gene_lookup: Looks up specific gene and closest peaks
In geneXtendeR: Optimized Functional Annotation Of ChIP-seq Data

Description Usage Arguments Value Examples

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.

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

`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

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

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