meanPeakLengthPlot: Produces line plots of mean (average) peak length within any...

Description Usage Arguments Value Examples

View source: R/meanPeakLengthPlot.r

Description

Makes line plots of mean peak lengths to show the average length of individual peaks within any genomic interval (e.g., 0-500 bp upstream of nearest gene for all genes throughout the genome).

Usage

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Arguments

organism

Object name assigned from readGFF() command.

start

Lower bound of upstream extension.

end

Upper bound of upstream extension.

by

Interval between consecutive extensions.

Value

Creates mean peak length line plots.

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")
allpeaks <- system.file("extdata", "totalpeaksfile.txt", package="geneXtendeR")
peaksInput(allpeaks)
meanPeakLengthPlot(rat, 0, 10000, 500)

geneXtendeR documentation built on Nov. 1, 2018, 3:34 a.m.