Merge pull request #719 from pablovgd/issue716

fix issue #716 in XcmsExperiment-functions.R
sneumann · Feb 19, 2024 · b1ae819 · b1ae819
2 parents 1cf7cda + b703edc
commit b1ae819
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Showing 4 changed files with 18 additions and 4 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,5 +1,5 @@
 Package: xcms
-Version: 4.1.7
+Version: 4.1.8
 Title: LC-MS and GC-MS Data Analysis
 Description: Framework for processing and visualization of chromatographically
     separated and single-spectra mass spectral data. Imports from AIA/ANDI NetCDF,
@@ -35,7 +35,11 @@ Authors@R: c(
 	   person(given = "Philippine", family = "Louail",
 	   email = "philippine.louail@eurac.edu",
 	   role = "aut",
-	   comment = c(ORCID = "0009-0007-5429-6846"))
+	   comment = c(ORCID = "0009-0007-5429-6846")),
+	   person(given = "Pablo", family = "Vangeenderhuysen",
+	   email = "pablo.vangeenderhuysen@ugent.be",
+	   role = "ctb",
+	   comment = c(ORCID = "0000-0002-5492-6904"))
 	   )
 Depends:
     R (>= 4.0.0),

diff --git a/R/XcmsExperiment.R b/R/XcmsExperiment.R
@@ -702,7 +702,7 @@
 NULL
 
 .empty_chrom_peaks <- function(sample = TRUE) {
-    cols <- c(.REQ_PEAKS_COLS, "maxo")
+    cols <- c(.REQ_PEAKS_COLS, "maxo","sn")
     if (!sample)
         cols <- cols[cols != "sample"]
     matrix(numeric(), ncol = length(cols), nrow = 0,

diff --git a/inst/NEWS b/inst/NEWS
@@ -1,3 +1,8 @@
+Changes in version 4.1.8
+----------------------
+- Fixing issue #716: edit of `.empty_chrom_peaks` function so an `sn` column is
+  returned. Fixes extracting and plotting of peaks after using `manualChromPeaks`
+
 Changes in version 4.1.7
 ----------------------
 

diff --git a/tests/testthat/test_XcmsExperiment.R b/tests/testthat/test_XcmsExperiment.R
@@ -4,7 +4,7 @@ mse_dia <- readMsExperiment(fl)
 test_that(".empty_chrom_peaks works", {
     res <- .empty_chrom_peaks()
     expect_true(nrow(res) == 0)
-    expect_equal(colnames(res), c(.REQ_PEAKS_COLS, "maxo"))
+    expect_equal(colnames(res), c(.REQ_PEAKS_COLS, "maxo","sn"))
 
     res <- .empty_chrom_peaks(sample = FALSE)
     expect_true(nrow(res) == 0)
@@ -995,8 +995,13 @@ test_that("manualChromPeaks,XcmsExperiment works", {
     expect_equal(unname(pks[, c("mz", "into", "maxo")]),
                  unname(pks_2[, c("mz", "into", "maxo")]))
 
+    chr_pks <- chromPeaks(res)
+    expect_true("sn" %in% colnames(chr_pks)
+
     res2 <- manualChromPeaks(tmp, pks, samples = 2)
     expect_equal(unname(chromPeaks(res2)), unname(pks_2))
+
+
 })
 
 test_that("filterChromPeaks,XcmsExperiment works", {