polysat: genIndex – R documentation

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genIndex

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

Examples

data(simgen)
genIndex(simgen, 1)

polysat

Tools for Polyploid Microsatellite Analysis

v1.7-4

GPL-2

Authors

Lindsay V. Clark [aut, cre] (<https://orcid.org/0000-0002-3881-9252>), Alistair J. Hall [ctb] (<https://orcid.org/0000-0001-9293-8909>), Handunnethi Nihal de Silva [ctb], Tyler William Smith [ctb] (<https://orcid.org/0000-0001-7683-2653>)

Initial release

2019-03-03