Man pages for StructuralVariantAnnotation
Variant annotations for structural variants
| align_breakpoints | Adjusting the nominal position of a pair of partnered... |
| breakendRanges | Extracting unpartnered breakend structural variants as a... |
| breakpointgr2bedpe | Converting breakpoint GRanges to BEDPE-like dataframe |
| breakpointGRangesToVCF | Converts the given breakpoint GRanges object to VCF format in... |
| breakpointRanges | Extracting the structural variants as a GRanges. |
| calculateReferenceHomology | Calculates the length of inexact homology between the... |
| countBreakpointOverlaps | Counting overlapping breakpoints between two breakpoint sets |
| dot-constrict | constrict |
| dot-isSymbolic | Determining whether the variant is a symbolic allele. |
| dot-pairwiseLCPrefix | vectorised pairwise longest common prefix Returns the length... |
| dot-svLen | Returns the structural variant length of the first allele |
| dot-testfile | Testthat helper utility to locate files used for package... |
| dot-testrecord | Loading a VCF containing the given records |
| dot-toVcfBreakendNotationAlt | Converts to breakend notation |
| dot-unXStringSet | converts an XStringSet to a character |
| 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... |
| grapes-na-grapes | Replaces the NA values in a with corresponding values in b |
| grapes-null-grapes | Uses b if a is NULL |
| isStructural | Determining whether the variant is a structural variant |
| isSymbolic | 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... |
| simpleEventLength | Length of event if interpreted as an isolated breakpoint. |
| simpleEventType | Type of simplest explaination of event. Possible types are: |... |
| StructuralVariantAnnotation | StructuralVariantAnnotation: a package for SV annotation |
