sommer (version 3.2)

build.HMM: Build a hybrid marker matrix using parental genotypes

Description

Uses the 2 marker matrices from both sets of parents and creates all possible combinations unless the user specifies which hybrid genotypes to build (custom.hyb argument). It returns the marker matrix for hybrids coded as additive (-1,0,1; homo,het,homo) and dominance (0,1,0; homo,het,homo).

Usage

build.HMM(M1,M2, custom.hyb=NULL, return.combos.only=FALSE)

Arguments

M1

Matrix (\(n \times m\)) of unphased genotypes for \(n\) lines and \(m\) biallelic markers, coded as {-1,0,1}. Fractional (imputed) and missing values (NA) are not allowed.

M2

Matrix (\(n \times m\)) of unphased genotypes for \(n\) lines and \(m\) biallelic markers, coded as {-1,0,1}. Fractional (imputed) and missing values (NA) are not allowed.

custom.hyb

A data frame with columns 'Var1' 'Var2', 'hybrid' which specifies which hybrids should be built using the M1 and M2 matrices provided.

return.combos.only

A TRUE/FALSE statement inicating if the function should skip building the geotype matrix for hybrids and only return the data frame with all possible combinations to be build. In case the user wants to subset the hybrids before building the marker matrix.

Value

It returns the marker matrix for hybrids coded as additive (-1,0,1; homo,het,homo) and dominance (0,1,0; homo,het,homo).

$HMM.add

marker matrix for hybrids coded as additive (-1,0,1; homo,het,homo)

$HMM.dom

marker matrix for hybrids coded as dominance (0,1,0; homo,het,homo)

$data.used

the data frame used to build the hybrid genotypes

Details

It returns the marker matrix for hybrids coded as additive (-1,0,1; homo,het,homo) and dominance (0,1,0; homo,het,homo).

References

Covarrubias-Pazaran G (2016) Genome assisted prediction of quantitative traits using the R package sommer. PLoS ONE 11(6): doi:10.1371/journal.pone.0156744

Nishio M and Satoh M. 2014. Including Dominance Effects in the Genomic BLUP Method for Genomic Evaluation. Plos One 9(1), doi:10.1371/journal.pone.0085792

Su G, Christensen OF, Ostersen T, Henryon M, Lund MS. 2012. Estimating Additive and Non-Additive Genetic Variances and Predicting Genetic Merits Using Genome-Wide Dense Single Nucleotide Polymorphism Markers. PLoS ONE 7(9): e45293. doi:10.1371/journal.pone.0045293

See Also

mmer and mmer2-- the core functions of the package

Examples

# NOT RUN {
####=========================================####
#### use Technow data as example
####=========================================####
data(Technow_data)
M.flint <- Technow_data$MF # Marker matrix Flint
M.dent <- Technow_data$MD # Marker matrix Dent

## first get all possible hybrids
res1 <- build.HMM(M.dent, M.flint, 
                  return.combos.only = TRUE)
head(res1$data.used)

## build the marker matrix for the first 50 hybrids
res2 <- build.HMM(M.dent, M.flint,
                 custom.hyb = res1$data.used[1:50,]
                 )
res2$HMM.add[1:5,1:5]
res2$HMM.dom[1:5,1:5]

## now you can use the A.mat(), D.mat() and E.mat() functions
# M <- res2$HMM.add
# A <- A.mat(M)
# D <- D.mat(M)

# }