linreg

This function is used by cit.cp to compute F test given a continuous outcome and full vs reduced sets of covariates

 nonparametric

 htest

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.

Joshua Millstein

Causal Inference Test

linreg function

<dl> <dt>nms.full</dt>
<dd>vector of variable names for all covariates included in the full model.</dd> <dt>nms.redu</dt>
<dd>vector of variable names for all covariates included in the reduced model. If nms.redu is NULL then the reduced model is fitted with the intercept only.</dd> <dt>nm.y</dt>
<dd>character string, which is the name of the outcome variable.</dd> <dt>mydat</dt>
<dd>the dataframe that includes all variables with each variable in a column.</dd></dl>

Arguments

Author

F Test for Linear Model — linreg

<dl>

 <dt>nms.full</dt>
<dd>vector of variable names for all covariates included in the full model.</dd>

 <dt>nms.redu</dt>
<dd>vector of variable names for all covariates included in the reduced model. If nms.redu is NULL then the reduced model is fitted with the intercept only.</dd>

 <dt>nm.y</dt>
<dd>character string, which is the name of the outcome variable.</dd>

 <dt>mydat</dt>
<dd>the dataframe that includes all variables with each variable in a column.</dd>

</dl>

linreg: F Test for Linear Model

Description

Usage

Value

Arguments

Author

Details

References

Examples