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:

1. 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.

2. convll. set convergence criteria according to log-likelihood, if its value set to 1

3. handle.miss. to handle missing data, if its value set to 1

4. eps. the actual convergence criteria, with default value 1e-5

5. tol. tolerance for genotype probabilities with default value 1e-8

6. maxit. maximum number of iterations, with default value 50

7. pl. criteria for trimming haplotypes according to posterior probabilities

8. assignment. filename containing haplotype assignment

9. 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 1.2.1 Index]