findNearest: Candidate backsplice data are split into donors and acceptors...
In KasperThystrup/circulaR: Characterization of circRNAs from Total RNA-seq data
Description
Candidate backsplice data are split into donors and acceptors as an GRanges object,
the annotation data are screened, to determine which individual donor and acceptor site maps to a nearby known junction.
The candidate backsplice data that overlaps or are near a known junction site are annotated and returned.
Following annotation are used for donors and acceptors:
* queryHit: The dataset postioin of a given backsplice candidate read.
* jID: The closest known junction unqiue ID (provided during 'constructSJDB')
* type: The closest known junction type (acceptor or donor)
* strand: The closest known junction strand position
* ToNearestJ: Minimum distance of the read donor or acceptor position to the nearest known donor or acceptor site.
Usage
1
findNearest(juncCand, kj, type, cbs)
KasperThystrup/circulaR documentation built on March 14, 2021, 12:44 p.m.
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Description
Candidate backsplice data are split into donors and acceptors as an GRanges object, the annotation data are screened, to determine which individual donor and acceptor site maps to a nearby known junction. The candidate backsplice data that overlaps or are near a known junction site are annotated and returned. Following annotation are used for donors and acceptors: * queryHit: The dataset postioin of a given backsplice candidate read. * jID: The closest known junction unqiue ID (provided during 'constructSJDB') * type: The closest known junction type (acceptor or donor) * strand: The closest known junction strand position * ToNearestJ: Minimum distance of the read donor or acceptor position to the nearest known donor or acceptor site.
Usage
1 | findNearest(juncCand, kj, type, cbs)
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R Package Documentation
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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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