deBruijn

DeBruijn-class

Classes for contructing de Bruijn graphs from collections of long read
 sequences mappe over brakpoints.

 manip 

Implements a method to combine multiple levels of multiple
sequence alignment to uncover the structure of complex DNA rearrangements.

Kevin Coombes

SVAlignR

Recovering Structure of Long Molecules from Structural Variation
Data

DeBruijn-class function

Objects should be defined using the <code>deBruijn</code> constructor.

Objects from the Class

<dl> <dt>rawseq</dt>
<dd>A character vecvtor of the long read sequences,
 expressed as hyphen-separated breakpoint ids.</dd> <dt>M</dt>
<dd>An integer; the length of the motifs/words to be used in
 constructing the graph.</dd></dl>

Arguments

<dl>
 <dt><code>G</code>:</dt>
<dd>An object of hhe <code><a href="/link/igraph?package=SVAlignR&version=0.9.2" data-mini-rdoc="SVAlignR::igraph">igraph</a></code> class</dd> <dt><code>adjmat</code>:</dt>
<dd>An adjacency matrix.</dd> <dt><code>motifs</code>:</dt>
<dd>A table of motifs/words.</dd> 
</dl>

Slots

Kevin R. Coombes &lt;krc@silicovore.com&gt;

Author

Class "DeBruijn" — DeBruijn-class

<dl>

 <dt>rawseq</dt>
<dd>A character vecvtor of the long read sequences,
 expressed as hyphen-separated breakpoint ids.</dd>

 <dt>M</dt>
<dd>An integer; the length of the motifs/words to be used in
 constructing the graph.</dd>

</dl>

<dl>
 <dt><code>G</code>:</dt>
<dd>An object of hhe <code><a href='https://rdrr.io/pkg/igraph/man/aaa-igraph-package.html'>igraph</a></code> class</dd>

 <dt><code>adjmat</code>:</dt>
<dd>An adjacency matrix.</dd>

 <dt><code>motifs</code>:</dt>
<dd>A table of motifs/words.</dd>

 
</dl>

DeBruijn-class: Class `"DeBruijn"`

Description

Usage

Value

Objects from the Class

Arguments

Slots

Author