R/build_geo_acc_urls.R

In Yunuuuu/rgeo: R interface for GEO database

#' Construct a URL to retrieve data from GEO Accession Display Bar
#'
#' @param scope A character string in one of "self", "gsm", "gpl", "gse" or
#' "all". allows you to display the GEO accession(s) which you wish to target
#' for display. You may display the GEO accession which is typed into the text
#' box itself ("Self"), or any ("Platform", "Samples", or "Series") or all
#' ("Family") of the accessions related to the accession number typed into the
#' text box.
#' @param amount A character string in one of "brief", "quick", "data" or
#' "full". Allows you to control the amount of data that you will see displayed.
#' "Brief" displays the accession's attributes only. "Quick" displays the
#' accession's attributes and the first twenty rows of its data table. "Full"
#' displays the accessions's attributes and the full data table. "Data" omits
#' the accession's attributes, showing only the links to other accessions as
#' well as the full data table
#' @param format A character string in one of "text", "xml" or "html".
#' Allows you to display the GEO accession in human readable, linked "HTML"
#' form, or in machine readable, "text" format, which is the same with "soft"
#' format. SOFT stands for "simple omnibus format in text".
#' @noRd
build_geo_acc_url <- function(ids, scope = "self", amount = "data", format = "text") {
    sprintf(
        "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=%s&targ=%s&view=%s&form=%s", 
        tolower(ids), scope, amount, format
        # match.arg(
        #     tolower(scope),
        #     c("self", "gsm", "gpl", "gse", "all")
        # ),
        # match.arg(
        #     tolower(amount),
        #     c("brief", "quick", "data", "full")
        # ),
        # GEO use "text" to refer to "soft" format
        # GEO use "xml" to refer to "miniml" format
        # match.arg(
        #     tolower(format),
        #     c("text", "html", "xml")
        # )
    )
}