Causal Inference Test
A likelihood-based hypothesis testing approach is implemented for
assessing causal mediation. Described in Millstein, Chen, and Breton (2016),
, it could be used to test for mediation
of a known causal association between a DNA variant, the 'instrumental variable',
and a clinical outcome or phenotype by gene expression or DNA methylation, the
potential mediator. Another example would be testing mediation of the effect
of a drug on a clinical outcome by the molecular target. The hypothesis test
generates a p-value or permutation-based FDR value with confidence intervals
to quantify uncertainty in the causal inference. The outcome can be represented
by either a continuous or binary variable, the potential mediator is continuous,
and the instrumental variable can be continuous or binary and is not limited to
a single variable but may be a design matrix representing multiple variables.
