PGS-TRI is for the analysis of polygenic scores (PGS) or polygenic risk scores (PRS) in case-parent trio studies for estimation of the risk of an index condition associated with direct effects of inherited PGS, indirect effects of parental PGS, and gene-environment interactions under a unified log-linear modeling framework. This tool can characterize genetic risks of diseases in the presence of population structure, assortative mating, and indirect genetic effects.
Installation
The package can be easily installed from Github
library(devtools)
install_github("ziqiaow/PGS.TRI")If you only want to use specific functions, you can also do this
rm(list = ls())
require(devtools)
source_url("https://github.com/ziqiaow/PGS.TRI/blob/main/R/PGS-TRI.R?raw=TRUE")
source_url("https://github.com/ziqiaow/PGS.TRI/blob/main/R/simulation.R?raw=TRUE")
#If directly downloaded the R files from Github to your local directory
source("./R/PGS-TRI.R")
source("./R/simulation.R")This software will be constantly updated, so please send your questions/suggestions to zwang389@jhu.edu to help improve the package.
Reference
- Ziqiao Wang, Luke Grosvenor, Debashree Ray, Ingo Ruczinski, Terri Beaty, Heather Volk, Christine Ladd-Acosta, Nilanjan Chatterjee (2024). Estimation of Direct and Indirect Polygenic Effects and Gene-Environment Interactions using Polygenic Scores in Case-Parent Trio Studies. medRxiv. https://doi.org/10.1101/2024.10.08.24315066