ngstk (version 0.1.0)

muts2mutation_mapper: Function to convert mutation data to MutationMapper http://www.cbioportal.org/mutation_mapper.jsp input format.

Description

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

Usage

muts2mutation_mapper(input_data, input_type = "iseq",
  config_file = system.file("extdata", "config/cbioportal.toml", package =
  "ngstk"), config_list = NULL, hander_confg_file = system.file("extdata",
  "config/hander.toml", package = "ngstk"),
  mhander_confg_file = system.file("extdata", "config/mhander.toml", package =
  "ngstk"), hander_funs = NULL, mhander_funs = NULL,
  hander_extra_params = NULL, mhander_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

hander_confg_file

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

mhander_confg_file

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

hander_funs

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

mhander_funs

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

hander_extra_params

Extra parameters pass to handler

mhander_extra_params

Extra parameters pass to mhandler

outfn

Default is NULL and not output the result to file

Value

A data frame

Examples

Run this code
# NOT RUN {
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')
# }

Run the code above in your browser using DataCamp Workspace