hap {gap}R Documentation

Haplotype reconstruction

Description

Haplotype reconstruction using sorting and trimming algorithms

Usage

hap(id,data,nloci,loci=rep(2,nloci),names=paste("loci",1:nloci,sep=""),
              control=hap.control())

Arguments

id a column of subject id
data genotype table
nloci number of loci
loci number of alleles at all loci
names locus names
control is a function with the following arguments,
  1. mb Maximum dynamic storage to be allocated, in Mb
  2. pr Prior (ie population) probability threshold
  3. po Posterior probability threshold
  4. to Log-likelihood convergence tolerance
  5. th Posterior probability threshold for output
  6. maxit Maximum EM iteration
  7. n Force numeric allele coding (1/2) on output (off)
  8. ss Tab-delimited speadsheet file output (off)
  9. rs Random starting points for each EM iteration (off)
  10. rp Restart from random prior probabilities
  11. ro Loci added in random order (off)
  12. rv Loci added in reverse order (off)
  13. sd Set seed for random number generator (use date+time)
  14. mm Repeat final maximization multiple times
  15. mi Create multiple imputed datasets. If set >0
  16. mc Number of MCMC steps between samples
  17. ds Starting value of Dirichlet prior parameter
  18. de Finishing value of Dirichlet prior parameter
  19. q Quiet operation (off)
  20. hapfile a file for haplotype frequencies
  21. 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.

Value

The returned value is a list containing:

l1 log-likelihood assuming linkage disequilibrium
converge convergence status, 0=failed, 1=succeeded
niter number of iterations

References

Clayton DG (2001) SNPHAP. http://www-gene.cimr.cam.ac.uk/clayton/software

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)

[Package gap version 1.0-22 Index]