ARACNE-AP output for Viper R package

ARACNE-AP output for Viper R package



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?






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