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haplo.stats (version 1.4.4)

loci: 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

loci(geno, locus.names, chrom.label=NULL, x.linked=FALSE, sex=NULL, 
     male.code="M", female.code="F", miss.val=NA, map=NA)

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.
locus.names
A vector containing the locus name for each locus.
chrom.label
Chromosome Label
x.linked
A logical value denoting whether the chromosome is X-linked.
sex
A vector containing the sex of each individual. If x.linked=F then argum ent sex is not required and may be left as the default value of NULL.
male.code
The code denoting a male in the sex vector.
female.code
The code denoting a female in the sex vector.
miss.val
A vector of codes denoting missing values for the allele labels. Note that NA will always be treated as a missing value, and alleles matching miss.val are assigned NA. Also note that the original missing value code for a specific individual can not be
map
An optional chromosome map of class "cmap"

Value

  • An object of class "model.matrix", with all alleles recoded to a numeric value. It contains the following attributes:
  • locus.namesA vector of labels for the loci, of length nloci.
  • mapWill be better defined later.
  • x.linkedA logical value denoting whether the chromosome is X-linked.
  • unique.allelesThe original allele labels 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.
  • male.codeThe code denoting a male in the sex vector.
  • female.codeThe code denoting a female in the sex vector.
  • chrom.labelChromosome Label

See Also

locus, setupGeno

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")

myloci <- data.frame(a1,a2,b1,b2,c1,c2)
myloci <- loci(myloci, locus.names=c("A","B","C"),miss.val=c(0,NA))
myloci

attributes(myloci)

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