Process Gene Ontology data into the right format

Helper function that takes in different files containing gene ontology data and puts them together for various gene set enrichment methods using the ontological information

Usage

process_go_data(go_info, go_genes, go_relationships)

Arguments

go_info

data.table. Contains go_id, go_name and namespace.

go_genes

data.table. Contains go_id and corresponding ensembl_id.

go_relationships

data.table. Contains parent, child and relationship

Value

data.table ready for usage in GeneOntologyElim().

Examples

# \donttest{
# assemble the packaged human GO data by hand
go_data <- load_go_human_data()
relationships <- data.table::setnames(
  data.table::copy(go_data$gene_ontology),
  old = c("from", "to"),
  new = c("parent", "child")
)
go_dt <- process_go_data(
  go_info = go_data$go_info,
  go_genes = go_data$go_to_genes,
  go_relationships = relationships[relationship %in% c("is_a", "part_of")]
)
dim(go_dt)
#> [1] 18841     6
# }