parmigene (version 1.1.1)

knnmi.cross: Parallel Mutual Information Estimation Between the Rows of Two Matrices

Description

A function that estimates the mutual information between all pairs of rows of matrices mat1 and mat2 using entropy estimates from K-nearest neighbor distances.

Usage

knnmi.cross(mat1, mat2, k=3, noise=1e-12)

Arguments

mat1

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

mat2

a numeric matrix with the same number of columns as mat1.

k

the number of nearest neighbors to consider to estimate the mutual information. Must be less than the number of columns of mat1.

noise

the magnitude of the random noise added to break ties.

Details

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.

References

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

See Also

knnmi

knnmi.all

Examples

mat1 <- matrix(rnorm(1000), nrow=10)
mat2 <- matrix(rnorm(1000), nrow=10)
knnmi.cross(mat1, mat2, 5)