partner {StructuralVariantAnnotation} | R Documentation |
GRanges representing the breakend coordinates of structural variants #@export Partner breakend for each breakend.
partner(gr, selfPartnerSingleBreakends = FALSE)
gr |
GRanges object of SV breakends |
selfPartnerSingleBreakends |
treat single breakends as their own partner. |
All breakends must have their partner breakend included in the GRanges.
A GRanges object in which each entry is the partner breakend of those in the input object.
#reading in a VCF file as \code{vcf} vcf.file <- system.file("extdata", "gridss.vcf", package = "StructuralVariantAnnotation") vcf <- VariantAnnotation::readVcf(vcf.file, "hg19") #parsing \code{vcf} to GRanges object \code{gr} gr <- breakpointRanges(vcf) #output partner breakend of each breakend in \code{gr} partner(gr)