getTsds {packFinder} | R Documentation

## Get Flanking Terminal Site Duplication Sequences

### Description

Gets the flanking TSD sequences of TIRs or predicted Pack-TYPE transposable elements. A dataframe of these elements can be in `tirMatches`.

### Usage

    getTsds(tirMatches, Genome, tsdLength, strand = "+", output = "character")

### Arguments

`tirMatches` | A dataframe containing genomic ranges and names referring to TIR sequences or predicted Pack-TYPE transposable elements. Should be in the format used by `packSearch`.
`Genome` | A `DNAStringSet` object containing sequences referred to in `tirMatches`.
`tsdLength` | The length of the TSD region to be retrieved (integer).
`strand` | The strand of the TIR; "+" for forward, "-" for reverse. If the TSD sequences of transposable elements are being predicted, then this parameter can be left as default ("+"); if the TSD sequences of TIRs are being found then the strand direction must be supplied.
`output` | The type of object to be returned: output = "DNAStringSet", returns a `DNAStringSet` object. output = "character", returns a `character` vector (default).

### Details

Called by `packSearch`. It is recommended to use the general pipeline function `packSearch` for identification of potential pack elements, which returns TSD sequences as a feature of results, however each stage may be called individually.

### Value

Flanking TSD sequences as a vector of characters, or if output is specified as "DNAStringSet", TSD sequences will be returned as a `DNAStringSet` object.

### Author(s)

Jack Gisby

### See Also

`DNAStringSet`, `packSearch`, `tirMatches`

### Examples

    data(arabidopsisThalianaRefseq)
    data(packMatches)

    tsdSeqs <- getTsds(packMatches, arabidopsisThalianaRefseq, 3)

[Package packFinder version 1.0.0 Index]