- Edited the convertToRDS() function to allow the deletion of one or …

…several channels in the dataset. The associated documentation was also edited as well

- Edited the version number
- Documented the argument of the checkNewVersion() function to meet the R package check

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: PICAFlow
 Title: PICAFlow: a complete R workflow dedicated to flow/mass cytometry data, from data pre-processing to deep and comprehensive analysis
-Version: 1.0.5
+Version: 1.0.6
 Authors@R: 
     person("Paul", "Régnier", , "paul.regnier@aphp.fr", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0002-9713-1132"))

R/0_Preprocessing.R

@@ -1,6 +1,7 @@
 #' Check new version
 #'
 #' This function checks whether there is a new available version for `PICAFlow` in the GitHub repository. If this is the case, users are notified.
+#' @param ... Useful to transfer other arguments to the function.
 #'
 #' @export
 
@@ -67,6 +68,8 @@ setupWorkingDirectory = function()
 #'
 #' Please note that the renaming both affects the parameters of each file AND the parameters in each self-contained compensation matrix.
 #'
+#' If needed, it is also possible to ask for the deletion of one or several channels in the dataset by specifying the word `DELETE` in the `to_desc` and `to_name` columns of the `conversionTable` table. In this case, it (or they) will simply be deleted from the samples which match with the associated pair of `from_desc` and `from_name` parameters used in the table.
+#'
 #' @return Generated `rds` files are saved to `rds` directory. The function also returns a matrix of all unique parameters (once correctly renamed) used in the dataset.
 #'
 #' @importFrom foreach %dopar%
@@ -143,6 +146,8 @@ convertToRDS = function(conversionTable = NULL)
 
         }
 
+        parametersToRemoveID = NULL
+
         foreach::foreach(b = 1:length(currentFileParameterDescriptions)) %do% {
           currentDescriptionFrom = currentFileParameterDescriptions[b]
           currentDescriptionName = currentFileParameterNames[b]
@@ -157,22 +162,37 @@ convertToRDS = function(conversionTable = NULL)
 
             rowToReplaceID = as.numeric(which(currentFileParameterDescriptions == currentDescriptionFrom))
 
-            currentData@parameters@data[rowToReplaceID, "desc"] = paste(currentDescriptionTo, "_replaced", sep = "")
-            currentData@parameters@data[rowToReplaceID, "name"] = paste(currentNameTo, "_replaced", sep = "")
+            if(currentDescriptionTo == "DELETE" & currentNameTo == "DELETE")
+            {
+              parametersToRemoveID = c(parametersToRemoveID, rowToReplaceID)
+              # currentData = currentData[, -rowToReplaceID]
+            } else
+            {
+              currentData@parameters@data[rowToReplaceID, "desc"] = paste(currentDescriptionTo, "_replaced", sep = "")
+              currentData@parameters@data[rowToReplaceID, "name"] = paste(currentNameTo, "_replaced", sep = "")
 
-            colToReplaceID = as.numeric(which(colnames(currentData@exprs) == currentNameFrom))
-            colnames(currentData@exprs)[colToReplaceID] = paste(currentNameTo, "_replaced", sep = "")
+              colToReplaceID = as.numeric(which(colnames(currentData@exprs) == currentNameFrom))
+              colnames(currentData@exprs)[colToReplaceID] = paste(currentNameTo, "_replaced", sep = "")
 
 
-            if (length(compensationMatricesSlotName) > 0)
-            {
-              matchingCompensationNameID = which(colnames(currentData@description[compensationMatricesSlotName][[1]]) == currentNameFrom)
+              if (length(compensationMatricesSlotName) > 0)
+              {
+                matchingCompensationNameID = which(colnames(currentData@description[compensationMatricesSlotName][[1]]) == currentNameFrom)
+
+                colnames(currentData@description[compensationMatricesSlotName][[1]])[matchingCompensationNameID] = paste(currentNameTo, "_replaced", sep = "")
+              }
 
-              colnames(currentData@description[compensationMatricesSlotName][[1]])[matchingCompensationNameID] = paste(currentNameTo, "_replaced", sep = "")
             }
+
+
           }
         }
 
+        if(is.null(parametersToRemoveID) == FALSE & length(parametersToRemoveID) > 0)
+        {
+          currentData = currentData[, -parametersToRemoveID]
+        }
+
         currentData@parameters@data[, "desc"] = gsub("_replaced", "", currentData@parameters@data[, "desc"])
         currentData@parameters@data[, "name"] = gsub("_replaced", "", currentData@parameters@data[, "name"])
         colnames(currentData@exprs) = gsub("_replaced", "", colnames(currentData@exprs))