extractInformationWhenNoIntersection: Extract information about nodes and edges to be used to...

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

Extract information about nodes and edges to be used to create network when interaction column is missing

Description

Create a list containing all node and edge information needed to create the network

Usage

extractInformationWhenNoIntersection(gostResults, gostObject)

Arguments

gostResults	a data.frame containing the terms retained for the creation of the network. The data.frame does not contain a column called "intersection".
gostObject	a list created by gprofiler2 that contains the results and meta-data from an enrichment analysis.

Value

list containing 2 entries:

• "geneNodes": a data.frame containing the information about the nodes present in the network. The nodes are genes.

• "termNodes": a data.frame containing the information about the nodes present in the network. The nodes are terms.

• "edges": a data.frame containing the information about the edges present in the network. The edges connect one gene to one term.

Author(s)

Astrid Deschênes

Examples

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

## Only retained the WikiPathways results
results <- demoGOST$result[demoGOST$result$source == "WP", ]

information <- enrichViewNet:::extractInformationWhenNoIntersection(
                gostResults=results, gostObject=demoGOST)

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