haplo {haplo.ccs}R Documentation

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. The order of the columns corresponds to the order of the loci on the chromosome, and each row corresponds to the alleles for each subject. The alleles should be numerically coded, i.e., 1, 2, 3, or 4 for 'A', 'C', 'G', or 'T'.
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.

Author(s)

Benjamin French and Thomas Lumley

Department of Biostatistics

University of Washington

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")


[Package haplo.ccs version 1.0 Index]