muts2oncoprinter: Function to convert mutation data to cbioportal Oncoprinter...

In JhuangLab/ngstk: Next-Generation Sequencing (NGS) Data Analysis Toolkit

Description

Function to convert mutation data to cbioportal Oncoprinter format.

Usage

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')

JhuangLab/ngstk documentation built on May 28, 2019, 12:43 p.m.