assess_decoy_rate: Assess decoy rate in data

Description Usage Arguments Details Value Author(s) Examples

View source: R/assess_decoy_rate.R

Description

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

Usage

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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

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

peterblattmann/SWATH2stats documentation built on April 20, 2021, 12:02 p.m.