diff --git a/R/motifs.R b/R/motifs.R index e173dc2..348731e 100644 --- a/R/motifs.R +++ b/R/motifs.R @@ -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) }