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

In ArrayExpress: Access the ArrayExpress Microarray Database at EBI and build Bioconductor data structures: ExpressionSet, AffyBatch, NChannelSet

Description

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

Usage

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

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.
local	if TRUE, files will be read from a local folder specified by sourcedir.
sourcedir	when local = TRUE, files will be read from this directory.

Value

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

Author(s)

Ibrahim Emam, Audrey Kauffmann

Maintainer: <[e-mail]>

See Also

ArrayExpress, ae2bioc, getcolproc, procset

Examples

mexp1422 = getAE("E-MEXP-1422", type = "full")

## Build a an ExpressionSet from the raw data
MEXP1422raw = ae2bioc(mageFiles = mexp1422)

## Build a an ExpressionSet from the processed data
cnames = getcolproc(mexp1422)
MEXP1422proc = procset(mexp1422, cnames[2])

ArrayExpress documentation built on Nov. 8, 2020, 6:26 p.m.