genetics: expectedGenotypes – R documentation

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expectedGenotypes

Construct expected genotypes/haplotypes according to known allele variants

Description

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.

Usage

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

Arguments

`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.

Details

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

Value

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.

Author(s)

Gregor Gorjanc

Examples

## 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]

genetics

Population Genetics

v1.3.8.1.3

GPL

Authors

Gregory Warnes, with contributions from Gregor Gorjanc, Friedrich Leisch, and Michael Man.

Initial release

2012-11-26