{qtl}R Documentation

Simulate a genetic map


Simulate the positions of markers on a genetic map.

Usage,20), n.mar=10,,
        include.x=TRUE, sex.sp=FALSE, eq.spacing=FALSE)


len A vector specifying the chromosome lengths (in cM)
n.mar A vector specifying the number of markers per chromosome. If true, markers at the two telomeres will always be included, so if n.mar = 1 or 2, we'll give just the two telomeric markers.
include.x Indicates whether the last chromosome should be considered the X chromosome.
sex.sp Indicates whether to create sex-specific maps, in which case the output will be a vector of 2-row matrices, with rows corresponding to the maps for the two sexes.
eq.spacing If TRUE, markers will be equally spaced.


Aside from the telomeric markers, marker positions are simulated as iid Uniform(0,L). If len or n.mar has just one element, it is expanded to the length of the other argument. If they both have just one element, only one chromosome is simulated.

If eq.spacing is TRUE, markers are equally spaced between 0 and L. If is FALSE, telomeric markers are not included.


A list of vectors, each specifying the locations of the markers. Each component of the list is given class A or X, according to whether it is autosomal or the X chromosome.


Karl W Broman,

See Also



# simulate 4 autosomes, each with 10 markers
map <-,90,80,40), 10, include.x=FALSE)

# equally spaced markers
map2 <-,90,80,40), 10, include.x=FALSE, eq.spacing=TRUE)

[Package qtl version 0.98-57 Index]