parse_MaxQuant {wilson}

Converting MaxQuant Output file proteinGroups.txt to CLARION format by creating a headline of metadata for each column

Description

List with columns of reduced version (see config.json file) If you only want the samples of a specific keyword write: column;exp For example: You got: Intensity Intensity 'experiment_name' Do you want both add "Intensity" to the list. Do you only want the sample add "Intensity;exp" to the list Anything else like 'Intensity;ex' or 'Intensity;' results in writing both. Only works if there are samples of that type. If not, column does not show up in file

Usage

parse_MaxQuant(
  proteinGroups_in,
  summary_in,
  outfile,
  outfile_reduced,
  config = system.file("extdata", "parser_MaxQuant_config.json", package = "wilson"),
  delimiter = ";",
  format = NULL,
  version = NULL,
  experiment_id = NULL
)

Arguments

proteinGroups_in

path of proteinGroup.txt file

summary_in

path of belonging summary.txt file

outfile

path of full CLARION output file

outfile_reduced

path of reduced CLARION output file

config

path of config file (containing information about metadata)

delimiter

delimiter (Default = ;)

format

pre-header information about format (optional)

version

pre-header information about version (optional)

experiment_id

pre-header information about experiment id (optional)

Value

TRUE on success

Author(s)

Rene Wiegandt