R: Pull out the genetic map from a cross

pull.map {qtl} | R Documentation

## Pull out the genetic map from a cross

### Description

Pull out the map portion of a cross object.

### Usage

    pull.map(cross, chr, as.table=FALSE)

### Arguments

`cross` | An object of class `cross`. See `read.cross` for details.
`chr` | Optional vector indicating the chromosomes to consider. 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.
`as.table` | If TRUE, return the genetic map as a table with chromosome assignments and marker names. If FALSE, return the map as a `"map"` object.

### Value

The genetic map: a list with each component containing the marker positions (in cM) for a chromosome. Each component has class `A` or `X` according to whether it is an autosome or the X chromosome. The components are either vectors of marker positions or, for a sex-specific map, 2-row matrices containing the female and male marker locations. The map itself is given class `map`.

### Author(s)

Karl W Broman, kbroman@biostat.wisc.edu

### See Also

`replace.map`, `plotMap`, `map2table`

### Examples

    data(fake.f2)
    map <- pull.map(fake.f2)
    plot(map)

[Package qtl version 1.41-6 Index]