From 09c8975c8642fa0cc37c33d563cbff544e02c0d3 Mon Sep 17 00:00:00 2001
From: Kostas Vilkelis <54437487+Kostusas@users.noreply.github.com>
Date: Fri, 17 Oct 2025 11:07:17 +0200
Subject: [PATCH] replace NAnnotated frame with AnnotatedFrame

---
 R/ROI_Extraction.R | 2 +-
 R/Spectra_Utils.R  | 2 +-
 R/Spectra_import.R | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/R/ROI_Extraction.R b/R/ROI_Extraction.R
index 102223c..a9e2a17 100644
--- a/R/ROI_Extraction.R
+++ b/R/ROI_Extraction.R
@@ -299,7 +299,7 @@ PerformROIExtraction <-
       raw_data <-
         tryCatch(read.MSdata(
           dda_file1,
-          pdata = new("NAnnotatedDataFrame", pd),
+          pdata = new("AnnotatedDataFrame", pd),
           msLevel. = 1L,
           mode = "inMemory"
         ), error = function(e) {e})
diff --git a/R/Spectra_Utils.R b/R/Spectra_Utils.R
index 2ae3c7d..d5eaf46 100644
--- a/R/Spectra_Utils.R
+++ b/R/Spectra_Utils.R
@@ -2511,7 +2511,7 @@ PerformPeakFiling <- function(mSet, BPPARAM=bpparam()){
         processingData = new("MSnProcess",
                              files = specdata@processingData@files[i]),
         featureData = new("AnnotatedDataFrame", fd),
-        phenoData = new("NAnnotatedDataFrame",
+        phenoData = new("AnnotatedDataFrame",
                         data.frame(sampleNames = "1")),
         experimentData = new("MIAPE",
                              instrumentManufacturer = "a",
diff --git a/R/Spectra_import.R b/R/Spectra_import.R
index e2590c9..098d0d4 100644
--- a/R/Spectra_import.R
+++ b/R/Spectra_import.R
@@ -270,7 +270,7 @@ ImportRawMSData <-
       raw_data <-
         tryCatch(read.MSdata(
           files = files,
-          pdata = new("NAnnotatedDataFrame", pd),
+          pdata = new("AnnotatedDataFrame", pd),
           mode = mode,
           msLevel. = 1
         ), error = function(e) {e})