Cut.off

Computes the cutoff threshold using the descriptive values generated by the bootstrap, also plots the empirical distribution and the sample wTO.

internal

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

Cut.off function

<dl><dt>wTO_value</dt>
<dd>is the table returned by the wTO with all the simulated values.</dd>
<dt>type</dt>
<dd>type of plot</dd>
<dt>plot</dt>
<dd>logical value indicating whether to plot the data.</dd></dl>

Arguments

Cut.off — Cut.off

<dl>

<dt>wTO_value</dt>
<dd>is the table returned by the wTO with all the simulated values.</dd>


<dt>type</dt>
<dd>type of plot</dd>


<dt>plot</dt>
<dd>logical value indicating whether to plot the data.</dd>

</dl>

Cut.off: Cut.off

Description

Usage

Value

Arguments