build_gene_annots: A helper function to build genic annotations.

In annotatr: Annotation of Genomic Regions to Genomic 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.

annotatr documentation built on Nov. 8, 2020, 8:16 p.m.