linkage.power: Power of a linkage study

Description

Power analysis of parametric linkage studies

Usage

linkage.power(x, N=100, available=x$available, afreq=c(0.5, 0.5), loop_breakers=NULL, threshold=NULL, seed=NULL)

Arguments

a linkdat object.

an integer; the number of markers to simulate.

available

a vector containing IDs of the available individuals, i.e. those whose genotypes should be simulated.

afreq

a vector of length 2 containing the population frequencies for the SNP alleles.

loop_breakers

a numeric containing IDs of individuals to be used as loop breakers. Relevant only if the pedigree has loops. See breakLoops.

threshold

a numeric of length 1, or NULL. If not NULL, and if maxonly=FALSE, the output includes the percentage of simulated markers having LOD larger than threshold.

seed

NULL, or a numeric seed for the random number generator.

Value

A linkres object, which is returned invisibly after a summary is printed

References

The marker simulation takes place in SNPsim, which implements the algorithm used by SLINK: http://linkage.rockefeller.edu/ott/SLINK.htm

Examples

Run this code

# Note: In the cases below, N is set very low. Increase to get more interesting results.
data(toyped)
x = linkdat(toyped, model=1)
linkage.power(x, N=5)
# X-linked example:
data(Xped)
y = linkdat(Xped, model=4)
linkage.power(y, N=1)

# Loop example:
z = addOffspring(cousinPed(1), father=7, mother=8, noffs=1, aff=2)
z = setModel(z, 2)
linkage.power(z, N=1, loop_breaker=7)

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