makeContrasts2: Make contrast DESeq2-style
In assaron/r-utils: Package with a bunch of useful R functions

Description Usage Arguments Value Examples

Make contrast DESeq2-style

1	makeContrasts2(contrast, levels)

contrast

vector of three elements (factor, level2, level1)

contrast table for level2-level1 comparison

es.design <- model.matrix(~0+condition, data=pData(es.norm))
fit <- lmFit(es.norm, es.design)
fit2 <- contrasts.fit(fit, makeContrasts2(c("condition", "Treatment", "Control"), 
                                         levels=es.design))
fit2 <- eBayes(fit2)
de <- topTable(fit2, adjust.method="BH", number=Inf)