rnb.execute.segmentation: rnb.execute.segmentation

In RnBeads: RnBeads

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.

RnBeads documentation built on March 3, 2021, 2 a.m.