gpiUtil: Utility functions for gpi()

In GeneticsPed: Pedigree and genetic relationship functions

Description

gpLong2Wide changes data.frame with genotype probabilities in long form (one genotype per row) to wide form (one individual per row) for use in gpi.

hwp calculates genotype probabilities according to Hardy-Weinberg law for use in gpi.

Usage

  gpLong2Wide(x, id, genotype, prob, trim=TRUE)
  hwp(x, trim=TRUE)

Arguments

x	data.frame for gpLong2Wide, genotype for hwp
id	character, column name in x holding individual identifications
genotype	character, column name in x holding genotypes
prob	character, column name in x holding genotype probabilities
trim	logical, remove last column (for gpLong2Wide) or value (for hwp) of a result

Details

Hardy-Weinberg probabilities for a gene with two alleles A and B, with probabilities Pr(A) and Pr(B) are:

• Pr(AA) = Pr(A)^2

• Pr(AB) = 2 * Pr(A) * Pr(A)

• Pr(BB) = Pr(B)^2

Value

gpLong2Wide returns a matrix with number of rows equal to number of individuals and number of columns equal to number of possible genotypes.

hwp returns a vector with Hardy-Weinberg genotype probabilities.

Author(s)

Gregor Gorjanc

See Also

gpi, genotype, expectedGenotypes

Examples

  if(require(genetics)) {
    gen <- genotype(c("A/A", "A/B"))
    hwp(x=gen)
    hwp(x=gen, trim=FALSE)
  }

GeneticsPed documentation built on Nov. 8, 2020, 5:54 p.m.