calculateReferenceHomology: Calculates the length of inexact homology between the...

In StructuralVariantAnnotation: Variant annotations for structural variants

Description

Calculates the length of inexact homology between the breakpoint sequence and the reference

Usage

calculateReferenceHomology(
  gr,
  ref,
  anchorLength = 300,
  margin = 5,
  match = 2,
  mismatch = -6,
  gapOpening = 5,
  gapExtension = 3
)

Arguments

gr	reakpoint GRanges
ref	reference BSgenome
anchorLength	Number of bases to consider for homology
margin	Number of additional reference bases include. This allows for inexact homology to be detected even in the presence of indels.
match	see Biostrings::pairwiseAlignment
mismatch	see Biostrings::pairwiseAlignment
gapOpening	see Biostrings::pairwiseAlignment
gapExtension	see Biostrings::pairwiseAlignment

Value

A dataframe containing the length of inexact homology between the breakpoint sequence and the reference.

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