From 3a351c93ecae50cbbfa92c3e9c0d735c6e60e1d2 Mon Sep 17 00:00:00 2001
From: Saket Choudhary <saketkc@gmail.com>
Date: Mon, 18 Sep 2023 13:15:17 -0400
Subject: [PATCH] Update documentation

---
 DESCRIPTION           | 4 ++--
 NEWS.md               | 1 +
 R/utils.R             | 3 ++-
 man/get_nz_median2.Rd | 3 +++
 4 files changed, 8 insertions(+), 3 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index fa87b7f..cb23425 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: sctransform
 Type: Package
 Title: Variance Stabilizing Transformations for Single Cell UMI Data
-Version: 0.3.5.9006
-Date: 2023-05-27
+Version: 0.3.5.9007
+Date: 2023-09-18
 Authors@R: c(
   person(given = "Christoph", family = "Hafemeister", email = "christoph.hafemeister@nyu.edu", role = "aut", comment = c(ORCID = "0000-0001-6365-8254")),
   person(given = "Saket", family = "Choudhary", email = "schoudhary@nygenome.org", role = c("aut", "cre"), comment = c(ORCID = "0000-0001-5202-7633")),
diff --git a/NEWS.md b/NEWS.md
index 11a8469..ae330b6 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -14,6 +14,7 @@ All notable changes will be documented in this file.
 - Changed `get_nz_median2` to support `genes` argument; thanks @boomanaiden154 and @ScreachingFire. [#155](https://github.com/satijalab/sctransform/pull/155)
 - Replaced `get_nz_median` with faster alternative `get_nz_median2` across all calls
 - Removed `get_nz_median` 
+- Updated `make_cell_attr` to be flexible for named vectors; thanks @moi-taga [#171](https://github.com/satijalab/sctransform/pull/171)
 
 ## [0.3.5] - 2022-09-21
 
diff --git a/R/utils.R b/R/utils.R
index 4b89e8d..1f10987 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -496,7 +496,8 @@ get_model_var <- function(vst_out, cell_attr = vst_out$cell_attr, use_nonreg = F
 #' Get median of non zero UMIs from a count matrix
 #'
 #' @param umi Count matrix
-#'
+#' @param genes A vector of genes to consider for calculating
+#' the median. Default is NULL which uses all genes.
 #' @return A numeric value representing the median of non-zero entries from the UMI matrix
 get_nz_median2 <- function(umi, genes = NULL){
   if (is.null(genes)) {
diff --git a/man/get_nz_median2.Rd b/man/get_nz_median2.Rd
index 8158d9a..01b1eb7 100644
--- a/man/get_nz_median2.Rd
+++ b/man/get_nz_median2.Rd
@@ -8,6 +8,9 @@ get_nz_median2(umi, genes = NULL)
 }
 \arguments{
 \item{umi}{Count matrix}
+
+\item{genes}{A vector of genes to consider for calculating
+the median. Default is NULL which uses all genes.}
 }
 \value{
 A numeric value representing the median of non-zero entries from the UMI matrix