cit: Causal Inference Test

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

View on CRAN

Man pages

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

Files in this package

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