v1.11.2: Fix bug affecting analysisQuantifications and other improvem…

…ents + Bug fix affecting {artmsAnalysisQuantifications()} + Allow {artmsAnalysisQuantifications()} to process previous versions of artMS + Change Extension of {artms_sessionInfo_quantification} file from {.txt} to {.log} + New parameters available in {artmsQuantification()}, including: - Parameter {printTables}. Default {TRUE}, prints tables. FALSE otherwise. - Parameter {return_results_object}. If TRUE, it returns a list of data frames with MSstats results. Default is FALSE - If both {printTables} and {printPDF} are FALSE, then {return_results_object} becames TRUE and a list of data frames is returned + Change default parameters of the configuration files: less verbose
biodavidjm · Jul 14, 2021 · 5fd14f8 · 5fd14f8
1 parent 55ea8f1
commit 5fd14f8
Show file tree

Hide file tree

Showing 15 changed files with 340 additions and 182 deletions.
diff --git a/.gitignore b/.gitignore
@@ -1,11 +1,17 @@
 Meta
 doc
+
 # History files
 **.Rhistory
 **.Rapp.history
 **.Rprofile
 **.DS_Store
 
+# TESTS
+tests/testthat/*log
+tests/testthat/*txt
+tests/testthat/*pdf
+
 # MSstats files
 msstats.log*
 sessionInfo.txt

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: artMS
 Type: Package
 Title: Analytical R tools for Mass Spectrometry
-Version: 1.11.1
-Date: 2021-07-08
+Version: 1.11.2
+Date: 2021-07-13
 Authors@R: c(person("David", "Jimenez-Morales", role = c("aut","cre"),
                      email = "[email protected]",
                      comment = c(ORCID = "0000-0003-4356-6461")),

diff --git a/NEWS b/NEWS
@@ -1,3 +1,13 @@
+Changes in version 1.10.2 (2021-07-13)
++ Bug fix affecting {artmsAnalysisQuantifications()}
++ Allow {artmsAnalysisQuantifications()} to process previous versions of artMS
++ Change Extension of {artms_sessionInfo_quantification} file from {.txt} to {.log}
++ New parameters available in {artmsQuantification()}, including:
+   - Parameter {printTables}. Default {TRUE}, prints tables. FALSE otherwise.
+   - Parameter {return_results_object}. If TRUE, it returns a list of data frames with MSstats results. Default is FALSE
+   - If both {printTables} and {printPDF} are FALSE, then {return_results_object} becames TRUE and a list of data frames is returned
++ Change default parameters of the configuration files: less verbose
+
 Changes in version 1.10.1 (2021-06-30)
 + Addressing major changes in MSstats
    - R version larger than 4.1 is now required

diff --git a/R/MSstats_functions.R b/R/MSstats_functions.R
@@ -477,7 +477,7 @@ artmsSILACtoLong <- function(evidence_file,
       cmmp = cmmp + 1
     }
     if(!any(grepl("^use_log_file$", names(config$msstats)))){
-      config$msstats$use_log_file = TRUE
+      config$msstats$use_log_file = FALSE
       cmmp = cmmp + 1
     }
     if(!any(grepl("^append$", names(config$msstats)))){

diff --git a/R/analysisQuantifications.R b/R/analysisQuantifications.R
@@ -231,7 +231,7 @@ artmsAnalysisQuantifications <- function(log2fc_file,
 
   ## CRAN -----
   required_bioc_packages <- c("ComplexHeatmap")
-  for(p in required_cran_packages){
+  for(p in required_bioc_packages){
     if(!(p %in% installed.packages())){
       message(paste0('- Package < ', p, ' > not installed in your system. 
                      Please, install running < BiocManager::install(\"',p,'\") >'))
@@ -315,7 +315,19 @@ artmsAnalysisQuantifications <- function(log2fc_file,
                        stringsAsFactors = FALSE)
     colnames(dfmq) <- toupper(colnames(dfmq))
   }
-
+
+  # ModelQC: fix old files-----
+  if("GROUP_ORIGINAL" %in% colnames(dfmq)){
+    if(verbose) message("\n------------------------------------------------------------")
+    if(verbose) message("(!) WARNING!")
+    if(verbose) message("Be aware that you are analyzing a dataset that was generated with an old version of MSstats (< 4.0)")
+    if(verbose) message("Some changes will be applied")
+    if(verbose) message(" ------------------------------------------------------------\n")
+    dfmq$GROUP <- NULL
+    dfmq$GROUP <- dfmq$GROUP_ORIGINAL
+    dfmq$SUBJECT <- NULL
+    dfmq$SUBJECT <- dfmq$SUBJECT_ORIGINAL
+  }
 
   # Removing the empty protein names-----
   if (any(dfmq$PROTEIN == "")) {
@@ -2019,7 +2031,8 @@ artmsAnalysisQuantifications <- function(log2fc_file,
     list_of_datasets,
     file = outexcel,
     asTable = FALSE,
-    headerStyle = hs
+    headerStyle = hs, 
+    overwrite = TRUE
   )
 
   if(verbose) message("Folder <", output_dir, "> ")

diff --git a/R/getMSstatsformat.R b/R/getMSstatsformat.R
@@ -9,12 +9,14 @@
 # '.txt' extension required
 # @param data_object (logical) if TRUE the output_name cannot be the evidence file
 # since it would be an data_object
+# @param printTables (logical) `TRUE` (default) prints results tables
 # @param verbose (logical) `TRUE` (default) shows function messages
 # @return (data.frame) MSstats compatible format
 # @keywords internal, MSstats, format, input, fractions
 .artms_getMSstatsFormat <- function(data_f, 
                                     output_name, 
                                     data_object = FALSE,
+                                    printTables = TRUE,
                                     verbose = TRUE) {
 
   Run = PeptideSequence = Condition_BioReplicate_Run = NULL
@@ -126,14 +128,15 @@
   }
 
   dmss <- as.data.frame(dmss)
-  if(verbose) message("-- Write out the MSstats input file (-mss.txt) ")
-  write.table(dmss,
-              file = gsub('.txt', '-mss.txt', output_name),
-              eol = "\n",
-              sep = "\t",
-              quote = FALSE,
-              row.names = FALSE,
-              col.names = TRUE)
-
+  if(printTables){
+    if(verbose) message("-- Write out the MSstats input file (-mss.txt) ")
+    write.table(dmss,
+                file = gsub('.txt', '-mss.txt', output_name),
+                eol = "\n",
+                sep = "\t",
+                quote = FALSE,
+                row.names = FALSE,
+                col.names = TRUE)
+  }
   return(dmss)
 }
diff --git a/R/main.R b/R/main.R
@@ -184,20 +184,44 @@ utils::globalVariables(
 #' is a string to a file that should be opened or config object (yaml). 
 #' Default is `FALSE`. Choose `TRUE` if `yaml_config_file` is a yaml object
 #' @param printPDF (logical) if `TRUE` (default), prints out pdf
+#' @param printTables (logical) `TRUE` (default) print results tables
 #' @param display_msstats (logical) if `TRUE`, prints MSstats outputs (default is `FALSE`)
+#' @param return_results_object (logical) Default is `FALSE`. 
+#' If `TRUE`, it returns a list of data frames with MSstats results, including:
+#' - `comparisonResult`: comparison results
+#' - `ModelQC`
+#' - `FittedModel`: fit model details
+#' - `power`: power calculations
+#' - `sample_size`: sample size estimations
 #' @param verbose (logical) `TRUE` (default) shows function messages
 #' @return The relative quantification of the conditions and comparisons
 #' specified in the keys/contrast file resulting from running MSstats, in
 #' addition to quality control plots (if selected)
 #' @keywords main, driver, function
-#' @examples \dontrun{
-#' artmsQuantification(yaml_config_file = "path/to/artms-ab-config.yaml")
-#' }
+#' @examples
+#' # Recommended
+#' # artmsQuantification(yaml_config_file = "your-config-file.yaml")
+#' 
+#' # Example to test this function using the example dataset available in artMS
+#' # Step 1: Add evidence, keys, and contrast to configuration object
+#' artms_data_ph_config$files$evidence <- artms_data_ph_evidence
+#' artms_data_ph_config$files$keys <- artms_data_ph_keys
+#' artms_data_ph_config$files$contrasts <- artms_data_ph_contrast
+#' 
+#' # Step 2: Run the quantification step
+#' quant_results <- artmsQuantification(yaml_config_file = artms_data_ph_config, 
+#'                                      data_object = TRUE, 
+#'                                      display_msstats = FALSE,
+#'                                      printPDF = FALSE,
+#'                                      printTables = FALSE)
+#' # Check the list of data frames "quant_results". Nothing should be printed out. 
 #' @export
 artmsQuantification <- function(yaml_config_file,
                                 data_object = FALSE,
                                 printPDF = TRUE,
+                                printTables = TRUE,
                                 display_msstats = FALSE,
+                                return_results_object = FALSE,
                                 verbose = TRUE) {
 
   # Check if the yaml file is already open first
@@ -231,10 +255,16 @@ artmsQuantification <- function(yaml_config_file,
     config$data$filters$modification <- toupper(config$data$filters$modification)
   }
 
-  session <- sessionInfo()
-  sink("artms_sessionInfo_quantification.txt")
-  print(session)
-  sink()
+  if(isFALSE(printTables) & isFALSE(printPDF) & isFALSE(return_results_object)){
+    return_results_object = TRUE
+  }
+
+  if(printTables){
+    session <- sessionInfo()
+    sink("artms_sessionInfo_quantification.log")
+    print(session)
+    sink()
+  }
 
   # Quality Control
   if (config$qc$basic) {
@@ -282,13 +312,15 @@ artmsQuantification <- function(yaml_config_file,
   # message("output_dir: ", output_dir) 
 
   # create output directory if it doesn't exist-----
-  if (!dir.exists(output_dir)) {
-    if(verbose) message("-- Folder: [", output_dir, "] created" )
-    dir.create(output_dir, recursive = TRUE)
+  if(printTables | printPDF){
+    if (!dir.exists(output_dir)) {
+      if(verbose) message("-- Folder: [", output_dir, "] created" )
+      dir.create(output_dir, recursive = TRUE)
+    }
   }
-  
+
   # process MaxQuant data, link with keys, and convert for MSStats format-----
-  if (config$data$enabled) {
+  if ( config$data$enabled ) {
     if(verbose) message(">> LOADING DATA ")
     ## Found more bugs in fread (issue submitted to data.table on github by
     ## JVD but it was closed with the excuse that 'is was not reproducible'
@@ -407,6 +439,7 @@ artmsQuantification <- function(yaml_config_file,
       dmss <- .artms_getMSstatsFormat(data_f = data_f,
                                       output_name = config$files$evidence,
                                       data_object = data_object,
+                                      printTables = printTables,
                                       verbose = verbose)
     } else {
       if(verbose) message(sprintf("\t+ READING PREPROCESSED FILE: %s ",
@@ -431,6 +464,8 @@ artmsQuantification <- function(yaml_config_file,
           suppressWarnings(results <- .artms_runMSstats(dmss = dmss,
                                                         contrasts = contrasts, 
                                                         config = config,
+                                                        printTables = printTables,
+                                                        printPDF = printPDF,
                                                         verbose = verbose)
                            )
           )
@@ -441,7 +476,11 @@ artmsQuantification <- function(yaml_config_file,
 
     if(data_object){
       return(results)
-    } 
+    }else{
+      if(return_results_object){
+        return(results)
+      }
+    }
 
   } else{
     if(verbose) message("\t+ MSstats not selected")