countBreakpointOverlaps {StructuralVariantAnnotation} | R Documentation |
Counting overlapping breakpoints between two breakpoint sets
countBreakpointOverlaps( querygr, subjectgr, countOnlyBest = FALSE, breakpointScoreColumn = "QUAL", maxgap = -1L, minoverlap = 0L, ignore.strand = FALSE, sizemargin = NULL, restrictMarginToSizeMultiple = NULL )
querygr, subjectgr, maxgap, minoverlap, ignore.strand, sizemargin, restrictMarginToSizeMultiple |
See |
countOnlyBest |
Default value set to FALSE. When set to TRUE, the result count each subject breakpoint as overlaping only the best overlapping query breakpoint. The best breakpoint is considered to be the one with the highest QUAL score. |
breakpointScoreColumn |
Query column defining a score for determining which query breakpoint is considered the best when countOnlyBest=TRUE. |
countBreakpointOverlaps()
returns the number of overlaps between breakpoint
objects, based on the output of findBreakpointOverlaps()
.
See GenomicRanges::countOverlaps-methods
An integer vector containing the tabulated query overlap hits.
truth_vcf = VariantAnnotation::readVcf(system.file("extdata", "na12878_chr22_Sudmunt2015.vcf", package = "StructuralVariantAnnotation")) crest_vcf = VariantAnnotation::readVcf(system.file("extdata", "na12878_chr22_crest.vcf", package = "StructuralVariantAnnotation")) caller_bpgr = breakpointRanges(crest_vcf) caller_bpgr$true_positive = countBreakpointOverlaps(caller_bpgr, breakpointRanges(truth_vcf), maxgap=100, sizemargin=0.25, restrictMarginToSizeMultiple=0.5, countOnlyBest=TRUE)