enrich_go-ClusterSet-method: Enrichment analysis using GO database of gene clusters from a...
In dputhier/dbfmcl: The scigenex package (Single-Cell Informative GENe Explorer)

enrich_go,ClusterSet-method

R Documentation

Enrichment analysis using GO database of gene clusters from a ClusterSet object

Description

This function performs enrichment analysis of all gene clusters from a ClusterSet object and store the results in the cluster_annotations slot.

Usage

## S4 method for signature 'ClusterSet'
enrich_go(object, species = "Hsapiens", ontology = "all")

Arguments

`object`	an object of class `ClusterSet`.
`species`	a character string indicating the species name, as a concatenation of the first letter of the name (uppercase) and the family name (lowercase), e.g human -> Hsapiens, mouse -> Mmusculus
`ontology`	a character string indicating the ontology to use for the enrichment analysis. One of "BP", "MF", and "CC" ontology, or "ALL".

Value

A ClusterSet object

Examples

load_example_dataset("7871581/files/pbmc3k_medium_clusters")
load_example_dataset("8028126/files/pbmc3k_medium_clusters_enr")
# pbmc3k_medium_clusters_enr <- enrich_go(pbmc3k_medium_clusters)
pbmc3k_medium_clusters_enr
is(pbmc3k_medium_clusters_enr@gene_cluster_annotations)

dputhier/dbfmcl documentation built on Dec. 24, 2024, 4:35 p.m.