getAreaFromGeneNames {AllelicImbalance} | R Documentation

## Get Gene Area

### Description

Given a character vector with genesymbols and an OrgDb object, this function returns a GRanges giving the coordinates of the genes.

### Usage

    getAreaFromGeneNames(genesymbols, ...)

    ## S4 method for signature 'character'
    getAreaFromGeneNames(
      genesymbols,
      OrgDb,
      leftFlank = 0,
      rightFlank = 0,
      na.rm = FALSE,
      verbose = TRUE
    )

### Arguments

`genesymbols` | A character vector that contains genesymbols of genes from which we wish to retrieve the coordinates
`...` | arguments to pass on
`OrgDb` | An `OrgDb` object containing gene annotation
`leftFlank` | A `integer` specifying number of additional nucleotides before the genes
`rightFlank` | A `integer` specifying number of additional nucleotides after the genes
`na.rm` | A `boolean` removing genes that returned NA from the annotation
`verbose` | Setting `verbose=TRUE` makes function more talkative

### Details

This function is a convenience function that can be used to determine which genomic coordinates to specify to e.g. `impBamGAL` when retrieving reads.

The function cannot handle genes that do not exist in the annotation. To remove these please set the na.rm=TRUE.

### Value

`getAreaFromGeneNames` returns a GRanges object with genomic coordinates around the specified genes

### Author(s)

Jesper R. Gadin, Lasse Folkersen

### Examples

    #load example data
    data(ASEset)

    #get counts at the three positions specified in GRvariants
    library(org.Hs.eg.db )
    searchArea<-getAreaFromGeneNames(c('PAX8','TLR7'), org.Hs.eg.db)

[Package AllelicImbalance version 1.25.2 Index]