Takes transposable elements detected by
packSearch and removes those with large
numbers of wildcard ("N") bases. Used by
remove poor quality sequences that may interfere with
the quality of sequence alignments.
filterWildcards(packMatches, Genome, maxWildcards = 0.05)
A dataframe containing genomic ranges and names referring to sequences to be extracted.
The original set of sequences used to generate the
transposons detected by
The maximal allowable proportion of wildcards in the
sequence of each match (defaults to
The original dataframe,
sequences removed that are found to contain a proportion
of wildcards ("N") greater than that specified in
data(arabidopsisThalianaRefseq) data(packMatches) filteredMatches <- filterWildcards( packMatches, arabidopsisThalianaRefseq, maxWildcards = 0.05 )
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