AnnotateExtra: Add annotations to a ExomeDepth object

In drramki-chop/edm: Scalable workflow to identify copy Number variants from exome sequencing data

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).

Details

A recent version of GenomicRanges (> 1.8.10) is required. Otherwise the function will return a warning and not update the ExomeDepth object.

Value

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

Author(s)

Vincent Plagnol

References

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

drramki-chop/edm documentation built on June 6, 2020, 8:48 a.m.