metagenomics_abundance

datasets

Computes the Weighted Topological Overlap with positive and negative signs (wTO) networks given a data frame containing the mRNA count/ expression/ abundance per sample, and a vector containing the interested nodes of interaction (a subset of the elements of the full data frame). It also computes the cut-off threshold or p-value based on the individuals bootstrap or the values reshuffle per individual. It also allows the construction of a consensus network, based on multiple wTO networks. The package includes a visualization tool for the networks.  More about the methodology can be found at <doi:10.1186/s12859-018-2351-7>.

Deisy Gysi

Computing Weighted Topological Overlaps (wTO) & Consensus wTO
Network

metagenomics_abundance function

<p>data.frame from The USC Microbial Observatory. The data is public available at &lt;https://www.ebi.ac.uk/metagenomics/projects/ERP013549&gt;</p>

metagenomics_abundance: metagenomics_abundance

Description

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