mglR (version 0.1.0)

addPtv: Add results from protein truncating variant algorithm made available by GTEx

Description

addPtv returns an 'mgl' list with the seventeenth element as a dataframe containing results from psiQTL algorithm; see http://www.gtexportal.org/home/.

Usage

addPtv(mgl, range = 0, download = T, saveDownload = F, 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 the data should be downloaded.

saveDownload

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

fpsource

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

Details

This gives the protein truncating variant results for each gene. Data was originally downloaded from the GTEx website http://www.gtexportal.org/static/datasets/gtex_analysis_pilot_v3/ptv_data/gtex_psiqtls.zip.

See Also

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

Examples

## Not run: buildFromRegion(chr = 2, start = 102314000, stop = 103435000) -> myMgl
## Not run: myMgl <- addPtv(myMgl, range = 0)