Description Usage Arguments Value Author(s) See Also Examples
Filter out peptide-to-spectrum MS/MS identifications.
1 | evaluate_filter(object, filter, level=c("PSM", "peptide", "accession"))
|
object |
An instance of class "MSnID". |
filter |
Either an instance of MSnIDFilter class or a |
level |
Level at which the filter will be evaluated. Possible values are "PSM", "peptide" and "accession". Multiple are OK. Default is all of them. |
Returns a matrix with with column names "fdr" and "n". Column "n" contains the number of features (spectra, peptides or proteins/accessions) passing the filter. Column "fdr" is the false discovery rate (i.e. identification confidence) for the corresponding features. Row names correspond to the provided levels.
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 | data(c_elegans)
## Filtering using string:
msnidObj <- assess_termini(msnidObj, validCleavagePattern="[KR]\\.[^P]")
table(msnidObj$numIrregCleavages)
evaluate_filter(msnidObj, "numIrregCleavages == 0")
## Filtering using filter object:
# first adding columns that will be used as filters
msnidObj$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)
evaluate_filter(msnidObj, filtObj)
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