dl_geo_raw: Download raw data from GEO for a GSE accession number
In russHyde/miiq: Microarrays Are Awesome: Get Them Analysed HERE!
Description
Usage
Arguments
Details
Value
View source: R/download_functions.R
Description
Given a GSE identifier, this function downloads the raw data for that
dataset from the Gene Expression Omnibus. Raw data is stored in
<dest_dir>/<gse_acc>/*_RAW.tar.
Usage
1
dl_geo_raw(acc, dest_dir = file.path("data", "ext", "GEOquery"))
Arguments
acc
A single GSE accession number of the form
"GSE12345".
dest_dir
An existing directory. The function dies if this
directory is missing. Data related to gse-id are stored either in this
directory (the processed data matrix and the annotation data) or in a
subdirectory <gse.id> of this directory (for the raw data).
Details
The function checks whether the raw data has already been
downloaded before pulling it from GEO again.
Value
A list giving the directories and filenames for all downloaded
files. The list contains some names that are relevant to array-express
downloads, rather than GEO downloads.
russHyde/miiq documentation built on Dec. 25, 2019, 10:56 a.m.
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Description Usage Arguments Details Value
View source: R/download_functions.R
Description
Given a GSE identifier, this function downloads the raw data for that dataset from the Gene Expression Omnibus. Raw data is stored in <dest_dir>/<gse_acc>/*_RAW.tar.
Usage
1 | dl_geo_raw(acc, dest_dir = file.path("data", "ext", "GEOquery"))
|
Arguments
acc |
A single GSE accession number of the form "GSE12345". |
dest_dir |
An existing directory. The function dies if this directory is missing. Data related to gse-id are stored either in this directory (the processed data matrix and the annotation data) or in a subdirectory <gse.id> of this directory (for the raw data). |
Details
The function checks whether the raw data has already been downloaded before pulling it from GEO again.
Value
A list giving the directories and filenames for all downloaded files. The list contains some names that are relevant to array-express downloads, rather than GEO downloads.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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