R/lmmlite is an R package for fitting linear mixed models for genome-wide association studies (GWAS) and quantitative trait locus (QTL) mapping.

I’m following the code in pylmm, and really I’m developing this package mostly so that I can better understand pylmm.

The code is on GitHub.

Vignettes

• User guide [source]

• Comparison of results to those of pylmm and regress. [source]

• Performance comparison with pylmm. [source]

Installation

You can install R/lmmlite from GitHub.

You first need to install the remotes pakcage.

install.packages("remotes")

Then use install_github() to install R/lmmlite.

library(remotes)
install_github("kbroman/lmmlite")

The Rcpp and RcppEigen packages will also be installed.

License

R/lmmlite is released under the GNU Affero GPL.

The code was developed following study of Nick Furlotte’s pylmm code.