1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
|
\name{getAE}
\alias{getAE}
\docType{data}
\title{ Download MAGE-TAB files from the ArrayExpress collection in a specified directory }
\description{
\code{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{
\item{accession}{ is an ArrayExpress experiment identifier. }
\item{path}{ is the name of the directory in which the files
downloaded on the ArrayExpress repository will be extracted.}
\item{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.}
\item{extract}{ if FALSE, the files are not extracted from the zip archive.}
\item{sourcedir}{ when local = TRUE, files will be read from this directory.}
\item{overwrite}{ if TRUE, overwrite files if they already exist in path, default FALSE.}
}
\value{
\code{ A list with the names of the files that
have been downloaded and extracted. }
}
\seealso{\code{\link[ArrayExpress]{ArrayExpress}},
\code{\link[ArrayExpress]{ae2bioc}},
\code{\link[ArrayExpress]{getcolproc}},
\code{\link[ArrayExpress]{procset}}}
\author{
Ibrahim Emam, Audrey Kauffmann
Maintainer: Jose Marugan <jcmarca@ebi.ac.uk>
}
\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])
}
\keyword{datasets}
|
