# Variant annotations for structural variants

## Documentation for package ‘StructuralVariantAnnotation’ version 1.3.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

StructuralVariantAnnotation-package | StructuralVariantAnnotation: a package for SV annotation
%na% | Replaces the NA values in a with corresponding values in b
%null% | Uses b if a is NULL
.breakpointRanges | Extracting the structural variants as a GRanges.
.constrict | constrict
.isSymbolic | Determining whether the variant is a symbolic allele.
.pairwiseLCPrefix | vectorised pairwise longest common prefix Returns the length of the longest common prefix for each string pair
.svLen | Returns the structural variant length of the first allele
.testfile | Testthat helper utility to locate files used for package tests
.testrecord | Loading a VCF containing the given records
.toVcfBreakendNotationAlt | Converts to breakend notation
.unXStringSet | converts an XStringSet to a character
align_breakpoints | Adjusting the nominal position of a pair of partnered breakpoint.
breakendRanges | Extracting unpartnered breakend structural variants as a GRanges
breakendRanges-method | Extracting unpartnered breakend structural variants as a GRanges
breakpointgr2bedpe | Converting breakpoint GRanges to BEDPE-like dataframe
breakpointgr2pairs | Converts a breakpoint GRanges object to a Pairs object
breakpointGRangesToVCF | Converts the given breakpoint GRanges object to VCF format in breakend notation.
breakpointRanges | Extracting the structural variants as a GRanges.
breakpointRanges-method | Extracting the structural variants as a GRanges.
calculateReferenceHomology | Calculates the length of inexact homology between the breakpoint sequence and the reference
countBreakpointOverlaps | Counting overlapping breakpoints between two breakpoint sets
elementExtract | Extracts the element of each element at the given position
extractBreakpointSequence | Extracts the breakpoint sequence.
extractReferenceSequence | Returns the reference sequence around the breakpoint position
findBreakpointOverlaps | Finding overlapping breakpoints between two breakpoint sets
isStructural | Determining whether the variant is a structural variant
isStructural-method | Determining whether the variant is a structural variant
isSymbolic | Determining whether the variant is a symbolic allele.
isSymbolic-method | Determining whether the variant is a symbolic allele.
pairs2breakpointgr | Converts a breakpoint GRanges object to a Pairs object
partner | GRanges representing the breakend coordinates of structural variants #@export Partner breakend for each breakend.
StructuralVariantAnnotation | StructuralVariantAnnotation: a package for SV annotation