Takes annotations in the GRanges format and adds these to the CNV calls in the ExomeDepth object.
AnnotateExtra(x, reference.annotation, min.overlap = 0.5, column.name = "overlap")An ExomeDepth object.
The list of reference annotations in GRanges format.
The minimum fraction of the CNV call that is covered by the reference call to declare that there is a significant overlap.
The name of the column used to store the overlap (in the slot CNV.calls).
A ExomeDepth object with the relevant annotations added to the CNVcalls slot.
A recent version of GenomicRanges (> 1.8.10) is required. Otherwise the function will return a warning and not update the ExomeDepth object.
A robust model for read count data in exome sequencing experiments and implications for copy number variant calling, Plagnol et al, Bioinformatics