OpenSWATHtoMSstatsFormat: Generate MSstats required input format for OpenSWATH output

Description Usage Arguments Value Author(s) Examples

View source: R/OpenSWATHtoMSstatsFormat.R

Description

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

Usage

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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 (mnchoi67@gmail.com)

Examples

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# Example will be ready in next version.

Example output



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