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% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/BreakpointGRanges.R
\name{findTransitiveCalls}
\alias{findTransitiveCalls}
\title{Identifies potential transitive imprecise calls that can be explained by
traversing multiple breakpoints.}
\usage{
findTransitiveCalls(
transitiveGr,
subjectGr,
maximumImpreciseInsertSize = 700,
minimumTraversedBreakpoints = 2,
maximumTraversedBreakpoints = 6,
positionalMargin = 8,
insertionLengthMargin = 50,
insLen = transitiveGr$insLen,
impreciseTransitiveCalls = (transitiveGr$HOMLEN == 0 | is.null(transitiveGr$HOMLEN))
& start(transitiveGr) != end(transitiveGr),
impreciseSubjectCalls = (subjectGr$HOMLEN == 0 | is.null(subjectGr$HOMLEN)) &
start(subjectGr) != end(subjectGr),
allowImprecise = FALSE
)
}
\arguments{
\item{transitiveGr}{a breakpoint GRanges object containing imprecise calls}
\item{subjectGr}{breakpoints to traverse}
\item{maximumImpreciseInsertSize}{Expected number of bases to traverse imprecise calls.}
\item{minimumTraversedBreakpoints}{Minimum number of traversed breakpoints to consider a transitive}
\item{maximumTraversedBreakpoints}{Maximum number of breakpoints to traverse when looking for an explanation of the transitive calls}
\item{positionalMargin}{Allowable margin of error when matching call positional overlaps.
A non-zero margin allows for matching of breakpoint with imperfect homology.}
\item{insertionLengthMargin}{Allowable difference in length between the inserted sequence and the traversed
path length.
Defaults to 50bp to allow for long read indel errors.}
\item{insLen}{Integer vector of same length as `transitiveGr` indicating the number
of bases inserted at the breakpoint.
Defaults to transitiveGr$insLen which will be present if the GRanges
was loaded from a VCF using breakpointRanges()}
\item{impreciseTransitiveCalls}{Boolean vector of same length as `transitiveGr` indicating which calls
are imprecise calls. Defaults to calls with a non-zero interval size
that have no homology.}
\item{impreciseSubjectCalls}{Boolean vector of same length as `subjectGr` indicating which calls
are imprecise calls. Defaults to calls with a non-zero interval size
that have no homology.}
\item{allowImprecise}{Allow traversal of imprecise calls.
Defaults to FALSE as to prevent spurious results which skip
some breakpoints when traversing multiple breakpoints
E.g. An A-D transitive from an underlying A-B-C-D rearrangement
will include A-B-D and A-C-D results if allowImprecise=TRUE.}
}
\value{
`DataFrame` containing the transitive calls traversed with the following columns:
| column | meaning |
| ------ | ------- |
| transitive_breakpoint_name | Name of the transitive breakpoint a path was found for |
| total_distance | Total length (in bp) of the path |
| traversed_breakpoint_names | `CharacterList` of names of breakpoint traversed in the path |
| distance_to_traversed_breakpoint | `IntegerList` of distances from start of path to end of traversing breakpoint |
}
\description{
Transitive calls are imprecise breakpoints or breakpoints with inserted sequence
that can be explained by a sequence of breakpoints.
That is, A-C calls in which additional sequence may be between A and C that
can be explained by A-B-C.
}
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