R: General likelihood ratio test for association between marker...

markerlrt {qtl} | R Documentation

## General likelihood ratio test for association between marker pairs

### Description

Calculate a LOD score for a general likelihood ratio test for each pair of markers, to assess their association.

### Usage

    markerlrt(cross)

### Arguments

`cross` | An object of class `cross`. See `read.cross` for details.

### Value

The input `cross` object is returned with a component, `rf`, added. This is a matrix of size (tot.mar x tot.mar). The diagonal contains the number of typed meioses per marker, the upper and lower triangles each contain the LOD scores.

### Author(s)

Karl W Broman, broman@wisc.edu

### See Also

`plotRF`, `est.rf`, `badorder`

### Examples

    data(badorder)
    badorder <- markerlrt(badorder)
    plotRF(badorder)

[Package qtl version 1.46-2 Index]