R/assayCount.R

In paodan/prideDownloader:

#' The number of assays in the projects
#' @param projectAccession character, a project accession number,
#' for example: PXD000001.
#' @return The number of assays in the projects.
#' @import RCurl
#' @import RJSONIO
#' @import XML
#' @export
#' @examples {
#' \dontrun{
#' # Search for one project accession
#' assayCount("PXD000001")
#'
#' # Search for two project accessions
#' assayCount(c("PXD000001", "PXD008959"))
#' }
#' }
assayCount = function(projectAccession = c("PXD000001", "PXD008959"),
                      accessionRownames = TRUE){
  # .assayCount = function(acc){
  #   # This URL is provided in PRIDE homepage -> Access data -> Web Service
  #   url = paste0('https://www.ebi.ac.uk:443/pride/ws/archive/assay/count/project/', acc)
  #   # https://www.ebi.ac.uk:443/pride/ws/archive/assay/count/project/PXD000001
  #   cat("The URL is:", url, "\n")
  #   count = suppressWarnings(as.numeric(getURL(url)))
  #   return(count)
  # }
  # res = data.frame(projectAccession = projectAccession,
  #                  fileNbr = unlist(lapply(projectAccession, function(x){
  #                    Sys.sleep(0.5)
  #                    .assayCount(x)
  #                  })))
  # if (accessionRownames)
  #   rownames(res) = projectAccession
  # return(res)
  #


  if (length(projectAccession) < 1){
    stop("Must provide at least one projectAccession!")
  }

  baseURL = "https://www.ebi.ac.uk:443/pride/ws/archive/assay/count/project/"
  count = entryCount(baseURL, projectAccession)

  colnames(count) = c("projectAccession", "assayNbr")
  if (accessionRownames)
    rownames(count) = projectAccession
  return(count)

}