filterWildcards: Remove Low Quality Sequences
In packFinder: de novo Annotation of Pack-TYPE Transposable Elements

Description Usage Arguments Value Author(s) See Also Examples

Takes transposable elements detected by packSearch and removes those with large numbers of wildcard ("N") bases. Used by packClust and packAlign to remove poor quality sequences that may interfere with the quality of sequence alignments.

1	filterWildcards(packMatches, Genome, maxWildcards = 0.05)

`packMatches`	A dataframe containing genomic ranges and names referring to sequences to be extracted.
`Genome`	The original set of sequences used to generate the transposons detected by `packSearch`.
`maxWildcards`	The maximal allowable proportion of wildcards in the sequence of each match (defaults to `0.05`).

The original dataframe, packMatches, with sequences removed that are found to contain a proportion of wildcards ("N") greater than that specified in maxWildcards.

Jack Gisby

packClust, packAlign, packMatches, data(arabidopsisThalianaRefseq)

data(arabidopsisThalianaRefseq)
data(packMatches)
    
filteredMatches <- filterWildcards(
    packMatches, 
    arabidopsisThalianaRefseq, 
    maxWildcards = 0.05
)