R: Summarize the results a genome scan to map a QTL to a...

summary.scanPhyloQTL {qtl} | R Documentation

## Summarize the results a genome scan to map a QTL to a phylogenetic tree

### Description

Print the maximum LOD scores for each partition on each chromosome, from the results of `scanPhyloQTL`.

### Usage

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

### Arguments

`object` | An object output by the function `scanPhyloQTL`.
`format` | Indicates whether to provide LOD scores or approximate posterior probabilities; see Details below.
`threshold` | A threshold determining which chromosomes should be output; see Details below.
`...` | Ignored at this point.

### Details

This function is used to report chromosomes deemed interesting from a one-QTL genome scan to map QTL to a phylogenetic tree (by `scanPhyloQTL`).

For `format="lod"`, the output contains the maximum LOD score for each partition on each chromosome (which do not necessarily occur at the same position). The position corresponds to the peak location for the partition with the largest LOD score on that chromosome. The last column is the overall maximum LOD (across partitions) on that chromosome. The second-to-last column is the inferred partition (i.e., that with the largest LOD score. The third-to-last column is the difference between the LOD score for the best partition and that for the second-best.

For `format="postprob"`, the final column contains the maximum LOD score across partitions. But instead of providing the LOD scores for each partition, these are converted to approximate posterior probabilities under the assumption of a single diallelic QTL on that chromosome: on each chromosome, we take 10^LOD for the partitions and rescale them to sum to 1.

The `threshold` argument is applied to the last column (the maximum LOD score across partitions).

### 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`, `max.scanPhyloQTL`, `summary.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]