Function to convert mutation data to Oncoprinter http://www.cbioportal.org/oncoprinter.jsp input format.

muts2oncoprinter(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) muts2oncoprinter(input_data, input_type = 'iseq')
#> Sample Gene Alteration Type #> 1 A1 IDH1 R132S MISSENSE #> 2 A2 PTPRC A694T MISSENSE #> 3 A3 PTPRC I281fs TRUNC #> 4 A4 ASPM L1061F MISSENSE #> 5 A5 ASPM Q2465R MISSENSE #> 6 A6 FAT1 L210F MISSENSE #> 7 A7 FAT1 H3955Y MISSENSE #> 8 A8 GNB4 H91delinsSH INFRAME #> 9 A9 KMT2C Y1348X TRUNC #> 10 A10 KMT2C P1855L MISSENSE #> 11 A11 KMT2C S2132F MISSENSE #> 12 A12 KMT2C R3850X TRUNC #> 13 A13 EZH2 T517I MISSENSE #> 14 A14 EZH2 L615delinsDL INFRAME #> 15 A15 EZH2 F616delinsCL INFRAME #> 16 A16 EZH2 V624M MISSENSE #> 17 A17 EZH2 R628C MISSENSE #> 18 A18 EZH2 R634H MISSENSE #> 19 A19 NOTCH1 M2392fs TRUNC #> 20 A20 NOTCH1 Q2393X TRUNC #> 21 A21 NOTCH1 P2462fs TRUNC #> 22 A22 NOTCH1 S2467fs TRUNC #> 23 A23 NOTCH1 S2467X TRUNC