getGenomicRatioSetFromGEO: Reading Illumina methylation array data from GEO.

In hansenlab/minfi: Analyze Illumina Infinium DNA methylation arrays

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. [e-mail].

See Also

If the data is already in memor you can use makeGenomicRatioSetFromMatrix

Examples

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

## End(Not run)

hansenlab/minfi documentation built on May 3, 2024, 3:49 p.m.