HIMA (version 2.2.2)

survHIMA: 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,
  M,
  COV = NULL,
  OT,
  status,
  FDRcut = 0.05,
  scale = TRUE,
  verbose = FALSE
)

Value

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

Index:

mediation name of selected significant mediator.

alpha_hat:

coefficient estimates of exposure (X) --> mediators (M) (adjusted for covariates).

alpha_se:

standard error for alpha.

beta_hat:

coefficient estimates of mediators (M) --> outcome (Y) (adjusted for covariates and exposure).

beta_se:

standard error for beta.

IDE:

mediation (indirect) effect, i.e., alpha*beta.

rimp:

relative importance of the mediator.

pmax:

joint raw p-value of selected significant mediator (based on HDMT pointwise FDR method).

Arguments

X

a vector of exposure.

M

a data.frame or matrix of high-dimensional mediators. Rows represent samples, columns represent mediator variables.

COV

a matrix of adjusting covariates. Rows represent samples, columns represent variables. Can be NULL.

OT

a vector of observed failure times.

status

a vector of censoring indicator (status = 1: uncensored; status = 0: censored)

FDRcut

HDMT pointwise FDR cutoff applied to 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.

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

if (FALSE) {
# 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$Treatment,
                M = himaDat$Example3$Mediator, 
                COV = himaDat$Example3$PhenoData[, c("Sex", "Age")], 
                OT = himaDat$Example3$PhenoData$Time, 
                status = himaDat$Example3$PhenoData$Status, 
                FDRcut = 0.05,
                scale = FALSE, # Disabled only for simulation data
                verbose = TRUE)
survHIMA.fit
}