rnb.plot.coverage.thresholds {RnBeads} | R Documentation

## 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`.

### 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.

### 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.

### Author(s)

Yassen Assenov

[Package RnBeads version 2.12.2 Index]