rnb.run.xml {RnBeads} | R Documentation

## rnb.run.xml

### Description

Starts the analysis pipeline from an XML configuration file. This function uses the XML package to parse the configuration file.

### Usage

    rnb.run.xml(fname, create.r.command = FALSE)

### Arguments

`fname` | XML configuration file to read.
`create.r.command` | Flag indicating if the R command(s) that correspond to the given XML configuration should be generated. If this is set to `TRUE`, a file named `"analysis.R"` is created in the reports directory.

### Details

Two values are required to be specified (as tags) in the configuration file - `data.source` and `dir.reports`. They define the input and output directory, respectively. In addition, the file may define analysis option values. The vignette Comprehensive DNA Methylation Analysis with RnBeads describes in details the syntax of the XML configuration file.

The sample annotation table must be stored as a file in `data.source`. For more information about the required parameters, see the documentation of `rnb.run.analysis`, which is called by this function.

### Value

Invisibly, the loaded, normalized and/or possibly filtered dataset as an object of type inheriting `RnBSet`.

### Author(s)

Yassen Assenov

### See Also

`rnb.run.analysis` for starting an analysis pipeline

[Package RnBeads version 2.2.0 Index]