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Merge DrugBank and HPO Gene-Phenotype Database Objects

Source: R/merge_helpers.R
merge_drugbank_hpo.Rd

Creates an integrated dvobject by linking DrugBank target gene data with HPO gene-phenotype associations using gene symbols as the bridge.

Usage

merge_drugbank_hpo(db_object, hpo_db)

Arguments

db_object

A dvobject from parseDrugBank() OR an existing merged dvobject (containing $drugbank).

hpo_db

A dvobject produced by dbparser::parseHPO().

Value

A new dvobject containing the integrated data.

Details

This function performs the following key steps: 1. Extracts gene names from DrugBank polypeptide data ($cett$targets$polypeptides$general_information). 2. Links gene names to DrugBank IDs via the target_id bridge ($cett$targets$general_information). 3. Optionally resolves DrugBank IDs to drug names. 4. Enriches the HPO gene-phenotype association table by adding drugbank_id and drug_name columns. 5. Assembles a merged object containing all original data plus the enriched table and the gene mapping bridge.

Supports piping and chaining with other merge functions.

See also

Other mergers: merge_drugbank_onsides(), merge_drugbank_twosides()

Examples

if (FALSE) { # \dontrun{
drugbank <- parseDrugBank("path/to/drugbank.xml")
hpo      <- parseHPO("path/to/gene_attribute_edges.tsv")

# Standalone merge
merged_db <- merge_drugbank_hpo(drugbank, hpo)

# Chained with other merges (any order)
full_db <- drugbank %>%
  merge_drugbank_hpo(hpo) %>%
  merge_drugbank_onsides(onsides) %>%
  merge_drugbank_twosides(twosides)

# --- Example: Find drugs targeting genes associated with seizures ---
seizure_drugs <- full_db$integrated_data$gene_phenotype_enriched %>%
  filter(grepl("seizure", phenotype_name, ignore.case = TRUE)) %>%
  filter(!is.na(drugbank_id)) %>%
  select(drug_name, drugbank_id, gene_symbol, phenotype_name) %>%
  distinct()
} # }