filterResults: Filter the results to retain only the selected terms

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

Filter the results to retain only the selected terms

Description

Filter the enrichment results to retain only the selected terms and remove root term if requested.

Usage

filterResults(gostResults, source, termIDs, removeRoot)

Arguments

gostResults	a data.frame containing the enriched terms that should be filtered.
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 or NULL.
removeRoot	a logical that specified if the root terms of the selected source should be removed (when present).

Value

a data.frame of filtered terms with or without the root term.

Author(s)

Astrid Deschênes

Examples

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

## Only retained the GO - Molecular Function results
results <- demoGOST$result

## Remove WIKIPATHWAYS root term
selected <- enrichViewNet:::filterResults(gostResults=results, source="WP", 
    termIDs=NULL, removeRoot=TRUE)

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