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.

### Author(s)

Karl W Broman, kbroman@biostat.wisc.edu

### See Also

`nmissing`

### Examples

    data(listeria)

    output <- comparegeno(listeria)

    # image of the proportions
    n.ind <- nind(listeria)
    image(1:n.ind, 1:n.ind, output, col=gray((0:99)/99),
          breaks=seq(0,1,len=101))

    # histogram
    hist(output, breaks=150, prob=TRUE,
         xlab="Proportion of matching genotypes")
    rug(output)

[Package qtl version 1.41-6 Index]