LOD thresholds from scantwo permutation results
Print the estimated genome-wide LOD thresholds on the basis of
permutation results from scantwo (with
n.perm > 0).
## S3 method for class 'scantwoperm' summary(object, alpha=c(0.05, 0.10), ...)
object |
Output from the function |
alpha |
Genome-wide significance levels. |
... |
Ignored at this point. |
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.
An object of class summary.scantwoperm, to be printed by
print.summary.scantwoperm.
Karl W Broman, broman@wisc.edu
Churchill, G. A. and Doerge, R. W. (1994) Empirical threshold values for quantitative trait mapping. Genetics 138, 963–971.
data(fake.f2) fake.f2 <- calc.genoprob(fake.f2, step=0) ## Not run: operm <- scantwo(fake.f2, n.perm=100, method="hk") summary(operm)
Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.