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feat: allow different jaspar DB sources #114

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25 changes: 15 additions & 10 deletions R/motifs.R
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Original file line number Diff line number Diff line change
@@ -1,28 +1,33 @@
#' getJasparMotifs
#'
#' Function to get motifs from JASPAR database
#' @param species Which species? use eithe jaspar code or latin name.
#' @param species Which species? use eithe jaspar code or latin name.
#' default is 'Homo sapiens'
#' @param collection Which collection to use? default is 'CORE'
#' @param ... additional arguments to opts for
#' @param jaspar_db Which JASPAR database? default is `JASPAR2016::JASPAR2016`
#' @param ... additional arguments to opts for
#' \code{\link[TFBSTools]{getMatrixSet}}
#' @details Simply a wrapper function for \code{\link[TFBSTools]{getMatrixSet}}
#' that calls JASPAR2016 database using \code{\link[JASPAR2016]{JASPAR2016}}
#' @return \code{\link[TFBSTools]{PFMatrixList}}
#' @export
#' @examples
#'
#' @examples
#'
#' motifs <- getJasparMotifs()
#'
#'
getJasparMotifs <- function(species = "Homo sapiens",
collection = "CORE", ...) {
#'
#' # use the JASPAR2020 database
#' motifs <- getJasparMotifs(jaspar_db = JASPAR2020::JASPAR2020)
#'
getJasparMotifs <- function(species = "Homo sapiens",
collection = "CORE",
jaspar_db = JASPAR2016::JASPAR2016,
...) {
opts <- list()
opts["species"] <- species
opts["collection"] <- collection
opts <- c(opts, list(...))
out <- TFBSTools::getMatrixSet(JASPAR2016::JASPAR2016, opts)
if (!isTRUE(all.equal(TFBSTools::name(out), names(out))))
out <- TFBSTools::getMatrixSet(jaspar_db, opts)
if (!isTRUE(all.equal(TFBSTools::name(out), names(out))))
names(out) <- paste(names(out), TFBSTools::name(out), sep = "_")
return(out)
}