Fix bug in selectBatchHVG

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.

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(