hap {gap}R Documentation

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())

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 function with the following arguments,
    mb
    Maximum dynamic storage to be allocated, in Mb
    pr
    Prior (ie population) probability threshold
    po
    Posterior probability threshold
    to
    Log-likelihood convergence tolerance
    th
    Posterior probability threshold for output
    maxit
    Maximum EM iteration
    n
    Force numeric allele coding (1/2) on output (off)
    ss
    Tab-delimited speadsheet file output (off)
    rs
    Random starting points for each EM iteration (off)
    rp
    Restart from random prior probabilities
    ro
    Loci added in random order (off)
    rv
    Loci added in reverse order (off)
    sd
    Set seed for random number generator (use date+time)
    mm
    Repeat final maximization multiple times
    mi
    Create multiple imputed datasets. If set >0
    mc
    Number of MCMC steps between samples
    ds
    Starting value of Dirichlet prior parameter
    de
    Finishing value of Dirichlet prior parameter
    q
    Quiet operation (off)
    hapfile
    a file for haplotype frequencies
    assignfile
    a file for haplotype assignment

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.

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

References

Clayton DG (2001) SNPHAP. http://www-gene.cimr.cam.ac.uk/clayton/software

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

Note

adapted from hap

See Also

genecounting

Examples

## Not run: 
# 4 SNP example, to generate hap.out and assign.out alone
data(fsnps)
hap(id=fsnps[,1],data=fsnps[,3:10],nloci=4)
dir()
file.show("hap.out")
file.show("assign.out")

# 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)

[Package gap version 1.0-17 Index]