gap (version 1.5-1)

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()
)

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

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 call to hap.control().

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.

References

Clayton DG (2001) SNPHAP. https://github.com/chr1swallace/snphap.

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

See Also

genecounting

Examples

if (FALSE) {
require(gap.datasets)
# 4 SNP example, to generate hap.out and assign.out alone
data(fsnps)
hap(id=fsnps[,1],data=fsnps[,3:10],nloci=4)
dir()

# 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()
}