LBRAT: R package for retrospective genetic association analysis of longitudinal binary outcomes in GWAS

LBRAT is an R program that performs retrospective association testing for longitudinal binary traits in population samples.

Installation Instructions:

Required software and packages

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

  2. Package nleqslv, lme4, geepack, mvtnorm, data.table, plyr

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

Install the required R package before you install LBRAT package. Install the LBRAT using the following steps.

Install LBRAT on LUNIX or Mac OSX

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

R CMD INSTALL LBRAT

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

Usage instructions:

Details for functions and examples in the LBRAT are available in the manual (https://github.com/ZWang-Lab/LBRAT/blob/master/LBRAT-manual.pdf) and in the vignettes(https://zwang-lab.github.io/LBRAT/articles/L-BRAT.html).

Citations:

Wu W., Wang Z., Xu K., Zhang X., Amei A., Gelernter J., Zhao H., Justice A.C., Wang Z., (2019) Retrospective association analysis of longitudinal binary traits identifies important loci and pathways in cocaine use. Genetics, in press.