haplo.design: Build a design matrix for haplotypes

In haplo.stats: Statistical Analysis of Haplotypes with Traits and Covariates when Linkage Phase is Ambiguous

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)

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.

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.

See Also

haplo.em

Examples

 ###------------------------------------------------
 ### 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,]

haplo.stats documentation built on May 29, 2024, 9:53 a.m.