Nothing
context("running full ddcorAll pipeline")
set.seed(42)
data(darmanis)
data(design_mat)
darmanis_test = darmanis[1:30, ]
test_that("full ddcorAll process yields correct results on this test data set", {
ddcor_res = ddcorAll(inputMat = darmanis_test, design = design_mat,
compare = c("oligodendrocyte", "neuron"),
adjust = "none", heatmapPlot = FALSE, nPerm = 0, nPairs = "all")
ddcor_res_spearman = ddcorAll(inputMat = darmanis_test, design = design_mat,
compare = c("oligodendrocyte", "neuron"), corrType = "spearman",
adjust = "none", heatmapPlot = FALSE, nPerm = 0, nPairs = "all")
expect_equal(ddcor_res[1, ]$Gene1, "ACSL3")
})
test_that("p-value adjustments work", {
ddcor_res = ddcorAll(inputMat = darmanis_test, design = design_mat, compare = c("oligodendrocyte", "neuron"), adjust = "none", heatmapPlot = FALSE, nPerm = 0)
expect_equal(sum("pValDiff_adj" %in% colnames(ddcor_res)), 0)
ddcor_res = ddcorAll(inputMat = darmanis_test, design = design_mat, compare = c("oligodendrocyte", "neuron"), adjust = "BH", nPerm = 0)
expect_equal(sum("pValDiff_adj" %in% colnames(ddcor_res)), 1)
expect_equal(round(ddcor_res$pValDiff_adj[1], 1), 0)
ddcor_res = ddcorAll(inputMat = darmanis_test, design = design_mat, compare = c("oligodendrocyte", "neuron"), adjust = "perm", heatmapPlot = FALSE, nPerm = 5)
expect_equal(sum("empPVals" %in% colnames(ddcor_res)), 1)
})
test_that("split set works", {
ddcor_res = ddcorAll(inputMat = darmanis_test, design = design_mat, compare = c("oligodendrocyte", "neuron"), adjust = "none", heatmapPlot = FALSE, nPerm = 0, splitSet = c("ACSL3", "ARHGAP5"), nPairs = "all")
expect_equal(nrow(ddcor_res), (nrow(darmanis_test)-2) * 2)
expect_true(all(ddcor_res$Gene2 %in% c("ACSL3", "ARHGAP5")))
darmanis_test_a = darmanis_test[!rownames(darmanis_test) %in% c("ACSL3", "ARHGAP5"), ]
darmanis_test_b = darmanis_test[c("ACSL3", "ARHGAP5"), ]
ddcor_res_b = ddcorAll(inputMat = darmanis_test_a, design = design_mat, inputMatB = darmanis_test_b, compare = c("oligodendrocyte", "neuron"), adjust = "none", heatmapPlot = FALSE, nPerm = 0, nPairs = "all")
expect_equal(ddcor_res, ddcor_res_b)
})
test_that("corr cutoff works", {
ddcor_res = ddcorAll(inputMat = darmanis_test, design = design_mat,
compare = c("oligodendrocyte", "neuron"), adjust = "none",
heatmapPlot = FALSE, nPerm = 0, corr_cutoff = 0.7)
#usually the zScore diff is greater than 5, but with the corr cutoff to 0.7, this is affected.
expect_lt(ddcor_res[1, ]$zScoreDiff, 5)
})
test_that("making design matrices works", {
n_oligo_samples = 38; n_neuron_samples = 120
cell_type = c(rep("oligodendrocyte", n_oligo_samples), rep("neuron", n_neuron_samples))
design_mat = model.matrix(~ cell_type + 0)
colnames(design_mat) = c("neuron", "oligodendrocyte")
design_mat2 = makeDesign(cell_type)
expect_equal(design_mat, design_mat2)
})
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