ld.design {ldDesign} | R Documentation |
Find the sample size required to detect linkage disequilibrium with a given Bayes factor, with a given power, or find the power of experimental designs to detect linkage equilibrium with a given Bayes factor.
ld.design(p, q, D, h2, phi, Bf, power, nmin = 50, nmax = 1e+05, ninterp = 50, missclass.rate = 0, print.it = FALSE) ld.power(n, p, q, D, h2, phi, Bf, missclass.rate = 0)
n |
ld.power: vector of sample sizes |
p |
Bi-allelic marker allele frequency |
q |
Bi-allelic QTL allele frequency |
D |
Linkage disequilibrium coefficient |
h2 |
QTL `heritability', i.e. proportion of total or phenotypic variance explained by the QTL |
phi |
Dominance ratio: phi = 0 denotes purely additive,
phi = 1 denotes purely dominant allele effects |
Bf |
Bayes factor |
power |
ld.design: Power, or probability of detecting an effect with Bayes
factor greater than Bf |
nmin |
ld.design: Lower bound for sample size |
nmax |
ld.design: Upper bound for sample size |
ninterp |
ld.design: Number of sample sizes to try |
missclass.rate |
Proportion of marker values which are missclassified, i.e. incorrect (to allow for genotyping errors) |
print.it |
If TRUE print results for sample sizes tried |
These functions implement the method described in Ball (2003) for
obtaining the power of designs for detecting linkage disequilibrium with
a given Bayes factor. The F values, (and hence significance levels)
corresponding to the given Bayes factors, sample sizes, and marker genotype
frequecies, are calculated using the method of Spiegelhalter and Smith (1982)
(R functions oneway.bf.alpha.required
,
SS.oneway.bf
). The power is obtained using a corrected
version of the classical deterministic power calculation from
Luo (1988) (R function luo.ld.power
).
For ld.power
, a matrix with columns:
n |
Sample sizes |
power |
Power of the design with the given sample sizes |
Additionally the return value has attributes indicating the
linkage disequilibrium parameters used.
For ld.design
the sample size is returned.
Rod Ball rod.ball@forestresearch.co.nz www.forestresearch.co.nz
Ball, R.D. 2003 Experimental designs for reliable detection of linkage disequilibrium in unstructured random population association studies.
Luo, Z.W. 1988 Detecting linkage disequilibrium between a polymorphic marker locus and a trait locus in natural populations. Heredity 80, 198–208
Spiegelhalter, D. and A.F.M. Smith 1982 Bayes factors for linear and log-linear models with vague prior information J. Royal Statist Soc. B 44: 377–387.
luo.ld.power
, ld.sim
, oneway.bf.alpha
,
oneway.bf.alpha.required
, SS.oneway.bf
ld.power(n=seq(100,1000,by=100),p=0.5,q=0.5,D=0.1,h2=0.1,phi=0,Bf=20) ld.design(p=0.5,q=0.5,D=0.1,h2=0.1,phi=0,Bf=20,power=0.9,print.it=TRUE,nmin=600,nmax=4000) ld.design(p=0.5,q=0.5,D=0.1,h2=0.1,phi=0,Bf=20,power=0.9,print.it=FALSE,nmin=1700,nmax=1900)