annotate {geneXtendeR} | R Documentation

## Annotate peaks file.

### Description

Annotate a user's peaks file (which has been preprocessed with the peaksInput() command) with gene information based on optimally chosen geneXtendeR upstream extension file. 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

    annotate(organism, extension)

### Arguments

`organism` | Object name assigned from readGFF() command.
`extension` | Desired upstream extension.

### Value

The gene coordinates are extended by 'extension' at the 5-prime end, and by 500 bp at the 3-prime end. The peaks file is then overlayed on these new gene coordinates, producing a file of peaks annotated with gene ID, gene name, and gene-to-peak genomic distance (in bp). Distance is calculated between 5-prime end of gene and 3-prime end of peak.

A data.table formatted version of the annotated file for checking or further calculations.

### 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")
    peaksInput(fpath)
    annotate(rat, 2500)

[Package geneXtendeR version 1.16.0 Index]