HIMA: High-dimensional Mediation Analysis

HIMA is an R package for estimating and testing high-dimensional mediation effects in omic studies.

Installation

HIMA is now available in R CRAN repository

## Install HIMA
install.packages("HIMA")

To install from GitHub

## Install HIMA from GitHub
library(devtools)
install_github("yinanzheng/HIMA")

If package "qvalue" is not found, please first install "qvalue" package through Bioconductor: https://www.bioconductor.org/packages/release/bioc/html/qvalue.html

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("qvalue")

Documentation

Explore the tutorial for the HIMA package, which provides detailed usage examples and guidelines, at the following tutorial link:

HIMA Tutorial

Citation:

1. Zhang H, Zheng Y, Zhang Z, Gao T, Joyce B, Yoon G, Zhang W, Schwartz J, Just A, Colicino E, Vokonas P, Zhao L, Lv J, Baccarelli A, Hou L, Liu L. Estimating and Testing High-dimensional Mediation Effects in Epigenetic Studies. Bioinformatics. 2016. DOI: 10.1093/bioinformatics/btw351. PMID: 27357171; PMCID: PMC5048064

2. 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

3. 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

4. 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

5. Perera C, Zhang H, Zheng Y, Hou L, Qu A, Zheng C, Xie K, Liu L. HIMA2: high-dimensional mediation analysis and its application in epigenome-wide DNA methylation data. BMC Bioinformatics. 2022. DOI: 10.1186/s12859-022-04748-1. PMID: 35879655; PMCID: PMC9310002

6. Zhang H, Hong X, Zheng Y, Hou L, Zheng C, Wang X, Liu L. High-Dimensional Quantile Mediation Analysis with Application to a Birth Cohort Study of Mother–Newborn Pairs. Bioinformatics. 2024. DOI: 10.1093/bioinformatics/btae055. PMID: 38290773; PMCID: PMC10873903

7. Bai X, Zheng Y, Hou L, Zheng C, Liu L, Zhang H. An Efficient Testing Procedure for High-dimensional Mediators with FDR Control. Statistics in Biosciences. 2024. DOI: 10.1007/s12561-024-09447-4.

Contact package maintainer:

Yinan Zheng

Email: y-zheng@northwestern.edu