Description Usage Arguments Details Value Author(s) References See Also

This function sets up two identical lists of three design matrices, one for each linear predictor of the logit of the three outcome levels defined by the combination of two dichotomous traits against the reference level (0,0) under a full model with main effects and product terms for two biallelic markers.

1 | ```
design.full(x, par.constrained, constraints)
``` |

`x` |
A 2-column matrix of numeric values representing genotypes of biallelic markers, with one column per marker and one row per subject. The two homozygous genotypes must be coded 0 and 1, and the heterozygous genotype value depends on the genetic model: 0 (recessive), 1/2 (allelic) or 1 (dominant). |

`par.constrained` |
Optional matrix of dimensions ( |

`constraints` |
Optional matrix of dimensions ( |

Let *Y[1]* and *Y[2]* be binary variables coding the presence (1) or absence (0) of the two traits (e.g. and endophenotype and a disease trait, respectively).
The linear predictors (without intercept) of the logistic functions between outcome levels and the reference level *Y[1] = 0* and *Y[2] = 0* for the full model are as follows:

*Y[1] = 1 , Y[2] = 0 : β[11] X[1] + β[12] X[2] + β[13] X[1] X[2]*

*Y[1] = 0 , Y[2] = 1 : β[21] X[1] + β[22] X[2] + β[23] X[1] X[2]*

*Y[1] = 1 , Y[2] = 1 : β[31] X[1] + β[32] X[2] + β[33] X[1] X[2]*

The design matrices for the above model are constructed by this function.

`x.e ` |
List of 3 design matrices containing all terms forming the full model |

`x.loc.e ` |
list of character strings containing the indices of the variables in |

`x.l ` |
identical to |

`x.loc.l ` |
identical to |

Alexandre Bureau <alexandre.bureau@msp.ulaval.ca>

Bureau A., Croteau J., Chagnon, Y.C., Roy, M.-A. and Maziade, M. Extension of the Generalized Disequilibrium Test to polytomous phenotypes and two locus models. Frontiers in Genetics, 5: Article 258.

`fat2Lpoly, design.endo2disease`

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