extractReferenceSequence: Returns the reference sequence around the breakpoint position

In StructuralVariantAnnotation: Variant annotations for structural variants

Description

Returns the reference sequence around the breakpoint position

Usage

extractReferenceSequence(
  gr,
  ref,
  anchoredBases,
  followingBases = anchoredBases
)

Arguments

gr	breakpoint GRanges
ref	Reference BSgenome
anchoredBases	Number of bases leading into breakpoint to extract
followingBases	Number of reference bases past breakpoint to extract

Details

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.

Value

Reference sequence around the breakpoint position.

StructuralVariantAnnotation documentation built on Nov. 8, 2020, 5:43 p.m.