R: Count number of obligate crossovers for each individual

countXO {qtl} | R Documentation

## Count number of obligate crossovers for each individual

### Description

Count the number of obligate crossovers for each individual in a cross, either by chromosome or overall.

### Usage

    countXO(cross, chr, bychr=FALSE)

### Arguments

`cross` | An object of class `cross`. See `read.cross` for details.
`chr` | Optional vector indicating the chromosomes to investigate. This should be a vector of character strings referring to chromosomes by name; numeric values are converted to strings. Refer to chromosomes with a preceding `-` to have all chromosomes but those considered. A logical (TRUE/FALSE) vector may also be used.
`bychr` | If TRUE, return counts for each individual chromosome; if FALSE, return the overall number across the selected chromosomes.

### Details

For each individual we count the minimal number of crossovers that explain the observed genotype data.

### Value

If `bychr=TRUE`, a matrix of counts is returned, with rows corresponding to individuals and columns corresponding to chromosomes.

If `bychr=FALSE`, a vector of counts (the total number of crossovers across all selected chromosomes) is returned.

### Author(s)

Karl W Broman, kbroman@biostat.wisc.edu

### See Also

`ripple`, `locateXO`, `cleanGeno`

### Examples

    data(hyper)
    plot(countXO(hyper))

[Package qtl version 1.41-6 Index]