MPGE: A Two-Step Approach to Testing Overall Effect of Gene-Environment Interaction for Multiple Phenotypes

Interaction between a genetic variant (e.g., a single nucleotide polymorphism) and an environmental variable (e.g., physical activity) can have a shared effect on multiple phenotypes (e.g., blood lipids). We implement a two-step method to test for an overall interaction effect on multiple phenotypes. In first step, the method tests for an overall marginal genetic association between the genetic variant and the multivariate phenotype. The genetic variants which show an evidence of marginal overall genetic effect in the first step are prioritized while testing for an overall gene-environment interaction effect in the second step. Methodology is available from: A Majumdar, KS Burch, S Sankararaman, B Pasaniuc, WJ Gauderman, JS Witte (2020) <doi:10.1101/2020.07.06.190256>.

Version: 1.0.0
Depends: R (≥ 3.5.0)
Imports: car, purrr, stats, utils
Suggests: knitr, rmarkdown, testthat
Published: 2020-10-23
Author: Arunabha Majumdar [aut, cre], Tanushree Haldar [aut]
Maintainer: Arunabha Majumdar <statgen.arunabha at gmail.com>
BugReports: https://github.com/ArunabhaCodes/MPGE/issues
License: GPL-3
URL: https://github.com/ArunabhaCodes/MPGE
NeedsCompilation: no
Materials: README NEWS
CRAN checks: MPGE results

Downloads:

Reference manual: MPGE.pdf
Vignettes: MPGE package: A two-step approach to testing overall effect of gene-environment interaction for multiple phenotypes
Package source: MPGE_1.0.0.tar.gz
Windows binaries: r-devel: MPGE_1.0.0.zip, r-release: MPGE_1.0.0.zip, r-oldrel: MPGE_1.0.0.zip
macOS binaries: r-release (arm64): MPGE_1.0.0.tgz, r-release (x86_64): MPGE_1.0.0.tgz, r-oldrel: MPGE_1.0.0.tgz

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