docs(progenesis): Add sample input data from Progenesis for converter

DESCRIPTION

@@ -32,4 +32,4 @@ biocViews: ImmunoOncology, MassSpectrometry, Proteomics, Software, DifferentialE
 BugReports: https://github.com/Vitek-Lab/MSstatsPTM/issues
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2

R/converters.R

@@ -929,18 +929,19 @@ PDtoMSstatsPTMFormat = function(input,
 #' required by MSstatsPTM.
 #' @examples
 #' 
-#' # Example annotation file
-#' annotation = data.frame('Condition' = c('Control', 'Control', 'Control',
-#'                          'Treatment', 'Treatment', 'Treatment'),
-#'                          'BioReplicate' = c(1,2,3,4,5,6),
-#'                          'Run' = c('prot_run_1', 'prot_run_2', 'prot_run_3',
-#'                                   'phos_run_1', 'phos_run_2', 'phos_run_3'),
-#'                          'Type' = c("Protein", "Protein", "Protein", "PTM", 
-#'                                     "PTM", "PTM"))
-#'                                     
-#' # The output should be in the following format.
-#' head(raw.input$PTM)
-#' head(raw.input$PROTEIN)
+#' input = system.file("tinytest/raw_data/Progenesis/progenesis_peptide.csv", 
+#'                                 package = "MSstatsPTM")
+#' input = data.table::fread(input)
+#' colnames(input) = unlist(input[1,])
+#' input = input[-1,]
+#' annot = system.file("tinytest/raw_data/Progenesis/phospho_annotation.csv", 
+#'                                 package = "MSstatsPTM")
+#' annot = data.table::fread(annot)
+#' prog_imported = ProgenesistoMSstatsPTMFormat(
+#'     input, 
+#'     annot
+#' )
+#' head(prog_imported$PTM)
 ProgenesistoMSstatsPTMFormat = function(ptm_input,
                                         annotation,
                                         global_protein_input = FALSE,

inst/tinytest/raw_data/Progenesis/phospho_annotation.csv

@@ -0,0 +1,10 @@
+Run,Condition,BioReplicate,Type
+001_PH003_G23,A,S1,PTM
+002_PH003_G23,B,S2,PTM
+003_PH003_G23,A,S3,PTM
+004_PH003_G23,A,S4,PTM
+005_PH003_G23,B,S5,PTM
+006_PH003_G23,B,S6,PTM
+007_PH003_G23,C,S7,PTM
+008_PH003_G23,C,S8,PTM
+009_PH003_G23,C,S9,PTM