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.

Version: 2.3.1
Depends: R (≥ 3.5.0)
Suggests: tinytest
Published: 2021-05-25
DOI: 10.32614/CRAN.package.cit
Author: Joshua Millstein ORCID iD [aut, cre]
Maintainer: Joshua Millstein <joshua.millstein at>
License: Artistic-2.0
NeedsCompilation: yes
SystemRequirements: gsl (with development libraries libgsl-dev)
Citation: cit citation info
Materials: README NEWS
In views: CausalInference
CRAN checks: cit results [issues need fixing before 2024-06-30]


Reference manual: cit.pdf


Package source: cit_2.3.1.tar.gz
Windows binaries: r-devel:, r-release:, r-oldrel:
macOS binaries: r-release (arm64): cit_2.3.1.tgz, r-oldrel (arm64): cit_2.3.1.tgz, r-release (x86_64): cit_2.3.1.tgz, r-oldrel (x86_64): cit_2.3.1.tgz
Old sources: cit archive


Please use the canonical form to link to this page.