getAE: Download MAGE-TAB files from the ArrayExpress collection in a...

In ebi-gene-expression-group/bioconductor-ArrayExpress: Access the ArrayExpress Collection at EMBL-EBI Biostudies and build Bioconductor data structures: ExpressionSet, AffyBatch, NChannelSet

Download MAGE-TAB files from the ArrayExpress collection in a specified directory

Description

getAE downloads and extracts the MAGE-TAB files from an ArrayExpress dataset.

Usage

getAE(accession, path = getwd(), type = "full", extract = TRUE, sourcedir = path, overwrite = FALSE)

Arguments

accession	is an ArrayExpress experiment identifier.
path	is the name of the directory in which the files downloaded on the ArrayExpress repository will be extracted.
type	can be 'raw' to download and extract only the raw data, 'processed' to download and extract only the processed data or 'full' to have both raw and processed data.
extract	if FALSE, the files are not extracted from the zip archive.
sourcedir	when local = TRUE, files will be read from this directory.
overwrite	if TRUE, overwrite files if they already exist in path, default FALSE.

Value

A list with the names of the files that have been downloaded and extracted.

Author(s)

Ibrahim Emam, Audrey Kauffmann

Maintainer: Jose Marugan <[e-mail]>

See Also

ArrayExpress, ae2bioc, getcolproc, procset

Examples

mexp21 = getAE("E-MEXP-21", type = "full")

## Build a an ExpressionSet from the raw data
MEXP21raw = ae2bioc(mageFiles = mexp21)

## Build a an ExpressionSet from the processed data
cnames = getcolproc(mexp21)
MEXP21proc = procset(mexp21, cnames[2])

ebi-gene-expression-group/bioconductor-ArrayExpress documentation built on April 9, 2023, 6:39 a.m.