mglR (version 0.1.0)

addGwasCatalog: Add GWAS data from NHGRI-EBI GWAS Catalog to list

Description

addGwasCatalog returns a list with the eighteenth element as a dataframe with GWAS data from the NHGRI-EBI GWAS Catalog.

Usage

addGwasCatalog(mgl, range = 0, download = TRUE, saveDownload = FALSE, fpsource = "./")

Arguments

mgl

List; see buildFromNames, buildFromRegion, or buildFromEnsgs

range

Number indicating distance upstream of start and downstream of stop that should be used for filtering SNPs.

download

A logical vector indicating if most recent version of the NHGRI-EBI GWAS Catalog should be downloaded.

saveDownload

A logical vector indicating if the data should be saved as 'RawData_GwasCatalog.RData'

fpsource

A character string of with the filepath where the data has been downloaded

Details

This gives basic information on trait associated variants as reported by the NHGRI-EBI GWAS Catalog for the gene of interest. It pulls data based on the gene name and position (i.e. any SNP that falls between the start and stop position). Note a wider range can be taken using the range flag.

See Also

Other elements: addAei, addAntisense, addCisEqtl, addDnase, addEnst, addExpression, addGo, addGrasp, addLoc, addPtv, addPubmed, addSqtlAltrans, addSqtlSeek, addTransEqtl, missNames

Examples

## Not run: buildFromRegion(chr = 2, start = 102314000, stop = 103435000) -> myMgl
## Not run: myMgl <- addGwasCatalog(myMgl, range = 0, download = TRUE, 
# saveDownload = TRUE, fpsource = "./")## End(Not run)