Tested devel after bugfix

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: extraChIPs
-Version: 1.8.1
+Version: 1.9.2
 Title: Additional functions for working with ChIP-Seq data
 Authors@R: person("Stevie", "Pederson", 
   email = "[email protected]", 

R/addDiffStatus.R

@@ -64,10 +64,11 @@ setMethod(
     stopifnot(is.numeric(x[[sig_col]]))
     sig <- x[[sig_col]] < alpha
     status <- case_when(
-      !sig ~ other[[1]],
       is.na(sig) | is.na(fc) ~ missing[[1]],
+      !sig ~ other[[1]],
       fc > abs(cutoff) ~ up[[1]],
-      fc < -abs(cutoff) ~ down[[1]]
+      fc < -abs(cutoff) ~ down[[1]],
+      TRUE ~ other[[1]]
     )
     ## Do we need to add an explicit NA value here?
     lv <- unique(c(other, down, up, missing))

R/colToRanges.R

@@ -29,6 +29,8 @@
 #' @param seqinfo A seqinfo object to be applied to the new GRanges object.
 #' Ignored if the column is already a GRanges object
 #' @param ... Used to pass arguments to lower-level functions
+#' @param keep_metadata logical(1) If the original object is a GRanges object,
+#' retain all metadata from the original ranges in the replaced ranges
 #'
 #' @importFrom methods as
 #' @import GenomicRanges
@@ -57,9 +59,11 @@ setMethod(
 #' @export
 setMethod(
     "colToRanges", signature = signature(x = "GRanges"),
-    function(x, var, ...) {
+    function(x, var, ..., keep_metadata = TRUE) {
         df <- mcols(x)
-        colToRanges(df, var, ...)
+        gr <- colToRanges(df, var, ...)
+        if (keep_metadata) metadata(gr) <- metadata(x)
+        gr
     }
 )
 #' @import GenomicRanges

tests/testthat/test_colToRanges.R

@@ -1,17 +1,20 @@
 sq <- Seqinfo("chr1", 100, FALSE, "test")
 x <- GRanges(c("chr1:1-10", "chr1:6-15", "chr1:51-60"), seqinfo = sq)
 df <- data.frame(logFC = rnorm(3), logCPM = rnorm(3,8), p = 10^-rexp(3))
-gr <-mergeByCol(x, df, col = "logCPM", pval = "p")
+gr <- mergeByCol(x, df, col = "logCPM", pval = "p")
+metadata(gr) <- list(check = TRUE)
 
 test_that("Coercion is correct where it should be", {
   new_gr <- colToRanges(gr, "keyval_range")
   expect_s4_class(new_gr, "GRanges")
+  expect_true(metadata(new_gr)$check)
   expect_equal(
     colnames(mcols(new_gr)),
     c("n_windows", "n_up", "n_down", "logCPM", "logFC", "p", "p_fdr")
   )
   expect_equal(length(new_gr), 2)
   df$gr <- as.character(x)
+  ## Now try using a df
   new_gr <- colToRanges(df, "gr", seqinfo = sq)
   expect_s4_class(new_gr, "GRanges")
   expect_equal(seqinfo(new_gr), sq)