From d9550c40e02b85ac9403f0010587001bd3bdc50c Mon Sep 17 00:00:00 2001
From: lingminhao <lingminhao31@gmail.com>
Date: Fri, 8 May 2026 10:33:07 +0800
Subject: [PATCH 1/3] export generateUniqueCountsSEFromQuantData &
 getSampleData

---
 NAMESPACE                      | 3 +++
 R/bambu-classes.R              | 4 ++--
 R/transcriptToGeneExpression.R | 2 +-
 3 files changed, 6 insertions(+), 3 deletions(-)

diff --git a/NAMESPACE b/NAMESPACE
index df261f3a..df57c91d 100755
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -6,6 +6,9 @@ export(plotBambu)
 export(prepareAnnotations)
 export(readFromGTF)
 export(transcriptToGeneExpression)
+export(generateUniqueCountsSEFromQuantData)
+export(getSampleData)
+exportMethods(getSampleData)
 export(writeBambuOutput)
 export(writeToGTF)
 export(writeAnnotationsToGTF)
diff --git a/R/bambu-classes.R b/R/bambu-classes.R
index e9ccaf43..6c9c235c 100644
--- a/R/bambu-classes.R
+++ b/R/bambu-classes.R
@@ -55,7 +55,7 @@ constructQuantData <- function(sampleData, readClassDt,
         readToTranscriptMap = readToTranscriptMap)
 }
 
-#' @noRd
+#' @export
 setGeneric("getSampleData",          function(x) standardGeneric("getSampleData"))
 #' @noRd
 setGeneric("getReadClassDt",         function(x) standardGeneric("getReadClassDt"))
@@ -66,7 +66,7 @@ setGeneric("getDistTable",           function(x) standardGeneric("getDistTable")
 #' @noRd
 setGeneric("getReadToTranscriptMap", function(x) standardGeneric("getReadToTranscriptMap"))
 
-#' @noRd
+#' @exportMethod getSampleData
 setMethod("getSampleData",          "quantData", function(x) x@sampleData)
 #' @noRd
 setMethod("getReadClassDt",         "quantData", function(x) x@readClassDt)
diff --git a/R/transcriptToGeneExpression.R b/R/transcriptToGeneExpression.R
index a76aa7d0..e39b9c8a 100644
--- a/R/transcriptToGeneExpression.R
+++ b/R/transcriptToGeneExpression.R
@@ -62,7 +62,7 @@ transcriptToGeneExpression <- function(se) {
 #' @return A SummarizedExperiment object with \code{assays$uniqueCounts},
 #'   \code{metadata$incompatibleCounts}, and \code{metadata$nonuniqueCounts}
 #' @import data.table
-#' @noRd
+#' @export
 generateUniqueCountsSEFromQuantData <- function(quantData, annotations) {
     uniqueCountsList <- lapply(quantData, function(x) {
         readClassDt <- getReadClassDt(x)

From 18673cfca96e104c550df59190dbcc0f060845f7 Mon Sep 17 00:00:00 2001
From: lingminhao <lingminhao31@gmail.com>
Date: Fri, 8 May 2026 11:26:16 +0800
Subject: [PATCH 2/3] export generateUniqueCountsSEFromQuantData

---
 NAMESPACE         | 2 --
 R/bambu-classes.R | 4 ++--
 2 files changed, 2 insertions(+), 4 deletions(-)

diff --git a/NAMESPACE b/NAMESPACE
index df57c91d..e9c86d79 100755
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -7,8 +7,6 @@ export(prepareAnnotations)
 export(readFromGTF)
 export(transcriptToGeneExpression)
 export(generateUniqueCountsSEFromQuantData)
-export(getSampleData)
-exportMethods(getSampleData)
 export(writeBambuOutput)
 export(writeToGTF)
 export(writeAnnotationsToGTF)
diff --git a/R/bambu-classes.R b/R/bambu-classes.R
index 6c9c235c..e9ccaf43 100644
--- a/R/bambu-classes.R
+++ b/R/bambu-classes.R
@@ -55,7 +55,7 @@ constructQuantData <- function(sampleData, readClassDt,
         readToTranscriptMap = readToTranscriptMap)
 }
 
-#' @export
+#' @noRd
 setGeneric("getSampleData",          function(x) standardGeneric("getSampleData"))
 #' @noRd
 setGeneric("getReadClassDt",         function(x) standardGeneric("getReadClassDt"))
@@ -66,7 +66,7 @@ setGeneric("getDistTable",           function(x) standardGeneric("getDistTable")
 #' @noRd
 setGeneric("getReadToTranscriptMap", function(x) standardGeneric("getReadToTranscriptMap"))
 
-#' @exportMethod getSampleData
+#' @noRd
 setMethod("getSampleData",          "quantData", function(x) x@sampleData)
 #' @noRd
 setMethod("getReadClassDt",         "quantData", function(x) x@readClassDt)

From 69ed2887e3ee23f66aa3460a43a0876f57ade49a Mon Sep 17 00:00:00 2001
From: lingminhao <lingminhao31@gmail.com>
Date: Fri, 8 May 2026 14:43:27 +0800
Subject: [PATCH 3/3] fix typo

---
 R/bambu-quantify.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/bambu-quantify.R b/R/bambu-quantify.R
index 65998cad..99f9eaaa 100644
--- a/R/bambu-quantify.R
+++ b/R/bambu-quantify.R
@@ -10,7 +10,7 @@ bambu.quantify <- function(readClassDt, columnIdx, incompatibleCounts, txid.inde
     # Calculate nobs for sample(s) columnIdx
     # Use data.table syntax for in-place creation of nobs column for the scope of this function
     readClassDt[, nobs := {
-        ids <- columnIdx[[1]]
+        ids <- columnIds[[1]]
         if (is.null(ids) || length(ids) == 0 || is.na(ids[1])) {
             0L
         } else if (length(columnIdx) == 1) {