peakLengthBoxplot {geneXtendeR} | R Documentation |
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).
peakLengthBoxplot(organism, start, end)
organism |
Object name assigned from readGFF() command. |
start |
Lower bound of upstream extension. |
end |
Upper bound of upstream extension. |
Creates boxplots showing how lengths of peaks are distributed within any given genomic interval. Also, creates character vector composed of individual peak lengths.
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)