From aca1681e4bea2ed988e74577547a0aff8781b3c2 Mon Sep 17 00:00:00 2001
From: Yichen Wang <wayichen@umich.edu>
Date: Wed, 15 Jan 2025 11:08:09 -0500
Subject: [PATCH] Fix bug in selectBatchHVG

---
 DESCRIPTION        | 4 ++--
 R/selectBatchHVG.R | 4 +++-
 2 files changed, 5 insertions(+), 3 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index f37c8bc..e9c26c1 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: rliger
-Version: 2.1.0.9003
-Date: 2024-12-04
+Version: 2.1.0.9004
+Date: 2025-01-07
 Type: Package
 Title: Linked Inference of Genomic Experimental Relationships
 Description: Uses an extension of nonnegative matrix factorization to identify shared and dataset-specific factors. See Welch J, Kozareva V, et al (2019) <doi:10.1016/j.cell.2019.05.006>, and Liu J, Gao C, Sodicoff J, et al (2020) <doi:10.1038/s41596-020-0391-8> for more details.
diff --git a/R/selectBatchHVG.R b/R/selectBatchHVG.R
index db2e612..f82e80b 100644
--- a/R/selectBatchHVG.R
+++ b/R/selectBatchHVG.R
@@ -148,7 +148,7 @@ selectBatchHVG.ligerDataset <- function(
     fm <- featureMeta(object)
     idx <- rep(FALSE, nrow(object))
     idx[features] <- TRUE
-    idx <- idx & (fm$nCell > 0)
+    # idx <- idx & (fm$nCell > 0)
     mat <- mat[idx, , drop = FALSE]
     stats <- selectBatchHVG(mat, nGenes = nGenes, verbose = verbose,
                             returnStats = TRUE, ...)
@@ -175,6 +175,8 @@ selectBatchHVG.dgCMatrix <- function(
         ...
 ) {
     # Get mean and var
+    idx <- Matrix::rowSums(object > 0) > 0
+    object <- object[idx, , drop = FALSE]
     means <- Matrix::rowMeans(object)
     vars <- rowVars_sparse_rcpp(object, means)
     stats <- .selectBatchHVG.by.metric(