microHIMA {HIMA}

High-dimensional mediation analysis for compositional microbiome data

Description

microHIMA is used to estimate and test high-dimensional mediation effects for compositional microbiome data.

Usage

microHIMA(X, Y, OTU, COV = NULL, FDRcut = 0.05, scale = TRUE, verbose = FALSE)

Arguments

X

a vector of exposure.

Y

a vector of outcome.

OTU

a data.frame or matrix of high-dimensional compositional OTUs (mediators). Rows represent samples, columns represent variables.

COV

a data.frame or matrix of adjusting covariates. Rows represent samples, columns represent microbiome variables. Can be NULL.

FDRcut

FDR cutoff applied to define and select significant mediators. Default = 0.05.

scale

logical. Should the function scale the data? Default = TRUE.

verbose

logical. Should the function be verbose? Default = FALSE.

Value

A data.frame containing mediation testing results of selected mediators (FDR < FDRcut).

• ID: index of selected significant mediator.

• alpha: coefficient estimates of exposure (X) –> mediators (M).

• alpha_se: standard error for alpha.

• beta: coefficient estimates of mediators (M) –> outcome (Y) (adjusted for exposure).

• beta_se: standard error for beta.

• FDR: false discovery rate of selected significant mediator.

References

Zhang H, Chen J, Feng Y, Wang C, Li H, Liu L. Mediation effect selection in high-dimensional and compositional microbiome data. Stat Med. 2021. DOI: 10.1002/sim.8808. PMID: 33205470; PMCID: PMC7855955.

Zhang H, Chen J, Li Z, Liu L. Testing for mediation effect with application to human microbiome data. Stat Biosci. 2021. DOI: 10.1007/s12561-019-09253-3. PMID: 34093887; PMCID: PMC8177450.

Examples

## Not run: 
# Note: In the following example, M1, M2, and M3 are true mediators.
data(himaDat)

head(himaDat$Example4$PhenoData)

microHIMA.fit <- microHIMA(X = himaDat$Example4$PhenoData$Treatment, 
                           Y = himaDat$Example4$PhenoData$Outcome, 
                           OTU = himaDat$Example4$Mediator, 
                           COV = himaDat$Example4$PhenoData[, c("Sex", "Age")],
                           scale = FALSE)
microHIMA.fit

## End(Not run)