create_upsetdata: Create a geneset upset dataset

In federicomarini/GeneTonic: Enjoy Analyzing And Integrating The Results From Differential Expression Analysis And Functional Enrichment Analysis

Create a geneset upset dataset

Description

Create a data frame that can be fed to the upset function

Usage

create_upsetdata(res_enrich, use_ids = FALSE)

Arguments

res_enrich	A data.frame object, storing the result of the functional enrichment analysis. See more in the main function, GeneTonic(), to see the formatting requirements.
use_ids	Logical - whether to use the gs_identifiers as names, or the values provided as gs_description. Defaults to FALSE, using the full descriptions

Value

A data.frame to be used in ComplexUpset::upset()

Examples

# res_enrich object
data(res_enrich_macrophage, package = "GeneTonic")
res_enrich <- shake_topGOtableResult(topgoDE_macrophage_IFNg_vs_naive)

create_upsetdata(res_enrich[1:20, ])
dim(create_upsetdata(res_enrich[1:20, ]))

create_upsetdata(res_enrich[1:5, ], use_ids = TRUE)

federicomarini/GeneTonic documentation built on Oct. 10, 2024, 8:49 p.m.