enrich_go_custom: Enriched ontologies for a custom organism

In OceaneCsn/DIANE: DIANE

Enriched ontologies for a custom organism

Description

Enriched custom Gene Ontology terms in a set of genes, from a dataframe giving Go terms to genes matching

Usage

enrich_go_custom(
  genes,
  universe = genes_to_GO[, 1],
  genes_to_GO,
  qvalue = 0.1,
  pvalue = 0.05,
  GO_type = "BP"
)

Arguments

genes	list of gene IDs, as present in the first column od genes_to_GO
universe	list of gene IDs as background, default is set to all the genes contained in genesto_GO
genes_to_GO	dataframe with gene IDs as first column, and GO IDs as second column. gene IDs must be the IDs present in your gene expresion file
qvalue	qvalue cutoff for enriched GO terms, default to 0.1
pvalue	qvalue cutoff for enriched GO terms, default to 0.05
GO_type	character between BP (Biological Process), CC(Cellular Component) or MF (Molecular Function), depending on the GO type to use in the analysis

Value

dataframe containing enriched go terms and their description

OceaneCsn/DIANE documentation built on Jan. 10, 2024, 6:43 p.m.