loci {haplo.stats} | R Documentation |
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.
loci(geno, locus.names, chrom.label=NULL, x.linked=FALSE, sex=NULL, male.code="M", female.code="F", miss.val=NA, map=NA)
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 retrieved from the returned object. |
map |
An optional chromosome map of class "cmap" |
An object of class "model.matrix", with all alleles recoded to a numeric value. It contains the following attributes:
locus.names |
A vector of labels for the loci, of length nloci. |
map |
Will be better defined later. |
x.linked |
A logical value denoting whether the chromosome is X-linked. |
unique.alleles |
The 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.code |
The code denoting a male in the sex vector. |
female.code |
The code denoting a female in the sex vector. |
chrom.label |
Chromosome Label |
A matrix that contains all elements of mode character will be sorted in alphabetic order.
locus, setupGeno
# 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)