hotspotPlot: Graphs hotspots of statistically significant peak activity.

In Bohdan-Khomtchouk/geneXtendeR_keepme: Optimized Functional Annotation Of ChIP-seq Data

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

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

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)

Bohdan-Khomtchouk/geneXtendeR_keepme documentation built on June 3, 2019, 10:09 p.m.