rmskbasicparser: Parser of RepeatMasker annotations
In functionalgenomics/atena: Analysis of Transposable Elements
rmskbasicparser R Documentation
Parser of RepeatMasker annotations
Description
Parser of RepeatMasker annotations
Usage
rmskbasicparser(gr)
Arguments
gr
A GRanges object with
RepeatMasker annotations from AnnotationHub
Details
Parses annotations by removing low complexity regions, simple repeats,
satellites, rRNA, scRNA, snRNA, srpRNA and tRNA. Also removes TEs with a
strand different than "+" or "-". Modifies "repFamily" and
"repClass" columns when a "?" is present or when they are defined
as "Unknown" or "Other". Finally, assigns a unique id to each TE instance
by adding the suffix "_dup" plus a number at the end of the "repName".
Value
A GRanges object.
Examples
rmskba <- annotaTEs(genome="dm6", parsefun=rmskbasicparser)
rmskba
functionalgenomics/atena documentation built on Nov. 4, 2024, 7:33 p.m.
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| rmskbasicparser | R Documentation |
Parser of RepeatMasker annotations
Description
Parser of RepeatMasker annotations
Usage
rmskbasicparser(gr)
Arguments
gr |
A GRanges object with RepeatMasker annotations from AnnotationHub |
Details
Parses annotations by removing low complexity regions, simple repeats, satellites, rRNA, scRNA, snRNA, srpRNA and tRNA. Also removes TEs with a strand different than "+" or "-". Modifies "repFamily" and "repClass" columns when a "?" is present or when they are defined as "Unknown" or "Other". Finally, assigns a unique id to each TE instance by adding the suffix "_dup" plus a number at the end of the "repName".
Value
A GRanges object.
Examples
rmskba <- annotaTEs(genome="dm6", parsefun=rmskbasicparser)
rmskba
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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