summary.scanoneperm {qtl} | R Documentation |
Print the estimated genome-wide LOD thresholds on the basis of
permutation results from scanone
(with
n.perm
> 0).
## S3 method for class 'scanoneperm': summary(object, alpha=c(0.05, 0.10), df=FALSE, ...)
object |
Output from the function scanone
with n.perm > 0. |
alpha |
Genome-wide significance levels. |
df |
If TRUE, the degrees of freedom associated with the LOD scores are shown. |
... |
Ignored at this point. |
If there were autosomal data only or scanone
was
run with perm.Xsp=FALSE
, genome-wide LOD thresholds are given;
these are the 1-alpha quantiles of the genome-wide maximum LOD
scores from the permutations.
If there were autosomal and X chromosome data and
scanone
was run with perm.Xsp=TRUE
,
autosome- and X-chromsome-specific LOD thresholds are given, by the
method described in Broman et al. (in press). Let L_A and
L_X be total the genetic lengths of the autosomes and X
chromosome, respectively, and let L_T = L_A + L_X
Then in place of alpha, we use
alpha_A = 1 - (1 - alpha)^(L_A/L_T)
as the significance level for the autosomes and
alpha_x = 1 - (1 - alpha)^(LX/LT)
as the significance level for the X chromosome. The result is a list with two matrices, one for the autosomes and one for the X chromosome.
An object of class summary.scanoneperm
, to be printed by
print.summary.scanoneperm
. If there were X chromosome data and
scanone
was run with perm.Xsp=TRUE
, there are two
matrices in the results, for the autosome and X-chromosome LOD
thresholds.
Karl W Broman, kbroman@biostat.wisc.edu
Broman, K. W., Sen, 'S, Owens, S. E., Manichaikul, A., Southard-Smith, E. M. and Churchill G. A. The X chromosome in quantitative trait locus mapping. Genetics, to appear.
Churchill, G. A. and Doerge, R. W. (1994) Empirical threshold values for quantitative trait mapping. Genetics 138, 963–971.
scanone
,
summary.scanone
,
plot.scanoneperm
data(fake.f2) fake.f2 <- calc.genoprob(fake.f2, step=2.5) operm1 <- scanone(fake.f2, n.perm=100, method="hk") summary(operm1) operm2 <- scanone(fake.f2, n.perm=100, method="hk", perm.Xsp=TRUE) summary(operm2)