extractReferenceSequence: Returns the reference sequence around the breakpoint position
In PapenfussLab/StructuralVariantAnnotation: Variant annotations for structural variants
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.
PapenfussLab/StructuralVariantAnnotation documentation built on Dec. 25, 2021, 1:20 a.m.
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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.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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