extractReferenceSequence: Returns the reference sequence around the breakpoint position

Description Usage Arguments Details Value

View source: R/BreakpointGRanges.R

Description

Returns the reference sequence around the breakpoint position

Usage

1
2
3
4
5
6
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.