Description Usage Arguments Details Value Author(s) See Also

View source: R/design.1locus.R

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 model with the main effect of a single biallelic marker.

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

`x` |
A numeric vector of values representing genotypes of a biallelic marker. 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* are as follows:

*Y[1] = 1 , Y[2] = 0 : β[11] X*

*Y[1] = 0 , Y[2] = 1 : β[21] X*

*Y[1] = 1 , Y[2] = 1 : β[31] X*

The vector *X* constitute the design matrix for each linear predictor of the above model.

`x.e ` |
List of 3 design matrices containing the vector |

`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>

`fat2Lpoly, design.full, design.endo2disease`

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