getPackSeqs {packFinder} | R Documentation

## Extract Sequences of Pack-TYPE Elements

### Description

Method to quickly extract the sequences of predicted Pack-TYPE elements (as created by `packSearch`).

### Usage

    getPackSeqs(packMatches, Genome, output = "DNAStringSet")

### Arguments

`packMatches` | A dataframe containing genomic ranges and names referring to sequences to be extracted. This dataframe is in the format produced by coercing a `link[GenomicRanges:GRanges-class]{GRanges}` object to a dataframe: `data.frame(GRanges)`. Must contain the following features: start - the predicted element's start base sequence position. end - the predicted element's end base sequence position. seqnames - character string referring to the sequence name in `Genome` to which `start` and `end` refer to.
`Genome` | A DNAStringSet object containing sequences referred to in `packMatches` (the object originally used to predict the transposons `packSearch`).
`output` | The type of object to be returned: output = "DNAStringSet", returns a `DNAStringSet` object (default). output = "character", returns a `character` vector.

### Value

transposon sequences extracted from `packMatches`. At default returns the sequences as a `DNAStringSet` or, if `output` is set to "character", returns a character vector.

### Author(s)

Jack Gisby

### See Also

`DNAStringSet`, `packSearch`, `DNAString`

### Examples

    data(arabidopsisThalianaRefseq)

    packMatches <- packSearch(
        Biostrings::DNAString("CACTACAA"),
        arabidopsisThalianaRefseq,
        elementLength = c(300, 3500),
        tsdLength = 3
    )

    packSeqs <- getPackSeqs(packMatches, arabidopsisThalianaRefseq)

[Package packFinder version 1.0.0 Index]