mglR (version 0.1.0)

addExpression: Add RNAsequencing expression data list

Description

addExpression returns a list with the eighth through the eleventh elements as lists containing dataframes with tissue specific expression data from GTEx; see http://www.gtexportal.org. Element 8 is a list of reads by gene, element 9 of reads by transcript, element 10 of RPKM by gene, and element 11 of RPKM by transcript.

Usage

addExpression(mgl, download = TRUE, saveDownload = FALSE, fpsource = "./", normalized = TRUE, xpGeneReads = TRUE, xpTranscriptReads = TRUE, xpGeneRpkm = TRUE, xpTranscriptRpkm = TRUE)

Arguments

mgl

List; see buildFromNames, buildFromRegion, or buildFromEnsgs

download

A logical vector indicating if expression data should be downloaded.

saveDownload

A logical vector indicating if the data should be saved

fpsource

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

normalized

A logical flag indicating if normalized gene expression data should be incorporated into the list. Note: this is both the gene expression values and covariates used by GTEx to calculate eQTLs

xpGeneReads

A logical flag indicating if gene read expression data should be incorporated into the list

xpTranscriptReads

A logical flag indicating if transcript read expression data should be incorporated into the list

xpGeneRpkm

A logical flag indicating if gene RPKM expression data should be incorporated into the list

xpTranscriptRpkm

A logical flag indicating if transcript RPKM expression data should be incorporated into the list

Details

This gives tissue specific RNAsequencing data as reported by GTEx for the gene of interest. It pulls data based on the gene name. Each element of the list is a separate tissue.

See Also

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

Examples

## Not run: buildFromRegion(chr = 2, start = 102314000, stop = 103435000) -> myMgl
## Not run: myMgl <- addEnst(myMgl)
## Not run: myMgl <- addExpression(myMgl, download = TRUE, saveDownload = FALSE, 
# fpsource = './', normalized = FALSE, xpGeneReads = TRUE, xpTranscriptReads = FALSE, 
# xpGeneRpkm = FALSE, xpTranscriptRpkm = FALSE)## End(Not run)