Function to convert mutation data to MutationMapper http://www.cbioportal.org/mutation_mapper.jsp input format.

muts2mutation_mapper(input_data, input_type = "iseq",
  config_file = system.file("extdata", "config/cbioportal.toml", package =
  "ngstk"), config_list = NULL, handler_confg_file = system.file("extdata",
  "config/handler.toml", package = "ngstk"),
  mhandler_confg_file = system.file("extdata", "config/mhandler.toml", package
  = "ngstk"), handler_funs = NULL, mhandler_funs = NULL,
  handler_extra_params = NULL, mhandler_extra_params = NULL, outfn = NULL)

Arguments

input_data

A mutation data.frame need to be converted to ProteinPaint input.

input_type

Point the input data format (iseq or others)

config_file

ngstk ProteinPaint configuration file path, default is system.file('extdata', 'config/proteinpaint.toml', package = 'ngstk')

config_list

ngstk ProteinPaint configuration, default is NULL and read from config_file

handler_confg_file

ngstk handler configuration file path, default is system.file('extdata', 'config/handler.toml', package = 'ngstk')

mhandler_confg_file

ngstk handler configuration file path, default is system.file('extdata', 'config/mhandler.toml', package = 'ngstk')

handler_funs

handler function for single colnum, default is NULL and get value from config_file

mhandler_funs

handler function for mulitple colnums, #' default is NULL and get value from config_file

handler_extra_params

Extra parameters pass to handler

mhandler_extra_params

Extra parameters pass to mhandler

outfn

Default is NULL and not output the result to file

Value

A data frame

Examples

demo_file <- system.file('extdata', 'demo/proteinpaint/muts2pp_iseq.txt', package = 'ngstk') input_data <- read.table(demo_file, sep = '\t', header = TRUE, stringsAsFactors = FALSE) disease <- 'T-ALL' input_data <- data.frame(input_data, disease) input_data$disease <- as.character(input_data$disease) muts2mutation_mapper(input_data, input_type = 'iseq')
#> Warning: Validation_Status were not exists or not be recognize correctly in input data!
#> Warning: Mutation_Status were not exists or not be recognize correctly in input data!
#> Warning: Center were not exists or not be recognize correctly in input data!
#> Hugo_Symbol Sample_ID Protein_Change Mutation_Type Chromosome #> 1 IDH1 A1 R132S Missense_Mutation chr2 #> 2 PTPRC A2 A694T Missense_Mutation chr1 #> 3 PTPRC A3 I281fs Frame_Shift_Ins chr1 #> 4 ASPM A4 L1061F Missense_Mutation chr1 #> 5 ASPM A5 Q2465R Missense_Mutation chr1 #> 6 FAT1 A6 L210F Missense_Mutation chr4 #> 7 FAT1 A7 H3955Y Missense_Mutation chr4 #> 8 GNB4 A8 H91delinsSH In_Frame_Ins chr3 #> 9 KMT2C A9 Y1348X Nonsense_Mutation chr7 #> 10 KMT2C A10 P1855L Missense_Mutation chr7 #> 11 KMT2C A11 S2132F Missense_Mutation chr7 #> 12 KMT2C A12 R3850X Nonsense_Mutation chr7 #> 13 EZH2 A13 T517I Missense_Mutation chr7 #> 14 EZH2 A14 L615delinsDL In_Frame_Ins chr7 #> 15 EZH2 A15 F616delinsCL In_Frame_Ins chr7 #> 16 EZH2 A16 V624M Missense_Mutation chr7 #> 17 EZH2 A17 R628C Missense_Mutation chr7 #> 18 EZH2 A18 R634H Missense_Mutation chr7 #> 19 NOTCH1 A19 M2392fs Frame_Shift_Ins chr9 #> 20 NOTCH1 A20 Q2393X Nonsense_Mutation chr9 #> 21 NOTCH1 A21 P2462fs Frame_Shift_Del chr9 #> 22 NOTCH1 A22 S2467fs Frame_Shift_Ins chr9 #> 23 NOTCH1 A23 S2467X Nonsense_Mutation chr9 #> Start_Position End_Position Reference_Allele Variant_Allele #> 1 209113113 209113113 G T #> 2 198711362 198711362 G A #> 3 198685843 198685843 - T #> 4 197093449 197093449 G A #> 5 197070987 197070987 T C #> 6 187630354 187630354 G A #> 7 187521292 187521292 G A #> 8 179132832 179132832 - GGA #> 9 151900067 151900067 G T #> 10 151879381 151879381 G A #> 11 151878550 151878550 G A #> 12 151856070 151856070 G A #> 13 148511184 148511184 G A #> 14 148507443 148507443 - ATC #> 15 148507439 148507439 - GGC #> 16 148506474 148506474 C T #> 17 148506462 148506462 G A #> 18 148506443 148506443 C T #> 19 139391015 139391015 - TGTTG #> 20 139391014 139391014 G A #> 21 139390805 139390805 G - #> 22 139390792 139390792 - CGAGGGAAAGCTCCACC #> 23 139390791 139390791 G T #> Validation_Status Mutation_Status Center #> 1 NA NA NA #> 2 NA NA NA #> 3 NA NA NA #> 4 NA NA NA #> 5 NA NA NA #> 6 NA NA NA #> 7 NA NA NA #> 8 NA NA NA #> 9 NA NA NA #> 10 NA NA NA #> 11 NA NA NA #> 12 NA NA NA #> 13 NA NA NA #> 14 NA NA NA #> 15 NA NA NA #> 16 NA NA NA #> 17 NA NA NA #> 18 NA NA NA #> 19 NA NA NA #> 20 NA NA NA #> 21 NA NA NA #> 22 NA NA NA #> 23 NA NA NA