hasPartner: Determines whether this breakend has a valid partner in this...

In PapenfussLab/StructuralVariantAnnotation: Variant annotations for structural variants

Description

Determines whether this breakend has a valid partner in this GRanges

Usage

hasPartner(gr, selfPartnerSingleBreakends = FALSE)

Arguments

gr	GRanges object of SV breakends
selfPartnerSingleBreakends	treat single breakends as their own partner.

Value

True/False for each row in the breakpoint GRanges

Examples

#Subset to chromosome 6 intra-chromosomal events \code{vcf}
vcf.file <- system.file("extdata", "COLO829T.purple.sv.ann.vcf.gz",
  package = "StructuralVariantAnnotation")
vcf <- VariantAnnotation::readVcf(vcf.file)
gr <- breakpointRanges(vcf)
gr <- gr[seqnames(gr) == "6"]
# We now need to filter out inter-chromosomal events to ensure
# our GRanges doesn't contain any breakpoints whose partner
# has already been filtered out and no longer exists in the GRanges.
gr <- gr[hasPartner(gr)]

PapenfussLab/StructuralVariantAnnotation documentation built on Dec. 25, 2021, 1:20 a.m.