Pipeline for GWAS Using MLMM

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Documentation for package ‘mlmm.gwas’ version 1.0.6

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

mlmm.gwas-package	mlmm.gwas
eBIC_allmodels	Compute eBIC and BIC criteria
Estimation_allmodels	Compute estimated effects
female	Dataset for examples with the mlmm.gwas package, male+female and male+female+interaction models
floweringDateAD	Dataset for examples with the mlmm.gwas package, additive and additive+dominance models
floweringDateFMI	Dataset for examples with the mlmm.gwas package, male+female and male+female+interaction models
fromeBICtoEstimation	Helper function that create the selec_XXclass argument of the Estimation_allmodels function
frommlmm_toebic	Helper that create the selec_XX argument of eBIC_allmodels()
genotypes.boxplot	Boxplots representation of the distributions of phenotypes according to allelic classes
hybrid	Dataset for examples with the mlmm.gwas package, male+female and male+female+interaction models
K.add	Dataset for examples with the mlmm.gwas package, additive and additive+dominance models
K.dom	Dataset for examples with the mlmm.gwas package, additive and additive+dominance models
K.female	Dataset for examples with the mlmm.gwas package, male+female and male+female+interaction models
K.hybrid	Dataset for examples with the mlmm.gwas package, male+female and male+female+interaction models
K.male	Dataset for examples with the mlmm.gwas package, male+female and male+female+interaction models
male	Dataset for examples with the mlmm.gwas package, male+female and male+female+interaction models
manhattan.plot	Manhattan plot
mlmm.gwas	mlmm.gwas
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
mlmm_allmodels	Multi-Locus Mixed-Model
run_entire_gwas_pipeline	MLMM, model selection and effects estimation
threshold_allmodels	Select significant marker thanks to a p-value threshold
Xa	Dataset for examples with the mlmm.gwas package, additive and additive+dominance models
Xd	Dataset for examples with the mlmm.gwas package, additive and additive+dominance models
Xf	Dataset for examples with the mlmm.gwas package, male+female and male+female+interaction models
Xfm	Dataset for examples with the mlmm.gwas package, male+female and male+female+interaction models
Xm	Dataset for examples with the mlmm.gwas package, male+female and male+female+interaction models