removeDecoyProteins: Removes decoy proteins from the protein group label

In SWATH2stats: Transform and Filter SWATH Data for Statistical Packages

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)

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