diffusion {CeTF} | R Documentation

## 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)

[Package CeTF version 1.2.4 Index]