R: Calculate LOD penalties

calc.penalties {qtl} | R Documentation

## Calculate LOD penalties

### Description

Derive penalties for the penalized LOD scores (used by `stepwiseqtl`) on the basis of permutation results from a two-dimensional, two-QTL scan (obtained by `scantwo`).

### Usage

    calc.penalties(perms, alpha=0.05, lodcolumn)

### Arguments

`perms` | Permutation results from `scantwo`.
`alpha` | Significance level.
`lodcolumn` | If the scantwo permutation results contain LOD scores for multiple phenotypes, this argument indicates which to use in the summary. This may be a vector. If missing, penalties for all phenotypes are calculated.

### Details

Thresholds derived from `scantwo` permutations (that is, for a two-dimensional, two-QTL genome scan) are used to calculate penalties on main effects and interactions.

The main effect penalty is the 1-`alpha` quantile of the null distribution of the genome-wide maximum LOD score from a single-QTL genome scan (as with `scanone`).

The "heavy" interaction penalty is the 1-`alpha` quantile of the null distribution of the maximum interaction LOD score (that is, the log10 likelihood ratio comparing the best model with two interacting QTL to the best model with two additive QTL) from a two-dimensional, two-QTL genome scan (as with `scantwo`).

The "light" interaction penality is the difference between the `"fv1"` threshold from the `scantwo` permutations (that is, the 1-`alpha` quantile of the LOD score comparing the best model with two interacting QTL to the best single-QTL model) and the main effect penalty.

If the permutations results were obtained with `perm.Xsp=TRUE`, to give X-chr-specific results, six penalties are calculated: main effect for autosomes, main effect for X chr, heavy penalty on A:A interactions, light penalty on A:A interactions, penalty on A:X interactions, and penalty on X:X interactions.

### Value

Vector of three values indicating the penalty on main effects and heavy and light penalties on interactions, or a matrix of such results, with each row corresponding to a different phenotype.

If the input permutations are X-chromosome-specific, the result has six values: main effect for autosomes, main effect for X chr, heavy penalty on A:A interactions, light penalty on A:A interactions, penalty on A:X interactions, and penalty on X:X interactions.

### Author(s)

Karl W Broman, broman@wisc.edu

### References

Manichaikul, A., Moon, J. Y., Sen, Ś, Yandell, B. S. and Broman, K. W. (2009) A model selection approach for the identification of quantitative trait loci in experimental crosses, allowing epistasis. Genetics, 181, 1077–1086.

### See Also

`scantwo`, `stepwiseqtl`

### Examples

    data(fake.f2)

    fake.f2 <- calc.genoprob(fake.f2, step=5)
    out.2dim <- scantwo(fake.f2, method="hk")

    # permutations

    ## Not run: permo.2dim <- scantwo(fake.f2, method="hk", n.perm=1000)
    summary(permo.2dim, alpha=0.05)

    # penalties
    calc.penalties(permo.2dim)

[Package qtl version 1.46-2 Index]