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 1.46.0 Index]