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mlmm.gwas (version 1.0.6)

Pipeline for GWAS Using MLMM

Description

Pipeline for Genome-Wide Association Study using Multi-Locus Mixed Model from Segura V, Vilhjlmsson BJ et al. (2012) . The pipeline include detection of associated SNPs with MLMM, model selection by lowest eBIC and p-value threshold, estimation of the effects of the SNPs in the selected model and graphical functions.

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Install

install.packages('mlmm.gwas')

Monthly Downloads

207

Version

1.0.6

License

GPL-3

Maintainer

Clement Mabire

Last Published

August 5th, 2019

Functions in mlmm.gwas (1.0.6)

eBIC_allmodels

Compute eBIC and BIC criteria
mlmm.gwas.AD

Dataset for examples with the mlmm.gwas package, additive and additive+dominance models
mlmm.gwas.FMI

Dataset for examples with the mlmm.gwas package, male+female and male+female+interaction models
run_entire_gwas_pipeline

MLMM, model selection and effects estimation
threshold_allmodels

Select significant marker thanks to a p-value threshold
manhattan.plot

Manhattan plot
genotypes.boxplot

Boxplots representation of the distributions of phenotypes according to allelic classes
frommlmm_toebic

Helper that create the selec_XX argument of eBIC_allmodels()
fromeBICtoEstimation

Helper function that create the selec_XXclass argument of the Estimation_allmodels function
mlmm_allmodels

Multi-Locus Mixed-Model
mlmm.gwas

mlmm.gwas
Estimation_allmodels

Compute estimated effects