breakpointgr2bedpe {StructuralVariantAnnotation} | R Documentation |
Converting breakpoint GRanges to BEDPE-like dataframe
breakpointgr2bedpe(gr)
gr |
A GRanges object. |
breakpointgr2bedpe
converts a breakpoint GRanges to a BEDPE-formatted
dataframe. The BEDPE format consists of two sets of genomic loci, optional
columns of name, score, strand1, strand2 and any user-defined fields.
See https://bedtools.readthedocs.io/en/latest/content/general-usage.html
for more details on the BEDPE format.
A BEDPE-formatted data frame.
#coverting a GRanges object to BEDPE-like dataframe vcf.file <- system.file("extdata", "gridss.vcf", package = "StructuralVariantAnnotation") vcf <- VariantAnnotation::readVcf(vcf.file, "hg19") gr <- breakpointRanges(vcf) breakpointgr2bedpe(gr)