From f601063e99e66374b41ffed95be91d7f4915934b Mon Sep 17 00:00:00 2001
From: Stevie Ped <stephen.pederson.au@gmail.com>
Date: Sat, 18 May 2024 23:02:18 +0930
Subject: [PATCH] Tested bugfix in release

---
 DESCRIPTION                       |  2 +-
 R/addDiffStatus.R                 | 10 +++++-----
 R/colToRanges.R                   |  8 ++------
 man/colToRanges-methods.Rd        |  5 +----
 tests/testthat/test_colToRanges.R |  5 +----
 5 files changed, 10 insertions(+), 20 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 1f1531ff..bd5b551f 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,5 +1,5 @@
 Package: extraChIPs
-Version: 1.9.2
+Version: 1.8.2
 Title: Additional functions for working with ChIP-Seq data
 Authors@R: person("Stevie", "Pederson", 
   email = "stephen.pederson.au@gmail.com", 
diff --git a/R/addDiffStatus.R b/R/addDiffStatus.R
index fa93ddda..6dd76f85 100644
--- a/R/addDiffStatus.R
+++ b/R/addDiffStatus.R
@@ -64,11 +64,11 @@ setMethod(
     stopifnot(is.numeric(x[[sig_col]]))
     sig <- x[[sig_col]] < alpha
     status <- case_when(
-      is.na(sig) | is.na(fc) ~ missing[[1]],
-      !sig ~ other[[1]],
-      fc > abs(cutoff) ~ up[[1]],
-      fc < -abs(cutoff) ~ down[[1]],
-      TRUE ~ other[[1]]
+        is.na(sig) | is.na(fc) ~ missing[[1]],
+        !sig ~ other[[1]],
+        fc > abs(cutoff) ~ up[[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))
diff --git a/R/colToRanges.R b/R/colToRanges.R
index 9cf10a61..2f3d8c6c 100644
--- a/R/colToRanges.R
+++ b/R/colToRanges.R
@@ -29,8 +29,6 @@
 #' @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
@@ -59,11 +57,9 @@ setMethod(
 #' @export
 setMethod(
     "colToRanges", signature = signature(x = "GRanges"),
-    function(x, var, ..., keep_metadata = TRUE) {
+    function(x, var, ...) {
         df <- mcols(x)
-        gr <- colToRanges(df, var, ...)
-        if (keep_metadata) metadata(gr) <- metadata(x)
-        gr
+        colToRanges(df, var, ...)
     }
 )
 #' @import GenomicRanges
diff --git a/man/colToRanges-methods.Rd b/man/colToRanges-methods.Rd
index 398225e8..3b67cf65 100644
--- a/man/colToRanges-methods.Rd
+++ b/man/colToRanges-methods.Rd
@@ -11,7 +11,7 @@ colToRanges(x, ...)
 
 \S4method{colToRanges}{DataFrame}(x, var, seqinfo = NULL, ...)
 
-\S4method{colToRanges}{GRanges}(x, var, ..., keep_metadata = TRUE)
+\S4method{colToRanges}{GRanges}(x, var, ...)
 
 \S4method{colToRanges}{data.frame}(x, var, seqinfo = NULL, ...)
 }
@@ -24,9 +24,6 @@ colToRanges(x, ...)
 
 \item{seqinfo}{A seqinfo object to be applied to the new GRanges object.
 Ignored if the column is already a GRanges object}
-
-\item{keep_metadata}{logical(1) If the original object is a GRanges object,
-retain all metadata from the original ranges in the replaced ranges}
 }
 \value{
 A GenomicRanges object
diff --git a/tests/testthat/test_colToRanges.R b/tests/testthat/test_colToRanges.R
index 71121469..eae54600 100644
--- a/tests/testthat/test_colToRanges.R
+++ b/tests/testthat/test_colToRanges.R
@@ -1,20 +1,17 @@
 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")
-metadata(gr) <- list(check = TRUE)
+gr <-mergeByCol(x, df, col = "logCPM", pval = "p")
 
 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)