genecounting {gap}R Documentation

Gene counting for haplotype analysis

Description

Gene counting for haplotype analysis with missing data

Usage

genecounting(data,weight=NULL,convll=1,handle.miss=0,eps=0.00001,maxit=50,pl=0.001)

Arguments

data genotype table
weight a column of frequency weights
convll set convergence criteria according to log-likelihood, if its value set to 1
handle.miss to handle missing data, if its value set to 1
eps the actual convergence criteria, with default value 1e-5
maxit maximum number of iterations, with default value 50
pl criteria for trimming haplotypes according to posterior probabilities

Value

The returned value is a list containing:

h haplotype frequency estimates under linkage disequilibrium (LD)
h0 haplotype frequency estimates under linkage equilibrium (no LD)
prob genotype probability estimates
l0 log-likelihood under linkage equilibrium
l1 log-likelihood under linkage disequilibrium
hapid unique haplotype identifier (defunct, see gc.em)
npusr number of parameters according user-given alleles
npdat number of parameters according to observed
htrtable design matrix for haplotype trend regression (defunct, see gc.em)
iter number of iterations used in gene counting
converge a flag indicating convergence status of gene counting
di0 haplotype diversity under no LD, defined as 1-sum (h0^2)
di1 haplotype diversity under LD, defined as 1-sum (h^2)
resid residuals in terms of frequency weights = o - e

References

Zhao, J. H., Lissarrague, S., Essioux, L. and P. C. Sham (2002). Gene-counting for haplotype analysis with missing genotypes. Bioinformatics 18(12):1694-1695

Zhao, J. H. and P. C. Sham (2003). Generic number systems and haplotype analysis. Comp Meth Prog Biomed 70: 1-9

Note

adapted from GENECOUNTING

Author(s)

Jing hua Zhao

See Also

gc.em, kbyl

Examples

## Not run: 
# Now we use the HLA data for testing
data(hla)
hla.gc<-genecounting(hla[,3:8])
summary(hla.gc)
hla.gc$l0
hla.gc$l1

# Now we use ALDH2 data
data(aldh2)
aldh2.gc<-genecounting(aldh2[,3:6],handle.miss=1)
summary(aldh2.gc)
aldh2.gc$l0
aldh2.gc$l1
## End(Not run)

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