removeDecoyProteins: Removes decoy proteins from the protein group label

Description Usage Arguments Value Author(s) Examples

View source: R/removeDecoyProteins.R

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

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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

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 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)

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