--- a +++ b/tests/testthat/test-modtest_ic.R @@ -0,0 +1,41 @@ +library(dplyr) +library(biotmleData) +library(SuperLearner) +library(SummarizedExperiment) +data(illuminaData) + +## SETUP TESTS ################################################################ +colData(illuminaData) <- colData(illuminaData) %>% + data.frame() %>% + mutate(age = as.numeric(age > median(age))) %>% + DataFrame() +varInt_index <- which(names(colData(illuminaData)) %in% "benzene") + +biomarkerTMLEout <- biomarkertmle( + se = illuminaData[1:2, ], + varInt = varInt_index, + bppar_type = BiocParallel::SerialParam(), + g_lib = c("SL.mean", "SL.glm"), + Q_lib = "SL.glm" +) +limmaTMLEout <- modtest_ic(biotmle = biomarkerTMLEout) + +## BEGIN TESTS ################################################################ +test_that("modtest_ic output object is of class type S4", { + expect_equivalent(typeof(limmaTMLEout), "S4") +}) + +test_that("modtest_ic output is of appropriate custom class", { + expect_equivalent(class(limmaTMLEout), "bioTMLE") +}) + +test_that("modtest_ic output contains data frame in topTable slot", { + expect_true(any(class(limmaTMLEout@topTable) == "data.frame")) +}) + +test_that("topTable slot has most column names produced by limma::topTable", { + expect_named( + limmaTMLEout@topTable, + c("ID", "AveExpr", "t", "P.Value", "adj.P.Val", "B", "var_bayes") + ) +})