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

In geneXtendeR: Optimized Functional Annotation Of ChIP-seq Data

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

meanPeakLengthPlot(organism, start, end, by)

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

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. 8, 2020, 11:09 p.m.