tests(converters): fix spectronaut and metamorpheus tests (#117)

Author: tonywu1999

R/MSstatsPTM.R

@@ -45,6 +45,6 @@
 #'    analysis and summarization
 #' }
 #'
-#' @docType package
 #' @name MSstatsPTM
-NULL
+#' @keywords internal
+"_PACKAGE"

R/converters.R

@@ -1436,22 +1436,26 @@ SpectronauttoMSstatsPTMFormat = function(
                                 bracket="[",
                                 replace_text=TRUE)
 
-  ptm_input = SpectronauttoMSstatsFormat(input, annotation, intensity, 
-                                         filter_with_Qvalue,
-                                         qvalue_cutoff, useUniquePeptide, 
-                                         removeFewMeasurements, 
-                                         removeProtein_with1Feature, 
-                                         summaryforMultipleRows)
+  ptm_input = SpectronauttoMSstatsFormat(input, annotation, 
+                                         intensity = intensity, 
+                                         filter_with_Qvalue = filter_with_Qvalue,
+                                         qvalue_cutoff = qvalue_cutoff, 
+                                         useUniquePeptide = useUniquePeptide, 
+                                         removeFewMeasurements = removeFewMeasurements, 
+                                         removeProtein_with1Feature = removeProtein_with1Feature, 
+                                         summaryforMultipleRows = summaryforMultipleRows)
 
   msstats_input = list(PTM = ptm_input)
   if (!is.null(protein_input)) {
     protein_input = SpectronauttoMSstatsFormat(protein_input, 
-                                               annotation_protein, intensity, 
-                                               filter_with_Qvalue,
-                                               qvalue_cutoff, useUniquePeptide, 
-                                               removeFewMeasurements, 
-                                               removeProtein_with1Feature, 
-                                               summaryforMultipleRows)
+                                               annotation_protein, 
+                                               intensity = intensity, 
+                                               filter_with_Qvalue = filter_with_Qvalue,
+                                               qvalue_cutoff = qvalue_cutoff, 
+                                               useUniquePeptide = useUniquePeptide, 
+                                               removeFewMeasurements = removeFewMeasurements, 
+                                               removeProtein_with1Feature = removeProtein_with1Feature, 
+                                               summaryforMultipleRows = summaryforMultipleRows)
 
     msstats_input = list(PTM = ptm_input, PROTEIN = protein_input)
   }
@@ -1584,28 +1588,28 @@ MetamorpheusToMSstatsPTMFormat = function(input,
 
     ptm_input = MetamorpheusToMSstatsFormat(input,
                                             annotation,
-                                            useUniquePeptide, 
-                                            removeFewMeasurements,
-                                            removeProtein_with1Feature, 
-                                            summaryforMultipleRows,
-                                            use_log_file, 
-                                            append, 
-                                            verbose, 
-                                            log_file_path)
+                                            useUniquePeptide = useUniquePeptide, 
+                                            removeFewMeasurements = removeFewMeasurements,
+                                            removeProtein_with1Feature = removeProtein_with1Feature, 
+                                            summaryforMultipleRows = summaryforMultipleRows,
+                                            use_log_file = use_log_file, 
+                                            append = append, 
+                                            verbose = verbose, 
+                                            log_file_path = log_file_path)
 
     msstats_format = list(PTM = ptm_input, PROTEIN = NULL)
 
     if (!is.null(input_protein)) {
         protein_input = MetamorpheusToMSstatsFormat(input_protein,
                                                     annotation_protein,
-                                                    useUniquePeptide, 
-                                                    removeFewMeasurements,
-                                                    removeProtein_with1Feature, 
-                                                    summaryforMultipleRows,
-                                                    use_log_file, 
-                                                    append, 
-                                                    verbose, 
-                                                    log_file_path)
+                                                    useUniquePeptide = useUniquePeptide, 
+                                                    removeFewMeasurements = removeFewMeasurements,
+                                                    removeProtein_with1Feature = removeProtein_with1Feature, 
+                                                    summaryforMultipleRows = summaryforMultipleRows,
+                                                    use_log_file = use_log_file, 
+                                                    append = append, 
+                                                    verbose = verbose, 
+                                                    log_file_path = log_file_path)
 
         ptm_input = ptm_input[grepl(mod_id, ptm_input$PeptideSequence),]
 

R/utils_converters.R

@@ -609,11 +609,14 @@ MSstatsPTMSiteLocator = function(data,
 
   return(data)
 }
-#' Add site location and aa
-#' @param data data.table
-#' @param fasta_file string or data.table
-#' @return data.table
-#' @keywords internal
+
+#' Fix terminus location adjustments
+#' @param data data.table containing peptide data
+#' @param terminus_id character string identifying the terminus 
+#' (e.g. N-terminus)
+#' @param unmod_pep_col character string specifying the column name containing 
+#' unmodified peptide sequences
+#' @return data.table with corrected Start positions
 .fixTerminus = function(data, terminus_id, unmod_pep_col){
 
   ## Terminus makes start location off