Gets the flanking TSD sequences of TIRs or predicted
Pack-TYPE transposable elements. A dataframe of these
elements can be in
getTsds(tirMatches, Genome, tsdLength, strand = "+", output = "character")
A dataframe containing genomic ranges and names referring
to TIR sequences or predicted Pack-TYPE transposable
elements. Should be in the format used by
The length of the TSD region to be retrieved (integer).
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.
The type of object to be returned:
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.
Flanking TSD sequences as a vector of characters, or if
output is specified as "DNAStringSet", TSD sequences
will be returned as a
data(arabidopsisThalianaRefseq) data(packMatches) tsdSeqs <- getTsds(packMatches, arabidopsisThalianaRefseq, 3)
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