R: Switch alleles at selected markers

switchAlleles {qtl} | R Documentation

## Switch alleles at selected markers

### Description

Switch alleles at selected markers in a cross object.

### Usage

    switchAlleles(cross, markers, switch=c("AB", "CD", "ABCD", "parents"))

### Arguments

`cross` | An object of class `cross`. See `read.cross` for details.
`markers` | Names of markers whose alleles are to be switched.
`switch` | For a 4-way cross, indicates how to switch the alleles (A for B, C for D, both A for B and C for D), or both A for C and B for D (`parents`).

### Details

For a backcross, we exchange homozygotes (AA) and heterozygotes (AB).

For doubled haploids and recombinant inbred lines, we exchange the two homozygotes.

For an intercross, we exchange the two homozygotes, and exchange C (i.e., not AA) and D (i.e., not BB). (The heterozygotes in an intercross are left unchanged.)

For a 4-way cross, we consider the argument `switch`, and the exchanges among the genotypes are more complicated.

### Value

The input cross object, with alleles at selected markers switched.

### Author(s)

Karl W Broman, kbroman@biostat.wisc.edu

### See Also

`checkAlleles`, `est.rf`, `geno.crosstab`

### Examples

    data(fake.f2)
    geno.crosstab(fake.f2, "D5M391", "D5M81")

    # switch homozygotes at marker D5M391
    fake.f2 <- switchAlleles(fake.f2, "D5M391")

    geno.crosstab(fake.f2, "D5M391", "D5M81")

    ## Not run: fake.f2 <- est.rf(fake.f2)
    checkAlleles(fake.f2)

    ## End(Not run)

[Package qtl version 1.41-6 Index]