filterWildcards {packFinder} | R Documentation

## Remove Low Quality Sequences

### Description

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.

### Usage

    filterWildcards(packMatches, Genome, maxWildcards = 0.05)

### Arguments

`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`).

### Value

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

### Author(s)

Jack Gisby

Jack Gisby

### See Also

`packClust`, `packAlign`, `packMatches`, data(arabidopsisThalianaRefseq)

### Examples

    data(arabidopsisThalianaRefseq)
    data(packMatches)

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

[Package packFinder version 1.6.0 Index]