Job PP plot.

Description

Plot the PP profile of a particular job.

Usage

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plot.PP(x, job, breaks = 150L, ...)

Arguments

x

Raw output from the bayespeak function.

job

Integer. Which of the jobs in the output should have its PP values plotted?

breaks

Integer. Analogous to the breaks argument in hist.

...

Additional arguments passed to the hist function.

Details

plot.PP plots a histogram of the PP values returned in a particular BayesPeak job. This can be used to identify overfitting in a particular job. It is not suitable for identifying the prevalence of overfitting in all of the jobs in a genome-wide analysis - for that, please see plot.overfitdiag.

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

bayespeak.

Examples

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##recreation of the plots in the vignette

data(raw.output) ##output from bayespeak()
plot.PP(raw.output, 324, ylim = c(0,50))
plot.PP(raw.output, 325, ylim = c(0,50))