randel / ofGEM

A Meta-Analysis Approach with Filtering for Identifying Gene-Level Gene-Environment Interactions

ofGEM

A Meta-Analysis Approach with Filtering for Identifying Gene-Level Gene-Environment Interactions with Genetic Association Data

This R package offers a gene-based meta-analysis test with filtering to detect gene-environment interactions (GxE) with association data, proposed by Wang et al. (2018) doi:10.1002/gepi.22115. It first conducts a meta-filtering test to filter out unpromising SNPs by combining all samples in the consortia data. It then runs a test of omnibus-filtering-based GxE meta-analysis (ofGEM) that combines the strengths of the fixed- and random-effects meta-analysis with meta-filtering. It can also analyze data from multiple ethnic groups.

Installation

• For the stable version from CRAN:

install.packages('ofGEM')

• For the development version (requiring the devtools package):

devtools::install_github('randel/ofGEM')

Reference

Wang, J., Liu, Q., Pierce, B. L., Huo, D., Olopade, O. I., Ahsan, H., & Chen, L. S. (2018). A meta‐analysis approach with filtering for identifying gene‐level gene–environment interactions. Genetic epidemiology.