drugannotR

drugannotR performs coordinate-level pharmacological annotation:

genomic region -> genomic feature -> gene -> drug-gene relationship

It answers which drug-associated genes or regulatory domains overlap each input region and preserves the relationship category, evidence scope, and source record. It does not predict whether a drug will work, whether an overlap is functional, or how treatment should change.

The four main operations are:

drug_sets <- buildDrugGeneSets(
    sources = c("ClinPGx", "DGIdb", "DrugCentral")
)

drug_ranges <- mapDrugGenes(
    drug_sets,
    genome = "GRCh38",
    features = c("gene_body", "promoter")
)

annotations <- annotateDrugRegions("regions.bed", drug_ranges)

report <- summariseDrugAnnotations(
    annotations,
    by = c("region", "drug", "relationship")
)

ClinPGx/PharmGKB summary annotations, DGIdb interactions, and DrugCentral targets are downloaded into a BiocFileCache. Local source files can be supplied to obtain a fixed, reproducible snapshot.

See vignette("drugannotR") for a fully local example and the expected input schemas.