R: An intercross with misplaced markers

badorder {qtl} | R Documentation

## An intercross with misplaced markers

### Description

Simulated data for an intercross with some markers out of order.

### Usage

    data(badorder)

### Format

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

### Details

There are 250 F2 individuals typed at a total of 36 markers on four chromosomes. The data were simulated with QTLs at the center of chromosomes 1 and 3.

The order of several markers on chromosome 1 is incorrect. Markers on chromosomes 2 and 3 are switched.

### Author(s)

Karl W Broman, broman@wisc.edu

### See Also

`est.rf`, `ripple`, `est.map`, `sim.cross`

### Examples

    data(badorder)

    # estimate recombination fractions
    badorder <- est.rf(badorder)
    plotRF(badorder)

    # re-estimate map
    newmap <- est.map(badorder)
    plotMap(badorder, newmap)

    # assess marker order on chr 1
    rip3 <- ripple(badorder, chr=1, window=3)
    summary(rip3)

[Package qtl version 1.46-2 Index]