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context("design matrix")
test_that("design can be a matrix", {
testthat::skip_if_not_installed("apeglm")
m <- matrix(rpois(12*100,100),ncol=12)
coldata <- data.frame(condition=factor(rep(1:2,each=6)),
batch=factor(rep(c(1,2,1,2),each=3)))
dm <- model.matrix(~condition, coldata)
dm2 <- model.matrix(~batch + condition, coldata)
dds <- DESeqDataSetFromMatrix(m, coldata, dm)
dds <- DESeq(dds, fitType="mean")
resultsNames(dds)
# specifying 'full' overrides...
dds2 <- DESeq(dds, full=dm2, fitType="mean")
resultsNames(dds2)
dds <- DESeqDataSetFromMatrix(m, coldata, dm2)
dds <- DESeq(dds, fitType="mean")
res <- results(dds)
res <- results(dds, contrast=list("condition2","batch2"))
res <- results(dds, contrast=c(0,-1,1))
expect_error(res <- results(dds, contrast=c("condition","2","1")), "only list- and numeric-type")
res <- lfcShrink(dds, coef="condition2", type="normal")
res <- lfcShrink(dds, coef="condition2", type="apeglm")
res <- lfcShrink(dds, coef="condition2", type="ashr")
# test replace with matrix
design(dds) <- dm
})
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