ProgenyArray-class: An S4 class that stores genotyping data from a progeny array...
In vsbuffalo/ProgenyArray: Some statistical genetics for progeny array experiments

An S4 class that stores genotyping data from a progeny array design.

ranges: a GenomicRanges object of loci
ref: reference alleles
alt: alternate alleles
progeny_geno: a matrix of bialleic progeny genotypes
parents_geno: a matrix of bialleic parents genotypes
supplied_mothers: integer vector indicating the mother of each progeny, supplied by user
mothers: integer vector indicating the inferred mother of each progeny
fathers: integer vector indicating the inferred father of each progeny
parents: dataframe with inferred parents and model information
complete_loci: which loci are not all missing or fixed in the parents
parent_lods: matrices from C++ parentage routine (for debugging)
lodcutoff: the LOD cutoff used in parentage inference
phased_parents: a list of parents' phased tiles for all chromosomes
phased_parents_metadata: a list of phasing parameters
tiles: a list of tiles for all chromosomes
sibfams: a list of sibling families for all phased parents