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)

Arguments

data

A data frame containing SWATH data.

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 1.12.1 Index]