Parsimnet-class: Class '"Parsimnet"' in the Package 'haplotypes'

In haplotypes: Manipulating DNA Sequences and Estimating Unambiguous Haplotype Network with Statistical Parsimony

Class "Parsimnet" in the Package haplotypes

Description

S4 class to store statistical parsimony networks and additional information.

Objects from the Class

Objects can be created by calls of the form new("Parsimnet", d, tempProbs, conlimit, prob, nhap, rowindex), however use function parsimnet instead.

Slots

d:

Object of class "list" containing the geodesic distance matrix of haplotypes and intermediates for each network.

tempProbs:

Object of class "numeric" giving the probabilities of parsimony for mutational steps beyond the connection limit.

conlimit:

Object of class "numeric" giving the number of maximum connection steps at connection limit.

prob:

Object of class "numeric" giving the user defined connection limit.

nhap:

Object of class "numeric" giving the number of haplotypes in each network.

rowindex:

Object of class "list" containing vectors giving the index of haplotypes in each network.

Methods

as.list

signature(x = "Parsimnet"): assigns slots of an object Parsimnet to list elements.

as.network

signature(x = "Parsimnet"): coerces Parsimnet object to network {network} object

as.networx

signature(x = "Parsimnet"): coerces Parsimnet object to networx {phangorn} object

length

signature(x = "Parsimnet"): returns the length of network(s).

names

signature(x = "Parsimnet"): gets names of networks in Parsimnet object

names<-

signature(x = "Parsimnet"): sets names of networks in Parsimnet object

plot

signature(x = "Parsimnet"): plots statistical parsimony networks.

pieplot

signature(x = "Parsimnet", y = "Haplotype"): plots pie charts on statistical parsimony networks

pielegend

signature(x = "Parsimnet", y = "Haplotype"): add legends to pie charts produced using pieplot.

rownames

signature(x = "Parsimnet"): gets names of vertices in networks.

rownames<-

signature(x = "Parsimnet"): gets names of vertices in networks

show

signature(object = "Parsimnet"): displays the object briefly.

Author(s)

Caner Aktas, [e-mail]

haplotypes documentation built on July 26, 2023, 5:22 p.m.