assess_decoy_rate {SWATH2stats} | R Documentation

## Assess decoy rate in data

### 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)

[Package SWATH2stats version 1.20.1 Index]