Retrieve representative transcript lengths from Ensembl — annotate_gene

This online convenience function queries BioMart for transcript lengths and summarizes multiple annotated transcripts per input gene. These annotation lengths are not sample-specific effective lengths; quantified RNA-seq data should preferentially use the length assay from import_tximport().

Usage

annotate_gene_lengths(
  ids,
  dataset = "hsapiens_gene_ensembl",
  id_type = "ensembl_gene_id",
  summary = c("median", "mean", "max"),
  strip_version = TRUE,
  biomart = "genes",
  mirror = NULL,
  version = NULL
)

Arguments

ids: Unique feature identifiers.
dataset: Ensembl dataset, for example hsapiens_gene_ensembl.
id_type: BioMart gene identifier attribute and filter.
summary: How to summarize multiple positive transcript lengths per gene.
strip_version: Remove terminal numeric Ensembl version suffixes before querying.
biomart, mirror, version: Passed to annotate_biomart().

Value

A feature-aligned data frame with source_id, query_id, gene_length, and n_transcripts. Missing genes retain NA lengths.