Description Usage Arguments Author(s)
View source: R/PDtoMSstatsFormat.R
Convert Proteome discoverer output into the required input format for MSstats.
1 2 3 4 5 6 7 | PDtoMSstatsFormat(input,
annotation,
useUniquePeptide=TRUE,
summaryforMultipleRows=max,
fewMeasurements="remove",
removeOxidationMpeptides=FALSE,
removeProtein_with1Peptide=FALSE)
|
input |
name of Proteome discover PSM output, which is long-format. "Protein.Group.Accessions", "#Proteins", "Sequence", "Modifications", "Charge", "Intensity", "Spectrum.File" are required. |
annotation |
name of 'annotation.txt' or 'annotation.csv' data which includes Condition, BioReplicate, Run information. 'Run' will be matched with 'Spectrum.File'. |
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)' in 'Modifications' column. FALSE is default. |
removeProtein_with1Peptide |
TRUE will remove the proteins which have only 1 peptide and charge. FALSE is default. |
Meena Choi, Olga Vitek.
Maintainer: Meena Choi (mnchoi67@gmail.com)
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