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

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`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 |

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. |

See hap

Adapted from HAP

Jing Hua Zhao

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