This function extracts haplotypes from phased genotypes.
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an object of class
a vector of integers giving the loci to analyse.
a logical value specifying whether to not print the
progress of the analysis (
by default only the unique haplotypes are returned
with their frequencies. If
a logical value specifying whether to check if the individual genotypes are phased.
arguments passed to and from methods.
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.
haplotype returns a matrix of mode character with the loci as
rows and the haplotypes as columns. The attribute
the counts of each haplotype and the class is
dist.haplotype.loci returns an object of class
haplotype is a generic function with methods for objects of
"DNAbin" and of class
"loci". Note that the class
returned by these methods is different:
"haplotype.loci", respectively. This and other details are
likely to change in the future.
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