ARACNE-AP output for Viper R package
Entering edit mode
2.3 years ago
Luna_P • 0


I am using ARACNE-AP via Docker to generate networks from my gene matrix. As an input, I am using a text file, with genes on rows and samples on columns and a gene list( the ones that I am mostly interested in whether to learn if they create hubs or not).

ARACNE-AP returns a network.txt file where the first column is regulators the second is target the third is mutual information score and the fourth is the p-value. According to what I read & understood, with MI we create a rank, and then according to this threshold, we decide whether it is a direct interaction or not. However, there are some things that I still can't wrap my head around.

My questions:

  • How does that threshold is decided? (sample number affect this but I can't understand how)
  • According to that threshold how does ARACNE-AP generates p-values?

For Viper, the network generated from ARACNE is used as an input and the format is in .adj. However, ARACNE-AP doesn't support this anymore. If anyone used ARACNE and Viper recently I would like to ask:

  • Would changing the extension manually from .txt to .adj cause problems?

Viper also accepts 3 column .txt file but what surprised me here is that my gene expression matrix has much more genes (rows) than my network file generated from ARACNE-AP which is probably because not all of them have pairwise direct interactions. For this part I would like to ask:

  • Would subsetting the gene matrix according to the network file is reasonable?

I guess this a bit more general question:

  • Which network file from which ARACNE could be given as an input for Viper?


ARACNE ARACNE-AP Viper • 1.6k views
Entering edit mode
2.1 years ago
Scott ▴ 10

You can use the .txt output from ARACNE-AP with the viper function aracne2regulon. You just have to include format = "3col".

regulons <- aracne2regulon(afile = "path/to/aracne_AP_output/network.txt", eset, format = "3col")

Also, I found that you need to go into the ARACNE-AP .txt output file and delete the first row containing the column headers "Regulator Target MI pvalue"


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