Primary filtering stage for the
algorithm. Identifies potential Pack-TYPE transposable
elements based on proximity of matching inverted repeats
and equality of TSD sequences.
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identifyPotentialPackElements( forwardMatches, reverseMatches, Genome, elementLength, tsdMismatch = 0 )
A dataframe containing genomic ranges and names referring to forwards-facing TIR sequences and their respective TSD sequences.
A dataframe containing genomic ranges and names referring to reverse-facing TIR sequences and their respective TSD sequences.
A DNAStringSet object containing the matches referred to
A vector of two integers containing the minimum and maximum transposable element length.
An integer referring to the allowable mismatch
(substitutions or indels) between a transposon's TSD
packSearch as a primariy filtering
stage. Identifies matches likely to be transposons based
on their TIR region, from
and their TSD region, from
getTsds. It is
recommended to use the general pipeline function
packSearch for identification of potential
pack elements, however each stage may be called
individually. Note that only exact TSD matches are
considered, so supplying long sequences for TSD elements
may lead to false-negative results.
packMatches, containing the locations
of potential Pack-TYPE transposable elements in
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data(arabidopsisThalianaRefseq) forwardMatches <- identifyTirMatches( Biostrings::DNAString("CACTACAA"), arabidopsisThalianaRefseq, tsdLength = 3, strand = "+" ) reverseMatches <- identifyTirMatches( Biostrings::reverseComplement(Biostrings::DNAString("CACTACAA")), arabidopsisThalianaRefseq, tsdLength = 3, strand = "-" ) packMatches <- identifyPotentialPackElements( forwardMatches, reverseMatches, arabidopsisThalianaRefseq, c(300, 3500) )
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