run_aracne {PRANA}

run_aracne

Description

A function to conduct co-expression analysis using ARACNE (Margolin et al. 2006). Uses the implementation from the minet package (Meyer et al. 2008). This function is from dnapath R package, which is archived in May 2024.

Usage

run_aracne(
  x,
  estimator = "spearman",
  disc = "none",
  nbins = NULL,
  eps = 0,
  ...
)

Arguments

x

A n by p matrix of gene expression data (n samples and p genes)

estimator

Argument is passed into minet::build.mim.

disc

Argument is passed into minet::build.mim.

nbins

Argument is passed into minet::build.mim.

eps

Argument is passed into minet::aracne.

...

Additional arguments are ignored.

Value

A p by p matrix of association scores.

References

Margolin AA, Nemenman I, Basso K, Wiggins C, Stolovitzky G, Dalla Favera R, Califano A (2006). “ARACNE: An Algorithm for the Reconstruction of Gene Regulatory Networks in a Mammalian Cellular Context.” In BMC Bioinformatics, volume 7(1), S7. BioMed Central.

Meyer PE, Lafitte F, Bontempi G (2008). “minet: A R/Bioconductor Package for Inferring Large Transcriptional Networks using Mutual Information.” BMC Bioinformatics, 9(1), 461.