n Force numeric allele coding (1/2) on output (off)
ss Tab-delimited speadsheet file output (off)
rs Random starting points for each EM iteration (off)
rp Restart from random prior probabilities
ro Loci added in random order (off)
rv Loci added in reverse order (off)
sd Set seed for random number generator (use date+time)
mm Repeat final maximization multiple times
mi Create multiple imputed datasets. If set >0
mc Number of MCMC steps between samples
ds Starting value of Dirichlet prior parameter
de Finishing value of Dirichlet prior parameter
q Quiet operation (off)
hapfile a file for haplotype frequencies
assignfile a file for haplotype assignment
Details
The package can hanlde much larger number of multiallelic loci.
For large sample size with relatively small number of multiallelic
loci, genecounting should be used.
Zhao JH and W Qian (2003) Association analysis of unrelated individuals
using polymorphic genetic markers. RSS 2003, Hassalt, Belgium
Zhao JH (2004). 2LD, GENECOUNTING and HAP: Computer programs for linkage
disequilibrium analysis. Bioinformatics 20: 1325-1326
Note
adapted from hap
See Also
genecounting
Examples
## Not run:
# 4 SNP example, to generate hap.out and assign.out alone
data(fsnps)
hap(id=fsnps[,1],data=fsnps[,3:10],nloci=4)
dir()
file.show("hap.out")
file.show("assign.out")
# to generate results of imputations
control <- hap.control(ss=1,mi=5,hapfile="h",assignfile="a")
hap(id=fsnps[,1],data=fsnps[,3:10],nloci=4,control=control)
dir()
## End(Not run)