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

Description Usage Arguments Value Examples

View source: R/peakLengthBoxplot.r

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

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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

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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)
peakLengthBoxplot(rat, 0, 500)

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