DIAUmpiretoMSstatsFormat: Generate MSstats required input format for DIA-Umpire output

Description Usage Arguments Value Author(s) Examples

View source: R/DIAUmpiretoMSstatsFormat.R

Description

Convert DIA-Umpire output into the required input format for MSstats.

Usage

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DIAUmpiretoMSstatsFormat(raw.frag, raw.pep, raw.pro,
    annotation,
    useSelectedFrag = TRUE,
    useSelectedPep = TRUE,
    fewMeasurements="remove",
    removeProtein_with1Feature = FALSE,
    summaryforMultipleRows=max)	

Arguments

raw.frag

name of FragSummary_date.xls data, which includes feature-level data.

raw.pep

name of PeptideSummary_date.xls data, which includes selected fragments information.

raw.pro

name of ProteinSummary_date.xls data, which includes selected peptides information.

annotation

name of annotation data which includes Condition, BioReplicate, Run information.

useSelectedFrag

TRUE will use the selected fragment for each peptide. 'Selected_fragments' column is required.

useSelectedPep

TRUE will use the selected peptide for each protein. 'Selected_peptides' column is required.

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 feature, which is the combination of peptide, precursor charge, fragment 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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# Manual will be updated.
# Output of DIAUmpiretoMSstatsFormat function 
# should have the same 10 columns as an example dataset.

head(DDARawData)

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