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().

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.

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.

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

Zhao JH (2004). “2LD. GENECOUNTING and HAP: computer programs for linkage disequilibrium analysis.” Bioinformatics, 20(8), 1325-6. doi:10.1093/bioinformatics/bth071 .

Examples

if (FALSE) { # \dontrun{
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()
} # }