getDbRegionsLoc: Gets the region location for the given database IDs.

In aertslab/RcisTarget: RcisTarget Identify transcription factor binding motifs enriched on a list of genes or genomic regions

Gets the region location for the given database IDs.

Description

Gets the region location based on the region ID. Only needed for drosophiladrosophila (fruit fly) regions.

For human/mouse the region locations are stored in a separate object (i.e. ). This function is not needed.

Usage

getDbRegionsLoc(featherFilePath, spltChr = "__", indexCol = NULL)

Arguments

featherFilePath	Path to the rankings database
spltChr	Character(s) used to split the prefix from the region location. The default is used for current Drosophila versions. Use NULL to skip.
indexCol	Column name including the motif/feature IDs. By default it will use the first column.

Value

The region locations in a GRanges object, with the original region ID as name.

See the package vignette for examples and more details: vignette("RcisTarget")

Examples

## Not run: 
featherFilePath <- "~/databases/dm6-regions-11species.mc9nr.feather"
dbRegionsLoc <- getDbRegionsLoc(featherFilePath)

## End(Not run)

aertslab/RcisTarget documentation built on March 7, 2024, 11:21 p.m.