validateCreateNetworkArguments: Validate arguments passed to creatNetwork() function

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

Validate arguments passed to creatNetwork() function

Description

Validate the arguments passed to creatNetwork() function. First, the object containing the enrichment results must correspond to a object created by gprofiler2 software. Second, the selected source must at least have one enriched term in the results. Then, if the source is 'TERM_ID', the listed terms must be present in the enrichment results.

Usage

validateCreateNetworkArguments(
  gostObject,
  source,
  termIDs,
  removeRoot,
  query,
  title,
  collection,
  fileName
)

Arguments

gostObject	a list created by gprofiler2 that contains the results from an enrichment analysis.
source	a character string representing the selected source that will be used to generate the network. To hand-pick the terms to be used, "TERM_ID" should be used and the list of selected term IDs should be passed through the termIDs parameter. The possible sources are "GO:BP" for Gene Ontology Biological Process, "GO:CC" for Gene Ontology Cellular Component, "GO:MF" for Gene Ontology Molecular Function, "KEGG" for Kegg, "REAC" for Reactome, "TF" for TRANSFAC, "MIRNA" for miRTarBase, "CORUM" for CORUM database, "HP" for Human phenotype ontology and "WP" for WikiPathways.
termIDs	a vector of character strings that contains the term IDs retained for the creation of the network. This parameter is only used when source is set to "TERM_ID".
removeRoot	a logical that specified if the root terms of the selected source should be removed (when present).
query	a character string that specified the retained query to generate the network or NULL.
title	a character string representing the name assigned to the network.
collection	a character string representing the collection name assigned to the network.
fileName	a character string representing the name of the CX JSON file that is created when Cytoscape is not running. The name must have a '.cx' extension.

Value

TRUE when all arguments are valid

Author(s)

Astrid Deschênes

Examples

## Load the result of an enrichment analysis done with gprofiler2
data(demoGOST)

## Check that all arguments are valid
enrichViewNet:::validateCreateNetworkArguments(gostObject=demoGOST,
    source="GO:BP", termIDs=NULL, removeRoot=FALSE, query=NULL, 
    title="Network graph Test",
    collection="test collection", fileName="test.cx")

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