BiBitR

BiBitR-package

BiBitR is a simple R wrapper which directly calls the original Java code for applying the BiBit algorithm.
The original Java code can be found at <a href="http://eps.upo.es/bigs/BiBit.html">http://eps.upo.es/bigs/BiBit.html</a> by Domingo S. Rodriguez-Baena, Antonia J. Perez-Pulido and Jesus S. Aguilar-Ruiz.
The BiBitR package also includes the following functions and/or workflows:<ul>
<li>A slightly adapted version of the original BiBit algorithm which now allows allows noise when adding rows to the bicluster (<code><a rd-options="" href="/link/bibit2?package=BiBitR&version=0.3.1" data-mini-rdoc="BiBitR::bibit2">bibit2</a></code>).</li>
<li>A function which accepts a pattern and, using the BiBit algorithm, will find biclusters fully or partly fitting the given pattern (<code><a rd-options="" href="/link/bibit3?package=BiBitR&version=0.3.1" data-mini-rdoc="BiBitR::bibit3">bibit3</a></code>).</li>
<li>A workflow which can discover larger patterns (and their biclusters) using BiBit and classic hierarchical clustering approaches (<code><a rd-options="" href="/link/BiBitWorkflow?package=BiBitR&version=0.3.1" data-mini-rdoc="BiBitR::BiBitWorkflow">BiBitWorkflow</a></code>).</li>
</ul>

A simple R wrapper for the Java BiBit algorithm from "A
biclustering algorithm for extracting bit-patterns from binary datasets"
from Domingo et al. (2011) <DOI:10.1093/bioinformatics/btr464>. An simple adaption for the BiBit algorithm which allows noise in the biclusters is also introduced as well as a function to guide the algorithm towards given (sub)patterns. Further, a workflow to derive noisy biclusters from discoverd larger column patterns is included as well.

Ewoud Troyer

R Wrapper for Java Implementation of BiBit

BiBitR function

BiBitR is a simple R wrapper which directly calls the original Java code for applying the BiBit algorithm.
The original Java code can be found at <a href = 'http://eps.upo.es/bigs/BiBit.html'>http://eps.upo.es/bigs/BiBit.html</a> by Domingo S. Rodriguez-Baena, Antonia J. Perez-Pulido and Jesus S. Aguilar-Ruiz.
The BiBitR package also includes the following functions and/or workflows:<ul>
<li>A slightly adapted version of the original BiBit algorithm which now allows allows noise when adding rows to the bicluster (<code><a rd-options='' href='bibit2'>bibit2</a></code>).</li>
<li>A function which accepts a pattern and, using the BiBit algorithm, will find biclusters fully or partly fitting the given pattern (<code><a rd-options='' href='bibit3'>bibit3</a></code>).</li>
<li>A workflow which can discover larger patterns (and their biclusters) using BiBit and classic hierarchical clustering approaches (<code><a rd-options='' href='BiBitWorkflow'>BiBitWorkflow</a></code>).</li>
</ul>

BiBitR: A biclustering algorithm for extracting bit-patterns from binary datasets

Description

Arguments

References