HIMA-package: High-Dimensional Mediation Analysis for 'Omic' Data
In HIMA: High-Dimensional Mediation Analysis

HIMA-package

R Documentation

High-Dimensional Mediation Analysis for 'Omic' Data

Description

HIMA is an R package for estimating and testing high-dimensional mediation effects in omic studies. HIMA can perform high-dimensional mediation analysis on a wide range of omic data types as potential mediators, including epigenetics, transcriptomics, proteomics, and metabolomics using function hima and microbiome data (function microHIMA). HIMA can also handle survival data (function survHIMA).

Package:	HIMA
Type:	Package
Version:	2.2.1
Date:	2023-09-10
License:	GPL-3

Details

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

Author(s)

Yinan Zheng y-zheng@northwestern.edu, Haixiang Zhang haixiang.zhang@tju.edu.cn, Lifang Hou l-hou@northwestern.edu Lei liu lei.liu@wustl.edu

Maintainer: Yinan Zheng y-zheng@northwestern.edu

References

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. 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

3. 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

4. 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

5. 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

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. 2023. (In press)

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