ProgenesistoMSstatsFormat: Generate MSstats required input format for Progenesis output

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

Description

Convert Progenesis output into the required input format for MSstats.

Usage

ProgenesistoMSstatsFormat(input,
      annotation,
      useUniquePeptide=TRUE,
      summaryforMultipleRows=max,
      fewMeasurements="remove",
      removeOxidationMpeptides=FALSE,
      removeProtein_with1Peptide=FALSE)	

Arguments

input	name of Progenesis output, which is wide-format. 'Accession', 'Sequence', 'Modification', 'Charge' and one column for each run are required.
annotation	name of 'annotation.txt' or 'annotation.csv' data which includes Condition, BioReplicate, Run information. It will be matched with the column name of input for MS runs.
useUniquePeptide	TRUE(default) removes peptides that are assigned for more than one proteins. We assume to use unique peptide for each protein.
summaryforMultipleRows	max(default) or sum - when there are multiple measurements for certain feature and certain run, use highest or sum of multiple intensities.
fewMeasurements	'remove'(default) will remove the features that have 1 or 2 measurements across runs.
removeOxidationMpeptides	TRUE will remove the modified peptides including 'Oxidation (M)' sequence. FALSE is default.
removeProtein_with1Peptide	TRUE will remove the proteins which have only 1 peptide and charge. FALSE is default.

Value

data.frame with the required format of MSstats.

Author(s)

Meena Choi, Olga Vitek.

Maintainer: Meena Choi ([e-mail])

Examples

# Please check section 4.4. 
# Suggested workflow with Progenesis output for DDA in MSstats user manual.
# Output of ProgenesistoMSstatsFormat function 
# should have the same 10 columns as an example dataset.

head(DDARawData)

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