Variant annotations for structural variants

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Documentation for package ‘StructuralVariantAnnotation’ version 1.13.0

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

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.breakpointRanges	Extracting the structural variants as a GRanges.
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
extractBreakpointSequence	Extracts the breakpoint sequence.
extractReferenceSequence	Returns the reference sequence around the breakpoint position
findBreakpointOverlaps	Finding overlapping breakpoints between two breakpoint sets
findInsDupOverlaps	Finds duplication events that are reported as inserts. As sequence alignment algorithms do no allow backtracking, long read-based variant callers will frequently report small duplication as insertion events. Whilst both the duplication and insertion representations result in the same sequence, this representational difference is problematic when comparing variant call sets.
findTransitiveCalls	Identifies potential transitive imprecise calls that can be explained by traversing multiple breakpoints.
hasPartner	Determines whether this breakend has a valid partner in this GRanges
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.
numtDetect	Detecting nuclear mitochondria fusion events.
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.
rtDetect	Detecting retrotranscript insertion in nuclear genomes.
simpleEventLength	Length of event if interpreted as an isolated breakpoint.
simpleEventType	Type of simplest explanation of event. Possible types are: | Type | Description | | BND | Single breakend | | CTX | Interchromosomal translocation | | INV | Inversion. | | DUP | Tandem duplication | | INS | Insertion | | DEL | Deletion |
StructuralVariantAnnotation	StructuralVariantAnnotation: a package for SV annotation