addRegionSubsegments: addRegionSubsegments

In RnBeads: RnBeads

Description

For the region annotation of a given RnBSet object. Subdivide each region into subsegments by hierarchical clustering on the site distances in a particular region and then splitting the region into subregions consisting of these site clusters. The number of clusters is determined in such way that the mean number of sites per cluster is given by the ns parameter.

Usage

addRegionSubsegments(
  rnb.set,
  annotation.dir,
  region.types = NULL,
  add.region.types.to.options = FALSE,
  ns = 10
)

Arguments

rnb.set	an RnBSet object
annotation.dir	a directory to save the annotation to for later reloading. (binary RData format.)
region.types	the region types to which subsegmentation should be applied. Must be a non-empty subset of summarized.regions(rnb.set). Defaults (NULL) to all region types in rnb.set
add.region.types.to.options	Flag indicating whether to add the newly created subregions to the package's region.types option
ns	the mean number of sites per cluster.

Value

the modified RnBSet object

Author(s)

Fabian Mueller

Examples

library(RnBeads.hg19)
data(small.example.object)
logger.start(fname=NA)
rnb.set.mod <- addRegionSubsegments(rnb.set.example,tempdir(),region.types=c("tiling","genes"))
summary(meth(rnb.set.mod,type="tiling.subsegments"))

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