GEOtoGDS: Download GEO data and pipe into a gdsfmt object

Description Usage Arguments Value Author(s) Examples

Description

Uses GEOquery to download a GSE Accession into the current working directory, only works for GSE's with raw idat files.

Usage

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

Arguments

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)

Value

A gds.class object, which points to the newly created .gds file.

Author(s)

Tyler Gorrie-Stone Who to contact: <[email protected]>

Examples

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#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)

Bioconductor-mirror/bigmelon documentation built on June 1, 2017, 4:26 a.m.