meanPeakLength: Calculates mean (average) peak length for any genomic region.

In Bohdan-Khomtchouk/geneXtendeR: Optimized Functional Annotation Of ChIP-seq Data

Description

Determines the average peak length of all peaks found within some genomic interval (e.g., 0-500 bp upstream of nearest gene for all genes throughout the genome).

Usage

meanPeakLength(organism, start, end)

Arguments

organism	Object name assigned from readGFF() command.
start	Lower bound of upstream extension.
end	Upper bound of upstream extension.

Value

A vector composed of a single number representing the average peak length found within a genomic interval.

Examples

library(rtracklayer)
rat <- readGFF("ftp://ftp.ensembl.org/pub/release-84/gtf/rattus_norvegicus/Rattus_norvegicus.Rnor_6.0.84.gtf.gz")
sigpeaks <- system.file("extdata", "significantpeaksfile.txt", package="geneXtendeR")
peaksInput(sigpeaks)
meanPeakLength(rat, 0, 500)

Bohdan-Khomtchouk/geneXtendeR documentation built on June 9, 2019, 2:53 a.m.