gene_lookup {geneXtendeR} | R Documentation

## Looks up specific gene and closest peaks

### Description

Looks up closest peak to a specified gene on the peaks file (which has been preprocessed with the peaksInput() command) based on the latest .bed file accessed or for a specified extension. This command requires a preprocessed "peaks.txt" file (generated using peaksInput()) to be present in the user's working directory, otherwise the user is prompted to rerun the peaksInput() command in order to regenerate it.

### Usage

    gene_lookup(organism, gene_name, n = 2, extension = NA, cutoff = Inf)

### Arguments

`organism` | Object name assigned from readGFF() command.
`gene_name` | Gene names or gene ids specified by user in a string form.
`n` | Number of closest peaks located to 'gene_name' on any given chromosome to be found. Default = 2
`extension` | Desired upstream extension. If left unspecified, the latest geneXtender bed file will be chosen. If no extension is specified and no bed file can be found, a default extension of 500 is selected.
`cutoff` | Optional arg to specify max bp distance to search around 'gene_name'. Default = Inf

### Value

A data.table with all peaks located within 'n' peaks and 'cutoff' bp distance away on every chromosome that contains 'gene_name'.

### Examples

    library(rtracklayer)
    rat <- readGFF("ftp://ftp.ensembl.org/pub/release-84/gtf/rattus_norvegicus/Rattus_norvegicus.Rnor_6.0.84.gtf.gz")
    fpath <- system.file("extdata", "somepeaksfile.txt", package="geneXtendeR")
    closest <- gene_lookup(rat, c("Vom2r3", "Vom2r5"), n = 7, extension = 1000)
    closest

[Package geneXtendeR version 1.13.0 Index]