GEOtoGDS {bigmelon} | R Documentation |
Uses GEOquery to download a GSE Accession into the current working directory, only works for GSE's with raw idat files.
geotogds(geo, gds, method = "wget", keepidat = F, keeptar = F, ...)
geo |
A GEO Accession number. "GSE########" or a tarball 'GSE######.tar.gz' |
gds |
A character string specifying the name of the .gds file to write to. |
method |
String to indicate what method to download data from GEO off. Default is 'wget' |
keepidat |
Logical, indicates whether or not to keep the raw idat files in the working directory after downloading - if FALSE, removed |
keeptar |
Logical, indicates whether or not to keep the downloaded tarball in the working directory - if FALSE, removed. |
... |
Additional Arguments to pass to other functions (if any) |
A gds.class object, which points to the newly created .gds file.
Tyler Gorrie-Stone Who to contact: <tgorri@essex.ac.uk>
#load example dataset # gfile <- geotogds("GSE*******", "Nameoffile.gds") # Will not work if gds has no idats submitted. May also fail if idats # are not deposited in a way readily readable by readEPIC(). # closefn.gds(gfile)