rmskatenaparser: atena annotation parser of RepeatMasker annotations

In functionalgenomics/atena: Analysis of Transposable Elements

atena annotation parser of RepeatMasker annotations

Description

atena annotation parser of RepeatMasker annotations

Usage

rmskatenaparser(gr, strict = FALSE, insert = 1000)

Arguments

gr	A GRanges object with RepeatMasker annotations from AnnotationHub
strict	(Default FALSE) A logical; if TRUE, the 80-80 rule is applied, i.e. only copies with more than 80 and more than 80 bp long are reported.
insert	(Default 1000L) An integer > 0. Fragments are assembled together if the distance between their closest extremities is equal or less than insert. When insert = 0, two fragments are assembled if they are in contact next to each other.

Details

atena annotation parser of RepeatMasker annotations. Parses RepeatMasker annotations from UCSC by assembling together fragments from the same transposable element (TE) that are close enough (determined by the insert parameter). For TEs from the LTR class, the parser tries to reconstruct full-length, when possible, or partial TEs following the LTR - internal region - LTR structure. Equivalences between LTR and internal regions are found by, first, identifying LTR regions (those with the "LTR" substring in their name) and internal regions (those with a suffix such as "-int", "-I", etc.). Then, LTR are assigned to internal regions for which the comparison of the two names are has a higher number of equal consecutive characters.

Value

A GRangesList object.

Examples

rmskat <- annotaTEs(genome="dm6", parsefun=rmskatenaparser,
                    strict=FALSE)
rmskat

functionalgenomics/atena documentation built on Nov. 4, 2024, 7:33 p.m.