paramlink (version 0.2-1)

simulSNP: Simulate SNP markers

Description

Simulates SNP markers conditional on the pedigree structure, affection statuses and disease model.

Usage

simulSNP(x, N = 1, init=NULL, unique=FALSE, seed=NULL)

Arguments

x

a linkdat object

N

a positive integer: the number of SNPs to be simulated

init

a non-negative integer indicating how many steps of genotype probability pre-calculating should be done. Increasing this can be a time saver for large N.

unique

a logical indicating if duplicates among the simulated markers should be removed.

seed

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

Value

• a linkdat object equal to x in all respects except its markerdata entry, which consists of the N simulated markers. (Markers already present in x$markerdata are deleted.)

Details

This is an implementation of the algortihm used in SLINK of the LINKAGE/FASTLINK suite.

References

G. M. Lathrop, J.-M. Lalouel, C. Julier, and J. Ott, Strategies for Multilocus Analysis in Humans, PNAS 81(1984), pp. 3443-3446.

See Also

linkage.power

Examples

data(toyped)
x=linkdat(toyped, model=1)
y=simulSNP(x, N=5)
plot(y, marker=1)