--- a +++ b/inst/tests/test-downloadAndProcessGEO.R @@ -0,0 +1,43 @@ +context("Download and process all DLBCL datasets") + + +data(DLBCL_overview) +deep_test <- FALSE # Do extensive testing --- SLOW! + +if (deep_test) { # deep_test is defined in ./test-all.R + exclude <- character(0) + for (geo_nbr in setdiff(DLBCL_overview$GSE, exclude)) { + + cat("\n\n\n\n\n\n\n\n #### ", geo_nbr, " #### \n\n\n\n") + + res <- downloadAndProcessGEO(geo_nbr = geo_nbr, + cdf = "brainarray", + target = "ensg", + clean = FALSE) + + cat("\n", geo_nbr, "downloaded and preprocessed successfully!\n") + + test_that(paste("downloadAndProcessGEO works for", geo_nbr), { + expect_that(res, is_a("list")) + expect_that(names(res), equals(c("es", "metadata", "call"))) + expect_that(res$es, is_a("list")) + expect_that(res$metadata, is_a(geo_nbr)) + expect_that(res$metadata, is_a("data.frame")) + expect_that(res$call, is_a("call")) + + # All expression values should not be na + expect_that(all(sapply(res$es, inherits, "ExpressionSet")), is_true()) + expect_that(any(sapply(res$es, function(x) anyNA(exprs(x)))), is_false()) + }) + } +} + +# GSE19246 downloaded and preprocessed successfully! +# GSE12195 downloaded and preprocessed successfully! +# GSE22895 downloaded and preprocessed successfully! +# GSE31312 downloaded and preprocessed successfully! +# GSE10846 downloaded and preprocessed successfully! +# GSE34171 downloaded and preprocessed successfully! +# GSE22470 downloaded and preprocessed successfully! +# GSE4475 downloaded and preprocessed successfully! +# GSE11318 downloaded and preprocessed successfully!