R: LOD thresholds from scantwo permutation results

summary.scantwoperm {qtl} | R Documentation

## LOD thresholds from scantwo permutation results

### Description

Print the estimated genome-wide LOD thresholds on the basis of permutation results from `scantwo` (with `n.perm` > 0).

### Usage

    ## S3 method for class 'scantwoperm'
    summary(object, alpha=c(0.05, 0.10), ...)

### Arguments

`object` | Output from the function `scantwo` with `n.perm` > 0.
`alpha` | Genome-wide significance levels.
`...` | Ignored at this point.

### Details

We take the 1-alpha quantiles of the individual LOD scores.

In the case of X-chr-specific permutations, we use the combined length of the autosomes, L_A, and the length of the X chromosome, L_X, and calculate the area of the A:A, A:X, and X:X regions as L_A^2/2, L_A L_X, and L_X^2/2, and then use the nominal significance levels of 1 - (1-alpha)^p, where p is the proportional area for that region.

### Value

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

### Author(s)

Karl W Broman, broman@wisc.edu

### References

Churchill, G. A. and Doerge, R. W. (1994) Empirical threshold values for quantitative trait mapping. Genetics 138, 963–971.

### See Also

`scantwo`, `summary.scantwo`, `plot.scantwoperm`

### Examples

    data(fake.f2)

    fake.f2 <- calc.genoprob(fake.f2, step=0)

    ## Not run: operm <- scantwo(fake.f2, n.perm=100, method="hk")
    summary(operm)

[Package qtl version 1.46-2 Index]