cit - Causal Inference Test
A likelihood-based hypothesis testing approach is
implemented for assessing causal mediation. Described in
Millstein, Chen, and Breton (2016),
<DOI:10.1093/bioinformatics/btw135>, 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.
