getGenomicRatioSetFromGEO {minfi} | R Documentation

## Reading Illumina methylation array data from GEO.

### Description

Reading Illumina methylation array data from GEO.

### Usage

    getGenomicRatioSetFromGEO(GSE = NULL, path = NULL, array = "IlluminaHumanMethylation450k",
                              annotation = .default.450k.annotation, what = c("Beta", "M"),
                              mergeManifest = FALSE, i = 1)

### Arguments

`GSE` | The GSE ID of the dataset to be downloaded from GEO.
`path` | If data already downloaded, the path with soft files. Either `GSE` or `path` are required.
`array` | Array name.
`annotation` | The feature annotation to be used. This includes the location of features thus depends on genome build.
`what` | Are `Beta` or `M` values being downloaded.
`mergeManifest` | Should the Manifest be merged to the final object.
`i` | If the GEO download results in more than one dataset, it pickes entry `i`.

### Details

This function downloads data from GEO using `getGEO` from the GEOquery package. It then returns a GenomicRatioSet object. Note that the rs probes (used for genotyping) are dropped.

### Value

A GenomicRatioSet object.

### Author(s)

Tim Triche Jr. and Rafael A. Irizarryrafa@jimmy.harvard.edu.

### See Also

If the data is already in memor you can use `makeGenomicRatioSetFromMatrix`

### Examples

    ## Not run:
    mset=getGenomicRatioSetFromGEO("GSE42752")

    ## End(Not run)

[Package minfi version 1.36.0 Index]