Q TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8ZM 
       44.05         8.09       185.13        92.84        47.54        65.42 
TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 
       12.69        21.90        10.95        48.39         1.94        37.32 
TCGA-WE-AAA4 TCGA-XV-AB01 TCGA-Z2-AA3S 
       24.99         6.61        91.23 

  DEL PEAK 30(16Q23.1) MUTATED DEL PEAK 30(16Q23.1) WILD-TYPE 
                          0.33                           0.00 
  DEL PEAK 30(16Q23.1) MUTATED DEL PEAK 30(16Q23.1) WILD-TYPE 
                        297.01                         346.49 
  DEL PEAK 30(16Q23.1) MUTATED DEL PEAK 30(16Q23.1) WILD-TYPE 
                         53.29                          43.53 
[1] "0.3 - 297.0 (53.3)" "0.0 - 346.5 (43.5)"
[1] "hr=" "1"  
D50V2, survival
                                sevent
clus2                              0   1
  DEL PEAK 30(16Q23.1) MUTATED    52  65
  DEL PEAK 30(16Q23.1) WILD-TYPE 114 127
  DEL PEAK 30(16Q23.1) MUTATED DEL PEAK 30(16Q23.1) WILD-TYPE 
                           117                            241 
  DEL PEAK 30(16Q23.1) MUTATED DEL PEAK 30(16Q23.1) WILD-TYPE 
                            65                            127 
$`DEL PEAK 30(16Q23.1) MUTATED`
TCGA-D3-A2JF TCGA-D3-A8GI TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A2GO TCGA-ER-A193 
       62.07        58.52        68.25        94.98       126.81        31.40 
TCGA-FS-A1ZF TCGA-FW-A3R5 TCGA-QB-AA9O TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-D3-A1Q4 
       15.45        36.95        18.05        61.15        21.40       112.04 
TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1QA TCGA-D3-A2J6 TCGA-D3-A2JB TCGA-D3-A2JC 
      112.57       133.25        90.90        43.43       168.00        86.76 
TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A3BZ TCGA-D3-A3CC TCGA-D3-A3CE 
      171.58        66.48        66.08       130.72        86.93        60.23 
TCGA-D3-A51N TCGA-D3-A8GD TCGA-D3-A8GM TCGA-D3-A8GS TCGA-D3-A8GV TCGA-D9-A148 
       22.62        23.61       107.15       117.17       167.70       151.53 
TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A3Z3 TCGA-D9-A6EC TCGA-DA-A1HW TCGA-DA-A1I2 
       54.67         3.65        22.29        77.56        36.03       176.55 
TCGA-DA-A1I4 TCGA-DA-A3F8 TCGA-DA-A95V TCGA-DA-A95X TCGA-EB-A44R TCGA-EB-A5UL 
       35.93        43.36        72.10        73.94        10.36        29.29 
TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20I TCGA-EE-A29B 
        8.65        33.73         4.96       151.27        13.55        85.08 
TCGA-EE-A29D TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29W TCGA-EE-A29X 
       13.97        64.64        56.84        56.42       195.02        17.92 
TCGA-EE-A2A0 TCGA-EE-A2A5 TCGA-EE-A2GC TCGA-EE-A2GH TCGA-EE-A2GP TCGA-EE-A2M5 
       46.82        39.29        67.43       220.24        13.91        21.67 
TCGA-EE-A2MD TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2MM 
       47.28       103.20       204.66        96.23       180.39       167.90 
TCGA-EE-A2MQ TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J4 
       43.23        53.26       122.73        54.51        13.81       127.20 
TCGA-EE-A3J5 TCGA-EE-A3JA TCGA-EE-A3JI TCGA-ER-A197 TCGA-ER-A19B TCGA-ER-A19F 
       36.95        53.19       152.81        13.94        98.40        26.37 
TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A2ND TCGA-ER-A3PL 
       44.09        50.89         8.88       148.18        23.34        33.21 
TCGA-ER-A42L TCGA-FR-A7U8 TCGA-FR-A8YC TCGA-FS-A1Z0 TCGA-FS-A1ZB TCGA-FS-A1ZP 
      149.03        27.85        34.82       202.65        48.85        74.73 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FW-A3I3 
       53.16        26.56        49.48        50.14        66.67        17.46 
TCGA-FW-A3TU TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A267 
       55.59        19.43         2.04       139.89       117.93        64.44 
TCGA-GN-A268 TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A8LK TCGA-LH-A9QB TCGA-OD-A75X 
       62.79        48.00       121.91        50.10       368.78       297.90 
TCGA-QB-A6FS TCGA-RP-A693 TCGA-W3-AA1R TCGA-WE-A8JZ TCGA-WE-A8ZQ TCGA-WE-A8ZX 
        7.23         0.33       111.09        24.03        63.22        35.80 
TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-AA3V 
       37.94        14.43        15.98 

$`DEL PEAK 30(16Q23.1) WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SH TCGA-EE-A184 TCGA-EE-A20H 
       27.65        46.32        13.87        54.02        68.15       168.26 
TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A198 TCGA-FR-A729 
        2.60       340.14       134.40        27.35        50.76       220.80 
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 
       17.03        66.48        12.99        14.93        16.57        16.67 
TCGA-D3-A1Q6 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QB TCGA-D3-A2J7 TCGA-D3-A2J8 
       71.80        28.08        31.59        95.74       103.10        65.49 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK 
       23.77       115.53        11.87       113.52        42.08        12.10 
TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CF TCGA-D3-A3MO 
       59.57        58.06        46.98       166.52        24.53         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
      103.59        39.75        45.30       174.84        55.73        56.35 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN 
      145.12        32.94        63.81        26.89       125.79       135.75 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GC 
      137.92       178.32        18.18       125.19        30.84        79.59 
TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GN TCGA-D3-A8GP 
       26.43       241.38       170.20        89.13       161.00       152.75 
TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D9-A1JX TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A4Z6 
       29.06       129.63         7.10        18.12        15.39        18.44 
TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I0 
        9.90        25.18        22.95        76.57       144.89        20.38 
TCGA-DA-A1I1 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
      222.51       135.02        88.87        53.92        65.92        40.60 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A95W TCGA-DA-A95Y 
       68.09        33.93        10.49       225.96        37.35        14.14 
TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 
       13.02        13.87        20.35        58.92         7.04        36.46 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20F 
       29.82        27.22        14.70        26.89       133.81        91.56 
TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29N TCGA-EE-A29Q 
       63.35        78.97        63.78        72.07        18.61        66.74 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A2A1 TCGA-EE-A2A2 
       14.47        61.28       369.93        25.87       115.96        59.64 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
       86.14        59.28       173.79        48.72       107.38        54.74 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT 
       79.66        75.48       102.12        42.77        81.21        44.88 
TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2ME 
       94.82       129.27        28.83        19.76        61.51       103.27 
TCGA-EE-A2MF TCGA-EE-A2MH TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MS 
      268.73        16.96       216.66        47.54       248.65       162.48 
TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AG TCGA-EE-A3AH 
       71.21       124.31        64.04        28.77        41.59       138.81 
TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JE TCGA-EE-A3JH 
      172.18        64.08        34.32       201.80        51.35       134.33 
TCGA-ER-A195 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E 
       35.44         9.17        77.75        48.89        12.59        13.02 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19P 
      302.07       152.35         6.44       131.51        61.05       162.08 
TCGA-ER-A19S TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
       49.48       105.07        43.82        20.15        28.83        48.99 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A42K TCGA-FR-A3YN 
       41.56       247.04        93.01        46.98        12.95        92.98 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YD TCGA-FR-A8YE 
      174.21        15.72        18.77        38.27        36.26       104.42 
TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 
      216.92        48.59       228.59        20.91        28.08         7.79 
TCGA-FS-A1ZA TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZH 
       27.72       357.37        53.52        46.45         9.70        32.75 
TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS 
       47.38        23.93       101.26       133.55        11.41       148.80 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 
       27.09        27.02        77.82        28.73       174.84        34.03 
TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
       26.73        54.41        80.68        13.51        19.30         9.90 
TCGA-GF-A6C9 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A26A TCGA-GN-A4U4 TCGA-GN-A4U7 
       15.78        96.92        10.13        32.48        39.35        10.42 
TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OG TCGA-HR-A2OH 
       48.89        22.13        21.37        59.41         0.23        65.88 
TCGA-RP-A690 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O 
        0.20         0.69       228.16        63.02       121.08         4.01 
TCGA-W3-AA1Q TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K6 
       69.07        42.08       219.16       105.04        49.05        17.95 
TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y 
      101.33        58.98        70.52        11.80        49.51        12.16 
TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-XV-AB01 TCGA-YD-A89C TCGA-YD-A9TA TCGA-Z2-A8RT 
       40.41        24.99        13.25         6.90        49.18        27.58 
TCGA-Z2-AA3S 
       96.99 

  DEL PEAK 30(16Q23.1) MUTATED DEL PEAK 30(16Q23.1) WILD-TYPE 
                          0.33                           0.20 
  DEL PEAK 30(16Q23.1) MUTATED DEL PEAK 30(16Q23.1) WILD-TYPE 
                        368.78                         369.93 
  DEL PEAK 30(16Q23.1) MUTATED DEL PEAK 30(16Q23.1) WILD-TYPE 
                         54.67                          49.18 
[1] "0.3 - 368.8 (54.7)" "0.2 - 369.9 (49.2)"
[1] "hr=" "1"  
D50V3, continuous
                                vv
clus                             I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB
  DEL PEAK 30(16Q23.1) MUTATED          4       3       6        7        8
  DEL PEAK 30(16Q23.1) WILD-TYPE        9       4      23       11       20
                                vv
clus                             STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK 30(16Q23.1) MUTATED          9         2        12         7
  DEL PEAK 30(16Q23.1) WILD-TYPE       17        12         7         8
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 30(16Q23.1) MUTATED          13          3          9         13
  DEL PEAK 30(16Q23.1) WILD-TYPE        26         12         26         41
                                vv
clus                             STAGE IV
  DEL PEAK 30(16Q23.1) MUTATED          8
  DEL PEAK 30(16Q23.1) WILD-TYPE       13
D50V4, multiclass
            clus
vv           DEL PEAK 30(16Q23.1) MUTATED DEL PEAK 30(16Q23.1) WILD-TYPE
  I/II NOS                              4                              9
  STAGE 0                               3                              4
  STAGE I                               6                             23
  STAGE IA                              7                             11
  STAGE IB                              8                             20
  STAGE II                              9                             17
  STAGE IIA                             2                             12
  STAGE IIB                            12                              7
  STAGE IIC                             7                              8
  STAGE III                            13                             26
  STAGE IIIA                            3                             12
  STAGE IIIB                            9                             26
  STAGE IIIC                           13                             41
  STAGE IV                              8                             13
[1] 14  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  DEL PEAK 30(16Q23.1) MUTATED      21 17 25 25
  DEL PEAK 30(16Q23.1) WILD-TYPE    43 56 56 42
D50V5, multiclass
       clus
vv      DEL PEAK 30(16Q23.1) MUTATED DEL PEAK 30(16Q23.1) WILD-TYPE
  T0+T1                           21                             43
  T2                              17                             56
  T3                              25                             56
  T4                              25                             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  N3
  DEL PEAK 30(16Q23.1) MUTATED    65  18  10  13
  DEL PEAK 30(16Q23.1) WILD-TYPE 112  47  29  32
D50V6, multiclass
    clus
vv   DEL PEAK 30(16Q23.1) MUTATED DEL PEAK 30(16Q23.1) WILD-TYPE
  N0                           65                            112
  N1                           18                             47
  N2                           10                             29
  N3                           13                             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"
D50V7, binary
                                cls
clus                               0   1
  DEL PEAK 30(16Q23.1) MUTATED    99   9
  DEL PEAK 30(16Q23.1) WILD-TYPE 220  13
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(16Q23.1) MUTATED     99    9
  DEL PEAK 30(16Q23.1) WILD-TYPE  220   13
   clus
vv  DEL PEAK 30(16Q23.1) MUTATED DEL PEAK 30(16Q23.1) WILD-TYPE
  0                           99                            220
  1                            9                             13
[1] 2 2
[1] FALSE
D50V8, binary
                                cls
clus                              0  1
  DEL PEAK 30(16Q23.1) MUTATED   48 30
  DEL PEAK 30(16Q23.1) WILD-TYPE 86 60
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(16Q23.1) MUTATED     48   30
  DEL PEAK 30(16Q23.1) WILD-TYPE   86   60
     clus
vv    DEL PEAK 30(16Q23.1) MUTATED DEL PEAK 30(16Q23.1) WILD-TYPE
  NO                            48                             86
  YES                           30                             60
[1] 2 2
[1] FALSE
D50V9, binary
                                cls
clus                               0   1
  DEL PEAK 30(16Q23.1) MUTATED    14 106
  DEL PEAK 30(16Q23.1) WILD-TYPE  33 214
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(16Q23.1) MUTATED     14  106
  DEL PEAK 30(16Q23.1) WILD-TYPE   33  214
     clus
vv    DEL PEAK 30(16Q23.1) MUTATED DEL PEAK 30(16Q23.1) WILD-TYPE
  NO                            14                             33
  YES                          106                            214
[1] 2 2
[1] FALSE
D50V10, continuous
D50V11, binary
                                cls
clus                               0   1
  DEL PEAK 30(16Q23.1) MUTATED    50  70
  DEL PEAK 30(16Q23.1) WILD-TYPE  88 159
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(16Q23.1) MUTATED     50   70
  DEL PEAK 30(16Q23.1) WILD-TYPE   88  159
        clus
vv       DEL PEAK 30(16Q23.1) MUTATED DEL PEAK 30(16Q23.1) WILD-TYPE
  FEMALE                           50                             88
  MALE                             70                            159
[1] 2 2
[1] FALSE
D50V12, binary
                                cls
clus                               0   1
  DEL PEAK 30(16Q23.1) MUTATED   105  15
  DEL PEAK 30(16Q23.1) WILD-TYPE 214  32
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(16Q23.1) MUTATED    105   15
  DEL PEAK 30(16Q23.1) WILD-TYPE  214   32
     clus
vv    DEL PEAK 30(16Q23.1) MUTATED DEL PEAK 30(16Q23.1) WILD-TYPE
  NO                           105                            214
  YES                           15                             32
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 30(16Q23.1) MUTATED       1                         1   114
  DEL PEAK 30(16Q23.1) WILD-TYPE     4                         0   239
D50V13, multiclass
                           clus
vv                          DEL PEAK 30(16Q23.1) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                              114
                           clus
vv                          DEL PEAK 30(16Q23.1) WILD-TYPE
  ASIAN                                                  4
  BLACK OR AFRICAN AMERICAN                              0
  WHITE                                                239
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V14, binary
                                cls
clus                               0   1
  DEL PEAK 30(16Q23.1) MUTATED     3 115
  DEL PEAK 30(16Q23.1) WILD-TYPE   4 237
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(16Q23.1) MUTATED      3  115
  DEL PEAK 30(16Q23.1) WILD-TYPE    4  237
                        clus
vv                       DEL PEAK 30(16Q23.1) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                          115
                        clus
vv                       DEL PEAK 30(16Q23.1) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            237
[1] 2 2
[1] FALSE

Clustering(51) Variable = DEL PEAK 31(16Q24.3) MUTATION ANALYSIS
D51V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 31(16Q24.3) MUTATED   46 44
  DEL PEAK 31(16Q24.3) WILD-TYPE 82 80
  DEL PEAK 31(16Q24.3) MUTATED DEL PEAK 31(16Q24.3) WILD-TYPE 
                            90                            162 
  DEL PEAK 31(16Q24.3) MUTATED DEL PEAK 31(16Q24.3) WILD-TYPE 
                            44                             80 
$`DEL PEAK 31(16Q24.3) MUTATED`
TCGA-D3-A2JF TCGA-D3-A8GI TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A2GO TCGA-ER-A193 
       62.07        13.41        33.24        31.96        52.90        19.04 
TCGA-FW-A3R5 TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 
       36.95        52.73         7.40        31.89       110.93       133.25 
TCGA-D3-A1QA TCGA-D3-A2J6 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JL 
       76.41        25.64        15.75       168.00        86.30       171.58 
TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3MU TCGA-D3-A8GC 
       64.83        66.08        40.01        59.70        23.67        78.21 
TCGA-D3-A8GD TCGA-D3-A8GJ TCGA-D3-A8GM TCGA-D9-A3Z3 TCGA-D9-A6EC TCGA-DA-A1I2 
       23.61       179.97        70.62        16.90        69.21       150.61 
TCGA-DA-A3F8 TCGA-DA-A95V TCGA-DA-A95X TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A20C 
        8.71        72.10        65.03        20.38        26.24        75.55 
TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29W 
       75.22        12.99        47.41        47.74        27.16       185.19 
TCGA-EE-A2GH TCGA-EE-A2GP TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
      201.60         0.76        94.19       171.85        63.25        89.26 
TCGA-EE-A2MM TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J4 
      145.45        53.26       122.73        54.51         6.28       111.85 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A197 TCGA-ER-A19B TCGA-ER-A19N TCGA-ER-A19Q 
       19.86       135.98        10.49        53.29        42.51        49.71 
TCGA-ER-A19W TCGA-ER-A2ND TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A7U8 TCGA-FR-A8YC 
      146.63         4.70        32.05        74.47        26.20        10.06 
TCGA-FS-A1Z0 TCGA-FS-A1ZJ TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
      195.98        36.33        35.28         4.47        23.21         5.29 
TCGA-FS-A4F4 TCGA-FW-A3TU TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A267 
       66.67        55.59        18.25         1.91        53.29        17.06 
TCGA-GN-A268 TCGA-GN-A4U3 TCGA-GN-A8LK TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS 
       42.48       120.53        43.23        85.05       297.01         7.23 
TCGA-RP-A693 TCGA-W3-AA1R TCGA-WE-A8K1 TCGA-WE-A8ZQ TCGA-YG-AA3O TCGA-Z2-AA3S 
        0.33        79.99        47.54        62.89        28.21        91.23 

$`DEL PEAK 31(16Q24.3) WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A3C8 TCGA-EE-A20H TCGA-EE-A2GD TCGA-EE-A2MR TCGA-EE-A3JD 
        9.76        38.76       166.75       269.03       134.40        27.35 
TCGA-FR-A729 TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 
      216.43        60.46        12.99        14.83         8.42        15.72 
TCGA-D3-A1Q6 TCGA-D3-A1Q8 TCGA-D3-A1QB TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JG 
       49.35        19.04        62.60        45.99        62.86       107.61 
TCGA-D3-A2JH TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CF TCGA-D3-A3MO 
       36.30        43.53        58.06       140.98        24.53         9.34 
TCGA-D3-A3MR TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R 
       90.21       173.85        30.67       144.46        31.76        62.70 
TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D3-A8GK 
       11.34        42.05        45.70       177.86       124.08       120.00 
TCGA-D3-A8GL TCGA-D3-A8GP TCGA-D3-A8GR TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A4Z6 
       69.53       135.12        36.53        10.78        15.02        18.44 
TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I5 TCGA-DA-A1I7 
       22.85        76.34       138.67        68.68       110.53        60.10 
TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A95W TCGA-DA-A95Y 
       64.83        58.85        30.44       225.11         0.76        14.14 
TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X 
       12.30         3.91        16.41        52.41        18.21        13.15 
TCGA-EE-A17Y TCGA-EE-A182 TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G 
       24.89         0.00        79.20        76.14         0.26        44.28 
TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB 
       61.12       346.49       115.43        30.02        77.98        26.14 
TCGA-EE-A2GE TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
       12.95        68.65        10.62        32.48        18.35        93.63 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
        0.20        71.31        81.99       103.13        15.25         5.75 
TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2ML TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT 
       23.77       209.79       104.78       227.01       143.93        23.51 
TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-EE-A3J8 
      124.31        64.04         4.41        67.89        45.90         3.35 
TCGA-EE-A3JB TCGA-ER-A195 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19C TCGA-ER-A19D 
      168.85        34.45         7.82         4.54        39.81        11.47 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19P TCGA-ER-A19S 
      184.60       150.12        99.06        59.84       120.76        47.18 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES 
       73.05        22.36        16.87        10.19        28.67       173.29 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7UA 
       68.52        15.48         4.50       174.21         4.14         5.65 
TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD 
      171.78        49.74         8.35        27.62       312.07        32.78 
TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZZ 
       43.92         7.82        78.61       130.95       136.27         3.06 
TCGA-FS-A4F0 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TV TCGA-FW-A5DY 
       30.90       173.19        13.28        80.68        11.54        19.30 
TCGA-GF-A3OT TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A26A TCGA-GN-A4U4 TCGA-GN-A4U8 
        9.90       117.93        96.92         7.59        34.49        46.92 
TCGA-GN-A9SD TCGA-RP-A690 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1Q 
       59.41         0.20       174.12         1.97       120.07        44.05 
TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO 
        8.09       185.13        92.84        65.42        12.69        21.90 
TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-XV-AB01 
       10.95        48.39         1.94        37.32        24.99         6.61 

  DEL PEAK 31(16Q24.3) MUTATED DEL PEAK 31(16Q24.3) WILD-TYPE 
                          0.33                           0.00 
  DEL PEAK 31(16Q24.3) MUTATED DEL PEAK 31(16Q24.3) WILD-TYPE 
                        297.01                         346.49 
  DEL PEAK 31(16Q24.3) MUTATED DEL PEAK 31(16Q24.3) WILD-TYPE 
                        52.815                         43.985 
[1] "0.3 - 297.0 (52.8)" "0.0 - 346.5 (44.0)"
[1] "hr=" "1"  
D51V2, survival
                                sevent
clus2                              0   1
  DEL PEAK 31(16Q24.3) MUTATED    59  70
  DEL PEAK 31(16Q24.3) WILD-TYPE 107 122
  DEL PEAK 31(16Q24.3) MUTATED DEL PEAK 31(16Q24.3) WILD-TYPE 
                           129                            229 
  DEL PEAK 31(16Q24.3) MUTATED DEL PEAK 31(16Q24.3) WILD-TYPE 
                            70                            122 
$`DEL PEAK 31(16Q24.3) MUTATED`
TCGA-D3-A2JF TCGA-D3-A8GI TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A2GO TCGA-ER-A193 
       62.07        58.52        68.25        94.98       126.81        31.40 
TCGA-FS-A1ZF TCGA-FW-A3R5 TCGA-QB-AA9O TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-D3-A1Q4 
       15.45        36.95        18.05        61.15        21.40       112.04 
TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A2J6 TCGA-D3-A2JA 
      112.57       133.25        31.59        90.90        43.43       115.53 
TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A3BZ 
      168.00        86.76       171.58        66.48        66.08       130.72 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3MU TCGA-D3-A51N TCGA-D3-A5GO TCGA-D3-A8GC 
       86.93        60.23        39.75        22.62       137.92        79.59 
TCGA-D3-A8GD TCGA-D3-A8GJ TCGA-D3-A8GM TCGA-D3-A8GS TCGA-D3-A8GV TCGA-D9-A148 
       23.61       241.38       107.15       117.17       167.70       151.53 
TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A3Z3 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HW 
       54.67         3.65        22.29        25.18        77.56        36.03 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A3F8 TCGA-DA-A95V TCGA-DA-A95X TCGA-EB-A44R 
      176.55        35.93        43.36        72.10        73.94        10.36 
TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20I 
        8.65        33.73        26.89         4.96       151.27        13.55 
TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29W 
       85.08        13.97        64.64        56.84        56.42       195.02 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A5 TCGA-EE-A2GC TCGA-EE-A2GH TCGA-EE-A2GP 
       17.92        46.82        39.29        67.43       220.24        13.91 
TCGA-EE-A2M5 TCGA-EE-A2MD TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
       21.67        47.28       103.20       204.66        96.23       180.39 
TCGA-EE-A2MM TCGA-EE-A2MQ TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AE TCGA-EE-A3AF 
      167.90        43.23        53.26       122.73        54.51        13.81 
TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3JA TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A197 
      127.20        36.95        53.19       134.33       152.81        13.94 
TCGA-ER-A19B TCGA-ER-A19F TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A19T TCGA-ER-A19W 
       98.40        26.37        44.09        50.89         8.88       148.18 
TCGA-ER-A2ND TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A7U8 TCGA-FR-A8YC TCGA-FS-A1Z0 
       23.34        33.21       149.03        27.85        34.82       202.65 
TCGA-FS-A1ZB TCGA-FS-A1ZJ TCGA-FS-A1ZP TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW 
       48.85        47.38        74.73        53.16        26.56        49.48 
TCGA-FS-A1ZY TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FW-A3TU TCGA-GF-A4EO TCGA-GF-A6C8 
       27.09        50.14        66.67        55.59        19.43         2.04 
TCGA-GN-A262 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A8LK 
      139.89        64.44        62.79        48.00       121.91        50.10 
TCGA-GN-A8LL TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A693 TCGA-W3-AA1R 
       21.37       368.78       297.90         7.23         0.33       111.09 
TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8ZQ TCGA-WE-A8ZX TCGA-YD-A9TA TCGA-YG-AA3O 
       24.03        49.05        63.22        35.80        49.18        37.94 
TCGA-YG-AA3P TCGA-Z2-AA3S TCGA-Z2-AA3V 
       14.43        96.99        15.98 

$`DEL PEAK 31(16Q24.3) WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SH TCGA-EE-A184 TCGA-EE-A20H 
       27.65        46.32        13.87        54.02        68.15       168.26 
TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A198 TCGA-FR-A729 
        2.60       340.14       134.40        27.35        50.76       220.80 
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 
       17.03        66.48        12.99        14.93        16.57        16.67 
TCGA-D3-A1Q6 TCGA-D3-A1Q8 TCGA-D3-A1QB TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 
       71.80        28.08        95.74       103.10        65.49        23.77 
TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JP TCGA-D3-A3C6 
       11.87       113.52        42.08        12.10        59.57        58.06 
TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MV 
       46.98       166.52        24.53         9.34       103.59        45.30 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R 
      174.84        55.73        56.35       145.12        32.94        63.81 
TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU 
       26.89       125.79       135.75       178.32        18.18       125.19 
TCGA-D3-A8GB TCGA-D3-A8GE TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GN TCGA-D3-A8GP 
       30.84        26.43       170.20        89.13       161.00       152.75 
TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D9-A1JX TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A4Z6 
       29.06       129.63         7.10        18.12        15.39        18.44 
TCGA-D9-A6E9 TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 
        9.90        22.95        76.57       144.89        20.38       222.51 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
      135.02        88.87        53.92        65.92        40.60        68.09 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A95W TCGA-DA-A95Y TCGA-DA-A95Z 
       33.93        10.49       225.96        37.35        14.14        13.02 
TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 
       13.87        20.35        29.29        58.92         7.04        36.46 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A182 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A29A 
       29.82        27.22        14.70       133.81        91.56        63.35 
TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29R 
       78.97        63.78        72.07        18.61        66.74        14.47 
TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 
       61.28       369.93        25.87       115.96        59.64        86.14 
TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       59.28       173.79        48.72       107.38        54.74        79.66 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU 
       75.48       102.12        42.77        81.21        44.88        94.82 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2ME TCGA-EE-A2MF 
      129.27        28.83        19.76        61.51       103.27       268.73 
TCGA-EE-A2MH TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT 
       16.96       216.66        47.54       248.65       162.48        71.21 
TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 
      124.31        64.04        28.77        41.59       138.81       172.18 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JE TCGA-ER-A195 TCGA-ER-A199 
       64.08        34.32       201.80        51.35        35.44         9.17 
TCGA-ER-A19A TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19G TCGA-ER-A19H 
       77.75        48.89        12.59        13.02       302.07       152.35 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19P TCGA-ER-A19S TCGA-ER-A1A1 
        6.44       131.51        61.05       162.08        49.48       105.07 
TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES 
       43.82        20.15        28.83        48.99        41.56       247.04 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       93.01        46.98        12.95        92.98       174.21        15.72 
TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YX 
       18.77        38.27        36.26       104.42       216.92        48.59 
TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZC 
      228.59        20.91        28.08         7.79        27.72       357.37 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZK TCGA-FS-A1ZM 
       53.52        46.45         9.70        32.75        23.93       101.26 
TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F5 
      133.55        11.41       148.80        27.02        77.82        28.73 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 
      174.84        34.03        26.73        54.41        80.68        17.46 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C9 TCGA-GN-A264 TCGA-GN-A265 
       13.51        19.30         9.90        15.78       117.93        96.92 
TCGA-GN-A266 TCGA-GN-A26A TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A4U9 
       10.13        32.48        39.35        10.42        48.89        22.13 
TCGA-GN-A9SD TCGA-HR-A2OG TCGA-HR-A2OH TCGA-RP-A690 TCGA-RP-A694 TCGA-W3-A824 
       59.41         0.23        65.88         0.20         0.69       228.16 
TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1Q TCGA-W3-AA1V TCGA-W3-AA1W 
       63.02       121.08         4.01        69.07        42.08       219.16 
TCGA-W3-AA21 TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT 
      105.04        17.95       101.33        58.98        70.52        11.80 
TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-XV-AB01 TCGA-YD-A89C 
       49.51        12.16        40.41        24.99        13.25         6.90 
TCGA-Z2-A8RT 
       27.58 

  DEL PEAK 31(16Q24.3) MUTATED DEL PEAK 31(16Q24.3) WILD-TYPE 
                          0.33                           0.20 
  DEL PEAK 31(16Q24.3) MUTATED DEL PEAK 31(16Q24.3) WILD-TYPE 
                        368.78                         369.93 
  DEL PEAK 31(16Q24.3) MUTATED DEL PEAK 31(16Q24.3) WILD-TYPE 
                         54.51                          49.48 
[1] "0.3 - 368.8 (54.5)" "0.2 - 369.9 (49.5)"
[1] "hr=" "1"  
D51V3, continuous
                                vv
clus                             I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB
  DEL PEAK 31(16Q24.3) MUTATED          4       4       7        8        9
  DEL PEAK 31(16Q24.3) WILD-TYPE        9       3      22       10       19
                                vv
clus                             STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK 31(16Q24.3) MUTATED         11         2        13         8
  DEL PEAK 31(16Q24.3) WILD-TYPE       15        12         6         7
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 31(16Q24.3) MUTATED          12          5         11         16
  DEL PEAK 31(16Q24.3) WILD-TYPE        27         10         24         38
                                vv
clus                             STAGE IV
  DEL PEAK 31(16Q24.3) MUTATED          7
  DEL PEAK 31(16Q24.3) WILD-TYPE       14
D51V4, multiclass
            clus
vv           DEL PEAK 31(16Q24.3) MUTATED DEL PEAK 31(16Q24.3) WILD-TYPE
  I/II NOS                              4                              9
  STAGE 0                               4                              3
  STAGE I                               7                             22
  STAGE IA                              8                             10
  STAGE IB                              9                             19
  STAGE II                             11                             15
  STAGE IIA                             2                             12
  STAGE IIB                            13                              6
  STAGE IIC                             8                              7
  STAGE III                            12                             27
  STAGE IIIA                            5                             10
  STAGE IIIB                           11                             24
  STAGE IIIC                           16                             38
  STAGE IV                              7                             14
[1] 14  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  DEL PEAK 31(16Q24.3) MUTATED      22 20 30 29
  DEL PEAK 31(16Q24.3) WILD-TYPE    42 53 51 38
D51V5, multiclass
       clus
vv      DEL PEAK 31(16Q24.3) MUTATED DEL PEAK 31(16Q24.3) WILD-TYPE
  T0+T1                           22                             42
  T2                              20                             53
  T3                              30                             51
  T4                              29                             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  N3
  DEL PEAK 31(16Q24.3) MUTATED    71  19  12  16
  DEL PEAK 31(16Q24.3) WILD-TYPE 106  46  27  29
D51V6, multiclass
    clus
vv   DEL PEAK 31(16Q24.3) MUTATED DEL PEAK 31(16Q24.3) WILD-TYPE
  N0                           71                            106
  N1                           19                             46
  N2                           12                             27
  N3                           16                             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"
D51V7, binary
                                cls
clus                               0   1
  DEL PEAK 31(16Q24.3) MUTATED   113   8
  DEL PEAK 31(16Q24.3) WILD-TYPE 206  14
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(16Q24.3) MUTATED    113    8
  DEL PEAK 31(16Q24.3) WILD-TYPE  206   14
   clus
vv  DEL PEAK 31(16Q24.3) MUTATED DEL PEAK 31(16Q24.3) WILD-TYPE
  0                          113                            206
  1                            8                             14
[1] 2 2
[1] FALSE
D51V8, binary
                                cls
clus                              0  1
  DEL PEAK 31(16Q24.3) MUTATED   52 34
  DEL PEAK 31(16Q24.3) WILD-TYPE 82 56
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(16Q24.3) MUTATED     52   34
  DEL PEAK 31(16Q24.3) WILD-TYPE   82   56
     clus
vv    DEL PEAK 31(16Q24.3) MUTATED DEL PEAK 31(16Q24.3) WILD-TYPE
  NO                            52                             82
  YES                           34                             56
[1] 2 2
[1] FALSE
D51V9, binary
                                cls
clus                               0   1
  DEL PEAK 31(16Q24.3) MUTATED    14 119
  DEL PEAK 31(16Q24.3) WILD-TYPE  33 201
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(16Q24.3) MUTATED     14  119
  DEL PEAK 31(16Q24.3) WILD-TYPE   33  201
     clus
vv    DEL PEAK 31(16Q24.3) MUTATED DEL PEAK 31(16Q24.3) WILD-TYPE
  NO                            14                             33
  YES                          119                            201
[1] 2 2
[1] FALSE
D51V10, continuous
D51V11, binary
                                cls
clus                               0   1
  DEL PEAK 31(16Q24.3) MUTATED    51  82
  DEL PEAK 31(16Q24.3) WILD-TYPE  87 147
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(16Q24.3) MUTATED     51   82
  DEL PEAK 31(16Q24.3) WILD-TYPE   87  147
        clus
vv       DEL PEAK 31(16Q24.3) MUTATED DEL PEAK 31(16Q24.3) WILD-TYPE
  FEMALE                           51                             87
  MALE                             82                            147
[1] 2 2
[1] FALSE
D51V12, binary
                                cls
clus                               0   1
  DEL PEAK 31(16Q24.3) MUTATED   116  17
  DEL PEAK 31(16Q24.3) WILD-TYPE 203  30
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(16Q24.3) MUTATED    116   17
  DEL PEAK 31(16Q24.3) WILD-TYPE  203   30
     clus
vv    DEL PEAK 31(16Q24.3) MUTATED DEL PEAK 31(16Q24.3) WILD-TYPE
  NO                           116                            203
  YES                           17                             30
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 31(16Q24.3) MUTATED       1                         1   127
  DEL PEAK 31(16Q24.3) WILD-TYPE     4                         0   226
D51V13, multiclass
                           clus
vv                          DEL PEAK 31(16Q24.3) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                              127
                           clus
vv                          DEL PEAK 31(16Q24.3) WILD-TYPE
  ASIAN                                                  4
  BLACK OR AFRICAN AMERICAN                              0
  WHITE                                                226
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V14, binary
                                cls
clus                               0   1
  DEL PEAK 31(16Q24.3) MUTATED     3 128
  DEL PEAK 31(16Q24.3) WILD-TYPE   4 224
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(16Q24.3) MUTATED      3  128
  DEL PEAK 31(16Q24.3) WILD-TYPE    4  224
                        clus
vv                       DEL PEAK 31(16Q24.3) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                          128
                        clus
vv                       DEL PEAK 31(16Q24.3) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            224
[1] 2 2
[1] FALSE

Clustering(52) Variable = DEL PEAK 32(17P13.3) MUTATION ANALYSIS
D52V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 32(17P13.3) MUTATED   44 39
  DEL PEAK 32(17P13.3) WILD-TYPE 84 85
  DEL PEAK 32(17P13.3) MUTATED DEL PEAK 32(17P13.3) WILD-TYPE 
                            83                            169 
  DEL PEAK 32(17P13.3) MUTATED DEL PEAK 32(17P13.3) WILD-TYPE 
                            39                             85 
$`DEL PEAK 32(17P13.3) MUTATED`
TCGA-D3-A8GI TCGA-EE-A180 TCGA-EE-A2MR TCGA-ER-A193 TCGA-FR-A729 TCGA-FW-A3R5 
       13.41        31.96       134.40        19.04       216.43        36.95 
TCGA-WE-AAA3 TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1QA TCGA-D3-A2J6 TCGA-D3-A2JA 
        7.40        60.46        12.99        76.41        25.64        15.75 
TCGA-D3-A2JB TCGA-D3-A2JG TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A51T 
      168.00       107.61       171.58        64.83        66.08        11.34 
TCGA-D3-A8GC TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GP TCGA-DA-A1HV TCGA-DA-A1HY 
       78.21        69.53        70.62       135.12        76.34       138.67 
TCGA-DA-A1I5 TCGA-DA-A3F5 TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A20C TCGA-EE-A29C 
      110.53       225.11        52.41        13.15        75.55        76.14 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29T TCGA-EE-A2A1 
        0.26        44.28        47.41        47.74       346.49       115.43 
TCGA-EE-A2A2 TCGA-EE-A2GP TCGA-EE-A2M6 TCGA-EE-A2MC TCGA-EE-A2MG TCGA-EE-A2MM 
       30.02         0.76       103.13        23.77        94.19       145.45 
TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AE 
      227.01       143.93        53.26       124.31        64.04        54.51 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH TCGA-ER-A195 TCGA-ER-A199 
       45.90         3.35       168.85        19.86        34.45         7.82 
TCGA-ER-A19C TCGA-ER-A19S TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A3EV TCGA-FR-A3YN 
       39.81        47.18        16.87        28.67        15.48         4.50 
TCGA-FR-A44A TCGA-FR-A7U8 TCGA-FR-A8YC TCGA-FS-A1YW TCGA-FS-A1Z4 TCGA-FS-A1ZQ 
      174.21        26.20        10.06       171.78        27.62       130.95 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F9 TCGA-GN-A265 
       35.28         4.47        23.21         5.29        13.28        96.92 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A4U3 TCGA-W3-AA1R TCGA-W3-AA21 TCGA-WE-A8K1 
       17.06        42.48       120.53        79.99        92.84        47.54 
TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-YG-AA3O 
       10.95        48.39         1.94        37.32        28.21 

$`DEL PEAK 32(17P13.3) WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A20H TCGA-EE-A2GD 
        9.76        62.07        38.76        33.24       166.75       269.03 
TCGA-EE-A2GO TCGA-EE-A3JD TCGA-WE-A8K5 TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 
       52.90        27.35        52.73        14.83         8.42        15.72 
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QB 
       31.89       110.93        49.35       133.25        19.04        62.60 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JC TCGA-D3-A2JH TCGA-D3-A2JP TCGA-D3-A3C6 
       45.99        62.86        86.30        36.30        43.53        58.06 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR 
      140.98        40.01        59.70        24.53         9.34        90.21 
TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R 
       23.67       173.85        30.67       144.46        31.76        62.70 
TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D3-A8GD TCGA-D3-A8GJ 
       42.05        45.70       177.86       124.08        23.61       179.97 
TCGA-D3-A8GK TCGA-D3-A8GR TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 
      120.00        36.53        10.78        15.02        16.90        18.44 
TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I7 TCGA-DA-A1IA 
       69.21        22.85        68.68       150.61        60.10        64.83 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F8 TCGA-DA-A95V TCGA-DA-A95W TCGA-DA-A95X 
       58.85        30.44         8.71        72.10         0.76        65.03 
TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A6L9 TCGA-EE-A17Y 
       14.14        12.30         3.91        16.41        18.21        24.89 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29D 
       20.38         0.00        26.24        79.20        75.22        12.99 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29W TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE 
       27.16        61.12       185.19        77.98        26.14        12.95 
TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
      201.60        68.65        10.62        32.48        18.35        93.63 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MF 
        0.20        71.31        81.99        15.25         5.75       209.79 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MT TCGA-EE-A3AB 
      171.85        63.25        89.26       104.78        23.51       122.73 
TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3JI TCGA-ER-A197 
        4.41         6.28        67.89       111.85       135.98        10.49 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L 
        4.54        53.29        11.47       184.60       150.12        99.06 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19W TCGA-ER-A1A1 
       59.84        42.51       120.76        49.71       146.63        73.05 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NF TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3PL 
       22.36         4.70        10.19       173.29        68.52        32.05 
TCGA-ER-A42L TCGA-FR-A69P TCGA-FR-A7UA TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
       74.47         4.14         5.65        49.74       195.98         8.35 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM 
      312.07        32.78        43.92         7.82        36.33        78.61 
TCGA-FS-A1ZS TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4FD 
      136.27         3.06        30.90        66.67       173.19        80.68 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
       55.59        11.54        19.30         9.90        18.25         1.91 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A26A TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-GN-A8LK 
       53.29       117.93         7.59        34.49        46.92        43.23 
TCGA-GN-A9SD TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 
       59.41        85.05       297.01         7.23         0.20         0.33 
TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1Q TCGA-W3-AA1V TCGA-W3-AA1W 
      174.12         1.97       120.07        44.05         8.09       185.13 
TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-AAA4 TCGA-XV-AB01 
       65.42        12.69        21.90        62.89        24.99         6.61 
TCGA-Z2-AA3S 
       91.23 

  DEL PEAK 32(17P13.3) MUTATED DEL PEAK 32(17P13.3) WILD-TYPE 
                          0.26                           0.00 
  DEL PEAK 32(17P13.3) MUTATED DEL PEAK 32(17P13.3) WILD-TYPE 
                        346.49                         312.07 
  DEL PEAK 32(17P13.3) MUTATED DEL PEAK 32(17P13.3) WILD-TYPE 
                         47.54                          44.05 
[1] "0.3 - 346.5 (47.5)" "0.0 - 312.1 (44.0)"
[1] "hr=" "1.2"
D52V2, survival
                                sevent
clus2                              0   1
  DEL PEAK 32(17P13.3) MUTATED    61  69
  DEL PEAK 32(17P13.3) WILD-TYPE 105 123
  DEL PEAK 32(17P13.3) MUTATED DEL PEAK 32(17P13.3) WILD-TYPE 
                           130                            228 
  DEL PEAK 32(17P13.3) MUTATED DEL PEAK 32(17P13.3) WILD-TYPE 
                            69                            123 
$`DEL PEAK 32(17P13.3) MUTATED`
TCGA-D3-A3ML TCGA-D3-A8GI TCGA-EE-A180 TCGA-EE-A184 TCGA-EE-A29L TCGA-EE-A2MR 
       13.87        58.52        94.98        68.15         2.60       134.40 
TCGA-ER-A193 TCGA-FR-A729 TCGA-FW-A3R5 TCGA-QB-AA9O TCGA-WE-AAA3 TCGA-3N-A9WB 
       31.40       220.80        36.95        18.05        21.40        17.03 
TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A2J6 TCGA-D3-A2JA 
       66.48        12.99        31.59        90.90        43.43       115.53 
TCGA-D3-A2JB TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
      168.00        11.87       113.52       171.58        66.48        66.08 
TCGA-D3-A51N TCGA-D3-A51T TCGA-D3-A5GO TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GL 
       22.62        26.89       137.92        30.84        79.59        89.13 
TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D9-A148 TCGA-D9-A1JW TCGA-D9-A6E9 
      107.15       161.00       152.75       151.53         3.65         9.90 
TCGA-D9-A6EA TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I5 TCGA-DA-A1I8 
       25.18        76.57        36.03       144.89       135.02        53.92 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-EB-A44R TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X 
       10.49       225.96        10.36        29.29        58.92        29.82 
TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H 
        4.96       151.27        78.97        63.78        72.07        64.64 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29X 
       56.84        18.61        61.28       369.93        25.87        17.92 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2GC TCGA-EE-A2GI TCGA-EE-A2GP 
      115.96        59.64        39.29        67.43        48.72        13.91 
TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2MG 
       44.88        21.67       129.27        61.51        47.28       103.20 
TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA 
      167.90       248.65        43.23       162.48        53.26       124.31 
TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB 
       64.04        54.51        36.95        64.08        34.32       201.80 
TCGA-EE-A3JH TCGA-ER-A195 TCGA-ER-A199 TCGA-ER-A19C TCGA-ER-A19F TCGA-ER-A19S 
      134.33        35.44         9.17        48.89        26.37        49.48 
TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A3EV TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A7U8 
       20.15        48.99        46.98        92.98       174.21        27.85 
TCGA-FR-A7U9 TCGA-FR-A8YC TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1Z4 TCGA-FS-A1ZH 
       18.77        34.82       216.92        48.59        28.08        32.75 
TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
       74.73       133.55        53.16        26.56        49.48        27.09 
TCGA-FS-A4F2 TCGA-FS-A4F9 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
       50.14        34.03        96.92        10.13        64.44        62.79 
TCGA-GN-A4U3 TCGA-GN-A4U9 TCGA-GN-A8LL TCGA-HR-A2OG TCGA-RP-A694 TCGA-W3-AA1R 
      121.91        22.13        21.37         0.23         0.69       111.09 
TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y 
      105.04        24.03        49.05        11.80        49.51        12.16 
TCGA-WE-AAA0 TCGA-YD-A9TA TCGA-YG-AA3O TCGA-Z2-AA3V 
       40.41        49.18        37.94        15.98 

$`DEL PEAK 32(17P13.3) WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A20H 
       27.65        62.07        46.32        68.25        54.02       168.26 
TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A3JD TCGA-ER-A198 TCGA-FS-A1ZF TCGA-WE-A8K5 
      340.14       126.81        27.35        50.76        15.45        61.15 
TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 
       14.93        16.57        16.67       112.04       112.57        71.80 
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QB TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 
      133.25        28.08        95.74       103.10        65.49        23.77 
TCGA-D3-A2JC TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 
       86.76        42.08        12.10        59.57       130.72        58.06 
TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO 
       46.98       166.52        86.93        60.23        24.53         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
      103.59        39.75        45.30       174.84        55.73        56.35 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR 
      145.12        32.94        63.81       125.79       135.75       178.32 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GK 
       18.18       125.19        23.61        26.43       241.38       170.20 
TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D3-A8GV TCGA-D9-A149 TCGA-D9-A1JX 
       29.06       129.63       117.17       167.70        54.67         7.10 
TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6EC TCGA-D9-A6EG 
       18.12        15.39        22.29        18.44        77.56        22.95 
TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I7 TCGA-DA-A1IA 
       20.38       222.51       176.55        35.93        88.87        65.92 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F8 TCGA-DA-A95V TCGA-DA-A95W 
       40.60        68.09        33.93        43.36        72.10        37.35 
TCGA-DA-A95X TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5VV 
       73.94        14.14        13.02        13.87        20.35         7.04 
TCGA-EB-A6L9 TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
       36.46        27.22         8.65        33.73        14.70        26.89 
TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29D 
      133.81        91.56        13.55        63.35        85.08        13.97 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29W TCGA-EE-A2A0 TCGA-EE-A2A6 
       56.42        66.74        14.47       195.02        46.82        86.14 
TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       59.28       173.79       220.24       107.38        54.74        79.66 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M7 
       75.48       102.12        42.77        81.21        94.82        28.83 
TCGA-EE-A2M8 TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ 
       19.76       103.27       268.73        16.96       204.66        96.23 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MT TCGA-EE-A3AB TCGA-EE-A3AD 
      180.39       216.66        47.54        71.21       122.73        28.77 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3JA 
       13.81        41.59       138.81       172.18       127.20        53.19 
TCGA-EE-A3JE TCGA-EE-A3JI TCGA-ER-A197 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19D 
       51.35       152.81        13.94        77.75        98.40        12.59 
TCGA-ER-A19E TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
       13.02       302.07       152.35         6.44       131.51        61.05 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 
       44.09       162.08        50.89         8.88       148.18       105.07 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NF TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
       43.82        23.34        28.83        41.56       247.04        93.01 
TCGA-ER-A3PL TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A69P TCGA-FR-A7UA TCGA-FR-A8YD 
       33.21        12.95       149.03        15.72        38.27        36.26 
TCGA-FR-A8YE TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z7 TCGA-FS-A1ZA 
      104.42       228.59       202.65        20.91         7.79        27.72 
TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ 
       48.85       357.37        53.52        46.45         9.70        47.38 
TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZZ TCGA-FS-A4F0 
       23.93       101.26        11.41       148.80        27.02        77.82 
TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD 
       66.67        28.73       174.84        26.73        54.41        80.68 
TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
       17.46        55.59        13.51        19.30         9.90        19.43 
TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A26A TCGA-GN-A26D 
        2.04        15.78       139.89       117.93        32.48        48.00 
TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A8LK TCGA-GN-A9SD TCGA-HR-A2OH 
       39.35        10.42        48.89        50.10        59.41        65.88 
TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 TCGA-W3-A824 
      368.78       297.90         7.23         0.20         0.33       228.16 
TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1Q TCGA-W3-AA1V TCGA-W3-AA1W 
       63.02       121.08         4.01        69.07        42.08       219.16 
TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZX 
       17.95       101.33        58.98        70.52        63.22        35.80 
TCGA-WE-AAA4 TCGA-XV-AB01 TCGA-YD-A89C TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S 
       24.99        13.25         6.90        14.43        27.58        96.99 

  DEL PEAK 32(17P13.3) MUTATED DEL PEAK 32(17P13.3) WILD-TYPE 
                          0.23                           0.20 
  DEL PEAK 32(17P13.3) MUTATED DEL PEAK 32(17P13.3) WILD-TYPE 
                        369.93                         368.78 
  DEL PEAK 32(17P13.3) MUTATED DEL PEAK 32(17P13.3) WILD-TYPE 
                        49.480                         54.215 
[1] "0.2 - 369.9 (49.5)" "0.2 - 368.8 (54.2)"
[1] "hr=" "1.1"
D52V3, continuous
                                vv
clus                             I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB
  DEL PEAK 32(17P13.3) MUTATED          6       4      14        9       10
  DEL PEAK 32(17P13.3) WILD-TYPE        7       3      15        9       18
                                vv
clus                             STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK 32(17P13.3) MUTATED          6         4         7         5
  DEL PEAK 32(17P13.3) WILD-TYPE       20        10        12        10
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 32(17P13.3) MUTATED          13          9         11         19
  DEL PEAK 32(17P13.3) WILD-TYPE        26          6         24         35
                                vv
clus                             STAGE IV
  DEL PEAK 32(17P13.3) MUTATED          5
  DEL PEAK 32(17P13.3) WILD-TYPE       16
D52V4, multiclass
            clus
vv           DEL PEAK 32(17P13.3) MUTATED DEL PEAK 32(17P13.3) WILD-TYPE
  I/II NOS                              6                              7
  STAGE 0                               4                              3
  STAGE I                              14                             15
  STAGE IA                              9                              9
  STAGE IB                             10                             18
  STAGE II                              6                             20
  STAGE IIA                             4                             10
  STAGE IIB                             7                             12
  STAGE IIC                             5                             10
  STAGE III                            13                             26
  STAGE IIIA                            9                              6
  STAGE IIIB                           11                             24
  STAGE IIIC                           19                             35
  STAGE IV                              5                             16
[1] 14  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  DEL PEAK 32(17P13.3) MUTATED      23 30 28 25
  DEL PEAK 32(17P13.3) WILD-TYPE    41 43 53 42
D52V5, multiclass
       clus
vv      DEL PEAK 32(17P13.3) MUTATED DEL PEAK 32(17P13.3) WILD-TYPE
  T0+T1                           23                             41
  T2                              30                             43
  T3                              28                             53
  T4                              25                             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  N3
  DEL PEAK 32(17P13.3) MUTATED    64  25  14  16
  DEL PEAK 32(17P13.3) WILD-TYPE 113  40  25  29
D52V6, multiclass
    clus
vv   DEL PEAK 32(17P13.3) MUTATED DEL PEAK 32(17P13.3) WILD-TYPE
  N0                           64                            113
  N1                           25                             40
  N2                           14                             25
  N3                           16                             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"
D52V7, binary
                                cls
clus                               0   1
  DEL PEAK 32(17P13.3) MUTATED   121   6
  DEL PEAK 32(17P13.3) WILD-TYPE 198  16
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 32(17P13.3) MUTATED    121    6
  DEL PEAK 32(17P13.3) WILD-TYPE  198   16
   clus
vv  DEL PEAK 32(17P13.3) MUTATED DEL PEAK 32(17P13.3) WILD-TYPE
  0                          121                            198
  1                            6                             16
[1] 2 2
[1] FALSE
D52V8, binary
                                cls
clus                              0  1
  DEL PEAK 32(17P13.3) MUTATED   55 34
  DEL PEAK 32(17P13.3) WILD-TYPE 79 56
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 32(17P13.3) MUTATED     55   34
  DEL PEAK 32(17P13.3) WILD-TYPE   79   56
     clus
vv    DEL PEAK 32(17P13.3) MUTATED DEL PEAK 32(17P13.3) WILD-TYPE
  NO                            55                             79
  YES                           34                             56
[1] 2 2
[1] FALSE
D52V9, binary
                                cls
clus                               0   1
  DEL PEAK 32(17P13.3) MUTATED    14 120
  DEL PEAK 32(17P13.3) WILD-TYPE  33 200
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 32(17P13.3) MUTATED     14  120
  DEL PEAK 32(17P13.3) WILD-TYPE   33  200
     clus
vv    DEL PEAK 32(17P13.3) MUTATED DEL PEAK 32(17P13.3) WILD-TYPE
  NO                            14                             33
  YES                          120                            200
[1] 2 2
[1] FALSE
D52V10, continuous
D52V11, binary
                                cls
clus                               0   1
  DEL PEAK 32(17P13.3) MUTATED    41  93
  DEL PEAK 32(17P13.3) WILD-TYPE  97 136
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 32(17P13.3) MUTATED     41   93
  DEL PEAK 32(17P13.3) WILD-TYPE   97  136
        clus
vv       DEL PEAK 32(17P13.3) MUTATED DEL PEAK 32(17P13.3) WILD-TYPE
  FEMALE                           41                             97
  MALE                             93                            136
[1] 2 2
[1] FALSE
D52V12, binary
                                cls
clus                               0   1
  DEL PEAK 32(17P13.3) MUTATED   121  13
  DEL PEAK 32(17P13.3) WILD-TYPE 198  34
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 32(17P13.3) MUTATED    121   13
  DEL PEAK 32(17P13.3) WILD-TYPE  198   34
     clus
vv    DEL PEAK 32(17P13.3) MUTATED DEL PEAK 32(17P13.3) WILD-TYPE
  NO                           121                            198
  YES                           13                             34
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 32(17P13.3) MUTATED       1                         1   129
  DEL PEAK 32(17P13.3) WILD-TYPE     4                         0   224
D52V13, multiclass
                           clus
vv                          DEL PEAK 32(17P13.3) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                              129
                           clus
vv                          DEL PEAK 32(17P13.3) WILD-TYPE
  ASIAN                                                  4
  BLACK OR AFRICAN AMERICAN                              0
  WHITE                                                224
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V14, binary
                                cls
clus                               0   1
  DEL PEAK 32(17P13.3) MUTATED     1 130
  DEL PEAK 32(17P13.3) WILD-TYPE   6 222
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 32(17P13.3) MUTATED      1  130
  DEL PEAK 32(17P13.3) WILD-TYPE    6  222
                        clus
vv                       DEL PEAK 32(17P13.3) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                          130
                        clus
vv                       DEL PEAK 32(17P13.3) WILD-TYPE
  HISPANIC OR LATINO                                  6
  NOT HISPANIC OR LATINO                            222
[1] 2 2
[1] FALSE

Clustering(53) Variable = DEL PEAK 33(19P13.3) MUTATION ANALYSIS
D53V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 33(19P13.3) MUTATED   34 37
  DEL PEAK 33(19P13.3) WILD-TYPE 94 87
  DEL PEAK 33(19P13.3) MUTATED DEL PEAK 33(19P13.3) WILD-TYPE 
                            71                            181 
  DEL PEAK 33(19P13.3) MUTATED DEL PEAK 33(19P13.3) WILD-TYPE 
                            37                             87 
$`DEL PEAK 33(19P13.3) MUTATED`
TCGA-D3-A8GI TCGA-EE-A20H TCGA-EE-A3JD TCGA-ER-A193 TCGA-D3-A1Q1 TCGA-D3-A1QB 
       13.41       166.75        27.35        19.04         8.42        62.60 
TCGA-D3-A2J6 TCGA-D3-A2JL TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A8GD 
       25.64       171.58        11.34        42.05        45.70        23.61 
TCGA-D3-A8GM TCGA-D3-A8GP TCGA-D3-A8GR TCGA-D9-A1X3 TCGA-D9-A3Z3 TCGA-D9-A4Z6 
       70.62       135.12        36.53        10.78        16.90        18.44 
TCGA-DA-A1HV TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F5 
       76.34       110.53        60.10        64.83        58.85       225.11 
TCGA-DA-A95V TCGA-DA-A95Y TCGA-EE-A17X TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29G 
       72.10        14.14        13.15        76.14        12.99        44.28 
TCGA-EE-A29H TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GM TCGA-EE-A2GS TCGA-EE-A2GU 
       47.41        77.98        26.14        18.35        71.31        81.99 
TCGA-EE-A2MG TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AB TCGA-EE-A3AC 
       94.19       227.01       143.93        23.51       122.73        64.04 
TCGA-EE-A3AD TCGA-EE-A3J4 TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19H TCGA-ER-A19M 
        4.41       111.85        53.29        39.81       150.12        59.84 
TCGA-ER-A19Q TCGA-ER-A19W TCGA-ER-A2ND TCGA-ER-A2NG TCGA-ER-A3EV TCGA-FR-A3YN 
       49.71       146.63         4.70        28.67        15.48         4.50 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1ZD TCGA-FS-A1ZQ TCGA-FS-A1ZT TCGA-FS-A1ZW 
      174.21         4.14        32.78       130.95        35.28        23.21 
TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV TCGA-GF-A4EO TCGA-GN-A262 TCGA-GN-A268 
       80.68        55.59        11.54        18.25        53.29        42.48 
TCGA-GN-A4U3 TCGA-W3-AA1R TCGA-W3-AA1V TCGA-WE-A8K1 TCGA-WE-A8ZM 
      120.53        79.99         8.09        47.54        65.42 

$`DEL PEAK 33(19P13.3) WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A2GD 
        9.76        62.07        38.76        33.24        31.96       269.03 
TCGA-EE-A2GO TCGA-EE-A2MR TCGA-FR-A729 TCGA-FW-A3R5 TCGA-WE-A8K5 TCGA-WE-AAA3 
       52.90       134.40       216.43        36.95        52.73         7.40 
TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
       60.46        12.99        14.83        15.72        31.89       110.93 
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A2J7 TCGA-D3-A2J8 
       49.35       133.25        19.04        76.41        45.99        62.86 
TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JN 
       15.75       168.00        86.30       107.61        36.30        64.83 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE 
       66.08        43.53        58.06       140.98        40.01        59.70 
TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F 
       24.53         9.34        90.21        23.67       173.85        30.67 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D3-A8GC 
      144.46        31.76        62.70       177.86       124.08        78.21 
TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D9-A3Z1 TCGA-D9-A6EC TCGA-D9-A6EG 
      179.97       120.00        69.53        15.02        69.21        22.85 
TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A3F2 TCGA-DA-A3F8 TCGA-DA-A95W 
      138.67        68.68       150.61        30.44         8.71         0.76 
TCGA-DA-A95X TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A6L9 
       65.03        12.30         3.91        16.41        52.41        18.21 
TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A20F 
       24.89        20.38         0.00        26.24        75.55        79.20 
TCGA-EE-A29B TCGA-EE-A29E TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T 
       75.22         0.26        47.74        27.16        61.12       346.49 
TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ 
      185.19       115.43        30.02        12.95       201.60        68.65 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2M6 
       10.62        32.48        93.63         0.76         0.20       103.13 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MI TCGA-EE-A2MJ 
       15.25         5.75        23.77       209.79       171.85        63.25 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AE 
       89.26       104.78       145.45        53.26       124.31        54.51 
TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH 
        6.28        67.89        45.90         3.35       168.85        19.86 
TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19D 
      135.98        34.45        10.49         7.82         4.54        11.47 
TCGA-ER-A19G TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19S TCGA-ER-A1A1 
      184.60        99.06        42.51       120.76        47.18        73.05 
TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3PL 
       22.36        16.87        10.19       173.29        68.52        32.05 
TCGA-ER-A42L TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FS-A1YW TCGA-FS-A1YY 
       74.47        26.20         5.65        10.06       171.78        49.74 
TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZE TCGA-FS-A1ZG 
      195.98         8.35        27.62       312.07        43.92         7.82 
TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A1ZZ 
       36.33        78.61       136.27         4.47         5.29         3.06 
TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FW-A5DY TCGA-GF-A3OT 
       30.90        66.67       173.19        13.28        19.30         9.90 
TCGA-GF-A6C8 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A4U4 
        1.91       117.93        96.92        17.06         7.59        34.49 
TCGA-GN-A4U8 TCGA-GN-A8LK TCGA-GN-A9SD TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS 
       46.92        43.23        59.41        85.05       297.01         7.23 
TCGA-RP-A690 TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1Q 
        0.20         0.33       174.12         1.97       120.07        44.05 
TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT 
      185.13        92.84        12.69        21.90        62.89        10.95 
TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-XV-AB01 TCGA-YG-AA3O 
       48.39         1.94        37.32        24.99         6.61        28.21 
TCGA-Z2-AA3S 
       91.23 

  DEL PEAK 33(19P13.3) MUTATED DEL PEAK 33(19P13.3) WILD-TYPE 
                          4.14                           0.00 
  DEL PEAK 33(19P13.3) MUTATED DEL PEAK 33(19P13.3) WILD-TYPE 
                        227.01                         346.49 
  DEL PEAK 33(19P13.3) MUTATED DEL PEAK 33(19P13.3) WILD-TYPE 
                         47.54                          45.90 
[1] "4.1 - 227.0 (47.5)" "0.0 - 346.5 (45.9)"
[1] "hr=" "1.2"
D53V2, survival
                                sevent
clus2                              0   1
  DEL PEAK 33(19P13.3) MUTATED    43  60
  DEL PEAK 33(19P13.3) WILD-TYPE 123 132
  DEL PEAK 33(19P13.3) MUTATED DEL PEAK 33(19P13.3) WILD-TYPE 
                           103                            255 
  DEL PEAK 33(19P13.3) MUTATED DEL PEAK 33(19P13.3) WILD-TYPE 
                            60                            132 
$`DEL PEAK 33(19P13.3) MUTATED`
TCGA-D3-A8GI TCGA-EB-A5SH TCGA-EE-A20H TCGA-EE-A3JD TCGA-ER-A193 TCGA-FS-A1ZF 
       58.52        54.02       168.26        27.35        31.40        15.45 
TCGA-D3-A1Q1 TCGA-D3-A1Q9 TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2JD TCGA-D3-A2JL 
       16.57        31.59        95.74        43.43        11.87       171.58 
TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A8GB TCGA-D3-A8GD TCGA-D3-A8GM 
       26.89       125.79       135.75        30.84        23.61       107.15 
TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D3-A8GV TCGA-D9-A148 
      161.00       152.75       129.63       117.17       167.70       151.53 
TCGA-D9-A1X3 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6EA TCGA-DA-A1HV TCGA-DA-A1HW 
       18.12        22.29        18.44        25.18        76.57        36.03 
TCGA-DA-A1I0 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IC 
       20.38       135.02        88.87        53.92        65.92        68.09 
TCGA-DA-A3F5 TCGA-DA-A95V TCGA-DA-A95Y TCGA-EB-A44R TCGA-EB-A5UL TCGA-EE-A17X 
      225.96        72.10        14.14        10.36        29.29        29.82 
TCGA-EE-A185 TCGA-EE-A20I TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29H 
        4.96        13.55        78.97        13.97        72.07        64.64 
TCGA-EE-A29N TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A6 TCGA-EE-A2GB 
       18.61        25.87        17.92        46.82        86.14        59.28 
TCGA-EE-A2GM TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2MG TCGA-EE-A2MP TCGA-EE-A2MQ 
       75.48        81.21        94.82       103.20       248.65        43.23 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3J4 
      162.48        71.21       122.73        64.04        28.77       127.20 
TCGA-EE-A3J5 TCGA-EE-A3JA TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19H TCGA-ER-A19M 
       36.95        53.19        98.40        48.89       152.35        61.05 
TCGA-ER-A19Q TCGA-ER-A19W TCGA-ER-A2ND TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3EV 
       50.89       148.18        23.34        48.99        41.56        46.98 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1ZD TCGA-FS-A1ZH TCGA-FS-A1ZQ 
       92.98       174.21        15.72        53.52        32.75       133.55 
TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A4FB TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV 
       53.16        49.48        26.73        80.68        55.59        13.51 
TCGA-GF-A4EO TCGA-GN-A262 TCGA-GN-A268 TCGA-GN-A4U3 TCGA-GN-A4U7 TCGA-GN-A8LL 
       19.43       139.89        62.79       121.91        10.42        21.37 
TCGA-W3-AA1R TCGA-W3-AA1V TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8ZM TCGA-YG-AA3P 
      111.09        42.08        24.03        49.05       101.33        14.43 
TCGA-Z2-AA3V 
       15.98 

$`DEL PEAK 33(19P13.3) WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SG TCGA-EE-A180 
       27.65        62.07        46.32        13.87        68.25        94.98 
TCGA-EE-A184 TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR TCGA-ER-A198 
       68.15         2.60       340.14       126.81       134.40        50.76 
TCGA-FR-A729 TCGA-FW-A3R5 TCGA-QB-AA9O TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-3N-A9WB 
      220.80        36.95        18.05        61.15        21.40        17.03 
TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
       66.48        12.99        14.93        16.67       112.04       112.57 
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A2J7 TCGA-D3-A2J8 
       71.80       133.25        28.08        90.90       103.10        65.49 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A2JH 
       23.77       115.53       168.00        86.76       113.52        42.08 
TCGA-D3-A2JK TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 
       12.10        66.48        66.08        59.57       130.72        58.06 
TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO 
       46.98       166.52        86.93        60.23        24.53         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
      103.59        39.75        45.30       174.84        55.73        56.35 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GO TCGA-D3-A5GR 
      145.12        32.94        22.62        63.81       137.92       178.32 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GC TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GK 
       18.18       125.19        79.59        26.43       241.38       170.20 
TCGA-D3-A8GL TCGA-D3-A8GQ TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 
       89.13        29.06        54.67         3.65         7.10        15.39 
TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 
        9.90        77.56        22.95       144.89       222.51       176.55 
TCGA-DA-A1I4 TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-DA-A95W 
       35.93        40.60        33.93        10.49        43.36        37.35 
TCGA-DA-A95X TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A5VV 
       73.94        13.02        13.87        20.35        58.92         7.04 
TCGA-EB-A6L9 TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
       36.46        27.22         8.65        33.73        14.70        26.89 
TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29E 
      133.81       151.27        91.56        63.35        85.08        63.78 
TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T 
       56.84        56.42        66.74        14.47        61.28       369.93 
TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2GC TCGA-EE-A2GE 
      195.02       115.96        59.64        39.29        67.43       173.79 
TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN 
      220.24        48.72       107.38        54.74        79.66       102.12 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 
       13.91        42.77        44.88        21.67       129.27        28.83 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MH 
       19.76        61.51        47.28       103.27       268.73        16.96 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN 
      204.66        96.23       180.39       216.66       167.90        47.54 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH 
       53.26       124.31        54.51        13.81        41.59       138.81 
TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JE TCGA-EE-A3JH 
      172.18        64.08        34.32       201.80        51.35       134.33 
TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19D 
      152.81        35.44        13.94         9.17        77.75        12.59 
TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19N 
       13.02        26.37       302.07         6.44       131.51        44.09 
TCGA-ER-A19P TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE 
      162.08        49.48         8.88       105.07        43.82        20.15 
TCGA-ER-A2NF TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3PL TCGA-ER-A42K TCGA-ER-A42L 
       28.83       247.04        93.01        33.21        12.95       149.03 
TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE 
       27.85        18.77        38.27        34.82        36.26       104.42 
TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 
      216.92        48.59       228.59       202.65        20.91        28.08 
TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZE TCGA-FS-A1ZG 
        7.79        27.72        48.85       357.37        46.45         9.70 
TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZS 
       47.38        23.93       101.26        74.73        11.41       148.80 
TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 
       26.56        27.09        27.02        77.82        50.14        66.67 
TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-FW-A5DY 
       28.73       174.84        34.03        54.41        17.46        19.30 
TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
        9.90         2.04        15.78       117.93        96.92        10.13 
TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-GN-A4U9 
       64.44        32.48        48.00        39.35        48.89        22.13 
TCGA-GN-A8LK TCGA-GN-A9SD TCGA-HR-A2OG TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X 
       50.10        59.41         0.23        65.88       368.78       297.90 
TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 
        7.23         0.20         0.33         0.69       228.16        63.02 
TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1Q TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K6 
      121.08         4.01        69.07       219.16       105.04        17.95 
TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-A8ZY 
       58.98        70.52        63.22        11.80        35.80        49.51 
TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-XV-AB01 TCGA-YD-A89C TCGA-YD-A9TA 
       12.16        40.41        24.99        13.25         6.90        49.18 
TCGA-YG-AA3O TCGA-Z2-A8RT TCGA-Z2-AA3S 
       37.94        27.58        96.99 

  DEL PEAK 33(19P13.3) MUTATED DEL PEAK 33(19P13.3) WILD-TYPE 
                          4.96                           0.20 
  DEL PEAK 33(19P13.3) MUTATED DEL PEAK 33(19P13.3) WILD-TYPE 
                        248.65                         369.93 
  DEL PEAK 33(19P13.3) MUTATED DEL PEAK 33(19P13.3) WILD-TYPE 
                         53.52                          50.14 
[1] "5.0 - 248.7 (53.5)" "0.2 - 369.9 (50.1)"
[1] "hr=" "1.2"
D53V3, continuous
                                vv
clus                             I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB
  DEL PEAK 33(19P13.3) MUTATED          6       1       7        6        8
  DEL PEAK 33(19P13.3) WILD-TYPE        7       6      22       12       20
                                vv
clus                             STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK 33(19P13.3) MUTATED          5         2         5         6
  DEL PEAK 33(19P13.3) WILD-TYPE       21        12        14         9
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 33(19P13.3) MUTATED          13          2         14         17
  DEL PEAK 33(19P13.3) WILD-TYPE        26         13         21         37
                                vv
clus                             STAGE IV
  DEL PEAK 33(19P13.3) MUTATED          4
  DEL PEAK 33(19P13.3) WILD-TYPE       17
D53V4, multiclass
            clus
vv           DEL PEAK 33(19P13.3) MUTATED DEL PEAK 33(19P13.3) WILD-TYPE
  I/II NOS                              6                              7
  STAGE 0                               1                              6
  STAGE I                               7                             22
  STAGE IA                              6                             12
  STAGE IB                              8                             20
  STAGE II                              5                             21
  STAGE IIA                             2                             12
  STAGE IIB                             5                             14
  STAGE IIC                             6                              9
  STAGE III                            13                             26
  STAGE IIIA                            2                             13
  STAGE IIIB                           14                             21
  STAGE IIIC                           17                             37
  STAGE IV                              4                             17
[1] 14  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  DEL PEAK 33(19P13.3) MUTATED      21 22 21 21
  DEL PEAK 33(19P13.3) WILD-TYPE    43 51 60 46
D53V5, multiclass
       clus
vv      DEL PEAK 33(19P13.3) MUTATED DEL PEAK 33(19P13.3) WILD-TYPE
  T0+T1                           21                             43
  T2                              22                             51
  T3                              21                             60
  T4                              21                             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  N3
  DEL PEAK 33(19P13.3) MUTATED    51  19  15  14
  DEL PEAK 33(19P13.3) WILD-TYPE 126  46  24  31
D53V6, multiclass
    clus
vv   DEL PEAK 33(19P13.3) MUTATED DEL PEAK 33(19P13.3) WILD-TYPE
  N0                           51                            126
  N1                           19                             46
  N2                           15                             24
  N3                           14                             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"
D53V7, binary
                                cls
clus                               0   1
  DEL PEAK 33(19P13.3) MUTATED    93   5
  DEL PEAK 33(19P13.3) WILD-TYPE 226  17
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 33(19P13.3) MUTATED     93    5
  DEL PEAK 33(19P13.3) WILD-TYPE  226   17
   clus
vv  DEL PEAK 33(19P13.3) MUTATED DEL PEAK 33(19P13.3) WILD-TYPE
  0                           93                            226
  1                            5                             17
[1] 2 2
[1] FALSE
D53V8, binary
                                cls
clus                              0  1
  DEL PEAK 33(19P13.3) MUTATED   40 27
  DEL PEAK 33(19P13.3) WILD-TYPE 94 63
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 33(19P13.3) MUTATED     40   27
  DEL PEAK 33(19P13.3) WILD-TYPE   94   63
     clus
vv    DEL PEAK 33(19P13.3) MUTATED DEL PEAK 33(19P13.3) WILD-TYPE
  NO                            40                             94
  YES                           27                             63
[1] 2 2
[1] FALSE
D53V9, binary
                                cls
clus                               0   1
  DEL PEAK 33(19P13.3) MUTATED    10  94
  DEL PEAK 33(19P13.3) WILD-TYPE  37 226
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 33(19P13.3) MUTATED     10   94
  DEL PEAK 33(19P13.3) WILD-TYPE   37  226
     clus
vv    DEL PEAK 33(19P13.3) MUTATED DEL PEAK 33(19P13.3) WILD-TYPE
  NO                            10                             37
  YES                           94                            226
[1] 2 2
[1] FALSE
D53V10, continuous
D53V11, binary
                                cls
clus                               0   1
  DEL PEAK 33(19P13.3) MUTATED    44  60
  DEL PEAK 33(19P13.3) WILD-TYPE  94 169
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 33(19P13.3) MUTATED     44   60
  DEL PEAK 33(19P13.3) WILD-TYPE   94  169
        clus
vv       DEL PEAK 33(19P13.3) MUTATED DEL PEAK 33(19P13.3) WILD-TYPE
  FEMALE                           44                             94
  MALE                             60                            169
[1] 2 2
[1] FALSE
D53V12, binary
                                cls
clus                               0   1
  DEL PEAK 33(19P13.3) MUTATED    89  15
  DEL PEAK 33(19P13.3) WILD-TYPE 230  32
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 33(19P13.3) MUTATED     89   15
  DEL PEAK 33(19P13.3) WILD-TYPE  230   32
     clus
vv    DEL PEAK 33(19P13.3) MUTATED DEL PEAK 33(19P13.3) WILD-TYPE
  NO                            89                            230
  YES                           15                             32
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 33(19P13.3) MUTATED       1                         0   101
  DEL PEAK 33(19P13.3) WILD-TYPE     4                         1   252
D53V13, multiclass
                           clus
vv                          DEL PEAK 33(19P13.3) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                              101
                           clus
vv                          DEL PEAK 33(19P13.3) WILD-TYPE
  ASIAN                                                  4
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                252
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V14, binary
                                cls
clus                               0   1
  DEL PEAK 33(19P13.3) MUTATED     1 101
  DEL PEAK 33(19P13.3) WILD-TYPE   6 251
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 33(19P13.3) MUTATED      1  101
  DEL PEAK 33(19P13.3) WILD-TYPE    6  251
                        clus
vv                       DEL PEAK 33(19P13.3) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                          101
                        clus
vv                       DEL PEAK 33(19P13.3) WILD-TYPE
  HISPANIC OR LATINO                                  6
  NOT HISPANIC OR LATINO                            251
[1] 2 2
[1] FALSE

Clustering(54) Variable = DEL PEAK 34(XP21.1) MUTATION ANALYSIS
D54V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 34(XP21.1) MUTATED    27  35
  DEL PEAK 34(XP21.1) WILD-TYPE 101  89
  DEL PEAK 34(XP21.1) MUTATED DEL PEAK 34(XP21.1) WILD-TYPE 
                           62                           190 
  DEL PEAK 34(XP21.1) MUTATED DEL PEAK 34(XP21.1) WILD-TYPE 
                           35                            89 
$`DEL PEAK 34(XP21.1) MUTATED`
TCGA-ER-A193 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q8 TCGA-D3-A2J6 TCGA-D3-A2JG 
       19.04        31.89       110.93        19.04        25.64       107.61 
TCGA-D3-A2JL TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A8GC 
      171.58        58.06        40.01        11.34        42.05        78.21 
TCGA-D3-A8GP TCGA-D3-A8GR TCGA-D9-A1X3 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-DA-A1I5 
      135.12        36.53        10.78        16.90        18.44       110.53 
TCGA-DA-A95X TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29D TCGA-EE-A29Q TCGA-EE-A2A2 
       65.03        75.55        79.20        12.99        61.12        30.02 
TCGA-EE-A2GR TCGA-EE-A2MF TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MS TCGA-EE-A3AD 
        0.20       209.79        89.26       145.45       143.93         4.41 
TCGA-EE-A3AF TCGA-EE-A3J8 TCGA-EE-A3JH TCGA-ER-A19L TCGA-ER-A2ND TCGA-ER-A2NE 
        6.28         3.35        19.86        99.06         4.70        16.87 
TCGA-ER-A2NF TCGA-FR-A7U8 TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1ZG TCGA-FS-A1ZQ 
       10.19        26.20       171.78        49.74         7.82       130.95 
TCGA-FS-A1ZS TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F9 TCGA-FW-A3TU 
      136.27         3.06        30.90        66.67        13.28        55.59 
TCGA-FW-A3TV TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A268 TCGA-GN-A8LK TCGA-LH-A9QB 
       11.54         1.91        53.29        42.48        43.23        85.05 
TCGA-OD-A75X TCGA-W3-AA1R TCGA-W3-AA1V TCGA-WE-A8ZM TCGA-WE-A8ZT TCGA-WE-A8ZY 
      297.01        79.99         8.09        65.42        10.95        48.39 
TCGA-WE-AA9Y TCGA-Z2-AA3S 
        1.94        91.23 

$`DEL PEAK 34(XP21.1) WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A8GI TCGA-EB-A5SG TCGA-EE-A180 
        9.76        62.07        38.76        13.41        33.24        31.96 
TCGA-EE-A20H TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-FR-A729 
      166.75       269.03        52.90       134.40        27.35       216.43 
TCGA-FW-A3R5 TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 
       36.95        52.73         7.40        60.46        12.99        14.83 
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1QA TCGA-D3-A1QB 
        8.42        15.72        49.35       133.25        76.41        62.60 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JH 
       45.99        62.86        15.75       168.00        86.30        36.30 
TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3CF 
       64.83        66.08        43.53       140.98        59.70        24.53 
TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51J 
        9.34        90.21        23.67       173.85        30.67       144.46 
TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D3-A8GD 
       31.76        62.70        45.70       177.86       124.08        23.61 
TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D9-A3Z1 TCGA-D9-A6EC 
      179.97       120.00        69.53        70.62        15.02        69.21 
TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I7 
       22.85        76.34       138.67        68.68       150.61        60.10 
TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-DA-A95V 
       64.83        58.85        30.44       225.11         8.71        72.10 
TCGA-DA-A95W TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN 
        0.76        14.14        12.30         3.91        16.41        52.41 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
       18.21        13.15        24.89        20.38         0.00        26.24 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M 
       75.22        76.14         0.26        44.28        47.41        47.74 
TCGA-EE-A29P TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A6 TCGA-EE-A2GB 
       27.16       346.49       185.19       115.43        77.98        26.14 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
       12.95       201.60        68.65        10.62        32.48        18.35 
TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 
       93.63         0.76        71.31        81.99       103.13        15.25 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2ML 
        5.75        23.77        94.19       171.85        63.25       104.78 
TCGA-EE-A2MP TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC 
      227.01        23.51        53.26       124.31       122.73        64.04 
TCGA-EE-A3AE TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3JB TCGA-EE-A3JI 
       54.51        67.89       111.85        45.90       168.85       135.98 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C 
       34.45        10.49         7.82         4.54        53.29        39.81 
TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P 
       11.47       184.60       150.12        59.84        42.51       120.76 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NG 
       49.71        47.18       146.63        73.05        22.36        28.67 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A3YN 
      173.29        68.52        15.48        32.05        74.47         4.50 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FS-A1Z0 TCGA-FS-A1Z3 
      174.21         4.14         5.65        10.06       195.98         8.35 
TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZJ TCGA-FS-A1ZM 
       27.62       312.07        32.78        43.92        36.33        78.61 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F8 TCGA-FS-A4FD 
       35.28         4.47        23.21         5.29       173.19        80.68 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 
       19.30         9.90        18.25       117.93        96.92        17.06 
TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-GN-A9SD TCGA-QB-A6FS 
        7.59       120.53        34.49        46.92        59.41         7.23 
TCGA-RP-A690 TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1Q 
        0.20         0.33       174.12         1.97       120.07        44.05 
TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ 
      185.13        92.84        47.54        12.69        21.90        62.89 
TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-XV-AB01 TCGA-YG-AA3O 
       37.32        24.99         6.61        28.21 

  DEL PEAK 34(XP21.1) MUTATED DEL PEAK 34(XP21.1) WILD-TYPE 
                          0.2                           0.0 
  DEL PEAK 34(XP21.1) MUTATED DEL PEAK 34(XP21.1) WILD-TYPE 
                       297.01                        346.49 
  DEL PEAK 34(XP21.1) MUTATED DEL PEAK 34(XP21.1) WILD-TYPE 
                       42.265                        47.295 
[1] "0.2 - 297.0 (42.3)" "0.0 - 346.5 (47.3)"
[1] "hr=" "1.4"
D54V2, survival
                               sevent
clus2                             0   1
  DEL PEAK 34(XP21.1) MUTATED    38  46
  DEL PEAK 34(XP21.1) WILD-TYPE 128 146
  DEL PEAK 34(XP21.1) MUTATED DEL PEAK 34(XP21.1) WILD-TYPE 
                           84                           274 
  DEL PEAK 34(XP21.1) MUTATED DEL PEAK 34(XP21.1) WILD-TYPE 
                           46                           146 
$`DEL PEAK 34(XP21.1) MUTATED`
TCGA-ER-A193 TCGA-FS-A1ZF TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q8 TCGA-D3-A2J6 
       31.40        15.45       112.04       112.57        28.08        43.43 
TCGA-D3-A2JG TCGA-D3-A2JL TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CC TCGA-D3-A51N 
      113.52       171.58        58.06        46.98        86.93        22.62 
TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GO TCGA-D3-A8GC TCGA-D3-A8GP TCGA-D3-A8GR 
       26.89       125.79       137.92        79.59       152.75       129.63 
TCGA-D9-A148 TCGA-D9-A1X3 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-DA-A1HW TCGA-DA-A1I5 
      151.53        18.12        22.29        18.44        36.03       135.02 
TCGA-DA-A1I8 TCGA-DA-A95X TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I 
       53.92        73.94         4.96       151.27        91.56        13.55 
TCGA-EE-A29D TCGA-EE-A29Q TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A2 TCGA-EE-A2GC 
       13.97        66.74        25.87        17.92        59.64        67.43 
TCGA-EE-A2GR TCGA-EE-A2MF TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MS TCGA-EE-A3AD 
       42.77       268.73       180.39       167.90       162.48        28.77 
TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J8 TCGA-EE-A3JH TCGA-ER-A19L TCGA-ER-A2ND 
       13.81       138.81        34.32       134.33       131.51        23.34 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NH TCGA-FR-A7U8 TCGA-FS-A1YW TCGA-FS-A1YY 
       20.15        28.83        41.56        27.85       216.92       228.59 
TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZZ 
        9.70        32.75       133.55        11.41       148.80        27.02 
TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FW-A3TU TCGA-FW-A3TV 
       77.82        66.67        34.03        26.73        55.59        13.51 
TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A268 TCGA-GN-A8LK TCGA-LH-A9QB 
        2.04        15.78       139.89        62.79        50.10       368.78 
TCGA-OD-A75X TCGA-W3-AA1R TCGA-W3-AA1V TCGA-WE-A8JZ TCGA-WE-A8ZM TCGA-WE-A8ZT 
      297.90       111.09        42.08        24.03       101.33        11.80 
TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-YD-A9TA TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S 
       49.51        12.16        49.18        14.43        27.58        96.99 

$`DEL PEAK 34(XP21.1) WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-D3-A8GI TCGA-EB-A5SG 
       27.65        62.07        46.32        13.87        58.52        68.25 
TCGA-EB-A5SH TCGA-EE-A180 TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD 
       54.02        94.98        68.15       168.26         2.60       340.14 
TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A198 TCGA-FR-A729 TCGA-FW-A3R5 
      126.81       134.40        27.35        50.76       220.80        36.95 
TCGA-QB-AA9O TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD 
       18.05        61.15        21.40        17.03        66.48        12.99 
TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 
       14.93        16.57        16.67        71.80       133.25        31.59 
TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA 
       90.90        95.74       103.10        65.49        23.77       115.53 
TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JN 
      168.00        86.76        11.87        42.08        12.10        66.48 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3CF 
       66.08        59.57       130.72       166.52        60.23        24.53 
TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F 
        9.34       103.59        39.75        45.30       174.84        55.73 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A5GR 
       56.35       145.12        32.94        63.81       135.75       178.32 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GJ 
       18.18       125.19        30.84        23.61        26.43       241.38 
TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GQ TCGA-D3-A8GS 
      170.20        89.13       107.15       161.00        29.06       117.17 
TCGA-D3-A8GV TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A6E9 
      167.70        54.67         3.65         7.10        15.39         9.90 
TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I0 
       25.18        77.56        22.95        76.57       144.89        20.38 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IB 
      222.51       176.55        35.93        88.87        65.92        40.60 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-DA-A95V 
       68.09        33.93        10.49       225.96        43.36        72.10 
TCGA-DA-A95W TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH 
       37.35        14.14        13.02        13.87        10.36        20.35 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
       29.29        58.92         7.04        36.46        29.82        27.22 
TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A29A 
        8.65        33.73        14.70        26.89       133.81        63.35 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M 
       85.08        78.97        63.78        72.07        64.64        56.84 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29W 
       18.61        56.42        14.47        61.28       369.93       195.02 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE 
       46.82       115.96        39.29        86.14        59.28       173.79 
TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
      220.24        48.72       107.38        54.74        79.66        75.48 
TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 
      102.12        13.91        81.21        44.88        94.82        21.67 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME 
      129.27        28.83        19.76        61.51        47.28       103.27 
TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MN 
      103.20        16.96       204.66        96.23       216.66        47.54 
TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB 
      248.65        43.23        71.21        53.26       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 
       64.04        54.51        41.59       172.18       127.20        36.95 
TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JE TCGA-EE-A3JI TCGA-ER-A195 
       64.08        53.19       201.80        51.35       152.81        35.44 
TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D 
       13.94         9.17        77.75        98.40        48.89        12.59 
TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19M 
       13.02        26.37       302.07       152.35         6.44        61.05 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W 
       44.09       162.08        50.89        49.48         8.88       148.18 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
      105.07        43.82        48.99       247.04        93.01        46.98 
TCGA-ER-A3PL TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       33.21        12.95       149.03        92.98       174.21        15.72 
TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YX 
       18.77        38.27        34.82        36.26       104.42        48.59 
TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB 
      202.65        20.91        28.08         7.79        27.72        48.85 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM 
      357.37        53.52        46.45        47.38        23.93       101.26 
TCGA-FS-A1ZP TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F2 
       74.73        53.16        26.56        49.48        27.09        50.14 
TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A5DY 
       28.73       174.84        54.41        80.68        17.46        19.30 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
        9.90        19.43       117.93        96.92        10.13        64.44 
TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 
       32.48        48.00       121.91        39.35        10.42        48.89 
TCGA-GN-A4U9 TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OG TCGA-HR-A2OH TCGA-QB-A6FS 
       22.13        21.37        59.41         0.23        65.88         7.23 
TCGA-RP-A690 TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 
        0.20         0.33         0.69       228.16        63.02       121.08 
TCGA-W3-AA1O TCGA-W3-AA1Q TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K6 
        4.01        69.07       219.16       105.04        49.05        17.95 
TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZX TCGA-WE-AAA0 TCGA-WE-AAA4 
       58.98        70.52        63.22        35.80        40.41        24.99 
TCGA-XV-AB01 TCGA-YD-A89C TCGA-YG-AA3O TCGA-Z2-AA3V 
       13.25         6.90        37.94        15.98 

  DEL PEAK 34(XP21.1) MUTATED DEL PEAK 34(XP21.1) WILD-TYPE 
                         2.04                          0.20 
  DEL PEAK 34(XP21.1) MUTATED DEL PEAK 34(XP21.1) WILD-TYPE 
                       368.78                        369.93 
  DEL PEAK 34(XP21.1) MUTATED DEL PEAK 34(XP21.1) WILD-TYPE 
                       49.805                        53.175 
[1] "2.0 - 368.8 (49.8)" "0.2 - 369.9 (53.2)"
[1] "hr=" "1"  
D54V3, continuous
                               vv
clus                            I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB
  DEL PEAK 34(XP21.1) MUTATED          4       3       4        1        7
  DEL PEAK 34(XP21.1) WILD-TYPE        9       4      25       17       21
                               vv
clus                            STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK 34(XP21.1) MUTATED          8         2        10         3
  DEL PEAK 34(XP21.1) WILD-TYPE       18        12         9        12
                               vv
clus                            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 34(XP21.1) MUTATED           5          2          7         15
  DEL PEAK 34(XP21.1) WILD-TYPE        34         13         28         39
                               vv
clus                            STAGE IV
  DEL PEAK 34(XP21.1) MUTATED          7
  DEL PEAK 34(XP21.1) WILD-TYPE       14
D54V4, multiclass
            clus
vv           DEL PEAK 34(XP21.1) MUTATED DEL PEAK 34(XP21.1) WILD-TYPE
  I/II NOS                             4                             9
  STAGE 0                              3                             4
  STAGE I                              4                            25
  STAGE IA                             1                            17
  STAGE IB                             7                            21
  STAGE II                             8                            18
  STAGE IIA                            2                            12
  STAGE IIB                           10                             9
  STAGE IIC                            3                            12
  STAGE III                            5                            34
  STAGE IIIA                           2                            13
  STAGE IIIB                           7                            28
  STAGE IIIC                          15                            39
  STAGE IV                             7                            14
[1] 14  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3 T4
  DEL PEAK 34(XP21.1) MUTATED      13 13 23 17
  DEL PEAK 34(XP21.1) WILD-TYPE    51 60 58 50
D54V5, multiclass
       clus
vv      DEL PEAK 34(XP21.1) MUTATED DEL PEAK 34(XP21.1) WILD-TYPE
  T0+T1                          13                            51
  T2                             13                            60
  T3                             23                            58
  T4                             17                            50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  DEL PEAK 34(XP21.1) MUTATED    42  16   5  12
  DEL PEAK 34(XP21.1) WILD-TYPE 135  49  34  33
D54V6, multiclass
    clus
vv   DEL PEAK 34(XP21.1) MUTATED DEL PEAK 34(XP21.1) WILD-TYPE
  N0                          42                           135
  N1                          16                            49
  N2                           5                            34
  N3                          12                            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"
D54V7, binary
                               cls
clus                              0   1
  DEL PEAK 34(XP21.1) MUTATED    70   8
  DEL PEAK 34(XP21.1) WILD-TYPE 249  14
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 34(XP21.1) MUTATED     70    8
  DEL PEAK 34(XP21.1) WILD-TYPE  249   14
   clus
vv  DEL PEAK 34(XP21.1) MUTATED DEL PEAK 34(XP21.1) WILD-TYPE
  0                          70                           249
  1                           8                            14
[1] 2 2
[1] FALSE
D54V8, binary
                               cls
clus                              0   1
  DEL PEAK 34(XP21.1) MUTATED    26  24
  DEL PEAK 34(XP21.1) WILD-TYPE 108  66
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 34(XP21.1) MUTATED     26   24
  DEL PEAK 34(XP21.1) WILD-TYPE  108   66
     clus
vv    DEL PEAK 34(XP21.1) MUTATED DEL PEAK 34(XP21.1) WILD-TYPE
  NO                           26                           108
  YES                          24                            66
[1] 2 2
[1] FALSE
D54V9, binary
                               cls
clus                              0   1
  DEL PEAK 34(XP21.1) MUTATED     8  78
  DEL PEAK 34(XP21.1) WILD-TYPE  39 242
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 34(XP21.1) MUTATED      8   78
  DEL PEAK 34(XP21.1) WILD-TYPE   39  242
     clus
vv    DEL PEAK 34(XP21.1) MUTATED DEL PEAK 34(XP21.1) WILD-TYPE
  NO                            8                            39
  YES                          78                           242
[1] 2 2
[1] FALSE
D54V10, continuous
D54V11, binary
                               cls
clus                              0   1
  DEL PEAK 34(XP21.1) MUTATED    37  49
  DEL PEAK 34(XP21.1) WILD-TYPE 101 180
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 34(XP21.1) MUTATED     37   49
  DEL PEAK 34(XP21.1) WILD-TYPE  101  180
        clus
vv       DEL PEAK 34(XP21.1) MUTATED DEL PEAK 34(XP21.1) WILD-TYPE
  FEMALE                          37                           101
  MALE                            49                           180
[1] 2 2
[1] FALSE
D54V12, binary
                               cls
clus                              0   1
  DEL PEAK 34(XP21.1) MUTATED    71  15
  DEL PEAK 34(XP21.1) WILD-TYPE 248  32
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 34(XP21.1) MUTATED     71   15
  DEL PEAK 34(XP21.1) WILD-TYPE  248   32
     clus
vv    DEL PEAK 34(XP21.1) MUTATED DEL PEAK 34(XP21.1) WILD-TYPE
  NO                           71                           248
  YES                          15                            32
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 34(XP21.1) MUTATED       0                         0    84
  DEL PEAK 34(XP21.1) WILD-TYPE     5                         1   269
D54V13, multiclass
                           clus
vv                          DEL PEAK 34(XP21.1) MUTATED
  ASIAN                                               0
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                              84
                           clus
vv                          DEL PEAK 34(XP21.1) WILD-TYPE
  ASIAN                                                 5
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                               269
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V14, binary
                               cls
clus                              0   1
  DEL PEAK 34(XP21.1) MUTATED     2  82
  DEL PEAK 34(XP21.1) WILD-TYPE   5 270
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 34(XP21.1) MUTATED      2   82
  DEL PEAK 34(XP21.1) WILD-TYPE    5  270
                        clus
vv                       DEL PEAK 34(XP21.1) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          82
                        clus
vv                       DEL PEAK 34(XP21.1) WILD-TYPE
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                           270
[1] 2 2
[1] FALSE
