ProgenesistoMSstatsFormat {MSstats} | R Documentation |
Convert Progenesis output into the required input format for MSstats.
ProgenesistoMSstatsFormat(input, annotation, useUniquePeptide=TRUE, summaryforMultipleRows=max, fewMeasurements="remove", removeOxidationMpeptides=FALSE, removeProtein_with1Peptide=FALSE)
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. |
data.frame with the required format of MSstats.
Meena Choi, Olga Vitek.
Maintainer: Meena Choi (mnchoi67@gmail.com)
# 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)