Man pages for StructuralVariantAnnotation
Variant annotations for structural variants

align_breakpointsAdjusting the nominal position of a pair of partnered...
breakendRangesExtracting unpartnered breakend structural variants as a...
breakpointgr2bedpeConverting breakpoint GRanges to BEDPE-like dataframe
breakpointGRangesToVCFConverts the given breakpoint GRanges object to VCF format in...
breakpointRangesExtracting the structural variants as a GRanges.
calculateReferenceHomologyCalculates the length of inexact homology between the...
countBreakpointOverlapsCounting overlapping breakpoints between two breakpoint sets
dot-isSymbolicDetermining whether the variant is a symbolic allele.
dot-pairwiseLCPrefixvectorised pairwise longest common prefix Returns the length...
dot-svLenReturns the structural variant length of the first allele
dot-testfileTestthat helper utility to locate files used for package...
dot-testrecordLoading a VCF containing the given records
dot-toVcfBreakendNotationAltConverts to breakend notation
dot-unXStringSetconverts an XStringSet to a character
elementExtractExtracts the element of each element at the given position
extractBreakpointSequenceExtracts the breakpoint sequence.
extractReferenceSequenceReturns the reference sequence around the breakpoint position
findBreakpointOverlapsFinding overlapping breakpoints between two breakpoint sets
findInsDupOverlapsFinds duplication events that are reported as inserts. As...
grapes-na-grapesReplaces the NA values in a with corresponding values in b
grapes-null-grapesUses b if a is NULL
isStructuralDetermining whether the variant is a structural variant
isSymbolicDetermining whether the variant is a symbolic allele.
pairs2breakpointgrConverts a breakpoint GRanges object to a Pairs object
partnerGRanges representing the breakend coordinates of structural...
simpleEventLengthLength of event if interpreted as an isolated breakpoint.
simpleEventTypeType of simplest explaination of event. Possible types are: |...
StructuralVariantAnnotationStructuralVariantAnnotation: a package for SV annotation
StructuralVariantAnnotation documentation built on Nov. 8, 2020, 5:43 p.m.