SMAHP {SMAHP}R Documentation

Main function

Description

An approach for survival mediation analysis of high-dimensional proteogenomic data.

Usage

SMAHP(
  X,
  M,
  C,
  time,
  status,
  model_option = "MCP",
  SIS_thres = "n/log(n)",
  p_adjust_option = "BH",
  p_thres = 0.05
)

Arguments

X

An n by p matrix of exposures.

M

An n by p matrix of mediators.

C

An n by p matrix of covariates. If there are no covariates, set C = NULL.

time

A vector of survival time of samples.

status

A vector of status indicator: 0=alive, 1=dead.

model_option

The penalization method used when selecting X for M. Options include MCP, elastic net and lasso. Default is MCP.

SIS_thres

SIS thresholds. Default is "n/log(n)". Other options include "n-1", "n/2log(n)", "2n/log(n)", "3n/log(n)".

p_adjust_option

The method for multiple correction. Option include q-value, holm, hochberg, hommel, bonferroni, BH, BY, and fdr. Default is BH.

p_thres

Threshold for determining significance.

Value

A list with the following components:

p_final_matrix

raw p-value matrix before adjustment

p_adjusted_matrix

adjusted p-value matrix

p_med_matrix

mediation-exposure matrix

outcome_model

coefficient estimates from outcome model

med_results

coefficient estimates from mediation model

Examples


data(example_dat)
surv_dat <- example_dat$surv_dat
SMAHP(example_dat$X, example_dat$M, example_dat$C, time = surv_dat$time, status = surv_dat$status)


[Package SMAHP version 0.0.5 Index]