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

Description Usage Arguments Value Examples

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

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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

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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.