wTO.rep_measure

Compute the wTO for a repeated measures expermiment and also the bootstraps. Proposed at arXiv:1711.04702. This is a quicker version of the wTO.Complete. It doesn'T contain diagnose plots nor a parallel version.

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.rep_measure function

<dl><dt>Data</dt>
<dd>data.frame containing the count / expression data for the correlation.</dd>
<dt>Overlap</dt>
<dd>Set of nodes of interest, where the Overlapping weights will be computed.</dd>
<dt>ID</dt>
<dd>a vector with the individuals identification</dd>
<dt>sign</dt>
<dd>Should the wTO be signed?</dd>
<dt>delta</dt>
<dd>expected difference between the real wTO and the bootstraped.</dd>
<dt>n</dt>
<dd>Number of resamplings, used to compute the empirical distribuitions of the links. Default is set to 100.</dd></dl>

Arguments

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

Author

wTO.rep_measure — wTO.rep_measure

<dl>

<dt>Data</dt>
<dd>data.frame containing the count / expression data for the correlation.</dd>


<dt>Overlap</dt>
<dd>Set of nodes of interest, where the Overlapping weights will be computed.</dd>


<dt>ID</dt>
<dd>a vector with the individuals identification</dd>


<dt>sign</dt>
<dd>Should the wTO be signed?</dd>


<dt>delta</dt>
<dd>expected difference between the real wTO and the bootstraped.</dd>


<dt>n</dt>
<dd>Number of resamplings, used to compute the empirical distribuitions of the links. Default is set to 100.</dd>

</dl>

wTO.rep_measure: wTO.rep_measure

Description

Usage

Arguments

Author

Examples