From 0d2af528634d4bbd22ca32d3fb2161897509d82f Mon Sep 17 00:00:00 2001
From: Tony Wu <ant.wu@northeastern.edu>
Date: Wed, 10 Jan 2024 10:55:48 -0500
Subject: [PATCH 1/4] feat(metamorpheus-converter): Add clean functionality of
 metamorpheus converter

---
 .gitignore                                    |   1 +
 DESCRIPTION                                   |   1 +
 R/MSstatsConvert_core_functions.R             |   7 +++++++
 R/clean_Metamorpheus.R                        |  18 ++++++++++++++++++
 .../Metamorpheus/AllQuantifiedPeaks.rds       | Bin 0 -> 24765 bytes
 .../Metamorpheus/ExperimentalDesign.tsv       |   5 +++++
 inst/tinytest/test_clean_Metamorpheus.R       |  12 ++++++++++++
 man/MSstatsClean.Rd                           |   7 +++++++
 man/dot-cleanRawMetamorpheus.Rd               |  18 ++++++++++++++++++
 9 files changed, 69 insertions(+)
 create mode 100644 R/clean_Metamorpheus.R
 create mode 100644 inst/tinytest/raw_data/Metamorpheus/AllQuantifiedPeaks.rds
 create mode 100644 inst/tinytest/raw_data/Metamorpheus/ExperimentalDesign.tsv
 create mode 100644 inst/tinytest/test_clean_Metamorpheus.R
 create mode 100644 man/dot-cleanRawMetamorpheus.Rd

diff --git a/.gitignore b/.gitignore
index 7c81cae0..ee6edbaa 100644
--- a/.gitignore
+++ b/.gitignore
@@ -5,3 +5,4 @@
 inst/doc
 *.Rproj
 *.DS_Store
+*.log
diff --git a/DESCRIPTION b/DESCRIPTION
index 365ec25c..89057915 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -29,6 +29,7 @@ Suggests:
     knitr,
     rmarkdown
 Collate: 
+    'clean_Metamorpheus.R'
     'clean_DIANN.R'
     'clean_Philosopher.R'
     'clean_Spectronaut.R'
diff --git a/R/MSstatsConvert_core_functions.R b/R/MSstatsConvert_core_functions.R
index 1bd59788..7141e231 100644
--- a/R/MSstatsConvert_core_functions.R
+++ b/R/MSstatsConvert_core_functions.R
@@ -271,6 +271,13 @@ setMethod("MSstatsClean", signature = "MSstatsPhilosopherFiles",
 #' @return data.table
 setMethod("MSstatsClean", signature = "MSstatsDIANNFiles", 
           .cleanRawDIANN)
+#' Clean Metamorpheus files
+#' @include clean_Metamorpheus.R
+#' @rdname MSstatsClean
+#' @inheritParams .cleanRawMetamorpheus
+#' @return data.table
+setMethod("MSstatsClean", signature = "MSstatsMetamorpheusFiles", 
+          .cleanRawMetamorpheus)
 
 
 #' Preprocess outputs from MS signal processing tools for analysis with MSstats
diff --git a/R/clean_Metamorpheus.R b/R/clean_Metamorpheus.R
new file mode 100644
index 00000000..1ebeb10d
--- /dev/null
+++ b/R/clean_Metamorpheus.R
@@ -0,0 +1,18 @@
+#' Clean raw Metamorpheus files
+#' @param msstats_object an object of class `MSstatsMetamorpheusFiles`.
+#' @return data.table
+#' @keywords internal
+.cleanRawMetamorpheus = function(msstats_object) {
+    metamorpheus_input = getInputFile(msstats_object, "input")
+    metamorpheus_input = data.table::as.data.table(metamorpheus_input)
+    req_cols = c('FileName', 'ProteinGroup', 'FullSequence', 
+                 'PrecursorCharge', 'Peakintensity')
+    metamorpheus_input = metamorpheus_input[, req_cols, with = FALSE]
+    data.table::setnames(
+        metamorpheus_input, 
+        c("ProteinGroup", "FullSequence", "PrecursorCharge", "FileName", "Peakintensity"),
+        c("ProteinName", "PeptideSequence", "PrecursorCharge", "Run", "Intensity"), 
+        skip_absent = TRUE)
+    .logSuccess("Metamorpheus", "clean")
+    metamorpheus_input
+}
\ No newline at end of file
diff --git a/inst/tinytest/raw_data/Metamorpheus/AllQuantifiedPeaks.rds b/inst/tinytest/raw_data/Metamorpheus/AllQuantifiedPeaks.rds
new file mode 100644
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diff --git a/inst/tinytest/raw_data/Metamorpheus/ExperimentalDesign.tsv b/inst/tinytest/raw_data/Metamorpheus/ExperimentalDesign.tsv
new file mode 100644
index 00000000..496eff7e
--- /dev/null
+++ b/inst/tinytest/raw_data/Metamorpheus/ExperimentalDesign.tsv
@@ -0,0 +1,5 @@
+Run	Condition	BioReplicate	Fraction	Techrep
+NEG1-calib	neg	1	1	1
+NEG2-calib	neg	2	1	1
+POS1-calib	pos	1	1	1
+POS2-calib	pos	2	1	1
\ No newline at end of file
diff --git a/inst/tinytest/test_clean_Metamorpheus.R b/inst/tinytest/test_clean_Metamorpheus.R
new file mode 100644
index 00000000..145459d6
--- /dev/null
+++ b/inst/tinytest/test_clean_Metamorpheus.R
@@ -0,0 +1,12 @@
+# Test Metamorpheus .cleanRawMetamorpheus ---------------------------
+
+file_path = system.file("tinytest/raw_data/Metamorpheus/AllQuantifiedPeaks.rds", package="MSstatsConvert")
+input = readRDS(file_path)
+output = MSstatsConvert:::.cleanRawMetamorpheus(input)
+expect_equal(ncol(output), 5)
+expect_true(nrow(output) > 0)
+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))
\ No newline at end of file
diff --git a/man/MSstatsClean.Rd b/man/MSstatsClean.Rd
index 5568bd5a..bca5ce16 100644
--- a/man/MSstatsClean.Rd
+++ b/man/MSstatsClean.Rd
@@ -13,6 +13,7 @@
 \alias{MSstatsClean,MSstatsSpectronautFiles-method}
 \alias{MSstatsClean,MSstatsPhilosopherFiles-method}
 \alias{MSstatsClean,MSstatsDIANNFiles-method}
+\alias{MSstatsClean,MSstatsMetamorpheusFiles-method}
 \title{Clean files generated by a signal processing tools.}
 \usage{
 MSstatsClean(msstats_object, ...)
@@ -57,6 +58,8 @@ MSstatsClean(msstats_object, ...)
 )
 
 \S4method{MSstatsClean}{MSstatsDIANNFiles}(msstats_object, MBR = TRUE)
+
+\S4method{MSstatsClean}{MSstatsMetamorpheusFiles}(msstats_object)
 }
 \arguments{
 \item{msstats_object}{object that inherits from \code{MSstatsInputFiles} class.}
@@ -125,6 +128,8 @@ data.table
 
 data.table
 
+data.table
+
 data.table
 }
 \description{
@@ -151,6 +156,8 @@ Clean Spectronaut files
 Clean Philosopher files
 
 Clean DIA-NN files
+
+Clean Metamorpheus files
 }
 \examples{
 evidence_path = system.file("tinytest/raw_data/MaxQuant/mq_ev.csv", 
diff --git a/man/dot-cleanRawMetamorpheus.Rd b/man/dot-cleanRawMetamorpheus.Rd
new file mode 100644
index 00000000..b977802d
--- /dev/null
+++ b/man/dot-cleanRawMetamorpheus.Rd
@@ -0,0 +1,18 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/clean_Metamorpheus.R
+\name{.cleanRawMetamorpheus}
+\alias{.cleanRawMetamorpheus}
+\title{Clean raw Metamorpheus files}
+\usage{
+.cleanRawMetamorpheus(msstats_object)
+}
+\arguments{
+\item{msstats_object}{an object of class \code{MSstatsMetamorpheusFiles}.}
+}
+\value{
+data.table
+}
+\description{
+Clean raw Metamorpheus files
+}
+\keyword{internal}

From 342e9b055e938ba155efc9dbbcf784d42dc2e7a6 Mon Sep 17 00:00:00 2001
From: Tony Wu <ant.wu@northeastern.edu>
Date: Wed, 10 Jan 2024 16:01:58 -0500
Subject: [PATCH 2/4] Modified metamorpheus annotation filename and removed
 techRep column from annotation file

---
 inst/tinytest/raw_data/Metamorpheus/Annotation.tsv         | 5 +++++
 inst/tinytest/raw_data/Metamorpheus/ExperimentalDesign.tsv | 5 -----
 2 files changed, 5 insertions(+), 5 deletions(-)
 create mode 100644 inst/tinytest/raw_data/Metamorpheus/Annotation.tsv
 delete mode 100644 inst/tinytest/raw_data/Metamorpheus/ExperimentalDesign.tsv

diff --git a/inst/tinytest/raw_data/Metamorpheus/Annotation.tsv b/inst/tinytest/raw_data/Metamorpheus/Annotation.tsv
new file mode 100644
index 00000000..3745fb78
--- /dev/null
+++ b/inst/tinytest/raw_data/Metamorpheus/Annotation.tsv
@@ -0,0 +1,5 @@
+Run	Condition	BioReplicate	Fraction
+NEG1-calib	neg	1	1
+NEG2-calib	neg	2	1
+POS1-calib	pos	3	1
+POS2-calib	pos	4	1
\ No newline at end of file
diff --git a/inst/tinytest/raw_data/Metamorpheus/ExperimentalDesign.tsv b/inst/tinytest/raw_data/Metamorpheus/ExperimentalDesign.tsv
deleted file mode 100644
index 496eff7e..00000000
--- a/inst/tinytest/raw_data/Metamorpheus/ExperimentalDesign.tsv
+++ /dev/null
@@ -1,5 +0,0 @@
-Run	Condition	BioReplicate	Fraction	Techrep
-NEG1-calib	neg	1	1	1
-NEG2-calib	neg	2	1	1
-POS1-calib	pos	1	1	1
-POS2-calib	pos	2	1	1
\ No newline at end of file

From d8336c3f8a4223acd150e2ad837a70a1120134d1 Mon Sep 17 00:00:00 2001
From: Tony Wu <ant.wu@northeastern.edu>
Date: Fri, 12 Jan 2024 13:01:07 -0500
Subject: [PATCH 3/4] Modify RDS filename to MSstatsMetamorpheusFilesObject for
 unit testing

---
 ...Peaks.rds => MSstatsMetamorpheusFilesObject.rds} | Bin
 inst/tinytest/test_clean_Metamorpheus.R             |   2 +-
 2 files changed, 1 insertion(+), 1 deletion(-)
 rename inst/tinytest/raw_data/Metamorpheus/{AllQuantifiedPeaks.rds => MSstatsMetamorpheusFilesObject.rds} (100%)

diff --git a/inst/tinytest/raw_data/Metamorpheus/AllQuantifiedPeaks.rds b/inst/tinytest/raw_data/Metamorpheus/MSstatsMetamorpheusFilesObject.rds
similarity index 100%
rename from inst/tinytest/raw_data/Metamorpheus/AllQuantifiedPeaks.rds
rename to inst/tinytest/raw_data/Metamorpheus/MSstatsMetamorpheusFilesObject.rds
diff --git a/inst/tinytest/test_clean_Metamorpheus.R b/inst/tinytest/test_clean_Metamorpheus.R
index 145459d6..49904f29 100644
--- a/inst/tinytest/test_clean_Metamorpheus.R
+++ b/inst/tinytest/test_clean_Metamorpheus.R
@@ -1,6 +1,6 @@
 # Test Metamorpheus .cleanRawMetamorpheus ---------------------------
 
-file_path = system.file("tinytest/raw_data/Metamorpheus/AllQuantifiedPeaks.rds", package="MSstatsConvert")
+file_path = system.file("tinytest/raw_data/Metamorpheus/MSstatsMetamorpheusFilesObject.rds", package="MSstatsConvert")
 input = readRDS(file_path)
 output = MSstatsConvert:::.cleanRawMetamorpheus(input)
 expect_equal(ncol(output), 5)

From 0199ea911413874c61342d0e27d12d30fbada1bd Mon Sep 17 00:00:00 2001
From: Tony Wu <ant.wu@northeastern.edu>
Date: Tue, 16 Jan 2024 21:26:21 -0500
Subject: [PATCH 4/4] create processed_data folder for testing

---
 .../Metamorpheus/MSstatsMetamorpheusFilesObject.rds | Bin
 inst/tinytest/test_clean_Metamorpheus.R             |   2 +-
 2 files changed, 1 insertion(+), 1 deletion(-)
 rename inst/tinytest/{raw_data => processed_data}/Metamorpheus/MSstatsMetamorpheusFilesObject.rds (100%)

diff --git a/inst/tinytest/raw_data/Metamorpheus/MSstatsMetamorpheusFilesObject.rds b/inst/tinytest/processed_data/Metamorpheus/MSstatsMetamorpheusFilesObject.rds
similarity index 100%
rename from inst/tinytest/raw_data/Metamorpheus/MSstatsMetamorpheusFilesObject.rds
rename to inst/tinytest/processed_data/Metamorpheus/MSstatsMetamorpheusFilesObject.rds
diff --git a/inst/tinytest/test_clean_Metamorpheus.R b/inst/tinytest/test_clean_Metamorpheus.R
index 49904f29..5bbc2136 100644
--- a/inst/tinytest/test_clean_Metamorpheus.R
+++ b/inst/tinytest/test_clean_Metamorpheus.R
@@ -1,6 +1,6 @@
 # Test Metamorpheus .cleanRawMetamorpheus ---------------------------
 
-file_path = system.file("tinytest/raw_data/Metamorpheus/MSstatsMetamorpheusFilesObject.rds", package="MSstatsConvert")
+file_path = system.file("tinytest/processed_data/Metamorpheus/MSstatsMetamorpheusFilesObject.rds", package="MSstatsConvert")
 input = readRDS(file_path)
 output = MSstatsConvert:::.cleanRawMetamorpheus(input)
 expect_equal(ncol(output), 5)