getPackSeqs: Extract Sequences of Pack-TYPE Elements
In packFinder: de novo Annotation of Pack-TYPE Transposable Elements

Description Usage Arguments Value Author(s) See Also Examples

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

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

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.

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

Jack Gisby

DNAStringSet, packSearch, DNAString

data(arabidopsisThalianaRefseq)

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

packSeqs <- getPackSeqs(packMatches, arabidopsisThalianaRefseq)