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

Description Usage Arguments

View source: R/BreakpointGRanges.R

Description

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

Usage

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

Arguments

gr

breakpoint 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

alignment

mismatch

see Biostrings::pairwiseAlignment

gapOpening

see Biostrings::pairwiseAlignment

gapExtension

see Biostrings::pairwiseAlignment

match

see Biostrings::pairwiseAlignment


lachlanmcintosh/SAP documentation built on May 21, 2017, 8:27 a.m.