survHIMA: High-dimensional mediation analysis for survival data

In HIMA: High-Dimensional Mediation Analysis

High-dimensional mediation analysis for survival data

Description

survHIMA is used to estimate and test high-dimensional mediation effects for survival data.

Usage

survHIMA(X, Z, M, OT, status, FDRcut = 0.05, scale = TRUE, verbose = FALSE)

Arguments

X	a vector of exposure.
Z	a matrix of adjusting covariates. Rows represent samples, columns represent variables. Can be NULL.
M	a data.frame or matrix of high-dimensional mediators. Rows represent samples, columns represent mediator variables.
OT	a vector of observed failure times.
status	a vector of censoring indicator (status = 1: uncensored; status = 0: censored)
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 <FDPcut).

• 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.

• p.joint: joint raw p-value of selected significant mediator (based on FDR).

References

Zhang H, Zheng Y, Hou L, Zheng C, Liu L. Mediation Analysis for Survival Data with High-Dimensional Mediators. Bioinformatics. 2021. DOI: 10.1093/bioinformatics/btab564. PMID: 34343267. PMCID: PMC8570823

Examples

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

head(himaDat$Example3$PhenoData)

survHIMA.fit <- survHIMA(X = himaDat$Example3$PhenoData$Treatment,
                Z = himaDat$Example3$PhenoData[, c("Sex", "Age")], 
                M = himaDat$Example3$Mediator, 
                OT = himaDat$Example3$PhenoData$Time, 
                status = himaDat$Example3$PhenoData$Status, 
                FDRcut = 0.05,
                scale = FALSE, 
                verbose = TRUE)
survHIMA.fit

## End(Not run)

HIMA documentation built on Sept. 10, 2023, 5:06 p.m.