mlmm.gwas {mlmm.gwas}

mlmm.gwas

Description

Pipeline for GWAS using Multi Locus Mixed Model (MLMM).

Details

This is a fork of the MLMM / MultLocMixMod package by Vincent Segura and Bjarni J. Vilhjalmsson.

The main differencies from the original package are:

• abandon of the multi-Bonferroni model selection

• abandon of the backward model search

• eBIC modified to be adapted to the rate between number of individuals and number of markers.

• function added to select significant SNP according to a p-value threshold at each mlmm step

• new models supported: additive+dominance, male+female and male+female+interaction. These models are described in Bonnafous et al. (2017).

• graphical functions: a new Manhattan plot and a boxplot representation of markers effects.

A vignette presents the usage of this package with the additive model.

References

Bonnafous, F., Fievet, G., Blanchet, N. et al. Theor Appl Genet (2018) 131: 319.

Segura V, Vilhjálmsson BJ, Platt A, Korte A, Seren Uuml, Long Q, et al. An efficient multi-locus mixed-model approach for genome-wide association studies in structured populations. Nat Genet. 2012;44:825–830.