Description Usage Arguments Details References See Also Examples

A function that computes the mutual information between all pairs
of rows of matrix `mat`

using entropy estimates from K-nearest neighbor distances.

1 | ```
knnmi.all(mat, k=3, noise=1e-12)
``` |

`mat` |
a numeric matrix (for the reconstruction of gene regulatory networks, genes on rows and samples on columns). |

`k` |
the number of nearest neighbors to consider to estimate the
mutual information. Must be less than the number of columns of |

`noise` |
the magnitude of the random noise added to break ties. |

The function adds a small random noise to the data in order to break ties due to limited numerical precision.

By default, the function uses all the available cores. You can
set the actual number of threads used to N by exporting the
environment variable `OMP_NUM_THREADS=N`

.

Kraskov, Alexander and Stogbauer, Harald and Grassberger, Peter.
*Estimating mutual information.* Phys. Rev. E, 2004.

1 2 |

parmigene documentation built on May 29, 2017, 11:58 a.m.

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