getProximalPromoter,Trena-method {trena} | R Documentation

## 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)
       }

[Package trena version 1.6.1 Index]