artmsEvidenceToSaintExpress {artMS}R Documentation

MaxQuant evidence file to SAINTexpress format

Description

Converts the MaxQuant evidence file to the 3 required files by SAINTexpress. One can choose to either use the spectral counts (use msspc) or the intensities (use msint) for the analysis.

Usage

artmsEvidenceToSaintExpress(evidence_file, keys_file, ref_proteome_file,
  quant_variable = c("msspc", "msint"), output_file, verbose = TRUE)

Arguments

evidence_file

(char) The evidence file path and name

keys_file

(char) Keys file with a SAINT column specifying test (T) and control (C) conditions

ref_proteome_file

(char) Reference proteome path file name in fasta format

quant_variable

(char) choose either

  • msspc (spectral counts, default) or

  • msint (MS Intensity)

output_file

(char) Output file name (must have extension .txt)

verbose

(logical) TRUE (default) shows function messages

Value

The 3 required files by SAINTexpress:

Examples

# Testing that the files cannot be empty
artmsEvidenceToSaintExpress(evidence_file = NULL, 
keys_file = NULL, ref_proteome_file = NULL)

[Package artMS version 1.2.5 Index]