hap.em: Gene counting for haplotype analysis

In gap: Genetic Analysis Package

Gene counting for haplotype analysis

Description

Gene counting for haplotype analysis

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.

Details

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

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)

gap documentation built on Aug. 26, 2023, 5:07 p.m.