DIAUmpiretoMSstatsFormat {MSstats} | R Documentation |
Convert DIA-Umpire output into the required input format for MSstats.
DIAUmpiretoMSstatsFormat(raw.frag, raw.pep, raw.pro, annotation, useSelectedFrag = TRUE, useSelectedPep = TRUE, fewMeasurements="remove", removeProtein_with1Feature = FALSE, summaryforMultipleRows=max)
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. |
data.frame with the required format of MSstats.
Meena Choi, Olga Vitek.
Maintainer: Meena Choi (mnchoi67@gmail.com)
# Manual will be updated. # Output of DIAUmpiretoMSstatsFormat function # should have the same 10 columns as an example dataset. head(DDARawData)