Harmonize assay-specific feature identifiers to common entities

Maps feature IDs within each omic to a shared entity identifier for entity-level cross-omic analysis (for example Ensembl RNA identifiers and UniProt proteins to a common gene symbol). Many-to-one mappings are rejected by default because collapsing isoforms/probes changes the scientific estimand.

Usage

harmonize_entities(
  data,
  mapping,
  collapse = c("error", "mean", "median"),
  min_mapped = 1L
)

Arguments

data

An `omics_braid_data` object.

mapping

Data frame with columns `omic`, `feature_id`, and `entity`.

collapse

How to handle multiple assay features mapping to one entity: `"error"` (default), `"mean"`, or `"median"`.

min_mapped

Minimum mapped entities required per retained omic.

Value

An `omics_braid_data` object with harmonized entity row names and a mapping report stored in `attr(x, "entity_harmonization")`.