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

Description Usage Arguments Value

View source: R/BreakpointGRanges.R

Description

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

Usage

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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.


d-cameron/StructuralVariantAnnotation documentation built on Dec. 26, 2021, 6:14 p.m.