getTsds: Get Flanking Terminal Site Duplication Sequences

In jackgisby/packFinder: de novo Annotation of Pack-TYPE Transposable Elements

Get Flanking Terminal Site Duplication Sequences

Description

Gets the flanking TSD sequences of TIRs or predicted Pack-TYPE transposable elements. A dataframe of these elements can be in tirMatches.

Usage

getTsds(tirMatches, Genome, tsdLength, strand = "+", output = "character")

Arguments

tirMatches	A dataframe containing genomic ranges and names referring to TIR sequences or predicted Pack-TYPE transposable elements. Should be in the format used by packSearch.
Genome	A DNAStringSet object containing sequences referred to in tirMatches.
tsdLength	The length of the TSD region to be retrieved (integer).
strand	The strand of the TIR; "+" for forward, "-" for reverse. If the TSD sequences of transposable elements are being predicted, then this parameter can be left as default ("+"); if the TSD sequences of TIRs are being found then the strand direction must be supplied.
output	The type of object to be returned: output = "DNAStringSet", returns a DNAStringSet object. output = "character", returns a character vector (default).

Details

Called by packSearch. It is recommended to use the general pipeline function packSearch for identification of potential pack elements, which returns TSD sequences as a feature of results, however each stage may be called individually.

Value

Flanking TSD sequences as a vector of characters, or if output is specified as "DNAStringSet", TSD sequences will be returned as a DNAStringSet object.

Author(s)

Jack Gisby

See Also

DNAStringSet, packSearch, tirMatches

Examples

data(arabidopsisThalianaRefseq)
data(packMatches)

tsdSeqs <- getTsds(packMatches, arabidopsisThalianaRefseq, 3)

jackgisby/packFinder documentation built on July 19, 2022, 2:25 a.m.