meanPeakLength {geneXtendeR}R Documentation

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

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

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)


[Package geneXtendeR version 1.6.0 Index]