Package: hdmed 1.0.1

hdmed

Our package offers a suite of functions for performing mediation analysis with high-dimensional mediators. Unlike methods for single-mediator mediation analysis—which have been distributed by packages such as “psych,” “mediation,” “medScan”—our package focuses on settings whether there are many potential mediators that need evaluating simultaneously, a topic which has recently become the focus of prolific and exciting methodological work.

Installation

You can install hdmed from GitHub with:

# install.packages("devtools")
devtools::install_github("dclarkboucher/hdmed")

Overview

To see how high-dimensional mediation analysis works mathematically, let $A$ be an exposure, $Y$ be an outcome, $\mathbf{C}$ be a set of $q$ covariates, and $\mathbf{M}$ be a set of $p$ potential mediators in the causal pathway between $A$ and $Y$. Then, supposing we have data on $n$ individuals, we can evaluate the mediating role of $\mathbf{M}$ with the equations

$$ \begin{equation} E[Y_i|A_i,\mathbf{M}_i,\mathbf{C_i}] = \beta_aA_i+\mathbf{\beta_m}^T\mathbf{M_i} + \mathbf{\beta_c}^T\mathbf{C_i} \end{equation} $$

and

$$ \begin{equation} E[\mathbf{M_i}|A_i,\mathbf{C_i}] =\mathbf{\alpha_a}A_i + \mathbf{\alpha_c}\mathbf{C_i}\text{,} \end{equation} $$

where the first equation is the outcome model and the second equation is the mediator model. In the outcome model, our primary estimands are $\beta_a$— the direct effect of the exposure on the outcome independent of $\mathbf{M}$— and $\mathbf{\beta_m}$, a $p$-vector of the association between each mediator and $Y$ given $A$ and $\mathbf{C}$. (Unlike many methods common to single-mediator analysis, all the methods included in our package assume there is no interaction effect between $\mathbf{M}$ and $A$ on $Y$.) Likewise, our primary concern in the mediator model is $\mathbf{\alpha_a}$, which is a $p$-vector of the conditional associations between each mediator and the exposure given $\mathbf{C}$. As for the other coefficients, $\mathbf{\beta_c}$ is a $q$-vector of the covariate-outcome effects, and $\mathbf{\alpha_c}$ is a $p\times q$ matrix of covariate-mediator associations.

Once the outcome and mediator models have been fitted, mediation analysis can be performed by assessing their estimated coefficients. The chief quantities of interest are:

1. $\mathbf{\alpha_a}^T \mathbf{\beta_m}$, the global mediation effect of $A$ on $Y$ through $M$;

2. $\beta_a$, the direct effect of $A$ on $Y$;

3. $\mathbf{\alpha_a}^T \mathbf{\beta_m} + \beta_a$, the total effect of $A$ on $Y$; and

4. $\frac{\mathbf{\alpha_a}^T \mathbf{\beta_m}}{\mathbf{\alpha_a}^T \mathbf{\beta_m}+\beta_a}$, the proportion of the total effect due to mediation (referred to as the proportion mediated.)

All the methods provided by our package can fit this model except for HDMM (mediate_hdmm) and LVMA (mediate_lvma), which instead of the typical model assumptions, assume the mediation between $A$ and $Y$ is transmitted by unmeasured latent variables. (See the documentation of those functions for more detail.) The other methods produce, at the very least, estimates of the direct effect, global mediation effect, and total effect, making them suitable for performing mediation analysis with the standard assumptions. Moreover, in the case of BSLMM (mediate_bslmm), HIMA (mediate_hima), HDMA (mediate_hdma), MedFix (mediate_medfix), and Pathway LASSO (mediate_pathway_lasso), we also report estimates of the mediation contributions, which are the contributions $(\mathbf{\alpha_a})_j(\mathbf{\beta_m})_j$ of each mediator to $\mathbf{\alpha_a}^T \mathbf{\beta_m}$, $j$ from $1$ to $p$. Though useful for identifying potentially important mediators, we stress that these contributions generally cannot be interpreted as causal effects unless the mediators are independent conditional on $A$ and $\mathbf{C}$. Conditions for when $\mathbf{\alpha_a}^T \mathbf{\beta_m}$ and $\beta_a$ can be interpreted causally are laid out by Song et al. (2019) (see mediate_bslmm for complete reference). Note also that, as programmed, the methods HIMA (mediate_hima), HDMA (mediate_hdma), MedFix (mediate_medfix), and BSLMM allow one to incorporate a small number of covariates directly, as specified in the above pair of models, whereas the other as programmed methods do not. If you are interested in adjusting for covariates with a method that does not allow them to be inputted to our mediation function directly, consider regressing those covariates out of the outcome, mediators, and exposures in advance, when doing so is appropriate. In addition, most functions in our package assume that the outcome variable is continuous; however, HIMA and HDMA have options for fitting a binary outcome model with a standard logistic link.

Example

The med_dat object provided by our package contains a simple toy dataset for practicing high-dimensional mediation (though in this case, we are using “high-dimensional” generously, as the dataset contains only 20 mediators to its 100 observations).

Let us take a look at the data. In Y we have the outcome, in A we have the exposure, and in M we have a named matrix of mediators.

library(hdmed)

# Process data
Y <- med_dat$Y
M <- med_dat$M
A <- med_dat$A

str(M)
#>  num [1:100, 1:20] -0.491 1.339 -0.194 -0.218 -0.108 ...
#>  - attr(*, "dimnames")=List of 2
#>   ..$ : NULL
#>   ..$ : chr [1:20] "m1" "m2" "m3" "m4" ...

Now we will perform mediation analysis. For a simple, fast mediation method we will use the method “high-dimensional mediation analysis” by Zhang et al. (2016), which we call “HIMA”. HIMA is a straightforward method that fits the mediator models using ordinary least squares and the outcome model using penalized regression with the minimax concave penalty. We don’t have covariates to include, so to use the default options, we input only A, M, and Y.

hima_out <- mediate_hima(A, M, Y)

Next let’s look at the mediation contributions, which are located in the contributions table. In this case, the function only returned one mediator, which happens if the others have an estimated contribution of zero and do not contribute to the estimated global mediation effect. Examining the table further, we see alpha as a shorthand for $(\mathbf{\alpha_a})_j$, beta as a shorthand for $(\mathbf{\beta_m})_j$, and alpha_beta as a shorthand for $(\mathbf{\alpha_a})_j(\mathbf{\beta_m})_j$. Notice that ab_pv is the $(\mathbf{\alpha_a})_j(\mathbf{\beta_m})_j$ p-value.

hima_out$contributions
#>   mediator      alpha   alpha_pv      beta      beta_pv alpha_beta      ab_pv
#> 1       m3 -0.2737383 0.01438887 0.6040214 1.364285e-07 -0.1653438 0.01438887

Finally, the estimated mediation effects are reported in effects table, which includes the indirect effect (the global mediation effect), the direct effect, and the total effect. In theory, one can use these estimates to report the proportion mediated, as described above, but since the proportion mediated is generally only useful when $\mathbf{\alpha_a}^T \mathbf{\beta_m}$ and $\beta_m$ have the same sign, we will not do so here.

hima_out$effects
#>     effect    estimate
#> 1 indirect -0.16534380
#> 2   direct  0.01018211
#> 3    total -0.15516169

Citation

This package serves as companion code for our paper, “Methods for Mediation Analysis with High-Dimensional DNA Methylation Data: Possible Choices and Comparison.” To give our work proper credit, please use the citation provided below:

Clark-Boucher D, Zhou X, Du J, Liu Y, Needham BL, Smith JA, et al. Methods for mediation analysis with high-dimensional DNA methylation data: Possible choices and comparisons. PLOS Genetics. 2023 Nov;19(11):1–26.