R/getPackSeqs.R

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

#' @title
#' Extract Sequences of Pack-TYPE Elements
#'
#' @description
#' Method to quickly extract the sequences of predicted 
#' Pack-TYPE elements (as created by \code{\link{packSearch}}).
#'
#' @param packMatches
#' A dataframe containing genomic ranges and names referring 
#' to sequences to be extracted. This dataframe is in the format 
#' produced by coercing a 
#' \code{link[GenomicRanges:GRanges-class]{GRanges}} 
#' object to a dataframe: \code{data.frame(GRanges)}. 
#' 
#' Must contain the following features:
#' \itemize{
#'     \item start - the predicted element's start base 
#'     sequence position.
#'     \item end - the predicted element's end base 
#'     sequence position.
#'     \item seqnames - character string referring to the 
#'     sequence name in \code{Genome} to which \code{start} 
#'     and \code{end} refer to.
#' }
#'
#' @param Genome
#' A DNAStringSet object containing sequences referred to 
#' in \code{packMatches} (the object originally used to 
#' predict the transposons \code{\link{packSearch}}).
#'
#' @param output
#' The type of object to be returned:
#' \itemize{
#'     \item output = "DNAStringSet", returns a 
#'     \code{\link[Biostrings:XStringSet-class]{DNAStringSet}} 
#'     object (default).
#'     \item output = "character", returns a 
#'     \code{character} vector.
#' }
#' 
#' @return
#' transposon sequences extracted from \code{packMatches}. 
#' At default returns the sequences as a 
#' \code{\link[Biostrings:XStringSet-class]{DNAStringSet}} 
#' or, if \code{output} is set to "character", returns a 
#' character vector. 
#'     
#' @seealso 
#' \code{\link[Biostrings:XStringSet-class]{DNAStringSet}},
#' \code{\link{packSearch}},
#' \code{\link[Biostrings:XString-class]{DNAString}}
#' 
#' @examples
#' data(arabidopsisThalianaRefseq)
#'
#' packMatches <- packSearch(
#'     Biostrings::DNAString("CACTACAA"),
#'     arabidopsisThalianaRefseq,
#'     elementLength = c(300, 3500),
#'     tsdLength = 3
#' )
#'
#' packSeqs <- getPackSeqs(packMatches, arabidopsisThalianaRefseq)
#'
#' @author
#' Jack Gisby
#'
#' @export

getPackSeqs <- function(packMatches, Genome, output = "DNAStringSet") {
    if (output != "string" & output != "DNAStringSet") {
        stop("Argument 'output' must be specified 
            as 'string' or 'DNAStringSet'")
    }

    # gets each sequence in packMatches
    seqs <- mapply(function(start, end, seqnames, Genome) {
            seq <- Genome[names(Genome) == seqnames][[1]][start:end]
            return(as.character(seq))
        },
        packMatches$start,
        packMatches$end,
        packMatches$seqnames,
        MoreArgs = list(Genome = Genome)
    )

    if (output == "string") {
        return(seqs)
    } else if (output == "DNAStringSet") {
        seqs <- Biostrings::DNAStringSet(seqs)
        names(seqs) <- as.character(packMatches$seqnames)
        return(seqs)
    }
}