From 5ce27013306f68b5cb42b437666deadde39574d1 Mon Sep 17 00:00:00 2001 From: Dariusz Scigocki Date: Wed, 4 Sep 2024 10:37:21 +0200 Subject: [PATCH 1/6] removed checkDimnames hack --- R/merge_SE.R | 7 +------ 1 file changed, 1 insertion(+), 6 deletions(-) diff --git a/R/merge_SE.R b/R/merge_SE.R index f8f658d4..c00e5fdb 100644 --- a/R/merge_SE.R +++ b/R/merge_SE.R @@ -70,8 +70,7 @@ merge_SE <- function(SElist, assays = lapply(merged_assays, "[[", "BM"), colData = data$condition_md, rowData = data$treatment_md, - metadata = metadata, - checkDimnames = FALSE + metadata = metadata ) av_pnames <- names(formals(SummarizedExperiment::SummarizedExperiment)) @@ -79,10 +78,6 @@ merge_SE <- function(SElist, do.call(SummarizedExperiment, f_list) } -# 2021.11.01 - param checkDimnames was added to Summarized Experiment in Bioc 3.14, -# to make it compatible with previous solution we re filtering it 'checkDimnames' if not present -# TODO: remove once all our envs are with Bioc 3.14 - #' Merge assay data #' #' @param SElist named list of Summarized Experiments From 3ac1ca23160428a27c37fcd41d3d742f18ba56f1 Mon Sep 17 00:00:00 2001 From: Dariusz Scigocki Date: Wed, 4 Sep 2024 10:38:25 +0200 Subject: [PATCH 2/6] bump version --- DESCRIPTION | 4 ++-- NEWS.md | 3 +++ 2 files changed, 5 insertions(+), 2 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 68a525a5..7096e0dc 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,8 +1,8 @@ Package: gDRutils Type: Package Title: A package with helper functions for processing drug response data -Version: 1.3.11 -Date: 2024-08-30 +Version: 1.3.12 +Date: 2024-08-04 Authors@R: c(person("Bartosz", "Czech", role=c("aut"), comment = c(ORCID = "0000-0002-9908-3007")), person("Arkadiusz", "Gladki", role=c("cre", "aut"), email="gladki.arkadiusz@gmail.com", diff --git a/NEWS.md b/NEWS.md index 27415faa..4a268457 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,6 @@ +## gDRutils 1.3.12 - 2024-09-04 +* remove hack with checkDimnames + ## gDRutils 1.3.11 - 2024-08-30 * remove GDS fit_source from gDRviz From 3f4689cc8913045bb8268e7b75d662bda285149c Mon Sep 17 00:00:00 2001 From: Dariusz Scigocki Date: Wed, 4 Sep 2024 22:59:49 +0200 Subject: [PATCH 3/6] CI From ebcd6caf8655723f14ba30f0fa75eb82794228e5 Mon Sep 17 00:00:00 2001 From: Dariusz Scigocki Date: Tue, 10 Sep 2024 10:09:04 +0200 Subject: [PATCH 4/6] updated assay rownames and colnames in merge_SE --- R/merge_SE.R | 10 +++++++++- 1 file changed, 9 insertions(+), 1 deletion(-) diff --git a/R/merge_SE.R b/R/merge_SE.R index c00e5fdb..5f053534 100644 --- a/R/merge_SE.R +++ b/R/merge_SE.R @@ -65,9 +65,17 @@ merge_SE <- function(SElist, metadata <- merge_metadata(SElist, metadataNames) metadata <- c(metadata, identifiers) + + assays = lapply(merged_assays, FUN = function(x) { + bm_assay <- x[["BM"]] + colnames(bm_assay) <- rownames(data$condition_md) + rownames(bm_assay) <- rownames(data$treatment_md) + bm_assay + }) + p_list <- list( - assays = lapply(merged_assays, "[[", "BM"), + assays = assays, colData = data$condition_md, rowData = data$treatment_md, metadata = metadata From 6e155e1c9ae2774b03e5f019ad2a1f43a7c38608 Mon Sep 17 00:00:00 2001 From: Dariusz Scigocki Date: Tue, 10 Sep 2024 10:32:26 +0200 Subject: [PATCH 5/6] linter --- R/merge_SE.R | 15 +++++++++------ 1 file changed, 9 insertions(+), 6 deletions(-) diff --git a/R/merge_SE.R b/R/merge_SE.R index 5f053534..a17ef0da 100644 --- a/R/merge_SE.R +++ b/R/merge_SE.R @@ -66,12 +66,15 @@ merge_SE <- function(SElist, metadata <- merge_metadata(SElist, metadataNames) metadata <- c(metadata, identifiers) - assays = lapply(merged_assays, FUN = function(x) { - bm_assay <- x[["BM"]] - colnames(bm_assay) <- rownames(data$condition_md) - rownames(bm_assay) <- rownames(data$treatment_md) - bm_assay - }) + assays <- lapply( + merged_assays, + FUN = function(x) { + bm_assay <- x[["BM"]] + colnames(bm_assay) <- rownames(data$condition_md) + rownames(bm_assay) <- rownames(data$treatment_md) + bm_assay + } + ) p_list <- list( From bc5617605027eab6ea57de93627589e2886c4ee1 Mon Sep 17 00:00:00 2001 From: darsoo Date: Tue, 10 Sep 2024 11:14:11 +0200 Subject: [PATCH 6/6] Update DESCRIPTION Co-authored-by: Bartek <32614650+bczech@users.noreply.github.com> --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 7096e0dc..ac2528f4 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -2,7 +2,7 @@ Package: gDRutils Type: Package Title: A package with helper functions for processing drug response data Version: 1.3.12 -Date: 2024-08-04 +Date: 2024-09-04 Authors@R: c(person("Bartosz", "Czech", role=c("aut"), comment = c(ORCID = "0000-0002-9908-3007")), person("Arkadiusz", "Gladki", role=c("cre", "aut"), email="gladki.arkadiusz@gmail.com",