R/getXref-methods.R

In cellbaseR: Querying annotation data from the high performance Cellbase web

###############################################################################
#' getXref
#' 
#' A method to query cross reference data from Cellbase web services.
#' @details This method retrieves cross references for genomic identifiers, eg
#' ENSEMBL ids, it also provide starts_with service that is useful for
#' autocomplete services.
#' @aliases getXref
#' @param object an object of class CellBaseR
#' @param ids a character vector of the ids to be queried, any crossrefereable
#'  ID, gene names, transcript ids, 
#' uniprot ids,etc.
#' @param resource a character vector to specify the resource to be queried
#' @param param a object of class CellBaseParam specifying additional param
#'  for the query
#' @return a dataframe with the results of the query
#' @examples
#'    cb <- CellBaseR()
#'    res <- getXref(object=cb, ids="ENST00000373644", resource="xref")
#' @seealso  \url{https://github.com/opencb/cellbase/wiki} 
#' and the RESTful API documentation 
#' \url{http://bioinfo.hpc.cam.ac.uk/cellbase/webservices/}
#' @export
setMethod("getXref", "CellBaseR", definition = function(object, ids, resource,
                                                        param=NULL) {
    
    categ <- "feature"
    subcateg<- "id"
    ids <- toupper(ids)
    resource <- resource
    if (!is.null(param)) {
      param <- c(assembly=param@assembly,feature=param@feature,region=param@region
                 ,rsid=param@rsid,so=param@so, trait=param@trait,
                 accession=param@accession, type=param@type,
                 mode_inheritance_labels=param@mode_inheritance_labels,
                 clinsig_labels=param@clinsig_labels, 
                 alleleOrigin=param@alleleOrigin, 
                 consistency_labels=param@consistency_labels,
                 limit=param@limit, include=param@include,
                 exclude=param@exclude, limit=param@limit)
      param <- paste(param, collapse = "&")
      }
    result <- fetchCellbase(object=object, file=NULL, meta=NULL, categ=categ,
                            subcateg=subcateg,
                            ids=ids, resource=resource, param=param)
    return(result)
})