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

setupGeno {haplo.stats} | R Documentation

## 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

[Package haplo.stats version 1.7.9 Index]