regions,RnBSet-method {RnBeads} | R Documentation |
Methylation regions, information for which is present in the RnBSet
object.
## S4 method for signature 'RnBSet' regions(object, type = NULL)
object |
Dataset of interest. |
type |
Region type(s) of interest as a |
Methylation site and region assignment. If type
is singleton, a matrix
is returned. The first
column corresponds to the methylation context index. The second column is the index of the chromosome in
the genome, and the third is the index of the region in the GRanges
object of the region type
annotation. When length(type)>1
, a list of such matrices is returned for each element of type
.
If type
is NULL
, matrices for all summarized region types are returned.
Methylation context index is an integer number denoting the sequence context of the cytosine of interest. Index
1
corresponds to CpG
, the only supported index in bisulfite sequencing datasets.
Pavlo Lutsik
summarized.regions
for all summarized region types in a dataset;
rnb.get.chromosomes
listing all supported chromosomes for a given genome assembly
library(RnBeads.hg19) data(small.example.object) head(regions(rnb.set.example))