hap {gap} | R Documentation |
Haplotype reconstruction
hap(
id,
data,
nloci,
loci = rep(2, nloci),
names = paste("loci", 1:nloci, sep = ""),
control = hap.control()
)
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(). |
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.
The returned value is a list containing:
l1 log-likelihood assuming linkage disequilibrium.
converge convergence status, 0=failed, 1=succeeded.
niter number of iterations.
adapted from hap.
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.
## 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)