Package: MPGE 1.0.0

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>.

Authors:Arunabha Majumdar [aut, cre], Tanushree Haldar [aut]

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MPGE.pdf |MPGE.html✨
MPGE/json (API)
NEWS

# Install 'MPGE' in R:
install.packages('MPGE', repos = c('https://arunabhacodes.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/arunabhacodes/mpge/issues

Datasets:
  • 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.
  • 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.

On CRAN:

3.70 score 1 stars 1 scripts 253 downloads 3 exports 60 dependencies

Last updated 4 years agofrom:80840fa3bb. Checks:OK: 1 NOTE: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 22 2024
R-4.5-winNOTENov 22 2024
R-4.5-linuxNOTENov 22 2024
R-4.4-winNOTENov 22 2024
R-4.4-macNOTENov 22 2024
R-4.3-winNOTENov 22 2024
R-4.3-macNOTENov 22 2024

Exports:mv_G_GESSTWHT

Dependencies:abindbackportsbootbroomcarcarDataclicolorspacecowplotcpp11DerivdoBydplyrfansifarverFormulagenericsggplot2gluegtableisobandlabelinglatticelifecyclelme4magrittrMASSMatrixMatrixModelsmgcvmicrobenchmarkminqamodelrmunsellnlmenloptrnnetnumDerivpbkrtestpillarpkgconfigpurrrquantregR6RColorBrewerRcppRcppEigenrlangscalesSparseMstringistringrsurvivaltibbletidyrtidyselectutf8vctrsviridisLitewithr

MPGE package: A two-step approach to testing overall effect of gene-environment interaction for multiple phenotypes

Arunabha Majumdar, Tanushree Haldar

Rendered frommpge.Rmdusingknitr::rmarkdownon Nov 22 2024.

Last update: 2020-10-14
Started: 2020-10-14

Readme and manuals

Help Manual

Help pageTopics
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.environment_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.genotype_data
MPGE: an R package to implement a two-step approach to testing overall effect of gene-environment interaction for multiple phenotypes.MPGE
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_GE
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.mv_G_GxE_pvalues
An example of phenotype data.phenotype_data
Subset multiple hypothesis testing procedure to combine two steps of testing gene-environment interaction in a two-step procedure.SST
Weighted multiple hypothesis testing procedure to combine two steps of testing gene-environment interaction in a two-step procedure.WHT