R: Find All Unique Genotypes for a Locus

genIndex {polysat} | R Documentation

## Find All Unique Genotypes for a Locus

### Description

This function will return all unique genotypes for a given locus (ignoring allele order, but taking copy number into account) and return those genotypes as well as an index indicating which genotype(s) each individual has. This is a generic function with methods for `"genambig"` objects and for arrays. The array method is primarily intended for internal use with `meandistance.matrix2`, processing the output of `genotypeProbs`.

### Usage

    genIndex(object, locus)

### Arguments

`object` | Typically, a `"genambig"` object. A two-dimentional list (array) can also be used here, where samples are in the first dimension and loci in the second dimension and each element of the list is output from `genotypeProbs`.
`locus` | A character string or integer indicating which locus to process.

### Value

A list with two elements:

`uniquegen` | A list, where each element in the list is a vector indicating a unique genotype that was found.
`genindex` | For `"genambig"` objects, an integer vector, with one value per sample. This is the index of that sample's genotype in `uniquegen`. For arrays, a list with one element per sample. Each element is a vector of indices of that sample's possible genotypes in `uniquegen`, in the same order as in the `genotypeProbs` output.

### Author(s)

Lindsay V. Clark

### See Also

`meandistance.matrix` uses the `"genambig"` method internally.

`.unal1loc`, `assignClones`

### Examples

    data(simgen)
    genIndex(simgen, 1)

[Package polysat version 1.7-6 Index]