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

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

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.

Value

data.frame with the required format of MSstats.

Author(s)

Meena Choi, Olga Vitek.

Maintainer: Meena Choi ([e-mail])

Examples

# 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.