hap {gap} | R Documentation |
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
Zhao JH (2004). “2LD. GENECOUNTING and HAP: computer programs for linkage disequilibrium analysis.” Bioinformatics, 20(8), 1325-6. ISSN 1367-4803 (Print) 1367-4803, doi:10.1093/bioinformatics/bth071.
See Also
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)