rnb.execute.segmentation {RnBeads} | R Documentation

## rnb.execute.segmentation

### Description

This function computes methylation segmentation by MethylSeekR into PMDs, UMRs/LMRs, and HMDs. It is recommened to only execute this function on WGBS data (with coverage >=10 according to the developer's recommendation), but could also be used with RRBS_HaeIII without guarantee and the results should be interpreted carefully.

### Usage

    rnb.execute.segmentation(
      rnb.set,
      sample.name,
      meth.level = 0.5,
      fdr = 5,
      min.cover = 5,
      n.cores = 1,
      chr.sel = "chr2",
      plot.path = getwd(),
      temp.dir = tempdir()
    )

### Arguments

`rnb.set` | An object of type `RnBiseqSet-class` containing methylation and coverage information.
`sample.name` | The sample for which segmentation is to be executed. Segemntation can only be exectued for each sample individually.
`meth.level` | Methylation cutoff to be used in UMR/LMR computation
`fdr` | False discovery rate cutoff to be used in percent
`min.cover` | The coverage threshold
`n.cores` | The number of cores available for analysis
`chr.sel` | Selected chromosome for model training in "chrAB" format. Defaults to "chr2".
`plot.path` | Location on disk on which diagnostic plots are to be stored. Defaults to the working directory.
`temp.dir` | The temporary directory. Defaults to the R temporary directory.

### Details

For further descriptions on the methods, see `MethylSeekR`-documentation. The new annotations can be accessed via `rnb.get.annotation("[PMDs,UMRs,LMRs,HMDs]_[sample.name]")`.

### Value

The input RnBSet object with segementation added as an additional region type. Furthermore, three new annotations are set globally containing segmentation into PMDs, UMRs/LMRs, and HMDs for the sample that was specified.

### Author(s)

Michael Scherer, based on a script by Abdulrahman Salhab

### References

1. Burger, Lukas, Gaidatzis, Dimos, Schuebeler, Dirk, and Stadler, Michael B. (2013) Identification of active regulatory regions from DNA methylation data. Nucleic Acids Research 41(16):e155.

[Package RnBeads version 2.12.2 Index]