A likelihood-based hypothesis testing approach is implemented for assessing causal mediation. For example, 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.

Author | Joshua Millstein |

Date of publication | 2016-11-15 07:16:48 |

Maintainer | Joshua Millstein <joshua.millstein@usc.edu> |

License | Artistic-2.0 |

Version | 2.1 |

**cit.bp:** Causal Inference Test for a Binary Outcome

**cit.cp:** Causal Inference Test for a Continuous Outcome

**cit-package:** Causal Inference Test

**fdr.cit:** Omnibus FDR Values for CIT

**fdr.od:** Permutation-Based FDR and Confidence Interval

**fdr.q.para:** Parametric tail-area FDR Values, q-values

**fdr.q.perm:** Nonparametric permutation-based tail-area FDR Values,...

**iuq:** Intersection/Union Q-Value

**linreg:** F Test for Linear Model

cit

cit/src

cit/src/Makevars

cit/src/citconlog3_perm_v5.cpp

cit/src/logisticfunc.h

cit/src/citconlog3cvr_perm_v6.cpp

cit/src/citconlog2cvr_v3.cpp

cit/src/Makevars.win

cit/src/citconlog2_v3.cpp

cit/src/logisticfunc.cpp

cit/NAMESPACE

cit/R

cit/R/C_CIT_V13.R
cit/MD5

cit/DESCRIPTION

cit/man

cit/man/fdr.q.perm.Rd
cit/man/cit.bp.Rd
cit/man/fdr.cit.Rd
cit/man/cit-package.Rd
cit/man/iuq.Rd
cit/man/fdr.od.Rd
cit/man/fdr.q.para.Rd
cit/man/cit.cp.Rd
cit/man/linreg.Rd
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