build_gene_annots: A helper function to build genic annotations.

In rcavalcante/annotatr: Annotation of Genomic Regions to Genomic Annotations

A helper function to build genic annotations.

Description

Using the TxDb.* group of packages, construct genic annotations consisting of any combination of 1-5kb upstream of a TSS, promoters (< 1kb from TSS), 5UTRs, CDS, exons, first exons, introns, intron/exon and exon/intron boundaries, 3UTRs, and intergenic.

Usage

build_gene_annots(
  genome = annotatr::builtin_genomes(),
  annotations = annotatr::builtin_annotations()
)

Arguments

genome	The genome assembly.
annotations	A character vector with entries of the form [genome]_genes_{1to5kb,promoters,5UTRs,cds,exons,firstexons,introns,intronexonboundaries,exonintronboundaries,3UTRs,intergenic}.

Value

A list of GRanges objects with unique id of the form [type]:i, tx_id being the UCSC knownGene transcript name, gene_id being the Entrez Gene ID, symbol being the gene symbol from the Entrez ID to symbol mapping in org.db for that species, and type being the annotation type.

rcavalcante/annotatr documentation built on March 25, 2023, 9:51 a.m.