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

View source: R/design.endo2disease.R

This function sets up two 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 the endophenotype-to-disease model of Bureau et al (2014). The design matrices in the first list contain all terms forming the model, and those in the second list contain all main effect and product terms appearing in the model.

1 | ```
design.endo2disease(x, par.constrained, constraints)
``` |

`x` |
A matrix of dimensions 2 x n 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 endophenotype and the 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* specified by the endophenotype-to-disease model are as follows:

*Y[1] = 1 , Y[2] = 0 : β[11] X[1] + β[e] X[1] (1 - X[2])*

*Y[1] = 0 , Y[2] = 1 : β[21] X[1]*

*Y[1] = 1 , Y[2] = 1 : β[31] X[1] + 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 endophenotype-to-disease model |

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

`x.l ` |
List of 3 design matrices containing the terms |

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

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.

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