apply_filter {MSnID} | R Documentation |
Filter out peptide-to-spectrum MS/MS identifications.
apply_filter(msnidObj, filterObj)
msnidObj |
An instance of class "MSnID". |
filterObj |
Either an instance of MSnIDFilter
class or a |
filterObj
argument
evaluated to a "logical"
for each entry of the
MS/MS results table.
Returns an instance of "MSnID" class with with peptide-to-spectrum
matches that pass criteria defined in filterObj
argument.
Vladislav A Petyuk vladislav.petyuk@pnnl.gov
data(c_elegans) ## Filtering using string: msnidObj <- assess_termini(msnidObj, validCleavagePattern="[KR]\\.[^P]") table(msnidObj$numIrregCleavages) # getting rid of any other peptides except fully tryptic msnidObj <- apply_filter(msnidObj, "numIrregCleavages == 0") show(msnidObj) ## Filtering using filter object: # first adding columns that will be used as filters msnidObj$msmsScore <- -log10(msnidObj$`MS-GF:SpecEValue`) msnidObj$mzError <- abs(msnidObj$experimentalMassToCharge - msnidObj$calculatedMassToCharge) # setting up filter object filtObj <- MSnIDFilter(msnidObj) filtObj$msmsScore <- list(comparison=">", threshold=10.0) filtObj$mzError <- list(comparison="<", threshold=0.1) # 0.1 Thomson show(filtObj) # applying filter and comparing MSnID object before and after show(msnidObj) msnidObj <- apply_filter(msnidObj, filtObj) show(msnidObj)