hotspotPlot {geneXtendeR} | R Documentation |
Makes line plots showing the ratio of statistically significant peaks to the total number of peaks at each genomic interval (e.g., 0-500 bp upstream of every gene in the genome, 500-1000 bp upstream of every gene in the genome, etc.).
hotspotPlot(totalpeaksfile, significantpeaksfile, organism, start, end, by)
totalpeaksfile |
Filename in user's working directory (or full path to filename) containing all peaks. |
significantpeaksfile |
Filename in user's working directory (or full path to filename) containing only significant peaks. |
organism |
Object name assigned from readGFF() command. |
start |
Lower bound of upstream extension. |
end |
Upper bound of upstream extension. |
by |
Interval between consecutive extensions. |
Line plot showing the ratio of significant to total peaks at each interval across the genome.
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") sigpeaks <- system.file("extdata", "significantpeaksfile.txt", package="geneXtendeR") hotspotPlot(allpeaks, sigpeaks, rat, 0, 10000, 500)