minor changes in strandSpecific function and properties

R/AllGenerics.R

@@ -155,14 +155,25 @@ setMethod("strandSpecific", "FraserDataSet", function(object) {
         warning("Strand is not specified. Please set the used RNA-seq",
                 " protocol by using 'strandSpecific(object) <- c(...)'.",
                 "\n\nWe assume as default a non stranded protocol.")
-        return(0)
+        return(rep(0, ncol(object)))
     }
     return(colData(object)$strand)
 })
 
 #' @export
 #' @rdname fds-methods
 setReplaceMethod("strandSpecific", "FraserDataSet", function(object, value) {
+    if (length(value) != ncol(object)){
+        if(length(value) == 1){
+            warning("Only one value is provided as strand for all samples.\n",
+                  "  We assume that all samples are of the same provided strand.")
+                  strandSpecific(object) <- rep(value, ncol(object))
+        }
+        else{
+            stop("Number of strand values should be equal to the number of samples: (",
+                  paste0(length(value), " != ", ncol(object), ")"))
+        }
+    }
     if(is.logical(value)){
         value <- as.integer(value)
     }

R/FraserDataSet-class.R

@@ -82,8 +82,8 @@ validateStrandSpecific <- function(object) {
     # Check mixed strand type
     ss <- strandSpecific(object)
     if ((any(ss == 0) && any(ss == 1)) || (any(ss == 0) && any(ss == 2))){
-      stop(paste("Error: Data contains a mix of stranded and unstranded samples.\n ",
-                 "Please consider analyzing them separately."))
+      stop(paste("Data contains a mix of stranded and unstranded samples.\n ",
+                 "Please analyse them separately to ensure consistency during counting."))
     }
     NULL
 }

R/annotationOfRanges.R

@@ -271,14 +271,8 @@ findAnnotatedJunction <- function(fds, annotation, annotateNames=TRUE,
     gr <- rowRanges(fds, type="psi5")
 
     # 
-    if(0 %in% stranded){
-        if(length(unique(stranded)) > 1){
-            warning("You use a mixture of stranded and unstranded data.", 
-                    " This is highly discouraged and ",
-                    " can lead to unwanted results. We treat all as stranded.")
-        } else {
-            strand(gr) <- "*"
-        }
+    if(isFALSE(as.logical(unique(stranded)))){
+        strand(gr) <- "*"
     }
 
     # set correct seq level names

R/helper-functions.R

@@ -547,8 +547,12 @@ getBPParam <- function(worker, tasks=0, ...){
 }
 
 getStrandString <- function(fds){
-    strand <- sapply(strandSpecific(fds)+1L, switch, "no", "yes", "reverse")
-    strand <- paste(collapse=", ", strand)
+    strand <- sapply(strandSpecific(fds)+1L, switch, "no", "yes (forward)", "yes (reverse)")
+    if (length(unique(strand)) == 2){
+        strand <- "yes (forward and reverse)"
+    } else {
+        strand <- unique(strand)
+    }
     return(strand)
 }