haplo.design: Build a design matrix for haplotypes

Description

Build a design matrix for haplotypes estimated from a haplo.em object.

Usage

haplo.design(obj, haplo.effect="additive", hapcodes=NA, min.count=5, haplo.base=NA)

Value

Matrix of columns for haplotype effects. Column names are "hap.k" where k is the row number of the unique haplotypes within the haplo.em object's "haplotypes" item.

Arguments

obj: an object created from haplo.em
haplo.effect: The "effect" pattern of haplotypes on the response. This parameter determines the coding for scoring the haplotypes. Valid coding options for heterozygous and homozygous carriers of a haplotype are "additive" (1, 2, respectively), "dominant" (1,1, respectively), and "recessive" (0, 1, respectively).
hapcodes: codes assigned in haplo.em, corresponding to the row numbers in the haplotypes matrix item in obj
min.count: The minimum number of estimated counts of the haplotype in the sample in order for a haplotype to be included in the design matrix.
haplo.base: code for which haplotype will be the reference group, or to be considered the baseline of a model. The code is the row number of the haplotypes matrix in obj. This haplotype is removed from the design matrix.

Details

First a matrix is made for the possible haplotypes for each person, coded for the haplo.effect, weighted by the posterior probability of those possible haplotypes per person, and then collapsed back to a single row per person.

Examples

Run this code


 ###------------------------------------------------
 ### See the user manual for more complete examples
 ###------------------------------------------------

 data(hla.demo)
 attach(hla.demo)

 geno <- hla.demo[,c(17,18,21:24)]
 label <-c("DQB","DRB","B")

 keep <- !apply(is.na(geno) | geno==0, 1, any)

 save.em.keep <- haplo.em(geno=geno[keep,], locus.label=label)

 save.df <- haplo.design(save.em.keep, min.count=10)
 dim(save.df)

 names(save.df)
 save.df[1:10,]