extractReferenceSequence {StructuralVariantAnnotation} | R Documentation |
Returns the reference sequence around the breakpoint position
extractReferenceSequence(gr, ref, anchoredBases, followingBases = anchoredBases)
gr |
breakpoint GRanges |
ref |
Reference BSgenome |
anchoredBases |
Number of bases leading into breakpoint to extract |
followingBases |
Number of reference bases past breakpoint to extract |
The sequence is the sequenced traversed from the reference anchor bases to the breakpoint. For backward (-) breakpoints, this corresponds to the reverse compliment of the reference sequence bases.
Reference sequence around the breakpoint position.