RnBeads (version 1.4.0)

addRegionSubsegments: addRegionSubsegments

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

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"))