import_MaxQuant: Import from MaxQuant

In squirrelandr/DEP: Differential Enrichment analysis of Proteomics data

Description

import_MaxQuant imports a protein table from MaxQuant and converts it into a SummarizedExperiment object.

Usage

import_MaxQuant(proteins, expdesign, filter = c("Reverse",
  "Potential.contaminant"), intensities = "LFQ", names = "Gene.names",
  ids = "Protein.IDs", delim = ";")

Arguments

proteins	Data.frame, Protein table originating from MaxQuant.
expdesign	Data.frame, Experimental design with 'label', 'condition' and 'replicate' information. See UbiLength_ExpDesign for an example experimental design.
filter	Character, Name of the column(s) containing features to be filtered on.
intensities	Character(1), Prefix of the columns containing sample intensities.
names	Character(1), Name of the column containing feature names.
ids	Character(1), Name of the column containing feature IDs.
delim	Character(1), Sets the delimiter separating the feature names within on protein group.

Value

A SummarizedExperiment object with log2-transformed values and "name" and "ID" columns containing unique names and identifiers.

Examples

# Load example data and experimental design
data <- UbiLength
exp_design <- UbiLength_ExpDesign

# Import data
se <- import_MaxQuant(data, exp_design)

squirrelandr/DEP documentation built on May 7, 2019, 9:31 a.m.