getAE {ArrayExpress} | R Documentation |
getAE
downloads and extracts the MAGE-TAB files from an
ArrayExpress dataset.
getAE(accession, path = getwd(), type = "full", extract = TRUE, local = FALSE, sourcedir = path)
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. |
A list with the names of the files that
have been downloaded and extracted.
Ibrahim Emam, Audrey Kauffmann
Maintainer: <iemam@ebi.ac.uk>
ArrayExpress
,
ae2bioc
,
getcolproc
,
procset
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])