Merge pull request satijalab#568 from satijalab/fix/UpdateSymbolList

UpdateSymbolList no longer searches aliases

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: Seurat
-Version: 4.0.2.9003
-Date: 2021-06-01
+Version: 4.0.2.9004
+Date: 2021-06-02
 Title: Tools for Single Cell Genomics
 Description: A toolkit for quality control, analysis, and exploration of single cell RNA sequencing data. 'Seurat' aims to enable users to identify and interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse types of single cell data. See Satija R, Farrell J, Gennert D, et al (2015) <doi:10.1038/nbt.3192>, Macosko E, Basu A, Satija R, et al (2015) <doi:10.1016/j.cell.2015.05.002>, Stuart T, Butler A, et al (2019) <doi:10.1016/j.cell.2019.05.031>, and Hao, Hao, et al (2020) <doi:10.1101/2020.10.12.335331> for more details.
 Authors@R: c(

NEWS.md

@@ -5,6 +5,7 @@
 ## Changes
 - Fix issues with `as.SingleCellExperiment.Seurat` for the latest verion of SingleCellExperiment ([#4532](https://github.com/satijalab/seurat/pull/4532))
 - Ensure proper reference.reduction is used in `MapQuery()`
+- Fix to `UpdateSymbolList()`, no longer searches aliases and exposes the `search.types` parameter in `GeneSymbolThesarus()` ([#4545](https://github.com/satijalab/seurat/issues/4545))
 
 # Seurat 4.0.2 (2020-03-20)
 ## Added

R/utilities.R

@@ -796,14 +796,25 @@ FastRowScale <- function(
 #' @note This function requires internet access
 #'
 #' @param symbols A vector of gene symbols
-#' @param timeout Time to wait before cancelling query in seconds
-#' @param several.ok Allow several current gene sybmols for each provided symbol
+#' @param timeout Time to wait before canceling query in seconds
+#' @param several.ok Allow several current gene symbols for each
+#' provided symbol
+#' @param search.types Type of query to perform:
+#' \describe{
+#'  \itemize{\dQuote{\code{alias_symbol}}}{Find alternate symbols for the genes
+#'  described by \code{symbols}}
+#'  \itemize{\dQuote{\code{prev_symbol}}}{Find new new symbols for the genes
+#'  described by \code{symbols}}
+#' }
+#' This parameter accepts multiple options and short-hand options
+#' (eg. \dQuote{\code{prev}} for \dQuote{\code{prev_symbol}})
 #' @param verbose Show a progress bar depicting search progress
 #' @param ... Extra parameters passed to \code{\link[httr]{GET}}
 #'
-#' @return For \code{GeneSymbolThesarus}, if \code{several.ok}, a named list
-#' where each entry is the current symbol found for each symbol provided and the
-#' names are the provided symbols. Otherwise, a named vector with the same information.
+#' @return \code{GeneSymbolThesarus}:, if \code{several.ok}, a named list
+#' where each entry is the current symbol found for each symbol provided and
+#' the names are the provided symbols. Otherwise, a named vector with the
+#' same information.
 #'
 #' @source \url{https://www.genenames.org/} \url{https://www.genenames.org/help/rest/}
 #'
@@ -827,11 +838,13 @@ GeneSymbolThesarus <- function(
   symbols,
   timeout = 10,
   several.ok = FALSE,
+  search.types = c('alias_symbol', 'prev_symbol'),
   verbose = TRUE,
   ...
 ) {
   db.url <- 'http://rest.genenames.org/fetch'
-  search.types <- c('alias_symbol', 'prev_symbol')
+  # search.types <- c('alias_symbol', 'prev_symbol')
+  search.types <- match.arg(arg = search.types, several.ok = TRUE)
   synonyms <- vector(mode = 'list', length = length(x = symbols))
   not.found <- vector(mode = 'logical', length = length(x = symbols))
   multiple.found <- vector(mode = 'logical', length = length(x = symbols))
@@ -1472,7 +1485,7 @@ RegroupIdents <- function(object, metadata) {
 
 #' @rdname UpdateSymbolList
 #'
-#' @return For \code{UpdateSymbolList}, \code{symbols} with updated symbols from
+#' @return \code{UpdateSymbolList}: \code{symbols} with updated symbols from
 #' HGNC's gene names database
 #'
 #' @export
@@ -1494,6 +1507,7 @@ UpdateSymbolList <- function(
     symbols = symbols,
     timeout = timeout,
     several.ok = several.ok,
+    search.types = 'prev_symbol',
     verbose = verbose,
     ...
   ))