plot.bed {BayesPeak} | R Documentation

## Plot bed file.

### Description

Plot the distribution of reads in a .bed file.

### Usage

    plot.bed(x, chr, start, end, strand = "+", bin = 50L, ...)

### Arguments

`x` | RangedData (from the IRanges package) with a value column entitled `"strand"`. The .bed file to plot. This could have been read in with `read.bed`, or alternatively by the `import` function in the rtracklayer library.
`chr` | Character. Chromosome to plot - should be exactly the same as a space in `bed`.
`start, end` | Integer. Start and end locations on chromosome.
`strand` | Character. Strand to plot - usually either "+" or "-". If the `bed` argument uses a different convention in its strand column, this can be used instead.
`bin` | Integer. The width of bin to plot.
`...` | Additional arguments, passed to `hist`.

### Details

This function takes the reads in a bed file, and plots a histogram of their locations. This allows us to see the peaks present in the data.

### Value

Plots a histogram on the active graphical device.

### Author(s)

Jonathan Cairns

### References

Spyrou C, Stark R, Lynch AG, Tavare S BayesPeak: Bayesian analysis of ChIP-seq data, BMC Bioinformatics 2009, 10:299 doi:10.1186/1471-2105-10-299

### See Also

`read.bed`

### Examples

    dir <- system.file("extdata", package="BayesPeak")
    treatment <- file.path(dir, "H3K4me3reduced.bed")
    bed <- read.bed(treatment)

    ##look at region chr16:91000000-94000000
    plot.bed(bed, "chr16", 9.1E7, 9.4E7)

[Package BayesPeak version 1.34.0 Index]