R: Gene counting for haplotype analysis

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`, `LDkl`

### Examples

    ## Not run:
    require(gap.datasets)
    # 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 <- system.file("tests/genecounting/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 1.2.3-1 Index]