hotspotPlot: Graphs hotspots of statistically significant peak activity.

Description Usage Arguments Value Examples

View source: R/hotspotPlot.r

Description

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.).

Usage

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hotspotPlot(totalpeaksfile, significantpeaksfile, organism, start, end, by)

Arguments

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.

Value

Line plot showing the ratio of significant to total peaks at each interval across the genome.

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")
sigpeaks <- system.file("extdata", "significantpeaksfile.txt", package="geneXtendeR")
hotspotPlot(allpeaks, sigpeaks, rat, 0, 10000, 500)

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