build_gene_annots {annotatr} | R Documentation

## 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.

[Package annotatr version 1.4.1 Index]