mglR (version 0.1.0)

addDnase: Add data from Maurano et. al. Nat Genet. 2015 regarding allele specific DNAse hypersensitivty.

Description

addDnase returns an 'mgl' list with the twelfth element as a dataframe containing results from Maurano et. al. Nat Genet. 2015

Usage

addDnase(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 the data should be downloaded.

saveDownload

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

fpsource

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

Warning

All results will be added. To view only SNPs with a significant imbalance use makeDnaseSig

Details

This gives the results for each gene, subsetting the data to reflect those SNPs that fall within the gene region. Data was originally downloaded from http://www.nature.com/ng/journal/v47/n12/extref/ng.3432-S5.txt.

See Also

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

Examples

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