genetics: Population Genetics

Description Usage Arguments Details Value Author(s) See Also Examples

expectedGenotypes constructs expected genotypes according to known allele variants, which can be quite tedious with large number of allele variants. It can handle different level of ploidy.

expectedGenotypes(x, alleles=allele.names(x), ploidy=2, sort=TRUE,
                  haplotype=FALSE)
expectedHaplotypes(x, alleles=allele.names(x), ploidy=2, sort=TRUE,
                   haplotype=TRUE)

`x`	genotype or haplotype
`alleles`	character, vector of allele names
`ploidy`	numeric, number of chromosome sets i.e. 2 for human autosomal genes
`sort`	logical, sort genotypes according to order of alleles in `alleles` argument
`haplotype`	logical, construct haplotypes i.e. ordered genotype

At least one of x or alleles must be given.

expectedHaplotypes() just calls expectedGenotypes() with argument haplotype=TRUE.

A character vector with genotype names as "alele1/alele2" for diploid example. Length of output is (n*(n+1))/2 for genotype (unordered genotype) and n*n for haplotype (ordered genotype) for n allele variants.

Gregor Gorjanc

allele.names, genotype

  ## On genotype
  prp <- c("ARQ/ARQ", "ARQ/ARQ", "ARR/ARQ", "AHQ/ARQ", "ARQ/ARQ")
  alleles <- c("ARR", "AHQ", "ARH", "ARQ", "VRR", "VRQ")
  expectedGenotypes(as.genotype(prp))
  expectedGenotypes(as.genotype(prp, alleles=alleles))
  expectedGenotypes(as.genotype(prp, alleles=alleles, reorder="yes"))

  ## Only allele names
  expectedGenotypes(alleles=alleles)
  expectedGenotypes(alleles=alleles, ploidy=4)

  ## Haplotype
  expectedHaplotypes(alleles=alleles)
  expectedHaplotypes(alleles=alleles, ploidy=4)[1:20]