haplo.ccs (version 1.0)

haplo: Specify an Allele Matrix and Inheritance Mode

Description

'haplo' specifies an allele matrix and an inheritance mode for the 'haplo.ccs' model formula.

Usage

haplo(..., mode)

Arguments

...

a matrix of alleles or list of columns of an allele matrix. Each locus on the chromosome has a pair of adjacent columns in the allele matrix, so that the number of columns of the allele matrix is twice the number of loci on the chromosome.

mode

the inheritance mode, either 'additive', 'dominant', or 'recessive'. Note that although 'haplo' does not specify a default inheritance mode, 'additive' is the default inheritance mode for 'haplo.ccs'.

Value

• A matrix of alleles with the inheritance mode assigned as an attribute.

See Also

haplo.ccs

Examples

data(Renin)

## Specify an allele matrix with additive inheritance in a model fit by
## 'haplo.ccs' to estimate haplotype effects.

m1 <- haplo.ccs(case ~ haplo(geno[,1:12], mode = "additive"),
                control = haplo.em.control(min.posterior=1e-4), referent = "223144")