Description
This function acts as a wrapper for
getGEO, to download the matrix
files of gene expression datasets from the GEO
database. It fixes two issues:
Usage
getGSE(GEO = NULL, filename = NULL, destdir = GEDtmp(), ..., verbose = FALSE, annotation = NULL,
simplify = TRUE)
Arguments
- ...
- extra parameters passed to
getGEO.
- verbose
- verbosity level
- annotation
- a character string that indicates the
Bioconductor annotation package to associate the dataset
with, e.g.,
'hgu133plus2.db'.
- simplify
- logical that indicates if the result for
GSEs that contain only one dataset should be simplified
and returned as an
ExpressionSet object
(TRUE) or as a list.
- GEO
- A character string representing a GEO object
for download and parsing. (eg.,
'GDS505','GSE2','GSM2','GPL96')
- filename
- The filename of a previously downloaded
GEO SOFT format file or its gzipped representation (in
which case the filename must end in .gz). Either one of
GEO or filename may be specified, not both. GEO series
matrix files are also handled. Note that since a single
file is being parsed, the return value is not a list of
esets, but a single eset when GSE matrix files are
parsed.
- destdir
- The destination directory for any
downloads. Defaults to the architecture-dependent
tempdir. You may want to specify a different directory
if you want to save the file for later use. Doing so is
a good idea if you have a slow connection, as some of the
GEO files are HUGE!
Details
- if the user is behind a proxy that
modifies the content of GEO's dataset index plain text
pages into HTML pages, then plain
getGEO breaks
with an error like:
Error in scan(file, what, nmax, sep, dec, quote,
skip, nlines, na.strings, : line 1 did not have 6
elements
- plain
getGEO do not honour the
destination directory for GPL files.
Moreover, this function installs GEOquery if necessary.
This function is a wrapper to
getGEO, which unlist the result
list in the common case of a single dataset, and installs
the GEOquery package if necessary.
Examples
## Not run:
##D dir.create('testGSE')
##D getGSE('GSE19830', destdir='testGSE')
## End(Not run)