Description Usage Arguments Details Methods References

Computes the dispersion coefficient of a – consensus –
matrix `object`

, generally obtained from multiple
NMF runs.

1 | ```
dispersion(object, ...)
``` |

`object` |
an object from which the dispersion is computed |

`...` |
extra arguments to allow extension |

The dispersion coefficient is based on the consensus matrix (i.e. the average of connectivity matrices) and was proposed by Kim et al. (2007) to measure the reproducibility of the clusters obtained from NMF.

It is defined as:

*ρ = ∑_{i,j=1}^n 4 (C_{ij} -
\frac{1}{2})^2 , *

where *n* is the total number of
samples.

By construction, *0 ≤q ρ ≤q 1* and *ρ =
1* only for a perfect consensus matrix, where all entries
0 or 1. A perfect consensus matrix is obtained only when
all the connectivity matrices are the same, meaning that
the algorithm gave the same clusters at each run. See
Kim et al. (2007).

- dispersion
`signature(object = "matrix")`

: Workhorse method that computes the dispersion on a given matrix.- dispersion
`signature(object = "NMFfitX")`

: Computes the dispersion on the consensus matrix obtained from multiple NMF runs.

Kim H and Park H (2007). "Sparse non-negative matrix factorizations via alternating non-negativity-constrained least squares for microarray data analysis." _Bioinformatics (Oxford, England)_, *23*(12), pp. 1495-502. ISSN 1460-2059, <URL: http://dx.doi.org/10.1093/bioinformatics/btm134>, <URL: http://www.ncbi.nlm.nih.gov/pubmed/17483501>.

NMF documentation built on March 18, 2018, 1:41 p.m.

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