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% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/BreakpointGRanges.R
\name{calculateReferenceHomology}
\alias{calculateReferenceHomology}
\title{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{
\item{gr}{reakpoint GRanges}
\item{ref}{reference BSgenome}
\item{anchorLength}{Number of bases to consider for homology}
\item{margin}{Number of additional reference bases include. This allows
for inexact homology to be detected even in the presence of indels.}
\item{match}{see Biostrings::pairwiseAlignment}
\item{mismatch}{see Biostrings::pairwiseAlignment}
\item{gapOpening}{see Biostrings::pairwiseAlignment}
\item{gapExtension}{see Biostrings::pairwiseAlignment}
}
\value{
A dataframe containing the length of inexact homology between the
breakpoint sequence and the reference.
}
\description{
Calculates the length of inexact homology between the breakpoint sequence
and the reference
}
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