Confident non-linear effect sizes using limma
limma_nonlinear_confects(object, design, effect, fdr = 0.05, step = 0.01, trend = FALSE)
An expression matrix or EList object, or anything limma's lmFit will accept.
A non-linear effect, created with one of the effect_... functions.
False Discovery Rate to control for.
Granularity of log2 fold changes to test.
Technical note: Signed confects are based on TREAT-style p-values. Unsigned confects (generally with df>1) are based on comparing the best fit within the H0 region to the best fit overall, which may up to double p-values.
nest_confects for details of how to interpret the result.