clr function

Context Likelihood or Relatedness Network

A function that infers the interaction network using the CLR algorithm.

clr(mi)

Arguments

• mi: matrix of the mutual information.

Returns

A square weighted adjacency matrix of the inferred network.

Details

CLR computes the score

for each pair of variables $i, j$, where

and $mean(Xi)$ and $sd(Xi)$ are the mean and the standard deviation of the mutual information values $I(Xi;Xk)$ for all $k=1,\ldots,n$.

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

Jeremiah J. Faith, Boris Hayete, Joshua T. Thaden, Ilaria Mogno, Jamey Wierzbowski, Guillaume Cottarel, Simon Kasif, James J. Collins, and Timothy S. Gardner. Large-scale mapping and validation of escherichia coli transcriptional regulation from a compendium of expression profiles. PLoS Biology, 2007.

See Also

aracne.a

aracne.m

mrnet

Examples

mat <- matrix(rnorm(1000), nrow=10)
mi  <- knnmi.all(mat)
grn <- clr(mi)