This function is a R port of the GENECOUNTING/PERMUTE program which generates EHPLUS-type statistics including z-tests for individual haplotypes

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`y` |
A column of 0/1 indicating cases and controls |

`cc` |
analysis indicator, 0 = marker-marker, 1 = case-control |

`g` |
the multilocus genotype data |

`handle.miss` |
a flag with value 1 indicating missing data are allowed |

`miss.val` |
missing value |

`n.sim` |
the number of permutations |

`locus.label` |
label of each locus |

`quietly` |
a flag if TRUE will suppress the screen output |

The returned value is a list containing (p.sim and ph when n.sim > 0):

`x2obs` |
the observed chi-squared statistic |

`pobs` |
the associated p value |

`zobs` |
the observed z value for individual haplotypes |

`p.sim` |
simulated p value for the global chi-squared statistic |

`ph` |
simulated p values for individual haplotypes |

Zhao JH, Curtis D, Sham PC (2000). Model-free analysis and permutation tests for allelic associations. Human Heredity 50(2): 133-139

Zhao JH (2004). 2LD, GENECOUNTING and HAP: Computer programs for linkage disequilibrium analysis. Bioinformatics 20: 1325-1326

Zhao JH, Qian WD Association analysis of unrelated individuals using polymorphic genetic markers – methods, implementation and application, Royal Statistical Society 2003, Hassallt-Diepenbeek, Belgium.

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Jing Hua Zhao

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