R: Simulate a genetic map

sim.map {qtl} | R Documentation

## Simulate a genetic map

### Description

Simulate the positions of markers on a genetic map.

### Usage

    sim.map(len=rep(100,20), n.mar=10, anchor.tel=TRUE,
            include.x=TRUE, sex.sp=FALSE, eq.spacing=FALSE)

### Arguments

`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.

### Details

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.

### Value

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.

### Author(s)

Karl W Broman, broman@wisc.edu

### See Also

`sim.cross`, `plotMap`, `replace.map`, `pull.map`

### Examples

    # simulate 4 autosomes, each with 10 markers
    map <- sim.map(c(100,90,80,40), 10, include.x=FALSE)
    plotMap(map)

    # equally spaced markers
    map2 <- sim.map(c(100,90,80,40), 10, include.x=FALSE, eq.spacing=TRUE)
    plot(map2)

[Package qtl version 1.46-2 Index]