R/url_ref.R

In Bioconductor/BiocSet: Representing Different Biological Sets

#' Functions to access reference urls for different identifiers
#' @rdname url_ref
#' @name url_ref
#' @param es A \code{BiocSet} object that the reference urls should be added to.
#' @return For \code{url_ref_element}, a \code{BiocSet} object with the url 
#'     column added to the element tibble.
#' @export
#' @examples
#' es <- BiocSet("GO:0000002" = c("TP53", "TNF"), "GO:0000003" = c("IL6"))
#' url_ref_element(es) 
url_ref_element <- function(es) 
{
    elements <- es_element(es)$element
    
    url <- ifelse(startsWith(elements, "ENSG"),
        "https://www.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=",
        "https://www.ncbi.nlm.nih.gov/gene/?term="
    )

    url <- paste0(url, elements)
    es %>% mutate_element(url = url)
}

#' @rdname url_ref
#' @name url_ref 
#' @return For \code{url_ref_set}, a \code{BiocSet} object with the url column 
#'     added to the set tibble.
#' @export
#' @examples
#' 
#' url_ref_set(es)
url_ref_set <- function(es)
{
    sets <- as.character(es_set(es)$set)    

    url <- ifelse(startsWith(sets, "GO"),
        "http://amigo.geneontology.org/amigo/medial_search?q=",
        "https://www.genome.jp/dbget-bin/www_bget?pathway:"
    )

    url <- paste0(url, sets)
    es %>% mutate_set(url = url)
}

#' @rdname url_ref
#' @name url_ref
#' @return For \code{url_ref}, a \code{BiocSet} object with the url column 
#'     added to both the element and set tibbles.
#' @export
#' @examples
#'
#' url_ref(es)
url_ref <- function(es)
{
    es %>% url_ref_element() %>% url_ref_set()
}