wTO.aux.each

wTO.aux.each calculate the wTO for each one of the resamplings.

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

wTO.aux.each function

<dl><dt>n</dt>
<dd>Number of bootstraps / reshuffles to be run for the estimates of the "Threshold" or "pval".</dd>
<dt>Data</dt>
<dd>data.frame containing the count / expression data for the correlation.</dd>
<dt>Overlap</dt>
<dd>Nodes of interested, where the Overlapping weights will be computed.</dd>
<dt>method</dt>
<dd>Type of the correlation that should be used. "s" / "spearman" will compute the rank spearman correlation, "p" / "pearson" will compute the linear correlation. If no value is given, the default is to use "s".</dd>
<dt>method_resampling</dt>
<dd>method of the resampling. Bootstrap or Reshuffle. Bootstrap null hypothesis is that the wTO is random, and Reshuffle tests if the wTO is equal to zero.</dd></dl>

Arguments

wTO.aux.each — wTO.aux.each

<dl>

<dt>n</dt>
<dd>Number of bootstraps / reshuffles to be run for the estimates of the "Threshold" or "pval".</dd>


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


<dt>Overlap</dt>
<dd>Nodes of interested, where the Overlapping weights will be computed.</dd>


<dt>method</dt>
<dd>Type of the correlation that should be used. "s" / "spearman" will compute the rank spearman correlation, "p" / "pearson" will compute the linear correlation. If no value is given, the default is to use "s".</dd>


<dt>method_resampling</dt>
<dd>method of the resampling. Bootstrap or Reshuffle. Bootstrap null hypothesis is that the wTO is random, and Reshuffle tests if the wTO is equal to zero.</dd>

</dl>

wTO.aux.each: wTO.aux.each

Description

Usage

Arguments