countBreakpointOverlaps: Counting overlapping breakpoints between two breakpoint sets

In StructuralVariantAnnotation: Variant annotations for structural variants

Description

Counting overlapping breakpoints between two breakpoint sets

Usage

countBreakpointOverlaps(
  querygr,
  subjectgr,
  countOnlyBest = FALSE,
  breakpointScoreColumn = "QUAL",
  maxgap = -1L,
  minoverlap = 0L,
  ignore.strand = FALSE,
  sizemargin = NULL,
  restrictMarginToSizeMultiple = NULL
)

Arguments

querygr, subjectgr, maxgap, minoverlap, ignore.strand, sizemargin, restrictMarginToSizeMultiple	See findBreakpointOverlaps().
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.

Details

countBreakpointOverlaps() returns the number of overlaps between breakpoint objects, based on the output of findBreakpointOverlaps(). See GenomicRanges::countOverlaps-methods

Value

An integer vector containing the tabulated query overlap hits.

Examples

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)

StructuralVariantAnnotation documentation built on Nov. 8, 2020, 5:43 p.m.