isMissing: Determine Whether Genotypes Are Missing

In polysat: Tools for Polyploid Microsatellite Analysis

Determine Whether Genotypes Are Missing

Description

isMissing returns Boolean values indicating whether the genotypes for a given set of samples and loci are missing from the dataset.

Usage

isMissing(object, samples = Samples(object), loci = Loci(object))

Arguments

object	An object of one of the subclasses of gendata, containing the genotypes to be tested.
samples	A character or numeric vector indicating samples to be tested.
loci	A character or numeric vector indicating loci to be tested.

Details

isMissing is a generic function with methods for genambig and genbinary objects.

For each genotype in a genambig object, the function evaluates and returns Genotype(object, sample, locus)[1] == Missing(object). For a genbinary object, TRUE %in% (Genotype(object, sample, locus) == Missing(object)) is returned for the genotype. If only one sample and locus are being evaluated, this is the Boolean value that is returned. If multiple samples and/or loci are being evaluated, the function creates an array of Boolean values and recursively calls itself to fill in the result for each element of the array.

Value

If both samples and loci are of length 1, a single Boolean value is returned, TRUE if the genotype is missing, and FALSE if it isn't. Otherwise, the function returns a named array with samples in the first dimension and loci in the second dimension, filled with Boolean values indicating whether the genotype for each sample*locus combination is missing.

Author(s)

Lindsay V. Clark

See Also

Missing, Missing<-, Genotype, find.missing.gen

Examples

# set up a genambig object for this example
mygen <- new("genambig", samples=c("a", "b"), loci=c("locD", "locE"))
Genotypes(mygen) <- array(list(c(122, 126), c(124, 128, 134),
                               Missing(mygen), c(156, 159)),
                          dim=c(2,2))
viewGenotypes(mygen)

# test if some individual genotypes are missing
isMissing(mygen, "a", "locD")
isMissing(mygen, "a", "locE")

# test an array of genotypes
isMissing(mygen, Samples(mygen), Loci(mygen))

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