Updated logic of calc_variance() for data with no replicates to consi…

…der expression_value
ruthkr · Mar 11, 2024 · 43ffccf · 43ffccf
1 parent b063da5
commit 43ffccf
Show file tree

Hide file tree

Showing 2 changed files with 2 additions and 2 deletions.
diff --git a/R/utils-calcs.R b/R/utils-calcs.R
@@ -87,7 +87,7 @@ calc_variance <- function(all_data, exp_sd = NA) {
 
     # Set variance for data with no replicates
     if (nrow(all_data_no_reps) > 0) {
-      all_data_no_reps[, var := 0.01]
+      all_data_no_reps[, var := pmax(expression_value / 10, 0.25), by = .(gene_id, accession, timepoint)]
     }
 
     # Combine data

diff --git a/tests/testthat/test-utils-calcs.R b/tests/testthat/test-utils-calcs.R
@@ -34,5 +34,5 @@ test_that("calc_variance works", {
 
   # Expected outputs
   expect_gt(length(unique(var_with_reps$var)), 1)
-  expect_equal(length(unique(var_with_no_reps$var)), 1)
+  expect_true(all(var_with_no_reps$var >= 0.25))
 })