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

## rnb.plot.biseq.coverage

### Description

Plots the sequencing coverage of the RnBiseqSet object across the genomic coordinate

### Usage

    rnb.plot.biseq.coverage(
      rnbs.set,
      sample,
      type = "sites",
      writeToFile = FALSE,
      numeric.names = FALSE,
      covg.lists = NULL,
      ...
    )

### Arguments

`rnbs.set` | RnBiseqSet object
`sample` | unique sample identifier. In case `rnb.getOption("identifiers.column")` is not `NULL`, `sample` should attain values from the corresponding column, or `colnames(meth(rnb.set))` otherwise
`type` | `character` singleton. If `site` the coverage information is plotted for each methylation site. Otherwise should be one of the regions returned by `rnb.region.types`
`writeToFile` | flag specifying whether the output should be saved as `ReportPlot`
`numeric.names` | if `TRUE` and `writeToFile` is `TRUE`substitute the plot options in the plot file name with digits
`covg.lists` | if available, the output of `rnb.execute.quality`
`...` | other arguments to `createReportPlot`

### Value

plot as an object of type `ReportPlot` if `writeToFile` is `TRUE` and of class `ggplot` otherwise.

### Author(s)

Pavlo Lutsik

[Package RnBeads version 2.12.2 Index]