From 5b447f26a535e465537817df0050e58444340670 Mon Sep 17 00:00:00 2001 From: mbstadler Date: Wed, 7 Aug 2024 08:14:06 +0200 Subject: [PATCH] update tests after limma's breaking changed calculation of degrees of freedom (https://code.bioconductor.org/browse/limma/commit/e8ff47777e7c25d6dcb9582d9fcb8f9c4fed9da1) --- DESCRIPTION | 2 +- tests/testthat/test_runEISA.R | 5 +++-- 2 files changed, 4 insertions(+), 3 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index b404f86..5ec044b 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: eisaR Title: Exon-Intron Split Analysis (EISA) in R -Version: 1.17.0 +Version: 1.17.1 Authors@R: c(person("Michael", "Stadler", email = "michael.stadler@fmi.ch", role = c("aut", "cre")), person("Dimos", "Gaidatzis", email = "dimosthenis.gaidatzis@fmi.ch", role = "aut"), person("Lukas", "Burger", email = "lukas.burger@fmi.ch", role = "aut"), diff --git a/tests/testthat/test_runEISA.R b/tests/testthat/test_runEISA.R index 5fa4293..c2b9c18 100644 --- a/tests/testthat/test_runEISA.R +++ b/tests/testthat/test_runEISA.R @@ -134,9 +134,10 @@ test_that("runEISA() gives expected results", { test.sig = res2$tab.ExIn$FDR < 0.01) # close to 1/nsig -> one false positive # no false positives or false negatives (except for selsig2 genes in t1) - nmissed1 <- t1["TRUE", "TRUE", "FALSE"] # expect to miss some genes with sample-specific effects + nmissed1 <- t1["FALSE", "TRUE", "FALSE"] # these are now missed after updated df calculation in limma (https://code.bioconductor.org/browse/limma/commit/e8ff47777e7c25d6dcb9582d9fcb8f9c4fed9da1) + nmissed2 <- t1["TRUE", "TRUE", "FALSE"] # expect to miss some genes with sample-specific effects expect_identical(as.vector(t1), - c(ngenes - nsig, 0L, 0L, nmissed1, 0L, 0L, nsig - nsig2, nsig2 - nmissed1)) + c(ngenes - nsig, 0L, nmissed1, nmissed2, 0L, 0L, nsig - nsig2 - nmissed1, nsig2 - nmissed2)) expect_identical(as.vector(t2), c(ngenes - nsig, 0L, 0L, 0L, 0L, 0L, nsig - nsig2, nsig2)) })