From 335f92e0ce6a7ad2d6d616d06280e26fa8efa6ae Mon Sep 17 00:00:00 2001
From: tonywu1999 <wu.anthon@northeastern.edu>
Date: Tue, 15 Jul 2025 16:23:47 -0400
Subject: [PATCH 1/7] feat(diann): Add support for DIANN 2.0

---
 R/clean_DIANN.R                     | 16 +++++++++++++++-
 R/converters_DIANNtoMSstatsFormat.R |  6 ++++--
 man/DIANNtoMSstatsFormat.Rd         |  6 ++++--
 man/MSstatsClean.Rd                 |  4 +++-
 man/dot-cleanRawDIANN.Rd            |  4 +++-
 5 files changed, 29 insertions(+), 7 deletions(-)

diff --git a/R/clean_DIANN.R b/R/clean_DIANN.R
index e972eb88..07a34db7 100644
--- a/R/clean_DIANN.R
+++ b/R/clean_DIANN.R
@@ -1,7 +1,9 @@
 #' Clean raw Diann files
 #' @param msstats_object an object of class `MSstatsDIANNFiles`.
 #' @param MBR True if analysis was done with match between runs
-#' @param quantificationColumn Use 'FragmentQuantCorrected'(default) column for quantified intensities. 'FragmentQuantRaw' can be used instead.
+#' @param quantificationColumn Use 'FragmentQuantCorrected'(default) column for quantified intensities. 
+#' 'FragmentQuantRaw' can be used instead. 
+#' 'auto' should be used for DIANN 2.0 where each fragment intensity is a separate column, e.g. Fr0Quantity.
 #' @return data.table
 #' @importFrom stats na.omit
 #' @keywords internal
@@ -10,6 +12,18 @@
   dn_input = getInputFile(msstats_object, "input")
   dn_input = data.table::as.data.table(dn_input)
   
+  # Auto-detect and collapse multiple fragment columns (DIANN 2.0 format)
+  if (quantificationColumn == "auto") {
+      fragment_columns <- grep("^Fr[0-9]+Quantity$", names(dn_input), value = TRUE)
+      if (length(fragment_columns) == 0) {
+          stop("No fragment quantification columns found. Please check your input.")
+      }
+      dn_input[, FragmentQuantCorrected := apply(.SD, 1, function(row) {
+          paste(as.character(row), collapse = ";")
+      }), .SDcols = fragment_columns]
+      quantificationColumn <- "FragmentQuantCorrected"
+  }
+
   if (!is.element("PrecursorMz", colnames(dn_input))) {
     dn_input[, PrecursorMz := NA]
   }
diff --git a/R/converters_DIANNtoMSstatsFormat.R b/R/converters_DIANNtoMSstatsFormat.R
index df3c4bd7..2c358b49 100644
--- a/R/converters_DIANNtoMSstatsFormat.R
+++ b/R/converters_DIANNtoMSstatsFormat.R
@@ -20,7 +20,9 @@
 #' @param removeFewMeasurements should proteins with few measurements be removed
 #' @param removeOxidationMpeptides should peptides with oxidation be removed
 #' @param removeProtein_with1Feature should proteins with a single feature be removed
-#' @param quantificationColumn Use 'FragmentQuantCorrected'(default) column for quantified intensities. 'FragmentQuantRaw' can be used instead.
+#' @param quantificationColumn Use 'FragmentQuantCorrected'(default) column for quantified intensities. 
+#' 'FragmentQuantRaw' can be used instead.
+#' 'auto' should be used for DIANN 2.0 where each fragment intensity is a separate column, e.g. Fr0Quantity.
 #' @param ... additional parameters to `data.table::fread`.
 #'  
 #' @return data.frame in the MSstats required format.
@@ -30,7 +32,7 @@
 #' @export
 #' 
 #' @examples 
-#' # See https://github.com/vdemichev/DiaNN/discussions/1525 for workaround for DIANN 2.0
+#' # For DIANN 2.0, set quantificationColumn = 'auto'
 #' input_file_path = system.file("tinytest/raw_data/DIANN/diann_input.tsv", 
 #'                                 package="MSstatsConvert")
 #' annotation_file_path = system.file("tinytest/raw_data/DIANN/annotation.csv", 
diff --git a/man/DIANNtoMSstatsFormat.Rd b/man/DIANNtoMSstatsFormat.Rd
index f7c2a68c..1719555a 100644
--- a/man/DIANNtoMSstatsFormat.Rd
+++ b/man/DIANNtoMSstatsFormat.Rd
@@ -67,7 +67,9 @@ If \code{append = TRUE}, has to be a valid path to a file.}
 
 \item{MBR}{True if analysis was done with match between runs}
 
-\item{quantificationColumn}{Use 'FragmentQuantCorrected'(default) column for quantified intensities. 'FragmentQuantRaw' can be used instead.}
+\item{quantificationColumn}{Use 'FragmentQuantCorrected'(default) column for quantified intensities.
+'FragmentQuantRaw' can be used instead.
+'auto' should be used for DIANN 2.0 where each fragment intensity is a separate column, e.g. Fr0Quantity.}
 
 \item{...}{additional parameters to \code{data.table::fread}.}
 }
@@ -78,7 +80,7 @@ data.frame in the MSstats required format.
 Import Diann files
 }
 \examples{
-# See https://github.com/vdemichev/DiaNN/discussions/1525 for workaround for DIANN 2.0
+# For DIANN 2.0, set quantificationColumn = 'auto'
 input_file_path = system.file("tinytest/raw_data/DIANN/diann_input.tsv", 
                                 package="MSstatsConvert")
 annotation_file_path = system.file("tinytest/raw_data/DIANN/annotation.csv", 
diff --git a/man/MSstatsClean.Rd b/man/MSstatsClean.Rd
index 93ce567e..7e94b964 100644
--- a/man/MSstatsClean.Rd
+++ b/man/MSstatsClean.Rd
@@ -116,7 +116,9 @@ removed based on the IsUnique column from Philosopher output}
 
 \item{MBR}{True if analysis was done with match between runs}
 
-\item{quantificationColumn}{Use 'FragmentQuantCorrected'(default) column for quantified intensities. 'FragmentQuantRaw' can be used instead.}
+\item{quantificationColumn}{Use 'FragmentQuantCorrected'(default) column for quantified intensities.
+'FragmentQuantRaw' can be used instead.
+'auto' should be used for DIANN 2.0 where each fragment intensity is a separate column, e.g. Fr0Quantity.}
 
 \item{qvalue_cutoff}{The q-value cutoff for filtering peaks detected by MBR}
 }
diff --git a/man/dot-cleanRawDIANN.Rd b/man/dot-cleanRawDIANN.Rd
index 109d3de9..c17556bb 100644
--- a/man/dot-cleanRawDIANN.Rd
+++ b/man/dot-cleanRawDIANN.Rd
@@ -15,7 +15,9 @@
 
 \item{MBR}{True if analysis was done with match between runs}
 
-\item{quantificationColumn}{Use 'FragmentQuantCorrected'(default) column for quantified intensities. 'FragmentQuantRaw' can be used instead.}
+\item{quantificationColumn}{Use 'FragmentQuantCorrected'(default) column for quantified intensities.
+'FragmentQuantRaw' can be used instead.
+'auto' should be used for DIANN 2.0 where each fragment intensity is a separate column, e.g. Fr0Quantity.}
 }
 \value{
 data.table

From 1b37ae529fdd8687e845c25689903ae90bc8e34b Mon Sep 17 00:00:00 2001
From: tonywu1999 <wu.anthon@northeastern.edu>
Date: Tue, 15 Jul 2025 17:01:30 -0400
Subject: [PATCH 2/7] add unit tests - pending test files

---
 R/converters_DIANNtoMSstatsFormat.R           | 11 ++++++++++
 .../test_converters_DIANNtoMSstatsFormat.R    | 20 +++++++++++++++++++
 man/DIANNtoMSstatsFormat.Rd                   | 11 ++++++++++
 3 files changed, 42 insertions(+)

diff --git a/R/converters_DIANNtoMSstatsFormat.R b/R/converters_DIANNtoMSstatsFormat.R
index 2c358b49..f771bea5 100644
--- a/R/converters_DIANNtoMSstatsFormat.R
+++ b/R/converters_DIANNtoMSstatsFormat.R
@@ -42,6 +42,17 @@
 #' output = DIANNtoMSstatsFormat(input, annotation = annot, MBR = FALSE, 
 #'                                 use_log_file = FALSE)
 #' head(output)
+#' 
+#' # For DIANN 2.0, set quantificationColumn = 'auto'
+#' input_file_path_2_0 = system.file("tinytest/raw_data/DIANN/diann_input_2.0.csv", 
+#'                                 package="MSstatsConvert")
+#' annotation_file_path_2_0 = system.file("tinytest/raw_data/DIANN/annotation_diann_2.0.csv", 
+#'                                 package = "MSstatsConvert")
+#' input_2_0 = data.table::fread(input_file_path_2_0)
+#' annot_2_0 = data.table::fread(annotation_file_path_2_0)
+#' output_2_0 = DIANNtoMSstatsFormat(input_2_0, annotation = annot_2_0, MBR = FALSE, 
+#'                                 use_log_file = FALSE, quantificationColumn = 'auto')
+#' head(output_2_0)
 DIANNtoMSstatsFormat = function(input, annotation = NULL,
                                 global_qvalue_cutoff = 0.01,
                                 qvalue_cutoff = 0.01, 
diff --git a/inst/tinytest/test_converters_DIANNtoMSstatsFormat.R b/inst/tinytest/test_converters_DIANNtoMSstatsFormat.R
index d54011ff..275bbeaf 100644
--- a/inst/tinytest/test_converters_DIANNtoMSstatsFormat.R
+++ b/inst/tinytest/test_converters_DIANNtoMSstatsFormat.R
@@ -16,4 +16,24 @@ expect_true("ProductCharge" %in% colnames(output))
 expect_true("IsotopeLabelType" %in% colnames(output))
 expect_true("Condition" %in% colnames(output))
 expect_true("BioReplicate" %in% colnames(output))
+expect_true("Fraction" %in% colnames(output))
+
+# Test DIANNtoMSstatsFormat DIANN 2.0 ------------------------
+input_file_path = system.file("tinytest/raw_data/DIANN/diann_input_2.0.csv", package="MSstatsConvert")
+annotation_file_path = system.file("tinytest/raw_data/DIANN/annotation_diann_2.0.csv", package = "MSstatsConvert")
+input = data.table::fread(input_file_path)
+annot = data.table::fread(annotation_file_path)
+output = DIANNtoMSstatsFormat(input, annotation = annot, MBR = FALSE, use_log_file = FALSE, quantificationColumn = 'auto')
+expect_equal(ncol(output), 11)
+expect_equal(nrow(output), 180)
+expect_true("Run" %in% colnames(output))
+expect_true("ProteinName" %in% colnames(output))
+expect_true("PeptideSequence" %in% colnames(output))
+expect_true("PrecursorCharge" %in% colnames(output))
+expect_true("Intensity" %in% colnames(output))
+expect_true("FragmentIon" %in% colnames(output))
+expect_true("ProductCharge" %in% colnames(output))
+expect_true("IsotopeLabelType" %in% colnames(output))
+expect_true("Condition" %in% colnames(output))
+expect_true("BioReplicate" %in% colnames(output))
 expect_true("Fraction" %in% colnames(output))
\ No newline at end of file
diff --git a/man/DIANNtoMSstatsFormat.Rd b/man/DIANNtoMSstatsFormat.Rd
index 1719555a..c702e644 100644
--- a/man/DIANNtoMSstatsFormat.Rd
+++ b/man/DIANNtoMSstatsFormat.Rd
@@ -90,6 +90,17 @@ annot = data.table::fread(annotation_file_path)
 output = DIANNtoMSstatsFormat(input, annotation = annot, MBR = FALSE, 
                                 use_log_file = FALSE)
 head(output)
+
+# For DIANN 2.0, set quantificationColumn = 'auto'
+input_file_path_2_0 = system.file("tinytest/raw_data/DIANN/diann_input_2.0.csv", 
+                                package="MSstatsConvert")
+annotation_file_path_2_0 = system.file("tinytest/raw_data/DIANN/annotation_diann_2.0.csv", 
+                                package = "MSstatsConvert")
+input_2_0 = data.table::fread(input_file_path_2_0)
+annot_2_0 = data.table::fread(annotation_file_path_2_0)
+output_2_0 = DIANNtoMSstatsFormat(input_2_0, annotation = annot_2_0, MBR = FALSE, 
+                                use_log_file = FALSE, quantificationColumn = 'auto')
+head(output_2_0)
 }
 \author{
 Elijah Willie

From 861beb6ed7d2cc6e5729ec217b720ce69b9e5df9 Mon Sep 17 00:00:00 2001
From: tonywu1999 <wu.anthon@northeastern.edu>
Date: Wed, 16 Jul 2025 11:44:37 -0400
Subject: [PATCH 3/7] optimize code for large datasets

---
 R/clean_DIANN.R                                  |  5 ++---
 .../raw_data/DIANN/annotation_diann_2.0.csv      |  9 +++++++++
 inst/tinytest/raw_data/DIANN/diann_input_2.0.csv | 16 ++++++++++++++++
 3 files changed, 27 insertions(+), 3 deletions(-)
 create mode 100644 inst/tinytest/raw_data/DIANN/annotation_diann_2.0.csv
 create mode 100644 inst/tinytest/raw_data/DIANN/diann_input_2.0.csv

diff --git a/R/clean_DIANN.R b/R/clean_DIANN.R
index 07a34db7..3759a7ce 100644
--- a/R/clean_DIANN.R
+++ b/R/clean_DIANN.R
@@ -18,9 +18,8 @@
       if (length(fragment_columns) == 0) {
           stop("No fragment quantification columns found. Please check your input.")
       }
-      dn_input[, FragmentQuantCorrected := apply(.SD, 1, function(row) {
-          paste(as.character(row), collapse = ";")
-      }), .SDcols = fragment_columns]
+      dn_input[, FragmentQuantCorrected := do.call(paste, c(.SD, sep = ";")),
+        .SDcols = fragment_columns]
       quantificationColumn <- "FragmentQuantCorrected"
   }
 
diff --git a/inst/tinytest/raw_data/DIANN/annotation_diann_2.0.csv b/inst/tinytest/raw_data/DIANN/annotation_diann_2.0.csv
new file mode 100644
index 00000000..d876c3bd
--- /dev/null
+++ b/inst/tinytest/raw_data/DIANN/annotation_diann_2.0.csv
@@ -0,0 +1,9 @@
+Run,BioReplicate,Condition
+Run1,1,Control
+Run2,2,Control
+Run3,3,Control
+Run4,4,Control
+Run5,5,Treatment
+Run6,6,Treatment
+Run7,7,Treatment
+Run8,8,Treatment
diff --git a/inst/tinytest/raw_data/DIANN/diann_input_2.0.csv b/inst/tinytest/raw_data/DIANN/diann_input_2.0.csv
new file mode 100644
index 00000000..33af2550
--- /dev/null
+++ b/inst/tinytest/raw_data/DIANN/diann_input_2.0.csv
@@ -0,0 +1,16 @@
+Run.Index,Run,Channel,Precursor.Id,Modified.Sequence,Stripped.Sequence,Precursor.Charge,Precursor.Lib.Index,Decoy,Proteotypic,Precursor.Mz,Protein.Ids,Protein.Group,Protein.Names,Genes,RT,iRT,Predicted.RT,Predicted.iRT,IM,iIM,Predicted.IM,Predicted.iIM,Precursor.Quantity,Precursor.Normalised,Ms1.Area,Ms1.Normalised,Ms1.Apex.Area,Ms1.Apex.Mz.Delta,Normalisation.Factor,Quantity.Quality,Empirical.Quality,Normalisation.Noise,Ms1.Profile.Corr,Evidence,Mass.Evidence,Channel.Evidence,Ms1.Total.Signal.Before,Ms1.Total.Signal.After,RT.Start,RT.Stop,FWHM,PG.TopN,PG.MaxLFQ,Genes.TopN,Genes.MaxLFQ,Genes.MaxLFQ.Unique,PG.MaxLFQ.Quality,Genes.MaxLFQ.Quality,Genes.MaxLFQ.Unique.Quality,Q.Value,PEP,Global.Q.Value,Lib.Q.Value,Peptidoform.Q.Value,Global.Peptidoform.Q.Value,Lib.Peptidoform.Q.Value,PTM.Site.Confidence,Site.Occupancy.Probabilities,Protein.Sites,Lib.PTM.Site.Confidence,Translated.Q.Value,Channel.Q.Value,PG.Q.Value,PG.PEP,GG.Q.Value,Protein.Q.Value,Global.PG.Q.Value,Lib.PG.Q.Value,Best.Fr.Mz,Best.Fr.Mz.Delta,Ms2.Scan,Fr.0.Index,Fr.0.Id,Fr.0.Quantity,Fr.0.Score,Fr.1.Index,Fr.1.Id,Fr.1.Quantity,Fr.1.Score,Fr.2.Index,Fr.2.Id,Fr.2.Quantity,Fr.2.Score,Fr.3.Index,Fr.3.Id,Fr.3.Quantity,Fr.3.Score,Fr.4.Index,Fr.4.Id,Fr.4.Quantity,Fr.4.Score,Fr.5.Index,Fr.5.Id,Fr.5.Quantity,Fr.5.Score,Fr.6.Index,Fr.6.Id,Fr.6.Quantity,Fr.6.Score,Fr.7.Index,Fr.7.Id,Fr.7.Quantity,Fr.7.Score,Fr.8.Index,Fr.8.Id,Fr.8.Quantity,Fr.8.Score,Fr.9.Index,Fr.9.Id,Fr.9.Quantity,Fr.9.Score,Fr.10.Index,Fr.10.Id,Fr.10.Quantity,Fr.10.Score,Fr.11.Index,Fr.11.Id,Fr.11.Quantity,Fr.11.Score
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From 6a053d4061670495baffcf2a9a2f1586d452f3c1 Mon Sep 17 00:00:00 2001
From: tonywu1999 <wu.anthon@northeastern.edu>
Date: Wed, 16 Jul 2025 12:00:32 -0400
Subject: [PATCH 4/7] use parquet file for input instead of CSV for examples

---
 DESCRIPTION                                     |   3 ++-
 R/converters_DIANNtoMSstatsFormat.R             |   5 ++---
 inst/tinytest/raw_data/DIANN/diann_2.0.parquet  | Bin 0 -> 51014 bytes
 .../tinytest/raw_data/DIANN/diann_input_2.0.csv |  16 ----------------
 .../test_converters_DIANNtoMSstatsFormat.R      |   4 ++--
 man/DIANNtoMSstatsFormat.Rd                     |   5 ++---
 6 files changed, 8 insertions(+), 25 deletions(-)
 create mode 100644 inst/tinytest/raw_data/DIANN/diann_2.0.parquet
 delete mode 100644 inst/tinytest/raw_data/DIANN/diann_input_2.0.csv

diff --git a/DESCRIPTION b/DESCRIPTION
index 4c4f60b6..a18e60bd 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -29,7 +29,8 @@ Suggests:
     tinytest,
     covr,
     knitr,
-    rmarkdown
+    rmarkdown,
+    arrow
 Collate: 
     'clean_ProteinProspector.R'
     'clean_Metamorpheus.R'
diff --git a/R/converters_DIANNtoMSstatsFormat.R b/R/converters_DIANNtoMSstatsFormat.R
index f771bea5..950c0b66 100644
--- a/R/converters_DIANNtoMSstatsFormat.R
+++ b/R/converters_DIANNtoMSstatsFormat.R
@@ -32,7 +32,6 @@
 #' @export
 #' 
 #' @examples 
-#' # For DIANN 2.0, set quantificationColumn = 'auto'
 #' input_file_path = system.file("tinytest/raw_data/DIANN/diann_input.tsv", 
 #'                                 package="MSstatsConvert")
 #' annotation_file_path = system.file("tinytest/raw_data/DIANN/annotation.csv", 
@@ -44,11 +43,11 @@
 #' head(output)
 #' 
 #' # For DIANN 2.0, set quantificationColumn = 'auto'
-#' input_file_path_2_0 = system.file("tinytest/raw_data/DIANN/diann_input_2.0.csv", 
+#' input_file_path_2_0 = system.file("tinytest/raw_data/DIANN/diann_2.0.parquet", 
 #'                                 package="MSstatsConvert")
 #' annotation_file_path_2_0 = system.file("tinytest/raw_data/DIANN/annotation_diann_2.0.csv", 
 #'                                 package = "MSstatsConvert")
-#' input_2_0 = data.table::fread(input_file_path_2_0)
+#' input_2_0 = arrow::read_parquet(input_file_path_2_0)
 #' annot_2_0 = data.table::fread(annotation_file_path_2_0)
 #' output_2_0 = DIANNtoMSstatsFormat(input_2_0, annotation = annot_2_0, MBR = FALSE, 
 #'                                 use_log_file = FALSE, quantificationColumn = 'auto')
diff --git a/inst/tinytest/raw_data/DIANN/diann_2.0.parquet b/inst/tinytest/raw_data/DIANN/diann_2.0.parquet
new file mode 100644
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diff --git a/inst/tinytest/raw_data/DIANN/diann_input_2.0.csv b/inst/tinytest/raw_data/DIANN/diann_input_2.0.csv
deleted file mode 100644
index 33af2550..00000000
--- a/inst/tinytest/raw_data/DIANN/diann_input_2.0.csv
+++ /dev/null
@@ -1,16 +0,0 @@
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diff --git a/inst/tinytest/test_converters_DIANNtoMSstatsFormat.R b/inst/tinytest/test_converters_DIANNtoMSstatsFormat.R
index 275bbeaf..94e3b617 100644
--- a/inst/tinytest/test_converters_DIANNtoMSstatsFormat.R
+++ b/inst/tinytest/test_converters_DIANNtoMSstatsFormat.R
@@ -19,9 +19,9 @@ expect_true("BioReplicate" %in% colnames(output))
 expect_true("Fraction" %in% colnames(output))
 
 # Test DIANNtoMSstatsFormat DIANN 2.0 ------------------------
-input_file_path = system.file("tinytest/raw_data/DIANN/diann_input_2.0.csv", package="MSstatsConvert")
+input_file_path = system.file("tinytest/raw_data/DIANN/diann_2.0.parquet", package="MSstatsConvert")
 annotation_file_path = system.file("tinytest/raw_data/DIANN/annotation_diann_2.0.csv", package = "MSstatsConvert")
-input = data.table::fread(input_file_path)
+input = arrow::read_parquet(input_file_path)
 annot = data.table::fread(annotation_file_path)
 output = DIANNtoMSstatsFormat(input, annotation = annot, MBR = FALSE, use_log_file = FALSE, quantificationColumn = 'auto')
 expect_equal(ncol(output), 11)
diff --git a/man/DIANNtoMSstatsFormat.Rd b/man/DIANNtoMSstatsFormat.Rd
index c702e644..93b27a88 100644
--- a/man/DIANNtoMSstatsFormat.Rd
+++ b/man/DIANNtoMSstatsFormat.Rd
@@ -80,7 +80,6 @@ data.frame in the MSstats required format.
 Import Diann files
 }
 \examples{
-# For DIANN 2.0, set quantificationColumn = 'auto'
 input_file_path = system.file("tinytest/raw_data/DIANN/diann_input.tsv", 
                                 package="MSstatsConvert")
 annotation_file_path = system.file("tinytest/raw_data/DIANN/annotation.csv", 
@@ -92,11 +91,11 @@ output = DIANNtoMSstatsFormat(input, annotation = annot, MBR = FALSE,
 head(output)
 
 # For DIANN 2.0, set quantificationColumn = 'auto'
-input_file_path_2_0 = system.file("tinytest/raw_data/DIANN/diann_input_2.0.csv", 
+input_file_path_2_0 = system.file("tinytest/raw_data/DIANN/diann_2.0.parquet", 
                                 package="MSstatsConvert")
 annotation_file_path_2_0 = system.file("tinytest/raw_data/DIANN/annotation_diann_2.0.csv", 
                                 package = "MSstatsConvert")
-input_2_0 = data.table::fread(input_file_path_2_0)
+input_2_0 = arrow::read_parquet(input_file_path_2_0)
 annot_2_0 = data.table::fread(annotation_file_path_2_0)
 output_2_0 = DIANNtoMSstatsFormat(input_2_0, annotation = annot_2_0, MBR = FALSE, 
                                 use_log_file = FALSE, quantificationColumn = 'auto')

From 2ed89d43005ec75ce7b3cf40ef30817adbd75174 Mon Sep 17 00:00:00 2001
From: tonywu1999 <wu.anthon@northeastern.edu>
Date: Tue, 22 Jul 2025 14:04:54 -0400
Subject: [PATCH 5/7] update documentation for quantificationColumn

---
 R/converters_DIANNtoMSstatsFormat.R | 6 +++---
 man/DIANNtoMSstatsFormat.Rd         | 6 +++---
 2 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/R/converters_DIANNtoMSstatsFormat.R b/R/converters_DIANNtoMSstatsFormat.R
index 950c0b66..56d1bf0d 100644
--- a/R/converters_DIANNtoMSstatsFormat.R
+++ b/R/converters_DIANNtoMSstatsFormat.R
@@ -20,9 +20,9 @@
 #' @param removeFewMeasurements should proteins with few measurements be removed
 #' @param removeOxidationMpeptides should peptides with oxidation be removed
 #' @param removeProtein_with1Feature should proteins with a single feature be removed
-#' @param quantificationColumn Use 'FragmentQuantCorrected'(default) column for quantified intensities. 
-#' 'FragmentQuantRaw' can be used instead.
-#' 'auto' should be used for DIANN 2.0 where each fragment intensity is a separate column, e.g. Fr0Quantity.
+#' @param quantificationColumn Use 'FragmentQuantCorrected'(default) column for quantified intensities for DIANN 1.8.x.
+#' Use 'FragmentQuantRaw' for quantified intensities for DIANN 1.9.x. 
+#' Use 'auto' for quantified intensities for DIANN 2.x where each fragment intensity is a separate column, e.g. Fr0Quantity.
 #' @param ... additional parameters to `data.table::fread`.
 #'  
 #' @return data.frame in the MSstats required format.
diff --git a/man/DIANNtoMSstatsFormat.Rd b/man/DIANNtoMSstatsFormat.Rd
index 93b27a88..269db0a3 100644
--- a/man/DIANNtoMSstatsFormat.Rd
+++ b/man/DIANNtoMSstatsFormat.Rd
@@ -67,9 +67,9 @@ If \code{append = TRUE}, has to be a valid path to a file.}
 
 \item{MBR}{True if analysis was done with match between runs}
 
-\item{quantificationColumn}{Use 'FragmentQuantCorrected'(default) column for quantified intensities.
-'FragmentQuantRaw' can be used instead.
-'auto' should be used for DIANN 2.0 where each fragment intensity is a separate column, e.g. Fr0Quantity.}
+\item{quantificationColumn}{Use 'FragmentQuantCorrected'(default) column for quantified intensities for DIANN 1.8.x.
+Use 'FragmentQuantRaw' for quantified intensities for DIANN 1.9.x.
+Use 'auto' for quantified intensities for DIANN 2.x where each fragment intensity is a separate column, e.g. Fr0Quantity.}
 
 \item{...}{additional parameters to \code{data.table::fread}.}
 }

From 41ea1aa3c0f350311b19902c57f01578518abb12 Mon Sep 17 00:00:00 2001
From: tonywu1999 <wu.anthon@northeastern.edu>
Date: Tue, 22 Jul 2025 14:37:13 -0400
Subject: [PATCH 6/7] edit docs for clean diann function

---
 R/clean_DIANN.R          | 6 +++---
 man/MSstatsClean.Rd      | 6 +++---
 man/dot-cleanRawDIANN.Rd | 6 +++---
 3 files changed, 9 insertions(+), 9 deletions(-)

diff --git a/R/clean_DIANN.R b/R/clean_DIANN.R
index 3759a7ce..525e5c94 100644
--- a/R/clean_DIANN.R
+++ b/R/clean_DIANN.R
@@ -1,9 +1,9 @@
 #' Clean raw Diann files
 #' @param msstats_object an object of class `MSstatsDIANNFiles`.
 #' @param MBR True if analysis was done with match between runs
-#' @param quantificationColumn Use 'FragmentQuantCorrected'(default) column for quantified intensities. 
-#' 'FragmentQuantRaw' can be used instead. 
-#' 'auto' should be used for DIANN 2.0 where each fragment intensity is a separate column, e.g. Fr0Quantity.
+#' @param quantificationColumn Use 'FragmentQuantCorrected'(default) column for quantified intensities for DIANN 1.8.x.
+#' Use 'FragmentQuantRaw' for quantified intensities for DIANN 1.9.x. 
+#' Use 'auto' for quantified intensities for DIANN 2.x where each fragment intensity is a separate column, e.g. Fr0Quantity.
 #' @return data.table
 #' @importFrom stats na.omit
 #' @keywords internal
diff --git a/man/MSstatsClean.Rd b/man/MSstatsClean.Rd
index 7e94b964..dbe04478 100644
--- a/man/MSstatsClean.Rd
+++ b/man/MSstatsClean.Rd
@@ -116,9 +116,9 @@ removed based on the IsUnique column from Philosopher output}
 
 \item{MBR}{True if analysis was done with match between runs}
 
-\item{quantificationColumn}{Use 'FragmentQuantCorrected'(default) column for quantified intensities.
-'FragmentQuantRaw' can be used instead.
-'auto' should be used for DIANN 2.0 where each fragment intensity is a separate column, e.g. Fr0Quantity.}
+\item{quantificationColumn}{Use 'FragmentQuantCorrected'(default) column for quantified intensities for DIANN 1.8.x.
+Use 'FragmentQuantRaw' for quantified intensities for DIANN 1.9.x.
+Use 'auto' for quantified intensities for DIANN 2.x where each fragment intensity is a separate column, e.g. Fr0Quantity.}
 
 \item{qvalue_cutoff}{The q-value cutoff for filtering peaks detected by MBR}
 }
diff --git a/man/dot-cleanRawDIANN.Rd b/man/dot-cleanRawDIANN.Rd
index c17556bb..118195e7 100644
--- a/man/dot-cleanRawDIANN.Rd
+++ b/man/dot-cleanRawDIANN.Rd
@@ -15,9 +15,9 @@
 
 \item{MBR}{True if analysis was done with match between runs}
 
-\item{quantificationColumn}{Use 'FragmentQuantCorrected'(default) column for quantified intensities.
-'FragmentQuantRaw' can be used instead.
-'auto' should be used for DIANN 2.0 where each fragment intensity is a separate column, e.g. Fr0Quantity.}
+\item{quantificationColumn}{Use 'FragmentQuantCorrected'(default) column for quantified intensities for DIANN 1.8.x.
+Use 'FragmentQuantRaw' for quantified intensities for DIANN 1.9.x.
+Use 'auto' for quantified intensities for DIANN 2.x where each fragment intensity is a separate column, e.g. Fr0Quantity.}
 }
 \value{
 data.table

From 67f51af4d699926bef59e200ef5bf9b191b6b889 Mon Sep 17 00:00:00 2001
From: tonywu1999 <wu.anthon@northeastern.edu>
Date: Tue, 22 Jul 2025 14:42:34 -0400
Subject: [PATCH 7/7] refactor DIANN code to be more readable

---
 R/clean_DIANN.R | 236 +++++++++++++++++++++++++++++++++++-------------
 1 file changed, 172 insertions(+), 64 deletions(-)

diff --git a/R/clean_DIANN.R b/R/clean_DIANN.R
index 525e5c94..97272d0e 100644
--- a/R/clean_DIANN.R
+++ b/R/clean_DIANN.R
@@ -7,69 +7,177 @@
 #' @return data.table
 #' @importFrom stats na.omit
 #' @keywords internal
-.cleanRawDIANN = function(msstats_object, MBR = TRUE, 
-                          quantificationColumn = "FragmentQuantCorrected") {
-  dn_input = getInputFile(msstats_object, "input")
-  dn_input = data.table::as.data.table(dn_input)
-  
-  # Auto-detect and collapse multiple fragment columns (DIANN 2.0 format)
-  if (quantificationColumn == "auto") {
-      fragment_columns <- grep("^Fr[0-9]+Quantity$", names(dn_input), value = TRUE)
-      if (length(fragment_columns) == 0) {
-          stop("No fragment quantification columns found. Please check your input.")
-      }
-      dn_input[, FragmentQuantCorrected := do.call(paste, c(.SD, sep = ";")),
-        .SDcols = fragment_columns]
-      quantificationColumn <- "FragmentQuantCorrected"
-  }
+.cleanRawDIANN <- function(msstats_object, MBR = TRUE, 
+                           quantificationColumn = "FragmentQuantCorrected") {
+    dn_input <- getInputFile(msstats_object, "input")
+    dn_input <- data.table::as.data.table(dn_input)
+    
+    # Process quantification columns
+    quantificationColumn <- .cleanDIANNProcessQuantificationColumns(dn_input, quantificationColumn)
+    
+    # Add missing columns
+    dn_input <- .cleanDIANNAddMissingColumns(dn_input)
+    
+    # Select required columns
+    dn_input <- .cleanDIANNSelectRequiredColumns(dn_input, quantificationColumn, MBR)
+    
+    # Split concatenated values
+    dn_input <- .cleanDIANNSplitConcatenatedValues(dn_input, quantificationColumn)
+    
+    # Process fragment information
+    dn_input <- .cleanDIANNProcessFragmentInfo(dn_input, quantificationColumn)
+    
+    # Clean and filter data
+    dn_input <- .cleanDIANNCleanAndFilterData(dn_input, quantificationColumn)
+    
+    # Rename columns
+    dn_input <- .cleanDIANNRenameColumns(dn_input, quantificationColumn)
+    
+    .logSuccess("DIANN", "clean")
+    dn_input
+}
+
+#' Process quantification columns for DIANN 2.0 format
+#' @param dn_input data.table input
+#' @param quantificationColumn quantification column name
+#' @return updated quantification column name
+#' @noRd
+.cleanDIANNProcessQuantificationColumns <- function(dn_input, quantificationColumn) {
+    if (quantificationColumn == "auto") {
+        fragment_columns <- grep("^Fr[0-9]+Quantity$", names(dn_input), value = TRUE)
+        if (length(fragment_columns) == 0) {
+            stop("No fragment quantification columns found. Please check your input.")
+        }
+        dn_input[, FragmentQuantCorrected := do.call(paste, c(.SD, sep = ";")),
+                 .SDcols = fragment_columns]
+        quantificationColumn <- "FragmentQuantCorrected"
+    }
+    return(quantificationColumn)
+}
+
+#' Add missing required columns
+#' @param dn_input data.table input
+#' @return data.table with missing columns added
+#' @noRd
+.cleanDIANNAddMissingColumns <- function(dn_input) {
+    if (!is.element("PrecursorMz", colnames(dn_input))) {
+        dn_input[, PrecursorMz := NA]
+    }
+    if (!is.element('FragmentInfo', colnames(dn_input))) {
+        dn_input[, FragmentInfo := NA]
+    }
+    return(dn_input)
+}
+
+#' Select required columns based on MBR setting
+#' @param dn_input data.table input
+#' @param quantificationColumn quantification column name
+#' @param MBR logical indicating if match between runs was used
+#' @return data.table with selected columns
+#' @noRd
+.cleanDIANNSelectRequiredColumns <- function(dn_input, quantificationColumn, MBR) {
+    base_cols <- c('ProteinNames', 'StrippedSequence', 'ModifiedSequence', 
+                   'PrecursorCharge', quantificationColumn, 'QValue', 
+                   'PrecursorMz', 'FragmentInfo', 'Run')
+    
+    mbr_cols <- if (MBR) {
+        c('LibQValue', 'LibPGQValue')
+    } else {
+        c('GlobalQValue', 'GlobalPGQValue')
+    }
+    
+    req_cols <- c(base_cols, mbr_cols)
+    return(dn_input[, req_cols, with = FALSE])
+}
 
-  if (!is.element("PrecursorMz", colnames(dn_input))) {
-    dn_input[, PrecursorMz := NA]
-  }
-  if (!is.element('FragmentInfo', colnames(dn_input))) {
-    dn_input[, FragmentInfo := NA]
-  }
-  req_cols = c('ProteinNames', 'StrippedSequence', 
-               'ModifiedSequence', 'PrecursorCharge',
-               quantificationColumn, 'QValue', 
-               'PrecursorMz', 'FragmentInfo', 'Run')
-  if (MBR) {
-    req_cols = c(req_cols, c('LibQValue', 'LibPGQValue'))
-  } else{
-    req_cols = c(req_cols, c('GlobalQValue', 'GlobalPGQValue'))
-  }
-  dn_input = dn_input[, req_cols, with = FALSE]
-  dn_input = dn_input[, lapply(.SD, function(x) unlist(tstrsplit(x, ";"))),
-                      .SDcols = c(quantificationColumn, "FragmentInfo"), 
-                      by = setdiff(colnames(dn_input), c("FragmentInfo", quantificationColumn))]
-  if (all(is.na(dn_input[["FragmentInfo"]]))) {
-    dn_input[, FragmentInfo := paste0("Frag", 1:.N),
-             by = c("ProteinNames", "ModifiedSequence", "PrecursorCharge", "Run")]
-  }
-  dn_input[, (quantificationColumn) := lapply(.SD, as.numeric), .SDcols = quantificationColumn]
-  dn_input[, FragmentIon := sub('\\^\\.\\*', '', FragmentInfo)]
-  if (any(grepl("/", dn_input$FragmentInfo))) {
-    dn_input[, ProductCharge := unlist(strsplit(FragmentInfo, split = "/"))[[1]], by = FragmentInfo]
-    dn_input[, ProductCharge := strtoi(sub("\\.\\*\\^", "", ProductCharge))]
-  } else {
-    dn_input[, ProductCharge := 1]
-  }
-  dn_input = dn_input[!grepl("NH3", FragmentIon), ]
-  dn_input = dn_input[!grepl("H2O", FragmentIon), ]
-  dn_input = na.omit(dn_input, cols = quantificationColumn)
-  data.table::setnames(dn_input, old = c('ProteinNames', 'StrippedSequence', 
-                                         'ModifiedSequence','PrecursorCharge',
-                                         quantificationColumn, 'QValue', 
-                                         'PrecursorMz', 'FragmentIon','Run', 
-                                         'ProductCharge'),
-                       new = c('ProteinName', 'PeptideSequence', 
-                               'PeptideModifiedSequence','PrecursorCharge',
-                               'Intensity', 'DetectionQValue', 
-                               'PrecursorMz', 'FragmentIon','Run',
-                               'ProductCharge'),
-                       skip_absent = TRUE)
-  dn_input[, PeptideSequence := NULL]
-  setnames(dn_input, "PeptideModifiedSequence", "PeptideSequence")
-  .logSuccess("DIANN", "clean")
-  dn_input
+#' Split concatenated values in quantification and fragment info columns
+#' @param dn_input data.table input
+#' @param quantificationColumn quantification column name
+#' @return data.table with split values
+#' @noRd
+.cleanDIANNSplitConcatenatedValues <- function(dn_input, quantificationColumn) {
+    split_cols <- c(quantificationColumn, "FragmentInfo")
+    by_cols <- setdiff(colnames(dn_input), split_cols)
+    
+    dn_input <- dn_input[, lapply(.SD, function(x) unlist(tstrsplit(x, ";"))),
+                         .SDcols = split_cols, 
+                         by = by_cols]
+    return(dn_input)
 }
+
+#' Process fragment information and add derived columns
+#' @param dn_input data.table input
+#' @param quantificationColumn quantification column name
+#' @return data.table with processed fragment info
+#' @noRd
+.cleanDIANNProcessFragmentInfo <- function(dn_input, quantificationColumn) {
+    # Generate fragment info if missing
+    if (all(is.na(dn_input[["FragmentInfo"]]))) {
+        dn_input[, FragmentInfo := paste0("Frag", 1:.N),
+                 by = c("ProteinNames", "ModifiedSequence", "PrecursorCharge", "Run")]
+    }
+    
+    # Convert quantification column to numeric
+    dn_input[, (quantificationColumn) := lapply(.SD, as.numeric), 
+             .SDcols = quantificationColumn]
+    
+    # Process fragment ion information
+    dn_input[, FragmentIon := sub('\\^\\.\\*', '', FragmentInfo)]
+    
+    # Extract product charge
+    if (any(grepl("/", dn_input$FragmentInfo))) {
+        dn_input[, ProductCharge := .cleanDIANNExtractProductCharge(FragmentInfo), by = FragmentInfo]
+    } else {
+        dn_input[, ProductCharge := 1]
+    }
+    
+    return(dn_input)
+}
+
+#' Extract product charge from fragment info
+#' @param fragment_info fragment information string
+#' @return numeric product charge
+#' @noRd
+.cleanDIANNExtractProductCharge <- function(fragment_info) {
+    charge_part <- unlist(strsplit(fragment_info, split = "/"))[[1]]
+    return(strtoi(sub("\\.\\*\\^", "", charge_part)))
+}
+
+#' Clean and filter data by removing unwanted fragments and NA values
+#' @param dn_input data.table input
+#' @param quantificationColumn quantification column name
+#' @return cleaned data.table
+#' @noRd
+.cleanDIANNCleanAndFilterData <- function(dn_input, quantificationColumn) {
+    # Remove NH3 and H2O loss fragments
+    dn_input <- dn_input[!grepl("NH3", FragmentIon)]
+    dn_input <- dn_input[!grepl("H2O", FragmentIon)]
+    
+    # Remove rows with NA in quantification column
+    dn_input <- na.omit(dn_input, cols = quantificationColumn)
+    
+    return(dn_input)
+}
+
+#' Rename columns to standardized names
+#' @param dn_input data.table input
+#' @param quantificationColumn quantification column name
+#' @return data.table with renamed columns
+#' @noRd
+.cleanDIANNRenameColumns <- function(dn_input, quantificationColumn) {
+    old_names <- c('ProteinNames', 'StrippedSequence', 'ModifiedSequence',
+                   'PrecursorCharge', quantificationColumn, 'QValue', 
+                   'PrecursorMz', 'FragmentIon', 'Run', 'ProductCharge')
+    
+    new_names <- c('ProteinName', 'PeptideSequence', 'PeptideModifiedSequence',
+                   'PrecursorCharge', 'Intensity', 'DetectionQValue', 
+                   'PrecursorMz', 'FragmentIon', 'Run', 'ProductCharge')
+    
+    data.table::setnames(dn_input, old = old_names, new = new_names, skip_absent = TRUE)
+    
+    # Clean up peptide sequence columns
+    dn_input[, PeptideSequence := NULL]
+    setnames(dn_input, "PeptideModifiedSequence", "PeptideSequence")
+    
+    return(dn_input)
+}
\ No newline at end of file