hap {gap} | R Documentation |
Haplotype reconstruction using sorting and trimming algorithms
hap(id,data,nloci,loci=rep(2,nloci),names=paste("loci",1:nloci,sep=""), mb=0,pr=0,po=0.001,to=0.001,th=1,maxit=100,n=0, ss=0,rs=0,rp=0,ro=0,rv=0,sd=0,mm=0,mi=0,mc=50,ds=0.1,de=0,q=0)
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) |
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 |
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
adapted from hap
## 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) # to generate results of imputations hap(id=fsnps[,1],data=fsnps[,3:10],nloci=4,ss=1,mi=5) ## End(Not run)