findTransitiveCalls: Identifies potential transitive imprecise calls that can be...

In PapenfussLab/StructuralVariantAnnotation: Variant annotations for structural variants

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.

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

transitiveGr	a breakpoint GRanges object containing imprecise calls
subjectGr	breakpoints to traverse
maximumImpreciseInsertSize	Expected number of bases to traverse imprecise calls.
minimumTraversedBreakpoints	Minimum number of traversed breakpoints to consider a transitive
maximumTraversedBreakpoints	Maximum number of breakpoints to traverse when looking for an explanation of the transitive calls
positionalMargin	Allowable margin of error when matching call positional overlaps. A non-zero margin allows for matching of breakpoint with imperfect homology.
insertionLengthMargin	Allowable difference in length between the inserted sequence and the traversed path length. Defaults to 50bp to allow for long read indel errors.
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()
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.
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.
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 |

PapenfussLab/StructuralVariantAnnotation documentation built on Dec. 25, 2021, 1:20 a.m.