tests/testthat/test-run_DGE.R

In NathanSkene/EWCE: Expression Weighted Celltype Enrichment

test_that("DGE works", {
    if (!is_32bit()) {
        set.seed(1234)
        cortex_mrna <- ewceData::cortex_mrna()
        n_genes <- 100
        exp <- cortex_mrna$exp[seq(1, n_genes), ]
        level2annot <- cortex_mrna$annot$level2class

        #### limma ####
        limma_res <- EWCE:::run_limma(
            exp = exp,
            level2annot = level2annot
        )
        testthat::expect_true(
            all(c("coefficients", "rank", "assign", "F", "p.value") %in% names(limma_res))
        )
        testthat::expect_true(EWCE:::is_matrix(limma_res$coefficients))
        testthat::expect_equal(sum(limma_res$q < .05), 100)

        #### DESeq2 ####
        deqseq2_res <- EWCE:::run_deseq2(
            exp = exp,
            level2annot = level2annot,
            test = "LRT"
        )
        testthat::expect_true(
            all(c("baseMean", "log2FoldChange", "pvalue", "padj") %in% 
                    names(deqseq2_res))
        )
        testthat::expect_length(deqseq2_res$padj, n_genes)
        testthat::expect_equal(nrow(subset(deqseq2_res, padj < .05)), 80)

        #### MAST ####
        mast_res <- EWCE:::run_mast(
            exp = exp,
            level2annot = level2annot
        )
        testthat::expect_true(
            all(c("Class", "lrstat", "p.value") %in% names(mast_res))
        )
        testthat::expect_true(is.data.frame(mast_res))
        testthat::expect_equal(nrow(subset(mast_res, q < .05)), 1917)
    }
})