From 1025edf89cd4b23885fa1ef33acc297a1f67a2fa Mon Sep 17 00:00:00 2001
From: timoast <4591688+timoast@users.noreply.github.com>
Date: Fri, 27 Aug 2021 12:50:07 -0400
Subject: [PATCH] Update to.upper documentation; #4576

---
 R/preprocessing.R      | 6 ++++--
 man/Load10X_Spatial.Rd | 6 ++++--
 2 files changed, 8 insertions(+), 4 deletions(-)

diff --git a/R/preprocessing.R b/R/preprocessing.R
index 16ba520bc..335dd78d4 100644
--- a/R/preprocessing.R
+++ b/R/preprocessing.R
@@ -468,8 +468,10 @@ GetResidual <- function(
 #' @param slice Name for the stored image of the tissue slice
 #' @param filter.matrix Only keep spots that have been determined to be over
 #' tissue
-#' @param to.upper Converts all feature names to upper case. Can be useful when
-#' analyses require comparisons between human and mouse gene names for example.
+#' @param to.upper Converts all feature names to upper case. This can provide an
+#' approximate conversion of mouse to human gene names which can be useful in an
+#' explorative analysis. For cross-species comparisons, orthologous genes should
+#' be identified across species and used instead.
 #' @param image An object of class VisiumV1. Typically, an output from \code{\link{Read10X_Image}}
 #' @param ... Arguments passed to \code{\link{Read10X_h5}}
 #'
diff --git a/man/Load10X_Spatial.Rd b/man/Load10X_Spatial.Rd
index 768c164b2..cfe5c63d6 100644
--- a/man/Load10X_Spatial.Rd
+++ b/man/Load10X_Spatial.Rd
@@ -28,8 +28,10 @@ and the image data in a subdirectory called \code{spatial}}
 \item{filter.matrix}{Only keep spots that have been determined to be over
 tissue}
 
-\item{to.upper}{Converts all feature names to upper case. Can be useful when
-analyses require comparisons between human and mouse gene names for example.}
+\item{to.upper}{Converts all feature names to upper case. This can provide an
+approximate conversion of mouse to human gene names which can be useful in an
+explorative analysis. For cross-species comparisons, orthologous genes should
+be identified across species and used instead.}
 
 \item{image}{An object of class VisiumV1. Typically, an output from \code{\link{Read10X_Image}}}