haplohh-class: Class "haplohh"

In rehh: Searching for Footprints of Selection using 'Extended Haplotype Homozygosity' Based Tests

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")

Example output

Loading required package: rehh.data
Loading required package: gplots

Attaching package: 'gplots'

The following object is masked from 'package:stats':

    lowess

Class "haplohh" [package "rehh"]

Slots:
                                                                  
Name:      haplo  position  snp.name  chr.name      nhap      nsnp
Class:    matrix   numeric character character   numeric   numeric

rehh documentation built on Sept. 15, 2021, 5:06 p.m.