Default wrapper function for the aracne network inference algorithm
Numeric matrix with the microarray dataset to infer the network.Columns contain variables and rows contain samples.
The motivation of the Algorithm for the Reconstruction of Accurate Cellular NEtworks (ARACNE) is that many similar measures between variables may be the result of indirect effects. In order to delete the indirect effect the algorithm relies on the “Data Processing Inequality”, this process removes the weakest link in every triplet of connected variables.
aracne.wrapper returns a matrix which is the weighted adjacency
matrix of the network inferred by aracne algorithm.
The wrapper uses the "spearman" correlation
(can be used with continuous data) to estimate the
entropy - see
Margolin, Adam A., et al. "ARACNE: an algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context." BMC Bioinformatics 7.Suppl 1 (2006): S7.
Meyer, Patrick E., Frederic Lafitte, and Gianluca Bontempi. "minet: AR/Bioconductor package for inferring large transcriptional networks using mutual information." BMC Bioinformatics 9.1 (2008): 461.
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