wb_load_exon_coords: Load exon coordinates

In AlexWeinreb/wbData: Download And Use WormBase Data

Load exon coordinates

Description

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

Usage

wb_load_exon_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:

• exon_id: Unique exon ID, composed of the transcript name with the exon number.

• transcript_id: Transcript ID, typically the sequence name, an isoform letter (if relevant) and a transcript number (if relevant).

• gene_id: Wormbase gene ID (WBGene).

• exon_number: An integer identifying exons of each transcript.

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

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

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

• transcript_biotype: Trtanscript biotype, usually the same as the gene biotype.

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

Examples

## Not run: 
exon_coords <- wb_load_exon_coords("WS277")
exon_coords[exon_coords$transcript_id == "K08H10.7.2", "position"]

## End(Not run)

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