id_quality: Identification quality

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

Description

Reports quality for a given level of identification (spectra, peptide or protein).

Usage

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

Arguments

object	An instance of class "MSnID".
filter	Optional argument. 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 evaluate_filter

Examples

data(c_elegans)
id_quality(msnidObj, level="peptide")
id_quality(msnidObj, filter="`MS-GF:PepQValue` < 0.01", level="peptide")

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