Variant annotations for structural variants


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Documentation for package ‘StructuralVariantAnnotation’ version 1.6.0

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%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
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.
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.
simpleEventLength Length of event if interpreted as an isolated breakpoint.
simpleEventType Type of simplest explaination of event. Possible types are: | Type | Description | | BND | Single breakend | | CTX | Interchromosomal translocation | | INV | Inversion. Note that both ++ and - breakpoint will be classified as inversion regardless of whether the matching breakpoint actually exists | | DUP | Tandem duplication | | INS | Insertion | | DEL | Deletion |
StructuralVariantAnnotation StructuralVariantAnnotation: a package for SV annotation