getAE {ArrayExpress}R Documentation

Download MAGE-TAB files from ArrayExpress in a specified directory

Description

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

Usage

getAE(input, path = ".", type = "full", extract = TRUE)

Arguments

input is an ArrayExpress 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.

Value

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

Author(s)

Audrey Kauffmann Maintainer: <audrey@ebi.ac.uk>

See Also

magetab2bioc, getcolproc

Examples

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

## Build a an ExpressionSet from the raw data
MEXP1422raw = magetab2bioc(files = mexp1422)

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


[Package ArrayExpress version 1.4.3 Index]