haplo: Specify an Allele Matrix, Inheritance Mode, and Grouping for Rare Haplotypes

Description

'haplo' specifies an allele matrix and an inheritance mode for the 'haplo.ccs' model formula. 'haplo' also specifies preferences for grouping rare haplotypes.

Usage

haplo(..., mode, group.rare=TRUE, rare.freq=0.02)

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 the default inheritance mode is 'additive'.

group.rare

a logical value indicating whether rare haplotypes should be grouped in the 'haplo.ccs' model. Note that the default is to group rare haplotypes.

rare.freq

the population haplotype frequency to define rare haplotypes. If 'group.rare=TRUE', then haplotypes with an estimated population frequency less than or equal to 'rare.freq' are grouped in the 'haplo.ccs' model. Note that the default haplotype frequency is 0.02. 'rare.freq' is automatically set to 0 if 'group.rare=FALSE'.

Value

A matrix of alleles with mode, group.rare, and rare.freq assigned as attributes.

References

French B, Lumley T, Monks SA, Rice KM, Hindorff LA, Reiner AP, Psaty BM. Simple estimates of haplotype relative risks in case-control data. Genetic Epidemiology 2006; 30(6):485-494.

Examples

Run this code


data(renin)

## Specify an allele matrix in a model fit by 'haplo.ccs'.

haplo.ccs(case ~ haplo(geno))

## Specify dominant inheritance and define rare haplotypes.

haplo.ccs(case ~ haplo(geno, mode="dominant", rare.freq=0.01))

## Specify the allele matrix without grouping rare haplotypes.

haplo.ccs(case ~ haplo(geno, group.rare=FALSE))