R: Compare individuals' genotype data

comparegeno {qtl} | R Documentation

## Compare individuals' genotype data

### Description

Count proportion of matching genotypes between all pairs of individuals, to look for unusually closely related individuals.

### Usage

    comparegeno(cross, what=c("proportion","number","both"))

### Arguments

`cross` | An object of class `cross`. See `read.cross` for details.
`what` | Indicates whether to return the proportion or number of matching genotypes (or both).

### Value

A matrix whose (i,j)th element is the proportion or number of matching genotypes for individuals i and j.

If called with `what="both"`, the lower triangle contains the proportion and the upper triangle contains the number.

If called with `what="proportion"`, the diagonal contains missing values. Otherwise, the diagonal contains the number of typed markers for each individual.

The output is given class `"comparegeno"` so that appropriate `summary` and `plot` functions may be used.

### Author(s)

Karl W Broman, broman@wisc.edu

### See Also

`nmissing`, `summary.comparegeno`, `plot.comparegeno`

### Examples

    data(listeria)

    cg <- comparegeno(listeria)

    summary(cg, 0.7)
    plot(cg)

[Package qtl version 1.46-2 Index]