meanPeakLengthPlot {geneXtendeR} | R Documentation |
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).
meanPeakLengthPlot(organism, start, end, by)
organism |
Object name assigned from readGFF() command. |
start |
Lower bound of upstream extension. |
end |
Upper bound of upstream extension. |
by |
Interval between consecutive extensions. |
Creates mean peak length line plots.
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)