qtl (version 1.66)

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"))

Value

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

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).

Author

Karl W Broman,

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.

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")

if (FALSE) fake.f2 <- est.rf(fake.f2)
checkAlleles(fake.f2)