createCXJSONForCytoscape: Create CX JSON text representing the network

In adeschen/gprofiler2cytoscape: From functional enrichment results to biological networks

Create CX JSON text representing the network

Description

Create a CX JSON text that represent the network which includes information about nodes and edges present in the network.

Usage

createCXJSONForCytoscape(nodeEdgeInfo, title)

Arguments

nodeEdgeInfo	a list created by gprofiler2 that contains the results from an enrichment analysis. TODO
title	a character string representing the name assigned to the network.

Value

character string that represent the network in a CX JSON format.

Author(s)

Astrid Deschênes

Examples

## Loading dataset containing result from an enrichment analysis done with
## gprofiler2
data(parentalNapaVsDMSOEnrichment)

## Only retained the GO Molecular Function results
results <- parentalNapaVsDMSOEnrichment$result[
        parentalNapaVsDMSOEnrichment$result$source == "GO:MF", ]

## Extract node and edge information
information <- enrichViewNet:::extractInformationWhenIntersection(
        gostResults=results)

jsonFormat <- enrichViewNet:::createCXJSONForCytoscape(
                nodeEdgeInfo=information, title="WikiPathways")

adeschen/gprofiler2cytoscape documentation built on Nov. 4, 2024, 3:16 p.m.