getRegionNearGenes {ELMER} | R Documentation

## Identifies nearest genes to a region

### Description

Auxiliary function for GetNearGenes This will get the closest genes (n=numFlankingGenes) for a target region (TRange) based on a genome of refenrece gene annotation (geneAnnot). If the transcript level annotation (tssAnnot) is provided the Distance will be updated to the distance to the nearest TSS.

### Usage

    getRegionNearGenes(TRange = NULL, numFlankingGenes = 20,
      geneAnnot = NULL, tssAnnot = NULL)

### Arguments

`TRange` | A GRange object contains coordinate of targets.
`numFlankingGenes` | A number determine how many gene will be collected from each
`geneAnnot` | A GRange object contains gene coordinates of for human genome.
`tssAnnot` | A GRange object contains tss coordinates of for human genome.

### Value

A data frame of nearby genes and information: genes' IDs, genes' symbols,

### Author(s)

Tiago C Silva (maintainer: tiagochst@usp.br)

### Examples

    geneAnnot <-  ELMER:::get.GRCh("hg38",as.granges = TRUE)
    tssAnnot <-  getTSS(genome = "hg38")
    probe <- GenomicRanges::GRanges(seqnames = c("chr1","chr2"),
    range=IRanges::IRanges(start = c(16058489,236417627), end= c(16058489,236417627)),
    name= c("cg18108049","cg17125141"))
    names(probe) <- c("cg18108049","cg17125141")
    NearbyGenes <- getRegionNearGenes(numFlankingGenes = 20,
                                 geneAnnot = geneAnnot,
                                 TRange = probe,
                                 tssAnnot = tssAnnot)

[Package ELMER version 2.10.0 Index]