medTest.SBMH: Test for multiple mediators which uses the Bogomolov and...

In SiminaB/MultiMed: Testing multiple biological mediators simultaneously

Description

Implements Heller/Sampson method of testing multiple biological mediators simultaneously, controlling either FWER or FDR.

Usage

medTest.SBMH(pEM,pMY,MCP.type="FWER",t1=0.05,t2=0.05,lambda=0)

Arguments

pEM	Vector of size m (where m = number of mediators). Entries are the p-values for the E,M_j relationship.
pMY	Vector of size m (where m = number of mediators). Entries are the p-values for the M_j,Y|E relationship.
MCP.type	Multiple comparison procedure - either "FWER" or "FDR".
t1	Threshold for determining the cutoff to be one of the top S_1 E/M_j relationships.
t2	Threshold for determining the cutoff to be one of the top S_2 M_j/Y relationships.
lambda	Threshold for estimating the proportion of false positives.

Details

See Heller/Sampson paper for a more in-depth description of this method.

Value

m x 1 matrix of either p-values (if MCP.type = "FWER") or q-values (if MCP.type = "FDR").

Author(s)

Ruth Heller, Joshua N. Sampson

References

Sampson JN, Boca SM, Moore SC, Heller R. FWER and FDR control when testing multiple mediators. Bioinformatics, 2018, 34(14), 2418-2424.

Examples

##load dataset - details are given in the accompanying vignette

data(NavyAdenoma)

##the exposure of interest is the daily intake of fish
##the possible mediators are 149 normalized serum metabolite values
##the outcome of interest is colorectal adenoma case-control status

##get all metabolites
metabs <- colnames(NavyAdenoma)[6:154]

##get exposure/mediator relationships
pEM <- sapply(NavyAdenoma[,metabs], 
              function(m,e){coef(summary(lm(m ~ e)))[2,4]}, 
              e=NavyAdenoma$Fish)

##get mediator/outcome relationship (conditional on exposure)
pMY <- sapply(NavyAdenoma[,metabs], 
              function(m,y,e){coef(summary(glm(y ~ m + e, family=binomial)))[2,4]}, 
              y=NavyAdenoma$Adenoma, e=NavyAdenoma$Fish)

##perform mediation test for both FWER and FDR procedures
medTest.FWER <- medTest.SBMH(pEM, pMY, MCP.type="FWER")
##get smallest p-value and corresponding metabolite
min(medTest.FWER)
metabs[which.min(medTest.FWER)]

medTest.FDR <- medTest.SBMH(pEM, pMY, MCP.type="FDR")
##get smallest p-value and corresponding metabolite
min(medTest.FDR)
metabs[which.min(medTest.FDR)]

SiminaB/MultiMed documentation built on June 1, 2019, 11:49 a.m.