From 349c581041cc67e0e7d869d3942753b4bafa362f Mon Sep 17 00:00:00 2001 From: Josh Campbell Date: Mon, 22 Apr 2024 10:36:13 -0400 Subject: [PATCH 1/2] Added GSVA version requirement, fixed one bug in runGSVA call, added explicit parameters in unit tests. --- DESCRIPTION | 4 ++-- R/runGSVA.R | 2 +- tests/testthat/test-pathway.R | 2 +- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index a73d0ce81..d3d4d0d60 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: singleCellTK Type: Package Title: Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data -Version: 2.13.2 +Version: 2.13.3 Authors@R: c(person(given="Yichen", family="Wang", email="wangych@bu.edu", role=c("aut"), comment = c(ORCID = "0000-0003-4347-5199")), person(given="Irzam", family="Sarfraz", email="isarfraz@bu.edu", role=c("aut"), @@ -62,7 +62,7 @@ Imports: ggrepel, ggtree, gridExtra, - GSVA (>= 1.26.0), + GSVA (>= 1.51.0), GSVAdata, igraph, KernSmooth, diff --git a/R/runGSVA.R b/R/runGSVA.R index 4dc205238..6a0e40f7c 100644 --- a/R/runGSVA.R +++ b/R/runGSVA.R @@ -35,7 +35,7 @@ runGSVA <- function(inSCE, useAssay = "logcounts", message(date(), " ... Running GSVA") - gsvaData <- as.matrix(expData(sce, useAssay)) + gsvaData <- as.matrix(expData(inSCE, useAssay)) gsvaPar <- GSVA::gsvaParam(gsvaData, gene.Set) gsvaRes <- t(GSVA::gsva(gsvaPar)) diff --git a/tests/testthat/test-pathway.R b/tests/testthat/test-pathway.R index 7aa557941..7eafa6f5e 100644 --- a/tests/testthat/test-pathway.R +++ b/tests/testthat/test-pathway.R @@ -33,7 +33,7 @@ test_that(desc = "Testing VAM", { }) test_that(desc = "Testing GSVA", { - sce <- runGSVA(sce, geneSetCollectionName = "GeneSetCollection") + sce <- runGSVA(sce, geneSetCollectionName = "GeneSetCollection", useAssay = "logcounts") testthat::expect_true("GSVA_GeneSetCollection_Scores" %in% reducedDimNames(sce)) gsvaPlot <- plotPathway(sce, resultName = "GSVA_GeneSetCollection_Scores", From 4c5ac48769efb0f137521fba8bae34054da9546a Mon Sep 17 00:00:00 2001 From: Josh Campbell Date: Mon, 22 Apr 2024 10:46:07 -0400 Subject: [PATCH 2/2] Downgraded GSVA version --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index d3d4d0d60..11a79d011 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -62,7 +62,7 @@ Imports: ggrepel, ggtree, gridExtra, - GSVA (>= 1.51.0), + GSVA (>= 1.50.0), GSVAdata, igraph, KernSmooth,