qtl (version 1.42-8)

countXO: Count number of obligate crossovers for each individual

Description

Count the number of obligate crossovers for each individual in a cross, either by chromosome or overall.

Usage

countXO(cross, chr, bychr=FALSE)

Arguments

cross

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

chr

Optional vector indicating the chromosomes to investigate. This should be a vector of character strings referring to chromosomes by name; numeric values are converted to strings. Refer to chromosomes with a preceding - to have all chromosomes but those considered. A logical (TRUE/FALSE) vector may also be used.

bychr

If TRUE, return counts for each individual chromosome; if FALSE, return the overall number across the selected chromosomes.

Value

If bychr=TRUE, a matrix of counts is returned, with rows corresponding to individuals and columns corresponding to chromosomes.

If bychr=FALSE, a vector of counts (the total number of crossovers across all selected chromosomes) is returned.

Details

For each individual we count the minimal number of crossovers that explain the observed genotype data.

See Also

ripple, locateXO, cleanGeno

Examples

# NOT RUN {
data(hyper)
plot(countXO(hyper))
# }