heritability (version 1.4)

heritability-package: Marker-Based Estimation of Heritability Using Individual Plant or Plot Data.

Description

The package implements marker-based estimation of heritability when observations on genetically identical replicates are available. These can be either observations on individual plants (e.g. in a growth chamber) or plot-level data in a field trial. The function marker_h2 estimates heritability using a mixed model for the individual plant or plot data, as proposed in Kruijer et al. For comparison, also mixed-model based estimation using genotypic means (marker_h2_means) and estimation of repeatability with ANOVA (repeatability) are implemented. For illustration the package contains several datasets for the model species Arabidopsis thaliana.

Author

Willem Kruijer Maintainer: Willem Kruijer <[e-mail]>

References

Kruijer, W. et al. (2015) Marker-based estimation of heritability in immortal populations. Genetics, Vol. 199(2), p. 1-20.

Examples

# A) marker-based estimation of heritability, given individual plant-data
# and a marker-based relatedness matrix:
data(LDV)
data(K_atwell)
# This may take up to 30 sec.
#out1 <- marker_h2(data.vector=LDV$LDV,geno.vector=LDV$genotype,
#                  covariates=LDV[,4:8],K=K_atwell)
#
# B) marker-based estimation of heritability, given genotypic means
# and a marker-based relatedness matrix:
data(means_LDV)
data(R_matrix_LDV)
data(K_atwell)
out2 <- marker_h2_means(data.vector=means_LDV$LDV,geno.vector=means_LDV$genotype,
                        K=K_atwell,Dm=R_matrix_LDV)
#
# C) estimation of repeatability using ANOVA:
data(LDV)
out3 <- repeatability(data.vector=LDV$LDV,geno.vector= LDV$genotype,
                      covariates.frame=as.data.frame(LDV[,3]))