run_aracne: run_aracne

In PRANA: Pseudo-Value Regression Approach for Network Analysis (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.

PRANA documentation built on Sept. 30, 2024, 9:25 a.m.