miic.write.network.cytoscape

The graph object returned by <a rd-options="=miic" href="/link/miic?package=miic&version=1.5.3&to=%3Dmiic" data-mini-rdoc="=miic::miic">miic</a>.

A string. Path to the output file containing file name without
extension (.graphml will be appended).

file

An optional data frame of 2 (or 3) columns containing the
coordinate <code>x</code> and <code>y</code> for each node. The optional first column can contain
node names. If node names is not given, the order of the input file will be
assigned to the list of positions.

layout

Convert miic graph to <a href="http://graphml.graphdrawing.org/">GraphML format</a>.

We report an information-theoretic method which learns a large
class of causal or non-causal graphical models from purely observational
data, while including the effects of unobserved latent variables, commonly
found in many datasets. Starting from a complete graph, the method
iteratively removes dispensable edges, by uncovering significant information
contributions from indirect paths, and assesses edge-specific confidences
from randomization of available data. The remaining edges are then oriented
based on the signature of causality in observational data. This approach can
be applied on a wide range of datasets and provide new biological insights
on regulatory networks from single cell expression data, genomic alterations
during tumor development and co-evolving residues in protein structures.
For more information you can refer to:
Cabeli et al. PLoS Comp. Bio. 2020 <doi:10.1371/journal.pcbi.1007866>,
Verny et al. PLoS Comp. Bio. 2017 <doi:10.1371/journal.pcbi.1005662>.

Vincent Cabeli

miic

Learning Causal or Non-Causal Graphical Models Using Information
Theory

Honghao Li

Marcel Ribeiro Dantas

Nadir Sella

Louis Verny

Severine Affeldt

Hervé Isambert

miic.write.network.cytoscape function

<dl><dt>g</dt>
<dd>The graph object returned by miic.</dd>
<dt>file</dt>
<dd>A string. Path to the output file containing file name without
extension (.graphml will be appended).</dd>
<dt>layout</dt>
<dd>An optional data frame of 2 (or 3) columns containing the
coordinate <code>x</code> and <code>y</code> for each node. The optional first column can contain
node names. If node names is not given, the order of the input file will be
assigned to the list of positions.</dd></dl>

Arguments

Convert miic graph to <a href='http://graphml.graphdrawing.org/'>GraphML format</a>.

GraphML converting function for miic graph — miic.write.network.cytoscape

<dl>

<dt>g</dt>
<dd>The graph object returned by miic.</dd>


<dt>file</dt>
<dd>A string. Path to the output file containing file name without
extension (.graphml will be appended).</dd>


<dt>layout</dt>
<dd>An optional data frame of 2 (or 3) columns containing the
coordinate <code>x</code> and <code>y</code> for each node. The optional first column can contain
node names. If node names is not given, the order of the input file will be
assigned to the list of positions.</dd>

</dl>

miic.write.network.cytoscape: GraphML converting function for miic graph

Description

Usage

Arguments