From 75ab574430f27412ddaa2d0b143749d4418da861 Mon Sep 17 00:00:00 2001
From: "Stephanie J. Spielman" <stephanie.spielman@gmail.com>
Date: Tue, 19 Dec 2023 12:29:16 -0500
Subject: [PATCH] doc update and redocument

---
 R/merge_sce_list.R              | 2 +-
 man/prepare_altexp_for_merge.Rd | 8 ++++++++
 man/prepare_sce_for_merge.Rd    | 6 +++---
 3 files changed, 12 insertions(+), 4 deletions(-)

diff --git a/R/merge_sce_list.R b/R/merge_sce_list.R
index a06fe93d..42be7801 100644
--- a/R/merge_sce_list.R
+++ b/R/merge_sce_list.R
@@ -229,7 +229,7 @@ merge_sce_list <- function(
 #' @param preserve_rowdata_cols A vector of rowData columns which should not be
 #'   renamed
 #' @param is_altexp Boolean if we are preparing an altExp or not.
-#'   Default is `FALSE`.
+#'   Default is `FALSE`. If FALSE, the SCE colnames will not be modified.
 #'
 #' @return An updated SCE that is prepared for merging
 prepare_sce_for_merge <- function(
diff --git a/man/prepare_altexp_for_merge.Rd b/man/prepare_altexp_for_merge.Rd
index 0dee95d8..baea7aa7 100644
--- a/man/prepare_altexp_for_merge.Rd
+++ b/man/prepare_altexp_for_merge.Rd
@@ -10,6 +10,8 @@ prepare_altexp_for_merge(
   altexp_name,
   expected_assays,
   expected_features,
+  batch_column,
+  cell_id_column,
   preserve_rowdata_cols = c("target_type")
 )
 }
@@ -24,6 +26,12 @@ prepare_altexp_for_merge(
 
 \item{expected_features}{Vector of features that should be in each altExp}
 
+\item{batch_column}{The name of the batch column which will be added to the
+colData slot.}
+
+\item{cell_id_column}{The name of the cell_id column which will be added to the
+colData slot.}
+
 \item{preserve_rowdata_cols}{altExp rowData columns which should not be renamed}
 }
 \value{
diff --git a/man/prepare_sce_for_merge.Rd b/man/prepare_sce_for_merge.Rd
index 195d8762..810cf19a 100644
--- a/man/prepare_sce_for_merge.Rd
+++ b/man/prepare_sce_for_merge.Rd
@@ -21,10 +21,10 @@ prepare_sce_for_merge(
 \item{sce_name}{The name of the SCE object}
 
 \item{batch_column}{The name of the batch column which will be added to the
-colData slot}
+colData slot.}
 
 \item{cell_id_column}{The name of the cell_id column which will be added to the
-colData slot}
+colData slot.}
 
 \item{shared_features}{A vector of features (genes) that all SCEs to be merged
 have in common}
@@ -38,7 +38,7 @@ populated with respective information.}
 renamed}
 
 \item{is_altexp}{Boolean if we are preparing an altExp or not.
-Default is `FALSE`.}
+Default is `FALSE`. If FALSE, the SCE colnames will not be modified.}
 }
 \value{
 An updated SCE that is prepared for merging