feat(diann): Enable DIANN 2.0 for DIANNtoMSstatsPTMFormat

DESCRIPTION

@@ -23,7 +23,7 @@ Authors@R: c(
 License: Artistic-2.0
 Depends: R (>= 4.3)
 Imports: dplyr, gridExtra, stringr, stats, ggplot2, stringi,
-            grDevices, MSstatsTMT, MSstatsConvert, MSstats,
+            grDevices, MSstatsTMT, MSstatsConvert (>= 1.19.1), MSstats,
             data.table, Rcpp, Biostrings, checkmate, ggrepel, plotly, htmltools,
             rlang
 Suggests: 
@@ -32,6 +32,7 @@ Suggests:
     tinytest,
     covr,
     mockery,
+    arrow,
     testthat (>= 3.0.0)
 LazyData: true
 LinkingTo: Rcpp

R/converters.R

@@ -7,10 +7,8 @@
 #' 
 #' @importFrom data.table as.data.table
 #' @importFrom MSstatsConvert DIANNtoMSstatsFormat
+#' @inheritParams MSstatsConvert::DIANNtoMSstatsFormat
 #' 
-#' @param input data.frame of `report.tsv` file produced by Philosopher
-#' @param annotation annotation with Run, Fraction, TechRepMixture, Mixture, Channel, 
-#' BioReplicate, Condition columns or a path to file. Refer to the example 'annotation' for the meaning of each column.
 #' @param input_protein same as `input` for global profiling run. Default is NULL.
 #' @param annotation_protein same as `annotation` for global profiling run. Default is NULL.
 #' @param fasta_path A string of path to a FASTA file, used to match PTM peptides.
@@ -22,25 +20,6 @@
 #' in `protein_id_col`. The protein names in these two columns must match in 
 #' order to join the FASTA file with the DIA-NN output. Default is "uniprot_ac"
 #' for uniprot ID. For uniprot mnemonic ID, use "entry_name"
-#' @param global_qvalue_cutoff The global qvalue cutoff. Default is 0.01.
-#' @param qvalue_cutoff local qvalue cutoff for library. Default is 0.01.
-#' @param pg_qvalue_cutoff local qvalue cutoff for protein groups Run should be 
-#' the same as filename. Default is 0.01.
-#' @param useUniquePeptide logical, if TRUE (default) removes peptides that are assigned for more than one proteins. 
-#' We assume to use unique peptide for each protein.
-#' @param removeFewMeasurements TRUE (default) will remove the features that have 1 or 2 measurements within each Run.
-#' @param removeOxidationMpeptides TRUE (default) will remove the peptides including oxidation (M) sequence.
-#' @param removeProtein_with1Feature TRUE will remove the proteins which have only 1 peptide and charge. Defaut is FALSE.
-#' @param MBR If analaysis was done with match between runs or not. Default is TRUE.
-#' @param use_log_file logical. If TRUE, information about data processing will 
-#' be saved to a file.
-#' @param append logical. If TRUE, information about data processing will be 
-#' added to an existing log file.
-#' @param verbose logical. If TRUE, information about data processing wil be 
-#' printed to the console.
-#' @param log_file_path character. Path to a file to which information about 
-#' data processing will be saved. If not provided, such a file will be created 
-#' automatically. If 'append = TRUE', has to be a valid path to a file.
 #' 
 #' @return `list` of one or two `data.frame` of class `MSstatsTMT`, named `PTM` and `PROTEIN`
 #' 
@@ -68,6 +47,28 @@
 #' 
 #' head(msstatsptm_format$PTM)
 #' 
+#' # Example DIANN 2.0
+#' input = system.file("tinytest/raw_data/DIANN/diann_2_ptm.parquet", 
+#'                                         package = "MSstatsPTM")
+#' input = arrow::read_parquet(input)
+#' annot = system.file("tinytest/raw_data/DIANN/annotation_diann_2.0_ptm.csv", 
+#'                                         package = "MSstatsPTM")
+#' annot = data.table::fread(annot)
+#' fasta_path = system.file("extdata", "diann.fasta", 
+#'                        package="MSstatsPTM")
+#' 
+#' msstatsptm_format = DIANNtoMSstatsPTMFormat(
+#'     input, 
+#'     annot, 
+#'     protein_id_col = "Protein.Names", 
+#'     fasta_path = fasta_path, 
+#'     fasta_protein_name = "entry_name", 
+#'     use_log_file = FALSE,
+#'     quantificationColumn = "auto"
+#' )
+#' 
+#' head(msstatsptm_format$PTM)
+#' 
 DIANNtoMSstatsPTMFormat = function(input,
                                    annotation,
                                    input_protein=NULL,
@@ -84,6 +85,7 @@ DIANNtoMSstatsPTMFormat = function(input,
                                    removeOxidationMpeptides = TRUE,
                                    removeProtein_with1Feature = FALSE,
                                    MBR=TRUE,
+                                   quantificationColumn = "FragmentQuantCorrected",
                                    use_log_file = TRUE,
                                    append = FALSE,
                                    verbose = TRUE,
@@ -120,41 +122,43 @@ DIANNtoMSstatsPTMFormat = function(input,
     input = input[input[,..protein_id_col][[1]] != input$ProteinNameUnmod]
   }
 
-  ptm_input = DIANNtoMSstatsFormat(input, 
-                                   annotation,
-                                   global_qvalue_cutoff,
-                                   qvalue_cutoff,
-                                   pg_qvalue_cutoff,
-                                   useUniquePeptide,
-                                   removeFewMeasurements,
-                                   removeOxidationMpeptides,
-                                   removeProtein_with1Feature,
-                                   use_log_file,
-                                   append,
-                                   verbose,
-                                   log_file_path,
-                                   MBR)
+  ptm_input = DIANNtoMSstatsFormat(input = input, 
+                                   annotation = annotation,
+                                   global_qvalue_cutoff = global_qvalue_cutoff,
+                                   qvalue_cutoff = qvalue_cutoff,
+                                   pg_qvalue_cutoff = pg_qvalue_cutoff,
+                                   useUniquePeptide = useUniquePeptide,
+                                   removeFewMeasurements = removeFewMeasurements,
+                                   removeOxidationMpeptides = removeOxidationMpeptides,
+                                   removeProtein_with1Feature = removeProtein_with1Feature,
+                                   use_log_file = use_log_file,
+                                   append = append,
+                                   verbose = verbose,
+                                   log_file_path = log_file_path,
+                                   MBR = MBR,
+                                   quantificationColumn = quantificationColumn)
 
   msstats_format = list(PTM=ptm_input, PROTEIN=NULL)
 
   if (!is.null(input_protein)){
     checkmate::assertTRUE(!is.null(input_protein) & 
                             !is.null(annotation_protein))
 
-    protein_input = DIANNtoMSstatsFormat(input_protein, 
-                                         annotation_protein,
-                                         global_qvalue_cutoff,
-                                         qvalue_cutoff,
-                                         pg_qvalue_cutoff,
-                                         useUniquePeptide,
-                                         removeFewMeasurements,
-                                         removeOxidationMpeptides,
-                                         removeProtein_with1Feature,
-                                         use_log_file,
-                                         append,
-                                         verbose,
-                                         log_file_path,
-                                         MBR)
+    protein_input = DIANNtoMSstatsFormat(input = input_protein, 
+                                         annotation = annotation_protein,
+                                         global_qvalue_cutoff = global_qvalue_cutoff,
+                                         qvalue_cutoff = qvalue_cutoff,
+                                         pg_qvalue_cutoff = pg_qvalue_cutoff,
+                                         useUniquePeptide = useUniquePeptide,
+                                         removeFewMeasurements = removeFewMeasurements,
+                                         removeOxidationMpeptides = removeOxidationMpeptides,
+                                         removeProtein_with1Feature = removeProtein_with1Feature,
+                                         use_log_file = use_log_file,
+                                         append = append,
+                                         verbose = verbose,
+                                         log_file_path = log_file_path,
+                                         MBR = MBR,
+                                         quantificationColumn = quantificationColumn)
 
     msstats_format = list(PTM=ptm_input, PROTEIN=protein_input)
 

inst/tinytest/raw_data/DIANN/annotation_diann_2.0_ptm.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