hasPartner {StructuralVariantAnnotation} | R Documentation |
Determines whether this breakend has a valid partner in this GRanges
hasPartner(gr, selfPartnerSingleBreakends = FALSE)
gr |
GRanges object of SV breakends |
selfPartnerSingleBreakends |
treat single breakends as their own partner. |
True/False for each row in the breakpoint GRanges
#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)]