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RnBeads (version 1.4.0)

rnb.plot.coverage.thresholds: rnb.plot.coverage.thresholds

Description

Plots the number of remaining CpGs after applying different thresholds for coverage and support.

Usage

rnb.plot.coverage.thresholds(rnb.set, min.coverages, fname = NA, ...)

Arguments

rnb.set
Methylation dataset as an object of type RnBiseqSet.
min.coverages
Non-empty integer vector storing the unique positive cutoff values to be applied for minimal coverage. Names, if present, are interpreted as colors that must be used to denote the corresponding values.
fname
File name to save the generated plot to. See the Details section for restrictions.
...
Additional named parameters related to saving the plot to files. These can include: report, width, height, create.pdf, low.png and high.png. These parameters are ignored when fname is NULL or NA.

Value

If fname is NULL or NA (default), the generated plot as an object of type ggplot2; otherwise, the initialized and closed ReportPlot object, invisibly.

Details

If fname is specified, this function calls createReportPlot to save the plot to PDF and/or PNG files. See its documentation for information on acceptable file names. Additional parameters - report, width, height, etc. - can also be given. If image width is not specified, it is set to a value between 4.7 and 9.2 (inches), depending on the number of samples in the dataset. The default image height is fixed to 7.2.