R: Pull out recombination fractions or LOD scores from a cross...

pull.rf {qtl} | R Documentation

## Pull out recombination fractions or LOD scores from a cross object

### Description

Pull out either the pairwise recombination fractions or the LOD scores, as calculated by `est.rf`, from a cross object.

### Usage

    pull.rf(cross, what=c("rf", "lod"), chr)

### Arguments

`cross` | An object of class `cross`. See `read.cross` for details.
`what` | Indicates whether to pull out a matrix of estimated recombination fractions or a matrix of LOD scores.
`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.

### Value

An object of class `"rfmatrix"`, which is a matrix of either estimated recombination fractions between all marker pairs or of LOD scores (for the test of rf=1/2) for all marker pairs.

The genetic map is included as an attribute.

### Author(s)

Karl W Broman, kbroman@biostat.wisc.edu

### See Also

`est.rf`, `plot.rfmatrix`, `plotRF`

### Examples

    data(fake.f2)

    fake.f2 <- est.rf(fake.f2)
    rf <- pull.rf(fake.f2)
    lod <- pull.rf(fake.f2, "lod")
    plot(rf[1,], lod[1,], xlab="rec frac", ylab="LOD score")
    marker <- markernames(fake.f2, chr=5)[6]
    par(mfrow=c(2,1))
    plot(rf, marker, bandcol="gray70")
    plot(lod, marker, bandcol="gray70")

[Package qtl version 1.41-6 Index]