The genetics Package

genotype 17that appear in the data, the rest (those in the data and possible combinations based on allele variants)is automatically added at the end of genotypeOrder. This puts "missing" genotype names atthe end of sort order. This feature is especially useful when there are a lot of allele variants andespecially in haplotypes. See examples.ValueThe genotype class extends "factor" and haplotype extends genotype. Both classes have the followingattributes:levelscharacter vector of possible genotype/haplotype values stored coded by paste(allele1, "/", allele2, sep="").allele.names character vector of possible alleles. For a SNP, these might be c("A","T"). For avariable length dinucleotyde repeat this might be c("136","138","140","148").allele.map matrix encoding how the factor levels correspond to alleles. See the source codeto allele.genotype() for how to extract allele values using this matrix.Better yet, just use allele.genotype().genotypeOrdercharacter, genotype/haplotype names in defined order that can used for sortingin various functions. Note that this slot stores both ordered and unordered genotypesi.e. "A/B" and "B/A".Author(s)Gregory R. Warnes 〈warnes@bst.rochester.edu〉 and Friedrich Leisch.See AlsoHWE.test, allele, homozygote, heterozygote, carrier, summary.genotype, allele.count,sort.genotype, genotypeOrder, locus, gene, marker, and %in% for default %in%methodExamples# several examples of genotype data in different formatsexample.data