estimatePloidy: Estimate Ploidies Based on Allele Counts

In polysat: Tools for Polyploid Microsatellite Analysis

Estimate Ploidies Based on Allele Counts

Description

estimatePloidy calculates the maximum and mean number of unique alleles for each sample across a given set of loci. These values are presented in a data editor, along with other pertinent information, so that the user can then edit the ploidy values for the object.

Usage

estimatePloidy(object, extrainfo, samples = Samples(object), 
               loci = Loci(object))

Arguments

object	The object containing genotype data, and to which ploidies will be written.
extrainfo	A named or unnamed vector or data frame containing extra information (such as morphological or flow cytometry data) to display in the data editor, to assist with making decisions about ploidy. If unnamed, the vector (or the rows of the data frame) is assumed to be in the same order as samples. An array can also be given as an argument here, and will be coerced to a data frame.
samples	A numeric or character vector indicating a subset of samples to evaluate.
loci	A numeric or character vector indicating a subset of loci to use in the calculation of mean and maximum allele number.

Details

estimatePloidy is a generic function with methods written for the genambig and genbinary classes.

If the Ploidies slot of object is not already a "ploidysample" object, the function will first convert the Ploidies slot to this format, deleting any data that is currently there. (Ploidies must be indexed by sample and not by locus.) If ploidies were already in the "ploidysample" format, any ploidy data already in the object is retained and put into the table (see below).

Population identities are displayed in the table only if more than one population identity is found in the dataset. Likewise, the current ploidies of the dataset are only displayed if there is more than one ploidy level already found in Ploidies(object).

Missing genotypes are ignored; maximum and mean allele counts are only calculted across genotypes that are not missing. If all genotypes for a given sample are missing, NA is displayed in the corresponding cells in the data editor.

The default values for new.ploidy are the maximum number of alleles per locus for each sample.

Value

object is returned, with Ploidies(object) now equal to the values set in the new.ploidy column of the data editor.

Author(s)

Lindsay V. Clark

See Also

genambig, genbinary, Ploidies

Examples

if(interactive()){ #this line included for automated checking on CRAN

# create a dataset for this example
mygen <- new("genambig", samples=c("a", "b", "c"),
             loci=c("loc1", "loc2"))
Genotypes(mygen, loci="loc1") <- list(c(122, 126, 128), c(124, 130),
                                      c(120, 122, 124))
Genotypes(mygen, loci="loc2") <- list(c(140, 148), c(144, 150), Missing(mygen))

# estimate the ploidies
mygen <- estimatePloidy(mygen)

# view the ploidies
Ploidies(mygen)

}

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