Update Maaslin2.R

biobakery · Nov 11, 2024 · 5ff4892 · 5ff4892
1 parent 0256ed9
commit 5ff4892
Showing 1 changed file with 2 additions and 2 deletions.
diff --git a/R/Maaslin2.R b/R/Maaslin2.R
@@ -879,8 +879,8 @@ Maaslin2 <-
         # Filter data based on variance #
         #################################
 
-        sds <- apply(filtered_data, 2, sd)
-        variance_filtered_data <- filtered_data[, which(sds > min_variance), drop = FALSE]
+        vars <- apply(filtered_data, 2, var)
+        variance_filtered_data <- filtered_data[, which(vars > min_variance), drop = FALSE]
         variance_filtered_features <- ncol(filtered_data) - ncol(variance_filtered_data)
         logging::loginfo("Total filtered features with variance filtering: %d", variance_filtered_features)
         variance_filtered_feature_names <- setdiff(names(filtered_data), names(variance_filtered_data))