Fix warnings related to strandSpecific on load and examples (#76)

* ensure old fds' load without warning about `strandSpecific`
* remove warning about missing strandSpecific field for empty and example fds
* fix loading again for new fds and remove warning for test data
* adjust example for merging with external counts to new strandSpecific vector

---------

Co-authored-by: Christian Mertes <mertes@in.tum.de>

R/AllGenerics.R

@@ -152,9 +152,11 @@ setReplaceMethod("workingDir", "FraserDataSet", function(object, value) {
 #' @rdname fds-methods
 setMethod("strandSpecific", "FraserDataSet", function(object) {
     if(!"strand" %in% colnames(colData(object))){
-        warning("Strand is not specified. Please set the used RNA-seq",
+        if(ncol(object) > 0){
+            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(rep(0, ncol(object)))
     }
     return(colData(object)$strand)

R/example_functions.R

@@ -43,6 +43,9 @@ createTestFraserSettings <- function(workingDir="FRASER_output"){
     # check that NHDF is NA group
     sampleTable[gene=='NHDF', condition:=NA]
 
+    # set strand specificity column in colData
+    sampleTable[, strand := 0L]
+
     # create FRASER object
     fds <- FraserDataSet(colData=sampleTable, workingDir=workingDir)
 

R/mergeExternalData.R

@@ -93,7 +93,7 @@ mergeExternalData <- function(fds, countFiles, sampleIDs, annotation=NULL){
     rownames(annotation) <- annotation[,"sampleID"]
     newColData <- DataFrame(rbind(fill=TRUE,
             as.data.table(colData(fds)),
-            as.data.table(annotation[sampleIDs,])))
+            as.data.table(annotation[sampleIDs,,drop=FALSE])))
     rownames(newColData) <- newColData[,"sampleID"]
 
     #

R/saveHDF5Objects.R

@@ -70,11 +70,12 @@ loadFraserDataSet <- function(dir, name=NULL, file=NULL, upgrade=FALSE){
     # can be removed later if the full pipeline is rerun
     attributes(fds)$class <- structure("FraserDataSet", package="FRASER")
 
-    # adapt type of strandSpecific if needed (changed from logical to integer)
-    if(is.logical(strandSpecific(fds))){
-        strandSpecific(fds) <- as.integer(strandSpecific(fds))
+    # ensure strandSpecific slot is up-to-date with new vector format
+    if("strandSpecific" %in% slotNames(fds)){
+        strandSpecific(fds) <- slot(fds, "strandSpecific")    
     }
 
+
     e <- try(assays(fds), silent=TRUE)
     if(is.error(e)){
         if(grepl("DelayedMatrix .* representation .* Please update it ",