annotate_n: Annotate peaks file.
In geneXtendeR: Optimized Functional Annotation Of ChIP-seq Data

Description Usage Arguments Value Examples

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.

1	annotate_n(organism, extension, n = 2)

`organism`	Object name assigned from readGFF() command.
`extension`	Desired upstream extension.
`n`	Number of Gene's closest away from the peak

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. File named "annotated_’extension'_'n'.txt".

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

## Not run: 
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_n(rat, 2500, n=3)

## End(Not run)