frommlmm_toebic {mlmm.gwas}

Helper that create the selec_XX argument of eBIC_allmodels()

Description

Helper function that create the selec_XX argument of eBIC_allmodels from the output of mlmm_allmodels.

Usage

frommlmm_toebic(XX, res.mlmm)

Arguments

XX

A list of length one, two or three matrices depending on the model. Matrices are n by m matrix, where n=number of individuals, m=number of SNPs, with rownames(X)=individual names, and colnames(X)=SNP names. Use the same XX you used with the mlmm_allmodels function

res.mlmm

Output from the mlmm_allmodels function

See Also

mlmm_allmodels eBIC_allmodels

Examples

### Additive model ###
## Not run: 
data("mlmm.gwas.AD")

XX = list(Xa)
KK = list(K.add)

# GWAS
res_mlmm <- mlmm_allmodels(floweringDateAD, XX, KK)
manhattan.plot(res_mlmm)

# Model selection
sel_XX <- frommlmm_toebic(XX, res_mlmm)
res.eBIC <- eBIC_allmodels(floweringDateAD, sel_XX, KK, ncol(Xa))

# Effects estimations with the selected model
sel_XXclass <- fromeBICtoEstimation(sel_XX, res.eBIC)
eff.estimations <- Estimation_allmodels(floweringDateAD, sel_XXclass, KK)
genotypes.boxplot(Xa, floweringDateAD, effects = eff.estimations)

## End(Not run)

### Additive + dominance model
## Not run: 
data("mlmm.gwas.AD")

XX = list(Xa, Xd)
KK = list(K.add, K.dom)

# GWAS
res_mlmm <- mlmm_allmodels(floweringDateAD, XX, KK)
manhattan.plot(res_mlmm)

# Model selection
sel_XX <- frommlmm_toebic(XX, res_mlmm)
res.eBIC <- eBIC_allmodels(floweringDateAD, sel_XX, KK, ncol(Xa))
#the selected model is the null model

## End(Not run)


### Female+Male model
## Not run: 
data("mlmm.gwas.FMI")

XX = list(Xf, Xm)
KK = list(K.female, K.male)

# GWAS
res_mlmm <- mlmm_allmodels(floweringDateFMI, XX, KK, female = female, male = male)
manhattan.plot(res_mlmm)

# Model selection
sel_XX <- frommlmm_toebic(XX, res_mlmm)
res.eBIC <- eBIC_allmodels(floweringDateFMI, sel_XX, KK, ncol(Xf), female = female, male = male)
#the selected model is the null model

## End(Not run)



### Female+Male+Interaction model
## Not run: 
data("mlmm.gwas.FMI")

XX = list(Xf, Xm, Xfm)
KK = list(K.female, K.male, K.hybrid)

# GWAS
res_mlmm <- mlmm_allmodels(floweringDateFMI, XX, KK, female = female, male = male)
manhattan.plot(res_mlmm)

# Model selection
sel_XX <- frommlmm_toebic(XX, res_mlmm)
res.eBIC <- eBIC_allmodels(floweringDateFMI, sel_XX, KK, ncol(Xf), female = female, male = male)
#the selected model is the null model

## End(Not run)