ExomeDepth (version 0.9.2)

AnnotateExtra: Add annotations to a ExomeDepth object

Description

Takes annotations in the GRanges format and adds these to the CNV calls in the ExomeDepth object.

Usage

AnnotateExtra(x, reference.annotation, min.overlap = 0.5, column.name = "overlap")

Arguments

x

An ExomeDepth object.

reference.annotation

The list of reference annotations in GRanges format.

min.overlap

The minimum fraction of the CNV call that is covered by the reference call to declare that there is a significant overlap.

column.name

The name of the column used to store the overlap (in the slot CNV.calls).

Value

• A ExomeDepth object with the relevant annotations added to the CNVcalls slot.

References

A robust model for read count data in exome sequencing experiments and implications for copy number variant calling, Plagnol et al, Bioinformatics