Use get_nz_median2 across all methods

satijalab · Jan 12, 2023 · 2cf8c9a · 2cf8c9a
1 parent 24b4ce6
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diff --git a/NEWS.md b/NEWS.md
@@ -1,6 +1,11 @@
 # News
 All notable changes will be documented in this file.
 
+## Unreleased
+
+### Fixed 
+- Replaced `get_nz_median` with faster alternative `get_nz_median2'
+
 ## [0.3.5] - 2022-09-21
 
 ### Fixed

diff --git a/R/utils.R b/R/utils.R
@@ -237,7 +237,7 @@ get_residuals <- function(vst_out, umi, residual_type = 'pearson',
   # min_variance estimated using median umi
   if (min_variance == "umi_median"){
     # Maximum pearson residual for non-zero median UMI is 5
-    min_var <- (get_nz_median(umi) / 5)^2
+    min_var <- (get_nz_median2(umi) / 5)^2
     if (verbosity > 0) {
       message(paste("Setting min_variance based on median UMI: ", min_var))
     }
@@ -359,7 +359,7 @@ get_residual_var <- function(vst_out, umi, residual_type = 'pearson',
   # min_variance estimated using median umi
   if (min_variance == "umi_median"){
     # Maximum pearson residual for non-zero median UMI is 5
-    min_var <- (get_nz_median(umi, genes) / 5)^2
+    min_var <- (get_nz_median2(umi, genes) / 5)^2
     if (verbosity > 0) {
       message(paste("Setting min_variance based on median UMI: ", min_var))
     }