consensus,NMFfitXn-method

plot.NMF.consensus

an object with a suitable
 <code><a rd-options="" href="/link/predict?package=NMF&version=0.24.0" data-mini-rdoc="NMF::predict">predict</a></code> method.

object

extra arguments to allow extension. They are
 passed to <code><a rd-options="" href="/link/predict?package=NMF&version=0.24.0" data-mini-rdoc="NMF::predict">predict</a></code>, except for the
 <code>vector</code> and <code>factor</code> methods.

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>).

no.attrib

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)

consensus,NMFfitXn-method function

<dl> <dt>object</dt>
<dd>an object with a suitable
 <code><a href="/link/predict?package=NMF&version=0.24.0" 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=0.24.0" 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