From cf32d0a0b6c097ef2f4e1a85d11d993d2ac53092 Mon Sep 17 00:00:00 2001 From: J Wokaty Date: Tue, 29 Oct 2024 11:14:34 -0400 Subject: [PATCH 1/4] bump x.y.z version to even y prior to creation of RELEASE_3_20 branch --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 38de8b35..5bd0b12a 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: gemma.R Title: A wrapper for Gemma's Restful API to access curated gene expression data and differential expression analyses -Version: 3.1.16 +Version: 3.2.0 Authors@R: c(person(given = "Javier", family = "Castillo-Arnemann", role = c("aut"), email = "javiercastilloar@gmail.com", From 04df853bef4c0140801e44dd9b34887e0e4344b1 Mon Sep 17 00:00:00 2001 From: J Wokaty Date: Tue, 29 Oct 2024 11:14:34 -0400 Subject: [PATCH 2/4] bump x.y.z version to odd y following creation of RELEASE_3_20 branch --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 5bd0b12a..41d5337e 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: gemma.R Title: A wrapper for Gemma's Restful API to access curated gene expression data and differential expression analyses -Version: 3.2.0 +Version: 3.3.0 Authors@R: c(person(given = "Javier", family = "Castillo-Arnemann", role = c("aut"), email = "javiercastilloar@gmail.com", From f8d1f0bbc7ab1c391988b51b185ab65f2f6cb40f Mon Sep 17 00:00:00 2001 From: OganM Date: Tue, 22 Oct 2024 14:02:55 -0700 Subject: [PATCH 3/4] test for get_dataset_object consolidation tests --- tests/testthat/testConvenience.R | 13 +++++++++++++ 1 file changed, 13 insertions(+) diff --git a/tests/testthat/testConvenience.R b/tests/testthat/testConvenience.R index 8bbbf619..548b1f5d 100644 --- a/tests/testthat/testConvenience.R +++ b/tests/testthat/testConvenience.R @@ -50,6 +50,19 @@ test_that("get_dataset_object with multiple datasets and genes",{ expect_true(tidy$NCBIid %>% unique %in% genes %>% all) }) +test_that('get_dataset_object with aggeration methods',{ + av <- get_dataset_object(549,consolidate = 'average') + mx <- get_dataset_object(549,consolidate = 'pickmax') + vr <- get_dataset_object(549,consolidate = 'pickvar') + + + expect_identical(av$`549` %>% dim,mx$`549` %>% dim) + expect_identical(av$`549` %>% dim,vr$`549` %>% dim) + + expect_true(all(av$`549`@elementMetadata$GeneSymbol %in% mx$`549`@elementMetadata$GeneSymbol)) + expect_true(all(av$`549`@elementMetadata$GeneSymbol %in% vr$`549`@elementMetadata$GeneSymbol)) +}) + test_that('get_dataset_object with resultSets',{ dea <- get_dataset_differential_expression_analyses(442) From 890574d309c12992cd22c0a1c7c9641e1006db13 Mon Sep 17 00:00:00 2001 From: ogan Mancarci Date: Tue, 26 Nov 2024 12:33:49 -0800 Subject: [PATCH 4/4] import kableExtra instead of suggest --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 41d5337e..7a6f2a1f 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -46,6 +46,7 @@ Imports: assertthat, digest, R.utils, + kableExtra, base64enc Suggests: testthat (>= 2.0.0), @@ -62,7 +63,6 @@ Suggests: pheatmap, viridis, poolr, - kableExtra, listviewer, shiny Config/testthat/edition: 2