R: Maximum peak in genome scan to map a QTL to a phylogenetic...

max.scanPhyloQTL {qtl} | R Documentation

## Maximum peak in genome scan to map a QTL to a phylogenetic tree

### Description

Print the chromosome with the maximum LOD score across partitions, from the results of `scanPhyloQTL`.

### Usage

    ## S3 method for class 'scanPhyloQTL'
    max(object, chr, format=c("postprob", "lod"),
            ...)

### Arguments

`object` | An object output by the function `scanPhyloQTL`.
`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.
`format` | Indicates whether to provide LOD scores or approximate posterior probabilities; see the help file for `summary.scanPhyloQTL`.
`...` | Ignored at this point.

### Details

The output, and the use of the argument `format`, is as in `summary.scanPhyloQTL`.

### Value

An object of class `summary.scanPhyloQTL`, to be printed by `print.summary.scanPhyloQTL`.

### Author(s)

Karl W Broman, broman@wisc.edu

### References

Broman, K. W., Kim, S., An\'e, C. and Payseur, B. A. Mapping quantitative trait loci to a phylogenetic tree. In preparation.

### See Also

`scanPhyloQTL`, `plot.scanPhyloQTL`, `summary.scanPhyloQTL`, `max.scanone`, `inferredpartitions`, `simPhyloQTL`

### Examples

    ## Not run:
    # example map; drop X chromosome
    data(map10)
    map10 <- map10[1:19]

    # simulate data
    x <- simPhyloQTL(4, partition="AB|CD", crosses=c("AB", "AC", "AD"),
                     map=map10, n.ind=150,
                     model=c(1, 50, 0.5, 0))

    # run calc.genoprob on each cross
    x <- lapply(x, calc.genoprob, step=2)

    # scan genome, at each position trying all possible partitions
    out <- scanPhyloQTL(x, method="hk")

    # maximum peak
    max(out, format="lod")

    # approximate posterior probabilities at peak
    max(out, format="postprob")

    # all peaks above a threshold for LOD(best) - LOD(2nd best)
    summary(out, threshold=1, format="lod")

    # all peaks above a threshold for LOD(best), showing approx post'r prob
    summary(out, format="postprob", threshold=3)

    # plot of results
    plot(out)

    ## End(Not run)

[Package qtl version 1.46-2 Index]