High-Dimensional Mediation Analysis

Allows to estimate and test high-dimensional mediation effects based on advanced mediator screening and penalized regression techniques. Methods used in the package refer to Haixiang Zhang, Yinan Zheng, Zhou Zhang, Tao Gao, Brian Joyce, Grace Yoon, Wei Zhang, Joel Schwartz, Allan Just, Elena Colicino, Pantel Vokonas, Lihui Zhao, Jinchi Lv, Andrea Baccarelli, Lifang Hou, Lei Liu (2016) .


GitHub release

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

Installation

HIMA is now available in R CRAN repository

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

Citation:

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: http://dx.doi.org/10.1093/bioinformatics/btw351. PubMed PMID: 27357171.

Contact package maintainer:

Yinan Zheng

Email: [email protected]

News

HIMA 1.0.0 (2016-07-09)

  • Initial package submission to GitHub

REMP 1.0.2 (2016-12-13)

  • Improvement: More powerful model fit when outcome variable is binary.
  • New: Generalized linear regression is now allowed in screening step.

REMP 1.0.3 (2017-03-30)

  • Improvement: Added error handler when no mediators were selected from penalized model.
  • Improvement: More transparent information returned during model fitting (when verbose = TRUE).

REMP 1.0.4 (2017-04-08)

  • Improvement: Benjamini-Hochberg FDR adjustment is available.

REMP 1.0.5 (2017-11-05)

  • Improvement: Two different sets of covariates are allowed for step 1 and step 2 separately.

REMP 1.0.7 (2018-03-06)

  • Allow low-dimensional mediator selections.

Reference manual

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install.packages("HIMA")

1.1.0 by Yinan Zheng, 4 months ago


https://github.com/YinanZheng/HIMA/


Report a bug at https://github.com/YinanZheng/HIMA/issues/


Browse source code at https://github.com/cran/HIMA


Authors: Yinan Zheng [aut, cre] , Haixiang Zhang [aut] , Lifang Hou [aut] , Lei Liu [aut, cph]


Documentation:   PDF Manual  


GPL-3 license


Imports utils, stats, MASS, survival, HDMT, iterators, parallel, foreach, doParallel

Depends on ncvreg, glmnet


See at CRAN