design.dichotomous: Setting-up the design matrix for a logistic model with two...
In fat2Lpoly: Two-Locus Family-Based Association Test with Polytomous Outcome

Description Usage Arguments Details Value Author(s) See Also

This function sets up two identical lists, each containing a design matrix for the linear predictor of the logit of a dichotomous outcome under a full logistic model with main effects and product terms for two biallelic markers.

1	design.dichotomous(x,...)

`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).
`...`	Additional arguments will be ignored, but must be allowed for compatibility with other design functions.

The linear predictors (without intercept) of the logistic function for Y = 1 against the reference level Y = 0 has the form:

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

The design matrix for the above model is constructed by this function.

`x.e`	List containing the single design matrix with all terms forming the full 2-locus logistic model
`x.loc.e`	list of character strings containing the indices of the variables in `x` involved in each term of the logistic model
`x.l`	identical to `x.e`
`x.loc.l`	identical to `x.l`