Description Usage Arguments Details Value Author(s) See Also Examples
Filter out peptide-to-spectrum MS/MS identifications.
1 | 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
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 | 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)
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