GEOtoGDS {bigmelon} | R Documentation

## 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: <t.gorrie-stone@qmul.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 1.13.14 Index]