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 |