annotateGRanges: Annotates a 'GRanges' object by means of a second 'GRanges'...
In BiSeq: Processing and analyzing bisulfite sequencing data

Description Usage Arguments Details Value Author(s) See Also Examples

Each genomic location of object is checked for overlapping with genomic ranges of regions. In case of an overlapping, this genomic location is marked as TRUE, or with the identifier of respective the regions object (if any).

1	annotateGRanges(object, regions, name, regionInfo)

`object`	A `GRanges`.
`regions`	A `GRanges`.
`name`	A string specifying the name of the metadata column with the overlapping information to be added to `object`. Usually the type of the `regions` object, e.g. 'Promoter'.
`regionInfo`	OPTIONAL: A string or integer specifying the metadata column column of `regions` object containing the identifiers, e.g. entrez gene IDs of the promoters. If not specified, the genomic locations of `object` are labeled as `TRUE` (overlap) or `FALSE` (no overlap).

If multiple ranges of regions overlap with a genomic region in object, the identifier names of the overlapping regions are seperated by ','.

A GRanges object similar to object containing an additional metadata column with the overlapping information.

Katja Hebestreit

GRanges-class

# load detected DMRs:
data(DMRs)

# annotate the DMRs with a GRanges object:
data(promoters)
DMRs.anno <- annotateGRanges(object = DMRs,
                             regions = promoters,
                             name = 'Promoter',
                             regionInfo = 'acc_no')
DMRs.anno