hotspotPlot {geneXtendeR} | R Documentation

## Graphs hotspots of statistically significant peak activity.

### 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)

[Package geneXtendeR version 1.12.0 Index]