Algorithms and framework for Nonnegative Matrix Factorization (NMF).

Description

This package provides a framework to perform Non-negative Matrix Factorization (NMF). It 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.

Details

nmf Run a given NMF algorithm

Author(s)

Renaud Gaujoux renaud@cbio.uct.ac.za

References

http://cran.r-project.org/

http://nmf.r-forge.project.org

See Also

nmf

Examples

# generate a synthetic dataset with known classes
n <- 50; counts <- c(5, 5, 8);
V <- syntheticNMF(n, counts)

# perform a 3-rank NMF using the default algorithm
res <- nmf(V, 3)

basismap(res)
coefmap(res)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(NMF)
Loading required package: pkgmaker
Loading required package: registry

Attaching package: 'pkgmaker'

The following object is masked from 'package:base':

    isNamespaceLoaded

Loading required package: rngtools
Loading required package: cluster
NMF - BioConductor layer [OK] | Shared memory capabilities [OK] | Cores 3/4
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/NMF/NMF-package.Rd_%03d_medium.png", width=480, height=480)
> ### Name: NMF-package
> ### Title: Algorithms and framework for Nonnegative Matrix Factorization
> ###   (NMF).
> ### Aliases: NMF NMF-package
> ### Keywords: package
> 
> ### ** Examples
> 
> ## Don't show: 
> # roxygen generated flag
> options(R_CHECK_RUNNING_EXAMPLES_=TRUE)
> ## End(Don't show)
> 
> # generate a synthetic dataset with known classes
> n <- 50; counts <- c(5, 5, 8);
> V <- syntheticNMF(n, counts)
> 
> # perform a 3-rank NMF using the default algorithm
> res <- nmf(V, 3)
> 
> basismap(res)
> coefmap(res)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>