R: Determine Whether Genotypes Are Missing

isMissing {polysat} | R Documentation

## 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))

[Package polysat version 1.7-6 Index]