Function to convert fusion data to ProteinPaint heatmap meta rows https://pecan.stjude.org/pp input format.

fusions2pp_meta(input_data, input_type = "fusioncatcher",
  config_file = system.file("extdata", "config/proteinpaint.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 gene fusions data.frame need to be converted to ProteinPaint input.

input_type

Point the input data format (fusioncatcher 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/fusions2pp_fusioncatcher.txt', package = 'ngstk') input_data <- read.table(demo_file, sep = '\t', header = TRUE, stringsAsFactors = FALSE) disease <- 'B-ALL' sampletype <- 'diagnose' input_data <- data.frame(input_data, disease, sampletype) input_data$disease <- as.character(input_data$disease) #handler_data <- fusions2pp_meta(input_data, input_type = 'fusioncatcher')