DIAUmpiretoMSstatsFormat {MSstats}R Documentation

Generate MSstats required input format for DIA-Umpire output

Description

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

Usage

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.

Author(s)

Meena Choi, Olga Vitek.

Maintainer: Meena Choi (mnchoi67@gmail.com)

Examples

# Manual will be updated.
# Output of DIAUmpiretoMSstatsFormat function 
# should have the same 10 columns as an example dataset.

head(DDARawData)

[Package MSstats version 3.10.6 Index]