haplotype.loci {pegas}

Haplotype Extraction and Frequencies From Allelic Data

Description

This function extracts haplotypes from phased genotypes.

Usage

## S3 method for class 'loci'
haplotype(x, locus = 1:2, quiet = FALSE, compress = TRUE,
           check.phase = TRUE, ...)
## S3 method for class 'haplotype.loci'
plot(x, ...)
dist.haplotype.loci(x)

Arguments

x

an object of class "loci" or of class "haplotype.loci".

locus

a vector of integers giving the loci to analyse.

quiet

a logical value specifying whether to not print the progress of the analysis (FALSE by default).

compress

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).

check.phase

a logical value specifying whether to check if the individual genotypes are phased.

...

arguments passed to and from methods.

Details

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.

Value

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".

Note

haplotype is a generic function with methods for objects of class "DNAbin" and of class "loci". Note that the class returned by these methods is different: c("haplotype", "DNAbin") and "haplotype.loci", respectively. This and other details are likely to change in the future.

Author(s)

Emmanuel Paradis

See Also

haplotype, LD