find.breaks {xoi}

Estimate crossover locations

Description

Estimate the locations of crossovers in a backcross.

Usage

find.breaks(cross, chr = NULL)

Arguments

cross

An object of class cross. (This must be a backcross, RIL, or intercross.) See qtl::read.cross() for details.

chr

Optional set of chromosomes on which to look for crossovers. If NULL, all chromosomes are considered.

Details

This works only a backcross, RIL, or intercross. We use the function qtl::locateXO() in R/qtl. Crossovers are estimated to be at the midpoint of the interval between the nearest flanking typed markers.

Value

If only one chromosome is considered, this is a list with one component for each individual. If multiple chromosomes were considered, this is a list with one element for each chromosome, each of which is a list with one element for each individual, as above.

For backcrosses and RIL, the componenets for the individuals are numeric(0) if there were no crossovers or a vector giving the crossover locations. The length of the chromosome (in cM) is saved as an attribute. (Note that the format is the same as the output of simStahl().)

For an intercross, the components for the individuals are themselves lists with all possible allocations of the crossovers to the two meiotic products; each component of this list is itself a list with two components, corresponding to the two meiotic products.

Author(s)

Karl W Broman, [e-mail]

See Also

convertxoloc(), fitGamma(), simStahl()

Examples

data(bssbsb)

# crossover locations on chromosome 1
xoloc1 <- find.breaks(bssbsb, chr=1)

# crossover locations on all chromosomes
xoloc <- find.breaks(bssbsb)