R: Context Likelihood or Relatedness Network

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(zi^2 + zj^2)

for each pair of variables i, j, where

zi = max(0, ( I(Xi;Xj)-mean(Xi) ) / sd(Xi))

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,…,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

`aracne.a`

`aracne.m`

`mrnet`

### Examples

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

[Package parmigene version 1.0.2 Index]