getPackSeqs: Extract Sequences of Pack-TYPE Elements

In jackgisby/packFinder: de novo Annotation of Pack-TYPE Transposable Elements

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)

jackgisby/packFinder documentation built on July 19, 2022, 2:25 a.m.