grouping-methods {haplotypes}

Groups haplotypes according to the grouping variable (populations, species, etc.)

Description

Function for creating a matrix with haplotypes as rows, grouping factor (populations, species, etc.) as columns and abundance as entries.

Usage

## S4 method for signature 'Haplotype'
grouping(x,factors)

Arguments

x

an object of class Haplotype.

factors

a vector or factor giving the grouping variable (populations, species, etc.), with one element per individual.

Value

a list with two components:

hapmat:

a matrix with haplotypes as rows, levels of the grouping factor (populations, species, etc.) as columns and abundance as entries.

hapvec:

a vector giving the haplotype identities of individuals.

Methods

signature(x = "Haplotype")

Author(s)

Caner Aktas, [e-mail]

See Also

haplotype

Examples

data("dna.obj")
x<-dna.obj[1:6,,as.matrix=FALSE]
# inferring haplotypes from DNA sequences
h<-haplotype(x) 

## Grouping haplotypes.
# character vector 'populations' is a grouping factor.
populations<-c("pop1","pop1","pop2","pop3","pop3","pop3") 

# length of the argument 'factor' is equal to the number of sequences
g<-grouping(h,factors=populations) 
g