qtl: switchAlleles – R documentation

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qtl

switchAlleles

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, broman@wisc.edu

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)

qtl

Tools for Analyzing QTL Experiments

v1.48-1

GPL-3

Authors

Karl W Broman <broman@wisc.edu> and Hao Wu, with ideas from Gary Churchill and Saunak Sen and contributions from Danny Arends, Robert Corty, Timothee Flutre, Ritsert Jansen, Pjotr Prins, Lars Ronnegard, Rohan Shah, Laura Shannon, Quoc Tran, Aaron Wolen, Brian Yandell, and R Core Team

Initial release

2021-03-24