fix loading again for new fds and remove warning for test data

gagneurlab · May 2, 2024 · 291cfcc · 291cfcc
1 parent 1397a9e
commit 291cfcc
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Showing 2 changed files with 12 additions and 2 deletions.
diff --git a/R/example_functions.R b/R/example_functions.R
@@ -43,9 +43,11 @@ 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)
-    strandSpecific(fds) <- 'no'
 
     # dont use hdf5 for example data set
     dontWriteHDF5(fds) <- TRUE

diff --git a/R/saveHDF5Objects.R b/R/saveHDF5Objects.R
@@ -71,7 +71,15 @@ loadFraserDataSet <- function(dir, name=NULL, file=NULL, upgrade=FALSE){
     attributes(fds)$class <- structure("FraserDataSet", package="FRASER")
 
     # ensure strandSpecific slot is up-to-date with new vector format
-    strandSpecific(fds) <- slot(fds, "strandSpecific")
+    if("strandSpecific" %in% slotNames(fds)){
+        strandSpecific(fds) <- slot(fds, "strandSpecific")    
+    } else{
+        # adapt type of strandSpecific if needed (changed logical -> integer)
+        if(is.logical(strandSpecific(fds))){
+            strandSpecific(fds) <- as.integer(strandSpecific(fds))
+        }
+    }
+
 
     e <- try(assays(fds), silent=TRUE)
     if(is.error(e)){