The sequences predicted by
overlap, which may be due to the presence of closely
interspersed elements or false TIR identification.
In such cases, these elements can be combined using
in order to collapse overlapping elements, preventing
over-estimation of transposon numbers. Also removes
duplicate elements that have been generated in the
case of multiple searches.
A dataframe containing genomic ranges and names referring
to sequences to be extracted. This dataframe is in the format
produced by coercing a
Must contain the following features:
A DNAStringSet object containing sequences referred to
A set of non-overlapping transposon sequences in the format of the input dataframe.
data(packMatches) data(arabidopsisThalianaRefseq) packMatches$start <- 1 packMatches$end <- 10 collapseSeqs(packMatches, arabidopsisThalianaRefseq)
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