wb_load_gene_coords: Load gene coordinates

In AlexWeinreb/wbData: Download And Use WormBase Data

Load gene coordinates

Description

Loads a data frame providing the genomic coordinates of all genes, built from the Wormbase GTF file. The GTF file will be downloaded as needed.

Usage

wb_load_gene_coords(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).

• chr: Chromosome name (I, II, III, IV, V, X, MtDNA).

• start, end, strand: Genomic position of the gene.

• position: Genomic position (compatible with JBrowse or IGV).

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

Examples

## Not run: 
  gene_coords <- wb_load_gene_coords("WS273")
  gene_coords[gene_coords$gene_id == "WBGene00004323", "position"]

## End(Not run)

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