assess_decoy_rate: Assess decoy rate in data

In SWATH2stats: Transform and Filter SWATH Data for Statistical Packages

Description

This function assesses the number of quantifications (typically peptides) that are decoys (false-positive) versus true identifications.

Usage

assess_decoy_rate(data, column = "FullPeptideName", column_decoy = "decoy")

Arguments

data	A data frame that contains at least a column named "FullPeptideName" and "decoy".
column	The column name of the Peptide identifier. Default: FullPeptideName.
column_decoy	The column name of the decoy column. Default: decoy.

Details

A printout is generated to indicate the number of non-decoy, decoy peptides and the rate of decoy vs non-decoy peptides. Unique peptides are counted, so a precursor with different charge states is counted as one peptide. In the column "decoy" the values need to be 1,0 or TRUE and FALSE.

Value

Message detailing the number of decoys, non-decoys, and the ratio.

Author(s)

Peter Blattmann

Examples

 data("OpenSWATH_data", package="SWATH2stats")
 data <- OpenSWATH_data
 assess_decoy_rate(data)

SWATH2stats documentation built on April 17, 2021, 6:01 p.m.