CorrelationOverlap

This function computes the correlation between Nodes and the Overlapping Nodes of interest.

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

CorrelationOverlap function

<dl><dt>Data</dt>
<dd>data.frame containing the expression data. Nodes on the Rows, Individuals on the Columns. Don't forget to give the names to the Nodes and to the Individuals. Nodes must have the row.names() with the Node Name.</dd>
<dt>Overlap</dt>
<dd>A vector containg the names of the Nodes of interest.</dd>
<dt>method</dt>
<dd>Spearman ("s", "spearman") or Pearson ("p", "pearson") correlation</dd></dl>

Arguments

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

Author

CorrelationOverlap — CorrelationOverlap

<dl>

<dt>Data</dt>
<dd>data.frame containing the expression data. Nodes on the Rows, Individuals on the Columns. Don't forget to give the names to the Nodes and to the Individuals. Nodes must have the row.names() with the Node Name.</dd>


<dt>Overlap</dt>
<dd>A vector containg the names of the Nodes of interest.</dd>


<dt>method</dt>
<dd>Spearman ("s", "spearman") or Pearson ("p", "pearson") correlation</dd>

</dl>

CorrelationOverlap: CorrelationOverlap

Description

Usage

Arguments

Author