alleleDiversity: Retrieve and Count Unique Alleles

In polysat: Tools for Polyploid Microsatellite Analysis

Retrieve and Count Unique Alleles

Description

alleleDiversity returns the number of unique alleles and/or a list of vectors of all unique alleles, indexed by locus and population.

Usage

alleleDiversity(genobject, samples = Samples(genobject),
                loci = Loci(genobject), alleles = TRUE, counts = TRUE)

Arguments

genobject	An object of the class "genambig".
samples	Optional. A character or numeric vector indicating samples to include in the analysis.
loci	Optional. A character or numeric vector indicating loci to include in the analysis.
alleles	Boolean, indicating whether or not to return the alleles themselves.
counts	Boolean, indicating whether or not to return the number of unique alleles.

Value

Under default settings, a list is returned:

alleles	A two dimensional list. The first dimension is indexed by population, with the additional element “overall” representing the entire dataset. The second dimension is indexed by locus. Each element of the list is a vector, containing all unique alleles found for that population and locus. Missing(genobject) is not counted as an allele.
counts	A matrix, indexed in the same way as alleles. Each element of the matrix is an integer indicating how many alleles were found at that population and locus.

If the argument alleles or counts is set to FALSE, then only one of the above list elements is returned.

Author(s)

Lindsay V. Clark

See Also

genotypeDiversity

Examples

# generate a dataset for this example
mygen <- new("genambig", samples=c("a","b","c","d"), loci=c("E","F"))
PopInfo(mygen) <- c(1,1,2,2)
Genotypes(mygen, loci="E") <- list(c(122,132),c(122,124,140),
                                   c(124,130,132),c(132,136))
Genotypes(mygen, loci="F") <- list(c(97,99,111),c(113,115),
                                   c(99,113),c(111,115))

# look at unique alleles
myal <- alleleDiversity(mygen)
myal$counts
myal$alleles
myal$alleles[["Pop1","E"]]
myal$alleles[["overall","F"]]

polysat documentation built on Aug. 23, 2022, 5:07 p.m.