wb_load_tx2gene: Load transcript to gene correspondence table

In AlexWeinreb/wbData: Download And Use WormBase Data

Load transcript to gene correspondence table

Description

Loads a data frame providing the transcripts and corresponding gene IDs, built from the Wormbase GTF file. The GTF file will be downloaded as needed.

Usage

wb_load_tx2gene(WS, dir_cache = NULL)

Arguments

WS	Wormbase release version.
dir_cache	Directory where the downloaded files are cached.

Value

A tibble obtained from reading the Wormbase GTF, containing the following fields:

• gene_id: Wormbase gene ID (WBGene).

• transcript_id: A transcript identifier, e.g. F46H6.2b.1 or T05A10.6.1.

• gene_biotype: Gene biotype (e.g. protein_coding or tRNA).

• transcript_biotype: Transcript biotype, usually the same as the gene biotype (see below).

Biotypes

The gene and transcrit biotypes are typically identical. However a few miRNA genes have their transcript annotated as pre_miRNA or miRNA_primary_transcript, some ncRNAs are contained within protein_coding genes, and there are a handful of tRNA and rRNA pseudogenes.

Examples

## Not run: 
  tx2g_tab <- wb_load_tx2gene("WS281")
  table(tx2g_tab$gene_biotype, tx2g_tab$transcript_biotype)
  wb_tx2g("MTCE.10", tx2g_tab)
  wb_g2tx("WBGene00014457", tx2g_tab)

## End(Not run)

AlexWeinreb/wbData documentation built on April 3, 2025, 1:24 p.m.