hap.em: 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

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

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.

References

See hap

Examples

Run this code

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