remove warning about missing strandSpecific field for empty and example fds

Author: ischeller

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

@@ -45,6 +45,7 @@ createTestFraserSettings <- function(workingDir="FRASER_output"){
 
     # create FRASER object
     fds <- FraserDataSet(colData=sampleTable, workingDir=workingDir)
+    strandSpecific(fds) <- 'no'
 
     # dont use hdf5 for example data set
     dontWriteHDF5(fds) <- TRUE