hap: Haplotype reconstruction

In gap: Genetic Analysis Package

Haplotype reconstruction

Description

Haplotype reconstruction

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 call to hap.control().

Details

Haplotype reconstruction using sorting and trimming algorithms.

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.

Note

adapted from hap.

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

\insertRef

zhao04gap

See Also

genecounting

Examples

## Not run: 
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()

## End(Not run)

gap documentation built on Aug. 26, 2023, 5:07 p.m.