🔄 convert_gene_id(): Convert gene identifiers using a reference table

Converts between Ensembl, Symbol, and Entrez gene IDs using a reference table. Supports both character vectors and data.frame columns. Automatically loads species-specific reference data from data/, or downloads if unavailable.

Usage

convert_gene_id(
  query,
  from = "symbol",
  to = c("ensembl_id", "entrez_id"),
  species = c("human", "mouse"),
  query_col = NULL,
  ref_table = NULL,
  keep_na = FALSE,
  preview = TRUE
)

Arguments

query

Character vector or data.frame to convert.

from

Source ID type (e.g., "symbol", "ensembl_id", "entrez_id").

to

Target ID type(s). Supports multiple.

species

Either "human" or "mouse". Default "human".

query_col

If query is a data.frame, the column name to convert.

ref_table

Optional reference table.

keep_na

Logical. Whether to keep unmatched rows. Default: FALSE.

preview

Logical. Whether to preview output. Default: TRUE.

Value

A data.frame containing original and converted columns.