setupGeno: Create a group of locus objects from a genotype matrix,...

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

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)

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

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.

Note

A matrix that contains all elements of mode character will be sorted in alphabetic order. This order may differ across platforms according to your setting of LC_COLLATE. See the note in haplo.em about how this sort order affects results.

See Also

locus, haplo.glm, haplo.em

Examples

# 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

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