genecounting {gap}R Documentation

Gene counting for haplotype analysis

Description

Gene counting for haplotype analysis with missing data

Usage

genecounting(data,weight=NULL,loci=NULL,control=gc.control())

Arguments

data genotype table
weight a column of frequency weights
loci an array containing number of alleles at each locus
control is a function with the following arguments:
    xdata
    a flag indicating if the data involves X chromosome, if so, the first column of data indicates sex of each subject: 1=male, 2=female. The marker data are no different from the autosomal version for females, but for males, two copies of the single allele present at a given locus.
    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
    tol
    tolerance for genotype probabilities with default value 1e-8
    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). GENECOUNTING: 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

Zhao, J. H. (2004). 2LD, GENECOUNTING and HAP: Computer programs for linkage disequilibrium analysis. Bioinformatics, 20, 1325-1326

Note

adapted from GENECOUNTING

Author(s)

Jing hua Zhao

See Also

gc.em, kbyl

Examples

## Not run: 
# HLA data
data(hla)
hla.gc <- genecounting(hla[,3:8])
summary(hla.gc)
hla.gc$l0
hla.gc$l1

# ALDH2 data
data(aldh2)
control <- gc.control(handle.miss=1)
aldh2.gc <- genecounting(aldh2[,3:6],control=control)
summary(aldh2.gc)
aldh2.gc$l0
aldh2.gc$l1

# Chromosome X data
# assuming allelic data have been extracted in columns 3-13
# and column 3 is sex
dat <- mao[,3:13]
loci <- c(12,9,6,5,3)
contr <- gc.control(xdata=TRUE,handle.miss=1)
mao.gc <- genecounting(dat,loci=loci,control=contr)
mao.gc$npusr
mao.gc$npdat
## End(Not run)

[Package gap version 1.0-3 Index]