R: Gene counting for haplotype analysis

hap.em {gap} | R Documentation

## Gene counting for haplotype analysis

### Description

Gene counting for haplotype analysis with missing data, adapted for hap.score.

### Usage

    hap.em(
      id,
      data,
      locus.label = NA,
      converge.eps = 1e-06,
      maxiter = 500,
      miss.val = 0
    )

### Arguments

`id` | a vector of individual IDs.
`data` | Matrix of alleles, such that each locus has a pair of adjacent columns of alleles, and the order of columns corresponds to the order of loci on a chromosome. If there are K loci, then ncol(data) = 2*K. Rows represent alleles for each subject.
`locus.label` | Vector of labels for loci, of length K (see definition of data matrix).
`converge.eps` | Convergence criterion, based on absolute change in log likelihood (lnlike).
`maxiter` | Maximum number of iterations of EM.
`miss.val` | missing value.

### Value

List with components:

converge

  Indicator of convergence of the EM algorithm (1=converged, 0 = failed).

niter

  Number of iterations completed in the EM alogrithm.

locus.info

  A list with a component for each locus. Each component is also a list, and the items of a locus- specific list are the locus name and a vector for the unique alleles for the locus.

locus.label

  Vector of labels for loci, of length K (see definition of input values).

haplotype

  Matrix of unique haplotypes. Each row represents a unique haplotype, and the number of columns is the number of loci.

hap.prob

  Vector of mle's of haplotype probabilities. The ith element of hap.prob corresponds to the ith row of haplotype.

lnlike

  Value of lnlike at last EM iteration (maximum lnlike if converged).

indx.subj

  Vector for index of subjects, after expanding to all possible pairs of haplotypes for each person. If indx=i, then i is the ith row of input matrix data. If the ith subject has n possible pairs of haplotypes that correspond to their marker phenotype, then i is repeated n times.

nreps

  Vector for the count of haplotype pairs that map to each subject's marker genotypes.

hap1code

  Vector of codes for each subject's first haplotype. The values in hap1code are the row numbers of the unique haplotypes in the returned matrix haplotype.

hap2code

  Similar to hap1code, but for each subject's second haplotype.

post

  Vector of posterior probabilities of pairs of haplotypes for a person, given thier marker phenotypes.

### Note

Adapted from HAP.

### Author(s)

Jing Hua Zhao

### See Also

`hap`, `LDkl`

### Examples

    ## Not run:
    data(hla)
    hap.em(id=1:length(hla[,1]),data=hla[,3:8],locus.label=c("DQR","DQA","DQB"))

    ## End(Not run)

[Package gap version 1.2.3-6 Index]