numberOverlappingDeletions: Tabulate the frequency a gene has a deletion

In cancer-genomics/trellis: Somatic structural variant analysis

Tabulate the frequency a gene has a deletion

Description

Multiple hit genes. Deletions do not necessarily have to overlap so long as the two deletions both hit the same gene.

Usage

numberOverlappingDeletions(tx, grl, maxgap = 5000)

Arguments

tx	a transcript object as provided by the svfilters package
grl	a GRangesList of deletions
maxgap	a length-one numeric vector indicating the amount of space between a deletion and a transcript allowed to consider overlapping. This argument is passed to overlapsAny.

Details

1. list transcripts by gene 2. reduce the deletion granges for each subject to avoid over-counting overlapping hemizygous deletions as 2 hits 3. count overlaps

Value

a data.frame of gene names with frequencies

a GRanges object. **The coordinates are of the reduced transcript and not the observed deletion.**

See Also

overlapsAny

cancer-genomics/trellis documentation built on Aug. 20, 2024, 5:48 p.m.