| clr {parmigene} | R Documentation |
Context Likelihood or Relatedness Network
Description
A function that infers the interaction network using the CLR algorithm.
Usage
clr(mi)
Arguments
mi |
matrix of the mutual information. |
Details
CLR computes the score
sqrt(z_i^2 + z_j^2)
for each pair of variables i, j, where
z_i = max(0, ( I(X_i;X_j)-mean(X_i) ) / sd(X_i))
and mean(X_i) and sd(X_i) are the mean
and the standard deviation of the mutual information values
I(X_i;X_k) 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.
Value
A square weighted adjacency matrix of the inferred network.
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
Examples
mat <- matrix(rnorm(1000), nrow=10)
mi <- knnmi.all(mat)
grn <- clr(mi)