miic.write.network.cytoscape

[a miic graph object] The graph object returned by the miic execution.

[a data frame]. An optional data frame of 2 (or 3) columns containing the coordinate x and y 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

[a string] The file path of the output file (containing the file name without extension).

file

This function writes the network using the graphml format (http://graphml.graphdrawing.org/).

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: Verny et al. Plos Comput Biol. (2017) <doi:10.1371/journal.pcbi.1005662>.

miic.write.network.cytoscape: Graphml writing function for the miic graph

Description

Usage

Arguments

Details