packsToFasta: Save packFinder Results in FASTA Format (.fasta)
In packFinder: de novo Annotation of Pack-TYPE Transposable Elements

Description Usage Arguments Value Author(s) See Also Examples

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

1	packsToFasta(packMatches, file, Genome)

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).

Save location of Fasta file.

Jack Gisby

getPacksFromFasta, packSearch

data(arabidopsisThalianaRefseq)
data(packMatches)

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