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)

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 fo

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.

Value

List with components:
convergeIndicator of convergence of the EM algorithm (1=converged, 0 = failed).
niterNumber of iterations completed in the EM alogrithm.
locus.infoA 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.labelVector of labels for loci, of length K (see definition of input values).
haplotypeMatrix of unique haplotypes. Each row represents a unique haplotype, and the number of columns is the number of loci.
hap.probVector of mle's of haplotype probabilities. The ith element of hap.prob corresponds to the ith row of haplotype.
lnlikeValue of lnlike at last EM iteration (maximum lnlike if converged).
indx.subjVector 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.
nrepsVector for the count of haplotype pairs that map to each subject's marker genotypes.
hap1codeVector 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.
hap2codeSimilar to hap1code, but for each subject's second haplotype.
postVector of posterior probabilities of pairs of haplotypes for a person, given thier marker phenotypes.

References

Clayton DG (2001) SNPHAP. http://www-gene.cimr.cam.ac.uk/clayton/software

Zhao JH and W Qian (2003) Association analysis of unrelated individuals using polymorphic genetic markers. RSS 2003, Hassalt, Belgium

Examples

Run this code

data(hla)
hap.em(id=1:length(hla[,1]),data=hla[,3:8])