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

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

## Documentation for package ‘MPGE’ version 1.0.1

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

MPGE-package | MPGE: an R package to implement a two-step approach to testing overall effect of gene-environment interaction for multiple phenotypes.
environment_data | An example of data of the environmental variable (e.g., smoking status). Here, environment_data is a data frame with single column for the environmental variable. The order of the 500 individuals in the row must be the same as provided in the phenotype and genotype data. Here, the environmental variable has two categories which were coded as 1 and 0 (e.g., smokers and non-smokers). Instead of numeric values, these can also be considered to be factors in the absence of a defined order in the categories.
genotype_data | An example of genotype data for two genetic variants (SNPs). Here, genotype_data is a data.frame with the columns as SNPs (e.g., rs1 and rs2 here). The rows correspond to the 500 individuals in the same order as in the phenotype data.
MPGE | MPGE: an R package to implement a two-step approach to testing overall effect of gene-environment interaction for multiple phenotypes.
mv_G_GE | Test for marginal overall genetic association with multivariate phenotype, and test for overall GxE effect on the multivariate phenotype in presence of marginal effect due to the genetic variant and a marginal effect due to the environmental variable.
mv_G_GxE_pvalues | An example of step 1 (marginal genetic association) and step 2 (GxE interaction) p-values across genetic variants (SNPs). Here, mv_G_GxE_pvalues is a data.frame with three columns. First column lists the set of 1000 genetic variants. Second column provides the vector of p-values obtained from testing the marginal multivariate genetic association for these SNPs. And the third column provides the vector of p-values obtained from testing the overall GxE effect in presence of possible marginal genetic effect and marginal environmental effect.
phenotype_data | An example of phenotype data.
SST | Subset multiple hypothesis testing procedure to combine two steps of testing gene-environment interaction in a two-step procedure.
WHT | Weighted multiple hypothesis testing procedure to combine two steps of testing gene-environment interaction in a two-step procedure.