import_MaxQuant: Import from MaxQuant

Description Usage Arguments Value Examples

View source: R/wrapper_functions.R

Description

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

Usage

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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

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# 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.