Enriched ontologies for a custom organism

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

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