MaxQtoMSstatsFormat: Generate MSstats required input format for MaxQuant output

In lindsaypino/MSstats-patch: Protein Significance Analysis in DDA, SRM and DIA for Label-free or Label-based Proteomics Experiments

Description

Convert MaxQuant output into the required input format for MSstats.

Usage

MaxQtoMSstatsFormat(evidence, 
      annotation,
      proteinGroups,
      proteinID="Proteins", 
      useUniquePeptide=TRUE, 
      summaryforMultipleRows=max, 
      fewMeasurements="remove", 
      removeMpeptides=FALSE,
      removeOxidationMpeptides=FALSE,
      removeProtein_with1Peptide=FALSE)	

Arguments

evidence	name of 'evidence.txt' data, which includes feature-level data.
annotation	name of 'annotation.txt' data which includes Raw.file, Condition, BioReplicate, Run, IsotopeLabelType information.
proteinGroups	name of 'proteinGroups.txt' data. It needs to matching protein group ID. If proteinGroups=NULL, use 'Proteins' column in 'evidence.txt'.
proteinID	'Proteins'(default) or 'proteinGroups' in 'proteinGroup.txt' for Protein ID.
useUniquePeptide	TRUE(default) removes peptides that are assigned for more than one proteins. We assume to use unique peptide for each protein.
summaryforMultipleRows	max(default) or sum - when there are multiple measurements for certain feature and certain run, use highest or sum of all.
fewMeasurements	'remove'(default) will remove the features that have 1 or 2 measurements across runs.
removeMpeptides	TRUE will remove the peptides including 'M' sequence. FALSE is default.
removeOxidationMpeptides	TRUE will remove the peptides including 'oxidation (M)' in modification. FALSE is default.
removeProtein_with1Peptide	TRUE will remove the proteins which have only 1 peptide and charge. FALSE is default.

Warning

MSstats does not support for metabolic labeling or iTRAQ experiments.

Author(s)

Meena Choi, Olga Vitek.

Maintainer: Meena Choi ([e-mail])

lindsaypino/MSstats-patch documentation built on May 24, 2019, 6 p.m.