R/abstract_search.R

In leekgroup/recount: Explore and download data from the recount project

#' Search the abstracts from the SRA studies available via the recount project
#'
#' Given a text query, find the SRA project ids (study accession numbers) that
#' contain the text in their abstract as provided by the SRAdb Bioconductor
#' package.
#'
#' @param query A character vector with the text to search for via
#' [grep][base::grep] in the abstract info available at [recount_abstract].
#' @param id_only Whether to only return the project id or to return summary
#' information for the project(s) that match the query.
#' @param ... Additional arguments passed to [grep][base::grep].
#'
#' @return If `id_only = TRUE` it returns a character vector with the
#' project SRA ids (accession numbers). If `id_only = FALSE` it returns a
#' subset of [recount_abstract] for the abstracts that contained the query.
#'
#' @details Both the query and the abstracts are searched in lower case.
#'
#' For a more powerful search use the recount project website at
#' <https://jhubiostatistics.shinyapps.io/recount/>.
#'
#' @seealso [browse_study], [recount_abstract]
#'
#' @author Leonardo Collado-Torres
#' @export
#'
#' @examples
#' ## Find the Geuvadis consortium project
#' project_info <- abstract_search("Geuvadis consortium")
#'
#' ## See some summary information for this project
#' project_info
abstract_search <- function(query, id_only = FALSE, ...) {
    ## Check input
    stopifnot(is.character(query))
    stopifnot(is.logical(id_only))
    stopifnot(length(id_only) == 1)

    ## Use table from the package
    abstract_table <- recount::recount_abstract

    ## Get abstracts
    abstracts <- tolower(abstract_table$abstract)
    query <- tolower(query)
    i <- grep(query, abstracts, ...)

    if (id_only) {
        return(abstract_table$project[i])
    } else {
        return(abstract_table[i, ])
    }
}