Calculates the weighted topologycal overlap (wTO)
between a set of Nodes and the Overlapping nodes. This function implements the method from Nowick (2009).

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

wTO function

<dl><dt>A_TF</dt>
<dd>Is the weighted adjency matrix (correlation matrix).</dd>
<dt>sign</dt>
<dd>("abs", "sign") if the user wants to use the absolute correlation or the signed correlation.</dd></dl>

Arguments

Deisy Morselli Gysi &lt;deisy at bioinf.uni-leipzig.de&gt;

Author

wTO — wTO

<dl>

<dt>A_TF</dt>
<dd>Is the weighted adjency matrix (correlation matrix).</dd>


<dt>sign</dt>
<dd>("abs", "sign") if the user wants to use the absolute correlation or the signed correlation.</dd>

</dl>

wTO: wTO

Description

Usage

Value

Arguments

Author

References