rnb.execute.segmentation {RnBeads} | R Documentation |
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.
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() )
rnb.set |
An object of type |
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. |
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]")
.
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.
Michael Scherer, based on a script by Abdulrahman Salhab
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.