manageNameDuplicationInEmap: Change name description in data frame when more than one term...

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

Change name description in data frame when more than one term as the same name

Description

The function adds the ID of the term at the name of the name description when terms with different ID share the same name. For example, "MAPK pathway" would become "MAPK pathway (KEGG:04010)".

Usage

manageNameDuplicationInEmap(clProfDF)

Arguments

clProfDF

a data.frame containing the enrichment terms that are going to be graphed as an enrichment map. The data.frame must contain at least one case of duplicated name descriptions for different term IDs.

Value

a data.frame with the name descriptions modified for terms with duplicated name descriptions but different term IDs.

Author(s)

Astrid Deschênes

Examples

## Data frame with duplicated name descriptions for different IDs
clustData <- data.frame(Cluster=c("group 1" , "group 1", "group 2"), 
    ID=c("WP:WP4925", "WP:WP382", "KEGG:04010"),
    Description=c("Unfolded protein response", 
                    rep("MAPK signaling pathway", 2)),
    GeneRatio=c("4/157", "3/157", "3/157"),
    BgRatio=c("4/24022", "3/24022", "3/24022"),
    pvalues=c(1.55e-4, 8.13e-8, 4.33e-5),
    p.adjust=c(1e-3, 1e-3, 1.4e-3), qvalue=c(1e-3, 1e-3, 1.4e-3), 
    geneID=c("ENSG000107968/ENSG000120129/ENSG000123358/ENSG000158050",
        "ENSG000107968/ENSG000120129/ENSG000158050",
        "ENSG000107968/ENSG000120129/ENSG000158050"),
    Count=c(4, 3, 3))

## Change the name descriptions for the duplicated terms
enrichViewNet:::manageNameDuplicationInEmap(clProfDF=clustData)
    

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