rnb.RnBSet.to.bedGraph {RnBeads} | R Documentation

## rnb.RnBSet.to.bedGraph

### Description

Exports the methylation data of an `RnBSet` object to `*.bedGraph` files.

### Usage

    rnb.RnBSet.to.bedGraph(rnb.set, out.dir = ".", reg.type = "sites",
      parameters = character(), digits = NULL)

### Arguments

`rnb.set` | Dataset as an instance of class `RnBSet`.
`out.dir` | One-element `character` vector signifying the output directory in which to create `bedGraph` files. Setting this to `"."` (default) uses the current working directory. If the output directory does not exist, this function attempts to create it. Any existing files in this directory could be overwritten.
`reg.type` | Site or region type to be exported.
`parameters` | Named `character` vector storing parameters (other than `"type"` and `"name"`) to include in the track definition line. The names of this vector must be the parameter names, and its elements - the corresponding values; missing values (`NA`s) are allowed neither for names, nor for values. This function does not test if all provided parameter names and values conform to the BedGraph track specification.
`digits` | Optionally, number of significant digits after the decimal point to round methylation values to. If specified, this parameter must be an `integer` between `0` and `10`.

### Details

The description of the BedGraph track format can be found here. Each methylation site is an entry in the resulting bedGraph file. The Score column corresponds to a site's methylation value in the interval `[0,1]`.

### Value

(invisibly) a summary list containing information on the conversion step. elements are `filenames` (a table containing information on which sample has been written to what filename) and `assembly` (a string indicating the assembly used by `rnb.set`).

### Author(s)

Fabian Mueller

### Examples

    library(RnBeads.hg19)
    data(small.example.object)
    logger.start(fname=NA)
    rnb.RnBSet.to.bedGraph(rnb.set.example,tempdir())

[Package RnBeads version 1.12.1 Index]