artmsEvidenceToSaintExpress: MaxQuant evidence file to SAINTexpress format

In kroganlab/artMS: Analytical R tools for Mass Spectrometry

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:

• interactions.txt

• preys.txt

• baits.txt

Examples

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

kroganlab/artMS documentation built on July 7, 2023, 5:35 a.m.