R: Build a design matrix for haplotypes

haplo.design {haplo.stats} | R Documentation

## 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 obj\$haplotypes matrix
`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 obj\$haplotypes matrix. 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,]

[Package haplo.stats version 1.7.9 Index]