Package: BreedingExperiment 0.99.4

BreedingExperiment: Container and Relationship Matrices for Breeding and Quantitative Genomics

Provides the BreedingExperiment class, a container that keeps marker genotypes, phenotypes, pedigree and marker coordinates together in one object, extending RangedSummarizedExperiment so that markers are addressable as genomic ranges. Relationship matrices central to quantitative genetics are computed as methods on the container: the pedigree numerator relationship matrix of Henderson (1976) <doi:10.2307/2529339>, the genomic relationship matrix of VanRaden (2008) <doi:10.3168/jds.2007-0980>, the dominance relationship matrix of Vitezica, Varona and Legarra (2013) <doi:10.1534/genetics.113.155176>, and the single-step matrix combining pedigree and genomic information of Legarra, Aguilar and Misztal (2009) <doi:10.3168/jds.2009-2061> and Christensen and Lund (2010) <doi:10.1186/1297-9686-42-2>, which allows genotyped and ungenotyped individuals to be analysed together as in Aguilar and others (2010) <doi:10.3168/jds.2009-2730>. Marker quality control, imputation, inbreeding coefficients and allele frequency summaries are included.

Authors:Muhammad Farooqi [aut, cre]