![[R logo]](../../../doc/html/Rlogo.svg)
![[Up]](../../../doc/html/left.jpg)
![[Top]](../../../doc/html/up.jpg)
| 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 |