R/getGene-methods.R

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

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#' getGene
#' 
#'   A method to query gene data from Cellbase web services.
#' @details This method retrieves various gene annotations including transcripts
#' and exons data as well as gene expression and clinical data
#' @aliases getGene
#' @param object an object of class CellBaseR
#' @param ids a character vector of gene ids to be queried
#' @param resource a character vector to specify the resource to be queried
#' @param param an object of class CellBaseParam specifying additional param
#'  for the CellBaseR
#' @return a dataframe with the results of the query
#' @examples
#'    cb <- CellBaseR()
#'    res <- getGene(object=cb, ids=c("TP73","TET1"), resource="info")
#' @seealso  \url{https://github.com/opencb/cellbase/wiki} 
#' and the RESTful API documentation 
#' \url{http://bioinfo.hpc.cam.ac.uk/cellbase/webservices/}
#' @export
setMethod("getGene", "CellBaseR", definition = function(object, ids, 
                                                             resource, 
                                                             param=NULL)
  {
 
    categ <- "feature"
    subcateg<- "gene"
    ids <- 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 = "&")
    }
    # TODO: param are not enabled
    result <- fetchCellbase(object=object,file=NULL, meta=NULL, 
                            categ=categ, subcateg=subcateg, 
                            ids=ids, resource=resource,
                            param=param)
    return(result)
})