LSRAT: Longitudinal variant-Set Retrospective Association Test

LSRAT is an R package that performs retrospective variant-set testing for longitudinal traits in GWA studies.

Installation Instructions:

Required software and packages

1. R (http://www.r-project.org/)

2. R Packages: snpStats, LBRAT, GENESIS, plyr, geepack, lme4, nlme, mvtnorm

3. PLINK 1.0 or 1.9 (https://www.cog-genomics.org/plink2)

Install the required R packages before you install LSRAT package. Instructions for installing "LBRAT" can be found here (https://github.com/ZWang-Lab/LBRAT). Install the LSRAT using the following steps.

Install LSRAT on LUNIX or Mac OSX

git clone https://github.com/ZWang-Lab/LSRAT.git

R CMD INSTALL LSRAT

Alternatively, one can install it in R using the following code.

Install LSRAT in R

library(devtools)
devtools::install_github(repo = 'ZWang-Lab/LSRAT')

Usage instructions:

Details for functions and examples in the LSRAT are available in the manual (LSRAT-manual.pdf)