OpenSWATHtoMSstatsFormat: Generate MSstats required input format for OpenSWATH output

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

Description

Preprocess MSstats input report from OpenSWATH and convert into the required input format for MSstats.

Usage

OpenSWATHtoMSstatsFormat(input,
    annotation = NULL,
    filter_with_mscore = TRUE,
    mscore_cutoff = 0.01,
    useUniquePeptide = TRUE,
    fewMeasurements="remove",
    removeProtein_with1Feature = FALSE,
    summaryforMultipleRows=max)	

Arguments

input	name of MSstats input report from OpenSWATH, which includes feature-level data.
annotation	name of 'annotation.txt' data which includes Condition, BioReplicate, Run. Run should be the same as filename.
filter_with_mscore	TRUE(default) will filter out the features that have greater than mscore_cutoff in m_score column. Those features will be removed.
mscore_cutoff	Cutoff for m_score. default is 0.01.
useUniquePeptide	TRUE(default) removes peptides that are assigned for more than one proteins. We assume to use unique peptide for each protein.
fewMeasurements	'remove' (default) will remove the features that have 1 or 2 measurements across runs.
removeProtein_with1Feature	TRUE will remove the proteins which have only 1 peptide and charge. FALSE is default.
summaryforMultipleRows	max(default) or sum - when there are multiple measurements for certain feature and certain run, use highest or sum of multiple intensities.

Value

data.frame with the required format of MSstats.

Author(s)

Meena Choi, Olga Vitek.

Maintainer: Meena Choi ([e-mail])

Examples

# Example will be ready in next version.

Example output

MSstats documentation built on Feb. 28, 2021, 2:01 a.m.