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 1.10.0 Index]