Correction

R/AllClasses.R

-library(SingleCellExperiment)
+checkTsneObject <- function(obj){
+    if (!class(obj) == "Tsne")
+        return(FALSE)
+}
 
+checkDbscanObject <- function(obj){
+    if (!class(obj) == "Dbscan")
+        return(FALSE)
+}
+
+
+## scRNAseq class
 scRNAseq <- setClass(
-    # Set the name for the class
     "scRNAseq",
-    
-    # Define the slots
     slots = c(
         experimentName = "character",
         countMatrix = "matrix", 
@@ -19,44 +26,191 @@ scRNAseq <- setClass(
         clusters = "SingleCellExperiment"
     ),
     
-        
-        # Make a function that can test to see if the data is consistent.
-        # This is not called if you have an initialize function defined!
-    validity = function(object)
-    {
+    prototype=list(
+        normalizedCountMatrix = SingleCellExperiment(),
+        tSNEList = list(),
+        dbscanList = list()
+        # cellsSimilarityMatrix = matrix(),
+        # clustersSimilarityMatrix = matrix(),
+        # clusters = SingleCellExperiment()
+    ),
+    
+    validity = function(object){
+        errors <- character()
+        ## Test experimentName slot
+        experimentName = getExperimentName(object)
+        if (!is.character(experimentName) | (grepl(" ", experimentName))){
+            msg <- paste("Experiment name should contain a single string ",
+                         "describing the experiment, '",
+                         experimentName,
+                         "' is not correct.\n",
+                         sep = "")
+            errors <- c(errors, msg)
+        }
+        ## Test countMatrix slot
+        countMatrix = getCountMatrix(object)
         if(ncol(countMatrix) < 100) {
-            return("Not enough cells in the count matrix")
+            msg <- paste("Not enough cells in the count matrix. ",
+                             "Should be at leat 100 cells. ",
+                             "The current count matrix contains ",
+                             ncol(countMatrix), " cells.\n",
+                             sep = "")
+            errors <- c(errors, msg)
+        }
+        ## Test normalizedCountMatrix slot
+        normalizedCountMatrix=getNormalizedCountMatrix(object)
+        if (!class(normalizedCountMatrix) == "SingleCellExperiment"){
+            msg <- paste("Normalized count matrix should be ",
+                         "SingleCellExperiment, ",
+                         "not '",
+                         class(normalizedCountMatrix),
+                         "'.\n",
+                         sep = "")
+            errors <- c(errors, msg)
+        }
+        ## Test colData slot
+        colData=getColData(object)
+        if ((!is.null(colData) & (!is.element('cellName', colnames(colData))))){
+            msg <- paste("colData should be a data frame containing ",
+                         "at least 'cellName' column.\n",
+                         sep = "")
+            errors <- c(errors, msg)
+        }
+        ## Test species slot
+        species=getSpecies(object)
+        if (!is.element(species, c("mmu","human"))){
+            msg <- paste("species should be 'mmu' or 'human'. '",
+                         species, "' is not available.\n",
+                         sep = "")
+            errors <- c(errors, msg)
+        }
+        ## Test tSNEList slot
+        tSNEList=getTSNEList(object)
+        if (!all(unlist(sapply(tSNEList, checkTsneObject)))){
+            msg <- paste("tSNE list should contain only objects ",
+                         "of 'Tsne class.'\n",
+                         sep = "")
+            errors <- c(errors, msg)
+        }
+        ## Test dbscan slot
+        dbscanList=getDbscanList(object)
+        if (!all(unlist(sapply(dbscanList, checkDbscanObject)))){
+            msg <- paste("dbscan list should contain only objects ",
+                         "of 'Dbscan class.'\n",
+                         sep = "")
+            errors <- c(errors, msg)
+        }
+        ## Validity return errors messages if they exist
+        if (length(errors) == 0) {
+            return(TRUE)
+        } else {
+            return(stop(errors))
         }
-        
-        # Vérifiez les types des slots
-        return(TRUE)
     }
 )
 
+
+## Tsne class
 Tsne <- setClass(
-    # Set the name for the class
     "Tsne",
-
-    # Define the slots
     slots = c(
         name = "character",
         pc = "numeric",
         perplexity = "numeric",
-        coordinates = "list"
-        )
+        coordinates = "matrix"
+        ),
+    prototype=list(
+        name = character(),
+        pc = numeric(),
+        perplexity = numeric(),
+        coordinates = matrix()
+    ),
+    validity = function(object){
+        errors <- character()
+        ## Test slot Name
+        name = getName(object)
+        if (!is.character(name)){
+            msg <- paste("Name of Tsne object'" , name , "' is incorrect. ",
+                         "It should be a string.\n",
+                         sep = "")
+            errors <- c(errors, msg)
+        }
+        ## Test slot pc
+        pc = getPC(object)
+        if (!is.numeric(pc)){
+            msg <- paste("PC '" , pc , "' is incorrect. ",
+                         "It should be a numeric.\n",
+                         sep = "")
+            errors <- c(errors, msg)
+        }
+        ## Test slot perplexity
+        perplexity = getPerplexity(object)
+        if (!is.numeric(perplexity)){
+            msg <- paste("Perplexity '" , perplexity , "' is incorrect. ",
+                         "It should be a numeric.\n",
+                         sep = "")
+            errors <- c(errors, msg)
+        }
+        ## Test slot coordinates
+        coordinates = getCoordinates(object)
+        if (!is.matrix(coordinates)){
+            msg <- paste("Coordinates should be matrix",
+                         sep = "")
+            errors <- c(errors, msg)
+        }
+    }
 )
 
+
+# Dbscan class
 Dbscan <- setClass(
-    # Set the name for the class
     "Dbscan",
-    
-    # Define the slots
     slots = c(
         name = "character",
-        clustering = "matrix",
         epsilon    = "numeric",
-        minPoints  = "numeric"
-    )
+        minPoints  = "numeric",
+        clustering = "matrix"
+    ),
+    prototype=list(
+        name = character(),
+        epsilon = numeric(),
+        minPoints = numeric(),
+        clustering = matrix()
+    ),
+    validity = function(object){
+        errors <- character()
+        ## Test slot Name
+        name = getName(object)
+        if (!is.character(name)){
+            msg <- paste("Name of Dbscan object '" , name , "' is incorrect. ",
+                         "It should be a string.\n",
+                         sep = "")
+            errors <- c(errors, msg)
+        }
+        ## Test slot epsilon
+        epsilon = getEpsilon(object)
+        if (!is.numeric(pc)){
+            msg <- paste("Epsilon '" , epsilon , "' is incorrect. ",
+                         "It should be a numeric.\n",
+                         sep = "")
+            errors <- c(errors, msg)
+        }
+        ## Test slot minPoints
+        minPoints = getMinPoints(object)
+        if (!is.numeric(minPoints)){
+            msg <- paste("minPoints '" , minPoints , "' is incorrect. ",
+                         "It should be a numeric.\n",
+                         sep = "")
+            errors <- c(errors, msg)
+        }
+        ## Test slot clustering
+        clustering = getClustering(object)
+        if (!is.matrix(clustering)){
+            msg <- paste("Coordinates should be matrix",
+                         sep = "")
+            errors <- c(errors, msg)
+            }
+        }
 )