haplohh-class {rehh}

Class "haplohh"

Description

An object of this class contains the information needed for computation of EHH based statistics.

Usage

## S4 method for signature 'haplohh'
chr.name(x)

## S4 method for signature 'haplohh'
positions(x)

## S4 method for signature 'haplohh'
haplo(x)

## S4 method for signature 'haplohh'
nmrk(x)

## S4 method for signature 'haplohh'
mrk.names(x)

## S4 method for signature 'haplohh'
nhap(x)

## S4 method for signature 'haplohh'
hap.names(x)

Arguments

x

an object of this class.

Details

This class is the basis for all calculations done by this package. Note that the matrix in slot haplo has to be of type integer, not numeric. Objects built by versions of rehh up to 2.0.4 coded this matrix as numeric and used a different coding scheme. They can be converted e.g. by haplohh <- update_haplohh(old_haplohh) in order be used with the present version.

Slots

chr.name

name of the chromosome/scaffold to which the markers belong.

positions

vector of type numeric containing the marker positions within the chromosome.

haplo

matrix of type integer containing haplotypes in rows and markers in columns.

See Also

data2haplohh, update_haplohh

Examples

showClass("haplohh")