gap (version 0.4)

hap: Haplotype reconstruction

Description

Haplotype reconstruction using sorting and trimming algorithms

Usage

hap(id,data,nloci,loci,names,mb,pr,po,to,th,maxit,n,ss,rs,rp,ro,rv,sd,mm,
           mi,mc,ds,de,q)

Arguments

id

a column of subject id

data

genotype table

nloci

number of loci

loci

number of alleles at all loci

names

locus names

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)

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

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.

See Also

genecounting

Examples

# 4 SNP example, to generate hap.out and assign.out alone
data(fsnps)
hap(id=fsnps[,1],data=fsnps[,3:10],nloci=4)

# to generate results of imputations
hap(id=fsnps[,1],data=fsnps[,3:10],nloci=4,ss=1,mi=5)