getProximalPromoter: Grab the region of the proximal promoter for a given gene...

In PriceLab/trena: Fit transcriptional regulatory networks using gene expression, priors, machine learning

Grab the region of the proximal promoter for a given gene symbol

Description

For the genome of a given Trena object, retrieve a data frame containing the region surrounding a target gene.

Usage

## S4 method for signature 'Trena'
getProximalPromoter(obj, geneSymbols, tssUpstream = 1000, tssDownstream = 1000)

Arguments

obj	An object of class Trena
geneSymbols	A vector containing genes of interest
tssUpstream	A designated distance upstream of the promoter to use as a shoulder (default = 1000)
tssDownstream	A designated distance downstream of the promoter to use as a shoulder (default = 1000)

Value

A dataframe containing the regions surrounding the proximal promoter

Examples

if(interactive()) {  # too slow for the bioc windows build
   # Retrieve the proximal promoter for MEF2C using a shoulder size of 2000 on each side
   trena <- Trena("hg38")
   regions <- getProximalPromoter(trena, "MEF2C", 2000, 2000)
   }

PriceLab/trena documentation built on March 16, 2023, 10:01 a.m.