R: Algorithm for the Reconstruction of Accurate Cellular...

aracne.m {parmigene} | R Documentation

## Algorithm for the Reconstruction of Accurate Cellular Networks

### Description

A function that implements the ARACNE algorithm for the reconstruction of gene interaction networks (multiplicative model).

### Usage

    aracne.m(mi, tau=0.15)

### Arguments

`mi` | matrix of the mutual information.
`tau` | a positive numeric value used to remove the weakest edge of each triple of nodes.

### Details

This algorithm considers each triple of edges independently and removes the weakest one if

MI(i;j) < MI(j;k) * (1 - tau)

and

MI(i;j) < MI(i;k) * (1 - tau)

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

Adam A. Margolin, Ilya Nemenman, Katia Basso, Chris Wiggins, Gustavo Stolovitzky, Riccardo Dalla Favera, and Andrea Califano. Aracne : An algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context. BMC Bioinformatics, 2006.

### See Also

`aracne.a`

`clr`

`mrnet`

### Examples

    mat <- matrix(rnorm(1000), nrow=10)
    mi  <- knnmi.all(mat)
    grn <- aracne.m(mi, 0.15)

[Package parmigene version 1.0.2 Index]