diffusion: Network diffusion analysis

In cbiagii/ceTF: Coexpression for Transcription Factors using Regulatory Impact Factors and Partial Correlation and Information Theory analysis

Network diffusion analysis

Description

Expand node selection using network propagation algorithms generating the expanded network for a core of genes and the network plot of this subnetwork.

Usage

diffusion(object, cond, genes, cyPath, name = "top_diffusion", label = TRUE)

Arguments

object	CeTF object resulted from runAnalysis function.
cond	Which conditions to be used to perform the diffusion analysis. The options are: network1 (1th condition) and network2 (2th condition).
genes	A single gene or a vector of characters indicating which genes will be used to perform diffusion analysis.
cyPath	System path of Cytoscape software (see details for further informations).
name	Network output name (default: top_diffusion)
label	If label is TRUE, shows the names of nodes (default: TRUE).

Details

To perform the diffusion analysis is necessary to install the latest Cytoscape software version (https://cytoscape.org/).

The cyPath argument varies depending on the operating system used, for example:

1. For Windows users: C:/Program Files/Cytoscape_v3.8.0/Cytoscape.exe

2. For Linux users: /home/user/Cytoscape_v3.8.0/Cytoscape

3. For macOS users: /Applications/Cytoscape_v3.8.0/cytoscape.sh

Value

Returns a list with the plot of the network and a table with the diffusion network.

Examples

## Not run:  
data(CeTFdemo)

result <- diffusion(object = CeTFdemo, 
                    cond = 'network1', 
                    genes = c('ENSG00000185591', 'ENSG00000179094'), 
                    cyPath = 'C:/Program Files/Cytoscape_v3.7.2/Cytoscape.exe', 
                    name = 'top_diffusion',
                    label = TRUE)

## End(Not run)

cbiagii/ceTF documentation built on Feb. 6, 2023, 9:05 p.m.