hwp {GeneticsPed}R Documentation

Utility functions for gpi()

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)
      }
    

    [Package GeneticsPed version 1.4.0 Index]