consensus,NMFfitXn-method

plot.NMF.consensus

This method returns <code>NULL</code> on an empty object. The
 result is a matrix with several attributes attached, that
 are used by plotting functions such as
 <code>consensusmap</code> to annotate the plots.

methods

Provides a framework to perform Non-negative Matrix
Factorization (NMF). The package implements a set of already published algorithms
and seeding methods, and provides a framework to test, develop and plug
new/custom algorithms. Most of the built-in algorithms have been optimized
in C++, and the main interface function provides an easy way of performing
parallel computations on multicore machines.

Nicolas Sauwen

Algorithms and Framework for Nonnegative Matrix Factorization
(NMF)

Renaud Gaujoux

Cathal Seoighe

consensus,NMFfitXn-method function

<dl> <dt>object</dt>
<dd>an object with a suitable
 <code><a href="/link/predict?package=NMF&version=0.28" data-mini-rdoc="NMF::predict">predict</a></code> method.</dd>
 <dt>...</dt>
<dd>extra arguments to allow extension. They are
 passed to <code><a href="/link/predict?package=NMF&version=0.28" data-mini-rdoc="NMF::predict">predict</a></code>, except for the
 <code>vector</code> and <code>factor</code> methods.</dd>
 <dt>no.attrib</dt>
<dd>a logical that indicates if attributes
 containing information about the NMF model should be
 attached to the result (<code>TRUE</code>) or not
 (<code>FALSE</code>).</dd></dl>

Arguments

Computes the consensus matrix of the set of fits stored in object, as
the mean connectivity matrix across runs. — consensus,NMFfitXn-method

<dl>

 <dt>object</dt>
<dd>an object with a suitable
 <code><a href='https://rdrr.io/r/stats/predict.html'>predict</a></code> method.</dd>


 <dt>...</dt>
<dd>extra arguments to allow extension. They are
 passed to <code><a href='https://rdrr.io/r/stats/predict.html'>predict</a></code>, except for the
 <code>vector</code> and <code>factor</code> methods.</dd>


 <dt>no.attrib</dt>
<dd>a logical that indicates if attributes
 containing information about the NMF model should be
 attached to the result (<code>TRUE</code>) or not
 (<code>FALSE</code>).</dd>

</dl>

consensus,NMFfitXn-method: Computes the consensus matrix of the set of fits stored in `object`, as the mean connectivity matrix across runs.

Description

Usage

Arguments