Construct limma-compatible contrasts from MAE sample metadata

This helper keeps design-column construction and contrast parsing inside bulkMAE. The returned matrix can be passed directly to de_voom() or de_limma().

Usage

de_contrast(x, experiment, formula, contrasts)

Arguments

x

A MultiAssayExperiment object.

experiment

Optional experiment name.

formula

Model formula evaluated against aligned sample metadata.

contrasts

Character contrast expressions accepted by limma::makeContrasts().

Value

A numeric contrast matrix whose rows match de_design() columns.