In fboehm/gemma2: GEMMA Multivariate Linear Mixed Model

Statuses

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "README-"
)

Overview

gemma2 is an implementation in R of the GEMMA v 0.97 EM algorithm that is part of the GEMMA algorithm for REML estimation of multivariate linear mixed effects models of the form:

$$vec(Y) = X vec(B) + vec(G) + vec(E)$$

where $E$ is a n by 2 matrix of random effects that follows the matrix-variate normal distribution

$$G \sim MN(0, K, V_g)$$

where $K$ is a relatedness matrix and $V_g$ is a 2 by 2 covariance matrix for the two traits of interest.

Additionally, the random errors matrix $E$ follows the distribution:

$$E \sim MN(0, I_n, V_e)$$

and $G$ and $E$ are independent.

Installation

To install gemma2, use the devtools R package from CRAN. If you haven't installed devtools, please run this line of code:

install.packages("devtools")

Then, run this line of code to install gemma2:

devtools::install_github("fboehm/gemma2")

References

X. Zhou & M. Stephens. Efficient multivariate linear mixed model algorithms for genome-wide association studies. Nature Methods volume 11, pages 407–409 (2014). https://www.nature.com/articles/nmeth.2848

https://github.com/genetics-statistics/GEMMA

fboehm/gemma2 documentation built on Oct. 28, 2020, 5:35 p.m.