GEOtoGDS {bigmelon} | R Documentation

## Download GEO data and pipe into a gdsfmt object

### Description

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

### Usage

    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: <tgorri@essex.ac.uk>

### 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)

[Package bigmelon version 1.8.0 Index]