GEOtoGDS: Download data from GEO and convert it into a gdsfmt object
In bigmelon: Illumina methylation array analysis for large experiments

Description Usage Arguments Value Author(s) Examples

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.

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

`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)

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

Tyler Gorrie-Stone Who to contact: <t.gorrie-stone@qmul.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)

bigmelon documentation built on Nov. 8, 2020, 7:40 p.m.