Update pseudocount (microbiome#571)

Signed-off-by: Daena Rys <[email protected]>
Daenarys8 · Jun 6, 2024 · bca93ac · bca93ac
1 parent 5ed79ef
commit bca93ac
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Showing 2 changed files with 6 additions and 3 deletions.
diff --git a/R/transformCounts.R b/R/transformCounts.R
@@ -420,8 +420,11 @@ setMethod("transformAssay", signature = c(x = "SummarizedExperiment"),
             stop("The assay contains missing or negative values. ",
                  "'pseudocount' must be specified manually.", call. = FALSE)
         }
-        # If pseudocount TRUE, set it to non-zero minimum value, else set it to zero
-        pseudocount <- ifelse(pseudocount, min(mat[mat>0]), 0)
+        # If pseudocount TRUE, set it to half of non-zero minimum value, else set 
+        # it to zero.
+        # Get min value
+        value <- min(mat[mat>0]) 
+        pseudocount <- ifelse(pseudocount, value / 2, 0)
         # Report pseudocount if positive value
         if ( pseudocount > 0 ){
             message("A pseudocount of ", pseudocount, " was applied.")

diff --git a/tests/testthat/test-5transformCounts.R b/tests/testthat/test-5transformCounts.R
@@ -215,7 +215,7 @@ test_that("transformAssay", {
         tse <- transformAssay(tse, method = "relabundance", pseudocount = TRUE, name = "pseudo_true")
         tse <- transformAssay(
             tse, method = "relabundance", name = "pseudo_min",
-            pseudocount = min(assay(tse, "counts")[assay(tse, "counts") > 0]),
+            pseudocount = (min(assay(tse, "counts")[assay(tse, "counts") > 0])) / 2,
         )
         tse <- transformAssay(tse, method = "relabundance", pseudocount = FALSE, name = "pseudo_false")
         tse <- transformAssay(tse, method = "relabundance", pseudocount = 0, name = "pseudo_zero")