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
    assignment
    filename containing haplotype assignment
    verbose
    If TRUE, yields print out from the C routine

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,assignment="ALDH2.out")
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
filespec <- file.path(.path.package("gap"),"tests/mao.dat")
mao2 <- read.table(filespec)
dat <- mao2[,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 1.0-17 Index]