R/phenotypes_byid.R

In rsnps: Get 'SNP' ('Single-Nucleotide' 'Polymorphism') Data on the Web

#' Get all openSNP known variations and all users sharing that phenotype for 
#' one phenotype(-ID).
#'
#' @export
#' @family opensnp-fxns
#' @param phenotypeid ID of openSNP phenotype.
#' @param return_ Return data.frame (`TRUE`) or not (`FALSE`). Default: `FALSE`
#' @param ... Curl options passed on to [crul::HttpClient]
#' @return List of description of phenotype, list of known variants, or 
#' data.frame of variants for each user with that phenotype.
#'
#' @examples \dontrun{
#' phenotypes_byid(phenotypeid=12, return_ = 'desc')
#' phenotypes_byid(phenotypeid=12, return_ = 'knownvars')
#' phenotypes_byid(phenotypeid=12, return_ = 'users')
#'
#' # pass on curl options
#' phenotypes_byid(phenotypeid=12, return_ = 'desc', verbose = TRUE)
#' }
phenotypes_byid <- function(phenotypeid = NA, 
  return_ = c('description','knownvars','users'), ...) {
  
  url2 <- paste0(paste0(osnp_base(), "phenotypes/json/variations/"), 
                 phenotypeid, '.json')
  res <- os_GET(url2, list(), ...)
  out <- jsonlite::fromJSON(res, FALSE)

  return_2 <- match.arg(return_, c('description','knownvars','users'), FALSE)

  if (return_2 == 'description') {
    out[c('id','characteristic','description')]
  } else if (return_2 == 'knownvars') {
      out[c('known_variations')]
    } else {
      ldply(out$users, data.frame, stringsAsFactors = FALSE)
    }
}