annotaTEsGetters: Getter functions of TE classes from parsed RepeatMasker...

In functionalgenomics/atena: Analysis of Transposable Elements

Getter functions of TE classes from parsed RepeatMasker annotations.

Description

Getter functions of TE classes from parsed RepeatMasker annotations.

Usage

getLTRs(
  annot,
  relLength = 0.9,
  fullLength = TRUE,
  partial = FALSE,
  soloLTR = FALSE,
  otherLTR = FALSE,
  returnMask = FALSE
)

getLINEs(annot, relLength = 0.9, returnMask = FALSE)

getSINEs(annot, relLength = 0.9, returnMask = FALSE)

getDNAtransposons(annot, relLength = 0.9, returnMask = FALSE)

Arguments

annot	A ['GRanges'] or ['GRangesList'] object obtained with the function 'annotaTES()', using either ['OneCodeToFindThemAll'] or ['rmskatenaparser'] as RepeatMasker parser functions. Alternatively, if 'annot' is a ['QuantifyParam'] or a ['SummarizedExperiment'] object produced by the 'qtex()' function, this function will attempt to extract the corresponding annotations from inside those objects.
relLength	(Default 0.9) Numeric value that can take values between 0 to 1. Sets the minimum relative length required for features. Elements with a lower relative length than relLength will be filtered. The relative length used is the one obtained by OneCodeToFindThemAll() or rmskatenaparser(). (length of the reconstructed TE / length of the reference).
fullLength	(Default TRUE) Logical value on whether reconstructed full-length LTR TEs (elements with structure LTR - internal region - LTR) should be selected.
partial	(Default FALSE) Logical value on whether partially reconstructed LTR TEs should be selected (structure LTR - internal region or internal region - LTR).
soloLTR	(Default FALSE) Logical value on whether solo LTRs should be selected. Note that only fragments unambiguously identified as LTRs thanks to the identification of their equivalent internal region are considered as LTRs.
otherLTR	(Default FALSE) Logical value on whether other TEs from the LTR class, not included in any of the previous three categories, should be selected. These include TEs from LTR class that cannot be unambiguously identified as LTR o internal region, and thus cannot be reconstructed into partial or full-length elements; as well as solo internal regions.
returnMask	(Default FALSE) Logical value indicating whether a subset of the input annotations should be returned (default) or a logical mask of the same length as the input annotations where TRUE values indicate what annotations belong to the TE class we want to obtain with the getter function.

Details

Retrieves annotations from the TE class corresponding to the getter function, using RepeatMasker annotations after parsing them with the OneCodeToFindThemAll() or rmskatenaparser() function. The relLength parameter can be used to filter out elements with a lower relative length. Further parameters can be used to fine-tune the type of elements to be reported.

Value

A GRangesList object with annotations from class corresponding to the getter function (LTRs, LINEs, SINEs or DNA transposons).

Examples

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

rmskatLTR <- getLTRs(rmskat, relLength=0.95, fullLength=TRUE,
                     partial=TRUE)
rmskatLTR
 
rmskat_line <- getLINEs(rmskat, relLength=0.95)
 
rmskat_sine <- getSINEs(rmskat, relLength=0.95)
 
rmskat_DNAtrans <- getDNAtransposons(rmskat, relLength=0.95)
 

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