identifyTirMatches {packFinder} | R Documentation

## Identify Terminal Inverted Repeat Matches

### Description

Searches a `DNAStringSet` for potential TIRs based on sequence similarity.

### Usage

    identifyTirMatches(tirSeq, Genome, mismatch = 0, strand = "*", tsdLength)

### Arguments

`tirSeq` | A `DNAString` object to be searched for.
`Genome` | A `DNAStringSet` object containing the `DNAString` objects to be searched.
`mismatch` | The allowable mismatch between `tirSeq` and a given slice of `Genome`. Includes indels.
`strand` | The directionality of the search string ("+" or "-"). Note that this does affect the search for tirSeqs, if you wish to search the reverse strand you should use the reverse complement of your sequence.
`tsdLength` | Integer referring to the length of the flanking TSD region.

### Details

Called by `packSearch`. Used by `packSearch` as an initial filtering stage. `matchPattern` from Biostrings is used for pattern matching. It is recommended to use the general pipeline function `packSearch` for identification of potential pack elements, however each stage may be called individually.

### Value

A dataframe, `tirMatches`, containing identified matches. The dataframe is in the format generated by `packSearch`.

### Author(s)

Jack Gisby

### See Also

`DNAStringSet`, `packSearch`, `matchPattern`, `DNAString`

### Examples

    data(arabidopsisThalianaRefseq)

    forwardMatches <- identifyTirMatches(
        Biostrings::DNAString("CACTACAA"),
        arabidopsisThalianaRefseq,
        tsdLength = 3,
        strand = "+"
    )

[Package packFinder version 1.0.0 Index]