addGwasCatalog: Add GWAS data from NHGRI-EBI GWAS Catalog to list
In mglR: Master Gene List

Description Usage Arguments Details See Also Examples

View source: R/addGwasCatalog_function.R

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

1 2	addGwasCatalog(mgl, range = 0, download = TRUE, saveDownload = FALSE, fpsource = "./")

`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

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.

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

## 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)