gap (version 1.1-2)

hap: 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

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

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.

See Also

genecounting

Examples

# 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()