ArrayExpress (version 1.32.0)

getAE: 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(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.

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])