rescueAmbiguous: The function used to identify nearest known junction...
In KasperThystrup/circulaR: Characterization of circRNAs from Total RNA-seq data
Description
The function used to identify nearest known junction ('IRange::nearest') reports the gap between two genomic positions and not the distance.
This means that a position (x) can be reported as nearest to three positions (x-1, x, x+1). If such ambiguities arise by using the nearest function,
we need to determine if the results can be disambiguated. This function will return reads where:
closest.donor.type == donor & closest.acceptor.type == acceptor
AND
shiftAcceptorToNearestJ == 0 | shiftDonorToNearestJ == 0
AND
donor/acceptor pairs that are closest to known junctions
Usage
1
rescueAmbiguous(acceptors, donors, ambiguousHits)
KasperThystrup/circulaR documentation built on March 14, 2021, 12:44 p.m.
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Description
The function used to identify nearest known junction ('IRange::nearest') reports the gap between two genomic positions and not the distance. This means that a position (x) can be reported as nearest to three positions (x-1, x, x+1). If such ambiguities arise by using the nearest function, we need to determine if the results can be disambiguated. This function will return reads where: closest.donor.type == donor & closest.acceptor.type == acceptor AND shiftAcceptorToNearestJ == 0 | shiftDonorToNearestJ == 0 AND donor/acceptor pairs that are closest to known junctions
Usage
1 | rescueAmbiguous(acceptors, donors, ambiguousHits)
|
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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