| sim.map {qtl} | R Documentation |
Simulate the positions of markers on a genetic map.
sim.map(len=rep(100,20), n.mar=10, anchor.tel=TRUE,
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. |
anchor.tel |
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 anchor.tel 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, kbroman@biostat.wisc.edu
sim.cross, plot.map,
replace.map, pull.map
# simulate 4 autosomes, each with 10 markers map <- sim.map(c(100,90,80,40), 10, include.x=FALSE) plot.map(map) # equally spaced markers map2 <- sim.map(c(100,90,80,40), 10, include.x=FALSE, eq.spacing=TRUE) plot(map2)