show-methods

show,Dna-method

show,Haplotype-method

show,Parsimnet-method

Show objects of classes <code>Dna</code>, <code>Haplotype</code>, and <code>Parsimnet</code>

DNA ANALYSIS

STATISTICAL PARSIMONY

HAPLOTYPE ANALYSIS

Provides S4 classes and methods for reading and manipulating aligned DNA sequences, supporting an indel coding methods (only simple indel coding method is available in the current version), showing base substitutions and indels, calculating absolute pairwise distances between DNA sequences, and collapses identical DNA sequences into haplotypes or inferring haplotypes using user provided absolute pairwise character difference matrix.  This package also includes S4 classes and methods for estimating genealogical relationships among haplotypes using statistical parsimony and plotting parsimony networks.

Caner Aktas

haplotypes

Manipulating DNA Sequences and Estimating Unambiguous Haplotype
Network with Statistical Parsimony

show-methods function

<dl><dt><code>signature(object = "Dna")</code></dt>
<dd>displays <code>Dna</code> object briefly: The total number of DNA sequences, names of the first six sequences (if nrow(x)&gt;=6), length of the shortest and longest sequences and the names of the slots.</dd>
<dt><code>signature(object = "Haplotype")</code></dt>
<dd>displays <code>Haplotype</code> object briefly: The list of individuals that share the same haplotypes, the total number of haplotypes and the names of the slots.</dd>
<dt><code>signature(object = "Parsimnet")</code></dt>
<dd>displays <code>Parsimnet</code> object briefly: The total number of networks, the maximum connection steps at chosen probability, the total number of haplotypes in each network,the total number of intermediates in each network, total network lengths (scores) of each network and the names of the slots.</dd></dl>

Methods

Methods for function show in the package haplotypes — show-methods

<dl>

<dt><code>signature(object = "Dna")</code></dt>
<dd>displays <code>Dna</code> object briefly: The total number of DNA sequences, names of the first six sequences (if nrow(x)&gt;=6), length of the shortest and longest sequences and the names of the slots.</dd>


<dt><code>signature(object = "Haplotype")</code></dt>
<dd>displays <code>Haplotype</code> object briefly: The list of individuals that share the same haplotypes, the total number of haplotypes and the names of the slots.</dd>


<dt><code>signature(object = "Parsimnet")</code></dt>
<dd>displays <code>Parsimnet</code> object briefly: The total number of networks, the maximum connection steps at chosen probability, the total number of haplotypes in each network,the total number of intermediates in each network, total network lengths (scores) of each network and the names of the slots.</dd>



</dl>

show-methods: Methods for function `show` in the package haplotypes

Description

Arguments

Methods