peakLengthBoxplot: Produces box-and-whisker plot of peak lengths within any...

In geneXtendeR: Optimized Functional Annotation Of ChIP-seq Data

Description

Makes boxplots of peak lengths to show how lengths of individual peaks are distributed within any genomic interval (e.g., 0-500 bp upstream of nearest gene for all genes throughout the genome).

Usage

peakLengthBoxplot(organism, start, end)

Arguments

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

Value

Creates boxplots showing how lengths of peaks are distributed within any given genomic interval. Also, creates character vector composed of individual peak lengths.

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)
peakLengthBoxplot(rat, 0, 500)

geneXtendeR documentation built on Nov. 8, 2020, 11:09 p.m.