From a08560b217ce5c46bb45fdde16ddbc3149d02441 Mon Sep 17 00:00:00 2001
From: thpralas <theotime.pralas@centrale-med.fr>
Date: Mon, 26 Feb 2024 11:05:24 +0200
Subject: [PATCH] up

---
 DESCRIPTION           | 2 +-
 man/transformAssay.Rd | 7 ++++---
 2 files changed, 5 insertions(+), 4 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 450b95cc0..2ae6ddcbe 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -84,5 +84,5 @@ Suggests:
 URL: https://github.com/microbiome/mia
 BugReports: https://github.com/microbiome/mia/issues
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.0
+RoxygenNote: 7.3.1
 VignetteBuilder: knitr
diff --git a/man/transformAssay.Rd b/man/transformAssay.Rd
index e5933e487..f49a71e98 100644
--- a/man/transformAssay.Rd
+++ b/man/transformAssay.Rd
@@ -120,9 +120,10 @@ reference sample's column in returned assay when calculating alr.
 (default: \code{ref_vals = NA})}
 }}
 
-\item{pseudocount}{TRUE or FALSE, should the minimum value of \code{assay.type}
-be added to assay values. Alternatively, a numeric value specifying the value
-to be added. (default: \code{pseudocount = FALSE})}
+\item{pseudocount}{TRUE, FALSE, or a numeric value. When TRUE,
+automatically adds the minimum positive value of \code{assay.type}.
+When FALSE, does not add any pseudocount (pseudocount = 0).
+Alternatively, a user-specified numeric value can be added as pseudocount.}
 
 \item{MARGIN}{A single character value for specifying whether the
 transformation is applied sample (column) or feature (row) wise.