find.breaks | R Documentation |
Estimate the locations of crossovers in a backcross.
find.breaks(cross, chr = NULL)
cross |
An object of class |
chr |
Optional set of chromosomes on which to look for crossovers. If NULL, all chromosomes are considered. |
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.
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.
Karl W Broman, broman@wisc.edu
convertxoloc()
, fitGamma()
,
simStahl()
data(bssbsb)
# crossover locations on chromosome 1
xoloc1 <- find.breaks(bssbsb, chr=1)
# crossover locations on all chromosomes
xoloc <- find.breaks(bssbsb)
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.