This function extracts haplotypes from phased genotypes.
# S3 method for loci
haplotype(x, locus = 1:2, quiet = FALSE, compress = TRUE,
check.phase = TRUE, ...)
# S3 method for haplotype.loci
plot(x, ...)
dist.haplotype.loci(x)an object of class "loci" or of class
"haplotype.loci".
a vector of integers giving the loci to analyse.
a logical value specifying whether to not print the
progress of the analysis (FALSE by default).
by default only the unique haplotypes are returned
with their frequencies. If compress = FALSE, a matrix with
all observed haplotypes is returned (with the number of columns
equals to the number of individuals times the ploidy level).
a logical value specifying whether to check if the individual genotypes are phased.
arguments passed to and from methods.
haplotype returns a matrix of mode character with the loci as
rows and the haplotypes as columns. The attribute "freq" gives
the counts of each haplotype and the class is "haplotype.loci".
dist.haplotype.loci returns an object of class "dist".
The individuals with at least one unphased genotype are ignored with a warning.
dist.haplotype.loci computes pairwise distances among
haplotypes by counting the number of different alleles.
Checking whether the genotypes are phased can be time consuming with
very big data sets. It may be useful to set check.phase = FALSE
if several analyses are done on the same data and no warning was
issued after the first scan, or you are sure that the genotypes are phased.