peakLengthBoxplot {geneXtendeR} | R Documentation

## Produces box-and-whisker plot of peak lengths within any genomic interval.

### Description

Makes boxplots of peak lengths to show how lengths of individual peaks are distributed within any genomic interval (e.g., 0-500 bp upstream of nearest gene for all genes throughout the genome).

### Usage

    peakLengthBoxplot(organism, start, end)

### Arguments

`organism` | Object name assigned from readGFF() command.
`start` | Lower bound of upstream extension.
`end` | Upper bound of upstream extension.

### Value

Creates boxplots showing how lengths of peaks are distributed within any given genomic interval. Also, creates character vector composed of individual peak lengths.

### 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")
    peaksInput(allpeaks)
    peakLengthBoxplot(rat, 0, 500)

[Package geneXtendeR version 1.12.0 Index]