Man pages for PapenfussLab/StructuralVariantAnnotation
VariantionAnnoration for Structural Variants

aggregateFunctionsForReturns a list of aggegration functions for the given variant...
bedpe2breakpointgrLoads a breakpoint GRanges from a BEDPE file
breakendRangesExtracts unpartnered breakend structural variants as a...
breakpointRangesExtracts the structural variants as a BreakendGRanges
calculateBlastHomologyIdentifies breakpoint sequences with signficant homology to...
calculateReferenceHomologyCalculates the length of inexact homology between the...
countBreakpointOverlapsFinds common breakpoints between the two breakpoint sets
elementExtractExtracts the element of each element at the given position
extractBreakpointSequenceExtracts the breakpoint sequence.
extractReferenceSequenceReturns the reference sequence around the breakpoint position
findBreakpointOverlapsFinds overlapping breakpoints by requiring that breakends on...
grapes-na-grapesReplaces the NA values in a with corresponding values in b
grapes-null-grapesUses b if a is NULL
isStructuralDetermines whether the variant is a structural variant
isSymbolicDetermines whether the variant is a symbolic allele
pairs2breakpointgrConverts a BEDPE Pairs containing pairs of GRanges loaded...
pairwiseLCPrefixvectorised pairwise longest common prefix Returns the length...
partnerGRanges representing the breakend coordinates of structural...
transformFunctionsForReturns a list of transformation functions for the given...
unpackExpands any columns with multiple values (such as Lists) into...
PapenfussLab/StructuralVariantAnnotation documentation built on May 24, 2018, 3:43 a.m.