GEOtoGDS: Download data from GEO and convert it into a gdsfmt object

In TJGorrie/bigmelon: Illumina methylation array analysis for large experiments

Download data from GEO and convert it into a gdsfmt object

Description

Uses the GEOquery R package to download a GSE Accession into the current working directory. This will only work for GSE's that have raw idat files associated with them.

Usage

geotogds(geo, gds, method = "wget", keepidat = F, keeptar = F, ...)

Arguments

geo	Either a GEO accession number ('GSE########') or a previously downloaded tarball 'GSE######.tar.gz'
gds	A character string that specifies the path and name of the .gds file you want to write to.
method	Character value to indicate which method should be used to download data from GEO. Default is 'wget'
keepidat	Logical, indicate whether or not raw idat files in the working directon should be removed after parsing, if FALSE: idat files will be removed.
keeptar	Logical, indicate whether or not the downloaded tarball should be removed after parsing, if FALSE: the tarball will be removed.
...	Additional Arguments to pass to other functions (if any)

Value

geotogds will return a gds.class object that will point towards a the newly created .gds file with majority of downloaded contents inside.

Author(s)

Tyler Gorrie-Stone Who to contact: <[e-mail]>

Examples

#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)

TJGorrie/bigmelon documentation built on Oct. 13, 2023, 9:51 p.m.