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 |
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 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
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)