get_genes return aliases and some doc fixes

R/processors.R

@@ -557,17 +557,18 @@ processElements <- function(d) {
 #' The fields of the output data.table are:
 #'
 #' \itemize{
-#'     \item \code{gene.Symbol}: Symbol for the gene
-#'     \item \code{gene.Ensembl}: Ensembl ID for the gene
+#'     \item \code{gene.symbol}: Symbol for the gene
+#'     \item \code{gene.ensembl}: Ensembl ID for the gene
 #'     \item \code{gene.NCBI}: NCBI id for the gene
-#'     \item \code{gene.Name}: Name of the gene
-#'     \item \code{gene.MFX.Rank}: Multifunctionality rank for the gene
-#'     \item \code{taxon.Name}: Name of the species
-#'     \item \code{taxon.Scientific}: Scientific name for the taxon
+#'     \item \code{gene.name}: Name of the gene
+#'     \item \code{gene.aliases}: Gene aliases. Each row includes a vector
+#'     \item \code{gene.MFX.rank}: Multifunctionality rank for the gene
+#'     \item \code{taxon.name}: Name of the species
+#'     \item \code{taxon.scientific}: Scientific name for the taxon
 #'     \item \code{taxon.ID}: Internal identifier given to the species by Gemma
 #'     \item \code{taxon.NCBI}: NCBI ID of the taxon
-#'     \item \code{taxon.Database.Name}: Underlying database used in Gemma for the taxon
-#'     \item \code{taxon.Database.ID}: ID of the underyling database used in Gemma for the taxon
+#'     \item \code{taxon.database.name}: Underlying database used in Gemma for the taxon
+#'     \item \code{taxon.database.ID}: ID of the underlying database used in Gemma for the taxon
 #' }
 #'
 #' @keywords internal
@@ -577,6 +578,9 @@ processGenes <- function(d) {
         gene.ensembl = accessField(d,'ensemblId',NA_character_),
         gene.NCBI = accessField(d,"ncbiId",NA_integer_),
         gene.name = accessField(d, "officialName",NA_character_),
+        gene.aliases = d %>% purrr::map(function(x){
+            x$aliases %>% unlist
+        }),
         # gene.Aliases = d[["aliases"]],
         # gene.GO = d[["numGoTerms"]],
         # gene.Homologues = d[["homologues"]],