R: Find Missing Genotypes

find.missing.gen {polysat} | R Documentation

## Find Missing Genotypes

### Description

This function returns a data frame listing the locus and sample names of all genotypes with missing data.

### Usage

    find.missing.gen(object, samples = Samples(object),
                     loci = Loci(object))

### Arguments

`object` | A `genambig` or `genbinary` object containing the genotypes of interest.
`samples` | A character vector of all samples to be searched. Must be a subset of `Samples(object)`.
`loci` | A character vector of all loci to be searched. Must be a subset of `Loci(object)`.

### Value

A data frame with no row names. The first column is named “Locus” and the second column is named “Sample”. Each row represents one missing genotype, and gives the locus and sample of that genotype.

### Author(s)

Lindsay V. Clark

### See Also

`isMissing`

### Examples

    # set up the genotype data
    samples <- paste("ind", 1:4, sep="")
    samples
    loci <- paste("loc", 1:3, sep="")
    loci
    testgen <- new("genambig", samples = samples, loci = loci)
    Genotypes(testgen, loci="loc1") <- list(c(-9), c(102,104),
                                            c(100,106,108,110,114),
                                            c(102,104,106,110,112))
    Genotypes(testgen, loci="loc2") <- list(c(77,79,83), c(79,85), c(-9),
                                            c(83,85,87,91))
    Genotypes(testgen, loci="loc3") <- list(c(122,128), c(124,126,128,132),
                                            c(120,126), c(124,128,130))

    # look up which samples*loci have missing genotypes
    find.missing.gen(testgen)

[Package polysat version 1.7-6 Index]