readProteinGroups: Read protein groups file from MaxQuant

In bartongroup/Proteus: Downstream analysis of the MaxQuant output

Read protein groups file from MaxQuant

Description

readProteinGroups reads a MaxQuant's protein groups file (usually named proteinGroups.txt), extracts intensity data and creates a proteusData object.

Usage

readProteinGroups(file, meta, measure.cols = NULL, data.cols = proteinColumns)

Arguments

file	Input file
meta	Metadata data frame. As a minimum, it should contain two columns: sample with unique sample names and condition with condition names.
measure.cols	A named list with measure columns to read. These are columns in the proteinGroup files containing intensity measurements per sample. Usually they are called Intensity <sample>. If not provided, column names will be created from metadata using a template paste("Intensity", meta$sample).
data.cols	A named list with columns to read in addition to measure columns. It should contain three columns named protein, which will be used as protein ID and reverse and contaminant, which will be used to filter data. The values of this named list are the actual column names in the file (including spaces). The default structure proteinColumns is provided with the package, though it might need modifying in case these columns are named differently in the protein groups file.

Details

This function allows to read MaxQuant's proteinGroups file directly, without reading and processing the evidence file. Apart from the proteinGroups file name, a metadata data frame needs to be provided.

Value

A proteusData object with protein intensity data.

Examples

library(proteusLabelFree)
proteinGroupsFile <- system.file("extdata", "proteinGroups.txt.gz", package="proteusLabelFree")
prot.MQ <- readProteinGroups(proteinGroupsFile, meta)

bartongroup/Proteus documentation built on April 22, 2023, 5:33 a.m.