removeDecoyProteins {SWATH2stats} | R Documentation

## Removes decoy proteins from the protein group label

### Description

There exist peptides annotated as protein groups with 2/ProteinA/DECOY_ProteinB. However these are in principal proteotypic peptides and should be annoated 1/ProteinA. This function changes these labels accordingly. The subfunction rmDecoyProt removes the Decoy protein, calling removeDecoyProteins also changes the nubmer before the protein group accordingly.

### Usage

    removeDecoyProteins(data, column = "ProteinName", decoy_string = "DECOY")

### Arguments

`data` | A data frame containing SWATH data.
`column` | Column to query for decoy string
`decoy_string` | String defining a decoy. Default: DECOY

### Value

Returns a data frame with changed protein labels

### Author(s)

Moritz Heusel

### Examples

     data("OpenSWATH_data", package="SWATH2stats")
     data("Study_design", package="SWATH2stats")
     data <- sample_annotation(OpenSWATH_data, Study_design)
     data.filtered.decoy <- filter_mscore(data, 0.01)
     data.2 <- removeDecoyProteins(data.filtered.decoy)

[Package SWATH2stats version 1.24.0 Index]