setupGeno: Create a group of locus objects from a genotype matrix, assign to 'model.matrix' class.

Description

The function makes each pair of columns a locus object, which recodes alleles to numeric and saves the original alleles as an attribute of the model.matrix.

Usage

setupGeno(geno, miss.val=c(0,NA), locus.label=NULL)

Value

A 'model.matrix' object with the alleles recoded to numeric values, and the original values are stored in the 'unique.alleles' attribute. The ith item of the unique.alleles list is a vector of unique alleles for the ith locus.

Arguments

geno: Matrix of alleles, such that each locus has a pair of adjacent columns of alleles, and the order of columns corresponds to the order of loci on a chromosome. If there are K loci, then ncol(geno) = 2*K. Rows represent alleles for each subject.
miss.val: A vector of codes denoting missing values for allele1 and allele2. Note that NA will always be treated as a missing value, even if not specified in miss.val. Also note that if multiple missing value codes are specified, the original missing value code for a specific individual can not be retrieved from the loci object.
locus.label: vector of labels for the loci

Details

This function contains the essential parts of the loci function, which is no longer within haplo.stats

Examples

Run this code

# Create some loci to work with
a1 <- 1:6
a2 <- 7:12

b1 <- c("A","A","B","C","E","D")
b2 <-c("A","A","C","E","F","G")

c1 <- c("101","10","115","132","21","112")
c2 <- c("100","101","0","100","21","110")

myGeno <- data.frame(a1,a2,b1,b2,c1,c2)
myGeno <- setupGeno(myGeno)
myGeno

attributes(myGeno)$unique.alleles