packsToFasta {packFinder} | R Documentation

## Save packFinder Results in FASTA Format (.fasta)

### Description

Saves a dataframe of potential Pack-TYPE elements, usually generated via `packSearch`. May be retrieved using `getPacksFromFasta`.

### Usage

    packsToFasta(packMatches, file, Genome)

### Arguments

`packMatches` | taframe containing genomic ranges and names referring to sequences to be extracted. Can be obtained from `packSearch` or generated from a `GRanges` object, after conversion to a dataframe. 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.
`file` | FASTA file save path.
`Genome` | A DNAStringSet object containing sequences referred to in `packMatches` (the object originally used to predict the transposons `packSearch`).

### Value

Save location of Fasta file.

### Author(s)

Jack Gisby

### See Also

`getPacksFromFasta`, `packSearch`

### Examples

    data(arabidopsisThalianaRefseq)
    data(packMatches)

    packsToFasta(
        packMatches,
        system.file("extdata", "packMatches.fasta", package = "packFinder"),
        arabidopsisThalianaRefseq
    )

[Package packFinder version 1.2.0 Index]