From 5e124e7c98e60bb61fad94534f4fbfc2abe5079d Mon Sep 17 00:00:00 2001 From: pablovgd <73334477+pablovgd@users.noreply.github.com> Date: Thu, 8 Feb 2024 10:00:46 +0100 Subject: [PATCH 01/10] fix issue #716 in XcmsExperiment-functions.R --- R/XcmsExperiment-functions.R | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/R/XcmsExperiment-functions.R b/R/XcmsExperiment-functions.R index e2b2957d5..837a81413 100644 --- a/R/XcmsExperiment-functions.R +++ b/R/XcmsExperiment-functions.R @@ -503,6 +503,7 @@ mzCenterFun = "weighted.mean", sampleIndex = integer(), cn = character(), ...) { + cn = c(cn,"sn") res <- matrix(NA_real_, ncol = length(cn), nrow = nrow(peakArea)) rownames(res) <- rownames(peakArea) colnames(res) <- cn @@ -525,10 +526,11 @@ maxi <- which.max(mat[, 2L])[1L] mmz <- do.call(mzCenterFun, list(mat[, 1L], mat[, 2L])) if (is.na(mmz)) mmz <- mat[maxi, 1L] - res[i, c("rt", "mz", "maxo", "into")] <- c( + res[i, c("rt", "mz", "maxo", "into","sn")] <- c( rts[maxi], mmz, mat[maxi, 2L], sum(mat[, 2L], na.rm = TRUE) * - ((rtr[2L] - rtr[1L]) / max(1L, (length(keep) - 1L))) + ((rtr[2L] - rtr[1L]) / max(1L, (length(keep) - 1L))), + mat[maxi, 2L]/ estimateChromNoise(mat[, 2L]) ) if ("beta_cor" %in% cn) res[i, c("beta_cor", "beta_snr")] <- .get_beta_values( From 5071cfbb22ecf684ed12d99224711f45a47c8815 Mon Sep 17 00:00:00 2001 From: pablovgd <73334477+pablovgd@users.noreply.github.com> Date: Fri, 9 Feb 2024 09:29:21 +0100 Subject: [PATCH 02/10] Update XcmsExperiment-functions.R Revert changes to .chrom_peak_intensity_centWave --- R/XcmsExperiment-functions.R | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/R/XcmsExperiment-functions.R b/R/XcmsExperiment-functions.R index 837a81413..e2b2957d5 100644 --- a/R/XcmsExperiment-functions.R +++ b/R/XcmsExperiment-functions.R @@ -503,7 +503,6 @@ mzCenterFun = "weighted.mean", sampleIndex = integer(), cn = character(), ...) { - cn = c(cn,"sn") res <- matrix(NA_real_, ncol = length(cn), nrow = nrow(peakArea)) rownames(res) <- rownames(peakArea) colnames(res) <- cn @@ -526,11 +525,10 @@ maxi <- which.max(mat[, 2L])[1L] mmz <- do.call(mzCenterFun, list(mat[, 1L], mat[, 2L])) if (is.na(mmz)) mmz <- mat[maxi, 1L] - res[i, c("rt", "mz", "maxo", "into","sn")] <- c( + res[i, c("rt", "mz", "maxo", "into")] <- c( rts[maxi], mmz, mat[maxi, 2L], sum(mat[, 2L], na.rm = TRUE) * - ((rtr[2L] - rtr[1L]) / max(1L, (length(keep) - 1L))), - mat[maxi, 2L]/ estimateChromNoise(mat[, 2L]) + ((rtr[2L] - rtr[1L]) / max(1L, (length(keep) - 1L))) ) if ("beta_cor" %in% cn) res[i, c("beta_cor", "beta_snr")] <- .get_beta_values( From 9af3da326ceca71ca63169c01d038b8870b7969b Mon Sep 17 00:00:00 2001 From: pablovgd <73334477+pablovgd@users.noreply.github.com> Date: Fri, 9 Feb 2024 09:30:29 +0100 Subject: [PATCH 03/10] Update XcmsExperiment.R Add "sn" to .empty_chrom_peaks function --- R/XcmsExperiment.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/XcmsExperiment.R b/R/XcmsExperiment.R index fdb94eddc..7b3672046 100644 --- 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, From 5d62852ceba8c1d9094c89cd67e58102f1e1db25 Mon Sep 17 00:00:00 2001 From: pablovgd <73334477+pablovgd@users.noreply.github.com> Date: Fri, 9 Feb 2024 09:31:37 +0100 Subject: [PATCH 04/10] Update DESCRIPTION update version to 4.1.8 --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 005b55868..5d933824c 100644 --- 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, From fd49fbe7ec4710b48bd88851727dea5e8cb242b7 Mon Sep 17 00:00:00 2001 From: pablovgd <73334477+pablovgd@users.noreply.github.com> Date: Fri, 9 Feb 2024 09:35:39 +0100 Subject: [PATCH 05/10] Update NEWS --- inst/NEWS | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/inst/NEWS b/inst/NEWS index 5fc15922b..28017d61b 100644 --- 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 ---------------------- From 21620fe19ea98b0d1bd857e20cea4d496c0f4399 Mon Sep 17 00:00:00 2001 From: pablovgd <73334477+pablovgd@users.noreply.github.com> Date: Fri, 9 Feb 2024 10:05:01 +0100 Subject: [PATCH 06/10] Update test_XcmsExperiment.R Edit tests for .empty_chrom_peaks and manualChromPeaks --- tests/testthat/test_XcmsExperiment.R | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/tests/testthat/test_XcmsExperiment.R b/tests/testthat/test_XcmsExperiment.R index 4aa26f58e..bfa8ffae7 100644 --- 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", { From 00e70625b681b4dfed750b760168a4252d726a2a Mon Sep 17 00:00:00 2001 From: pablovgd <73334477+pablovgd@users.noreply.github.com> Date: Wed, 14 Feb 2024 12:26:46 +0100 Subject: [PATCH 07/10] Update DESCRIPTION --- DESCRIPTION | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/DESCRIPTION b/DESCRIPTION index 5d933824c..153a8aabd 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -37,6 +37,11 @@ Authors@R: c( role = "aut", 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), BiocParallel (>= 1.8.0), From c30b27751f5e020df2d516d5de27826cab1953ce Mon Sep 17 00:00:00 2001 From: pablovgd <73334477+pablovgd@users.noreply.github.com> Date: Wed, 14 Feb 2024 12:28:06 +0100 Subject: [PATCH 08/10] Update DESCRIPTION --- DESCRIPTION | 1 - 1 file changed, 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 153a8aabd..4f3d37864 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -36,7 +36,6 @@ Authors@R: c( email = "philippine.louail@eurac.edu", role = "aut", comment = c(ORCID = "0009-0007-5429-6846")) - ) person(given = "Pablo", family = "Vangeenderhuysen", email = "pablo.vangeenderhuysen@ugent.be", role = "ctb", From b703edcc77961e4a6260249a90701ff93ba1dffc Mon Sep 17 00:00:00 2001 From: pablovgd <73334477+pablovgd@users.noreply.github.com> Date: Fri, 16 Feb 2024 08:51:24 +0100 Subject: [PATCH 09/10] Update DESCRIPTION --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 4f3d37864..c8ca2bc7a 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -35,7 +35,7 @@ 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", From 4fcb331b60d1ce869c226582ed314fb21969e4cf Mon Sep 17 00:00:00 2001 From: Steffen Neumann Date: Mon, 19 Feb 2024 13:53:40 +0100 Subject: [PATCH 10/10] Fix missing closing bracket --- tests/testthat/test_XcmsExperiment.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/testthat/test_XcmsExperiment.R b/tests/testthat/test_XcmsExperiment.R index bfa8ffae7..f2b0e6303 100644 --- a/tests/testthat/test_XcmsExperiment.R +++ b/tests/testthat/test_XcmsExperiment.R @@ -996,7 +996,7 @@ test_that("manualChromPeaks,XcmsExperiment works", { unname(pks_2[, c("mz", "into", "maxo")])) chr_pks <- chromPeaks(res) - expect_true("sn" %in% colnames(chr_pks) + expect_true("sn" %in% colnames(chr_pks)) res2 <- manualChromPeaks(tmp, pks, samples = 2) expect_equal(unname(chromPeaks(res2)), unname(pks_2))