refactor(converters): Load MSstatsConvert converters when calling lib…

…rary(MSstats) (#146)

* refactor(converters): Load MSstatsConvert converters when calling library(MSstats)

* refactor(converters): Reexport converters to MSstats namespace

.gitignore

@@ -5,4 +5,6 @@
 .DS_Store
 *.log
 *.txt
+.codiumai
+.idea
 

NAMESPACE

@@ -54,12 +54,22 @@ import(ggplot2)
 import(limma)
 import(lme4)
 importFrom(MASS,rlm)
+importFrom(MSstatsConvert,DIANNtoMSstatsFormat)
+importFrom(MSstatsConvert,DIAUmpiretoMSstatsFormat)
+importFrom(MSstatsConvert,FragPipetoMSstatsFormat)
 importFrom(MSstatsConvert,MSstatsBalancedDesign)
 importFrom(MSstatsConvert,MSstatsClean)
 importFrom(MSstatsConvert,MSstatsImport)
 importFrom(MSstatsConvert,MSstatsLogsSettings)
 importFrom(MSstatsConvert,MSstatsMakeAnnotation)
 importFrom(MSstatsConvert,MSstatsPreprocess)
+importFrom(MSstatsConvert,MaxQtoMSstatsFormat)
+importFrom(MSstatsConvert,OpenMStoMSstatsFormat)
+importFrom(MSstatsConvert,OpenSWATHtoMSstatsFormat)
+importFrom(MSstatsConvert,PDtoMSstatsFormat)
+importFrom(MSstatsConvert,ProgenesistoMSstatsFormat)
+importFrom(MSstatsConvert,SkylinetoMSstatsFormat)
+importFrom(MSstatsConvert,SpectronauttoMSstatsFormat)
 importFrom(Rcpp,sourceCpp)
 importFrom(data.table,as.data.table)
 importFrom(data.table,melt)

R/utils_documentation.R

@@ -0,0 +1,30 @@
+#' A dummy function to store shared documentation items.
+#' 
+#' @import data.table
+#' @importFrom MSstatsConvert MSstatsImport MSstatsClean MSstatsPreprocess 
+#' MSstatsBalancedDesign MSstatsMakeAnnotation MSstatsLogsSettings
+#' 
+#' @param removeFewMeasurements TRUE (default) will remove the features that have 1 or 2 measurements across runs.
+#' @param useUniquePeptide TRUE (default) removes peptides that are assigned for more than one proteins. 
+#' We assume to use unique peptide for each protein.
+#' @param summaryforMultipleRows max(default) or sum - when there are multiple measurements for certain feature and certain run, use highest or sum of multiple intensities.
+#' @param removeProtein_with1Feature TRUE will remove the proteins which have only 1 feature, which is the combination of peptide, precursor charge, fragment and charge. FALSE is default.
+#' @param removeProtein_with1Peptide TRUE will remove the proteins which have only 1 peptide and charge. FALSE is default.
+#' @param removeOxidationMpeptides TRUE will remove the peptides including 'oxidation (M)' in modification. FALSE is default.
+#' @param removeMpeptides TRUE will remove the peptides including 'M' sequence. FALSE is default.
+#' @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.
+#' 
+#' @keywords internal
+#' 
+.documentFunction = function() {
+    NULL
+}

R/utils_onAttach.R

@@ -0,0 +1,14 @@
+#' Load core packages when loading MSstats
+#' @noRd
+#' @keywords internal
+.onAttach = function(libname, pkgname) {
+    # Load core packages dynamically
+    to_load <- c("MSstatsConvert")
+
+    # Attach them quietly
+    if (length(to_load) > 0) {
+        lapply(to_load, function(pkg) {
+            suppressPackageStartupMessages(library(pkg, character.only = TRUE))
+        })
+    }
+}