Gene Ontology data

This class is used to store the gene ontology information for usage in GSE elimination methods.

Usage

GeneOntologyElim(go_data_dt, min_genes)

Arguments

go_data_dt

A data.table that contains the gene ontology information. This can be extract with for example get_go_data_human().

min_genes

data.frame. Meta-data information in form of a data.frame.

Value

Returns the class for subsequent usage.

Properties

go_info

data.table. Contains the gene ontology identifiers and names.

go_to_genes

List. Contains the genes within each gene ontology term.

ancestry

List. Contains the ancestors for each gene ontology term.

levels

List. Which gene ontology terms sit at which level.

min_genes

Integer, the minimum genes in the gene ontology term to conduct the test.

Examples

# \donttest{
# human GO restricted to terms with at least 25 genes
go_obj <- GeneOntologyElim(
  get_go_data_human(.verbose = FALSE),
  min_genes = 25L
)
go_obj
#> Gene ontology enrichment class:
#>  Contains 1974 gene ontology terms.
#>  Total of 14 levels represented in the ontology.
#>  Minimum genes per term set to 25.
# }