evaluate_filter: Filters the MS/MS identifications

In MSnID: Utilities for Exploration and Assessment of Confidence of LC-MSn Proteomics Identifications

Description

Filter out peptide-to-spectrum MS/MS identifications.

Usage

    evaluate_filter(object, filter, level=c("PSM", "peptide", "accession"))

Arguments

object	An instance of class "MSnID".
filter	Either an instance of MSnIDFilter class or a "character".
level	Level at which the filter will be evaluated. Possible values are "PSM", "peptide" and "accession". Multiple are OK. Default is all of them.

Value

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.

Author(s)

Vladislav A Petyuk [e-mail]

See Also

MSnID id_quality

Examples

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)

MSnID documentation built on Nov. 8, 2020, 8:03 p.m.