build_lncrna_annots {annotatr} | R Documentation

## A helper function to build lncRNA annotations.

### Description

Using the `AnnotationHub` package, retrieve transcript level lncRNA annotations for either human (GRCh38) or mouse (GRCm38). If the genome is 'hg19', use the permalink from GENCODE and `rtracklayer::import()` to download and process.

### Usage

    build_lncrna_annots(genome = c("hg19", "hg38", "mm10"))

### Arguments

`genome` | The genome assembly.

### Value

A `GRanges` object with `id` giving the `transcript_type` from the GENCODE file, `tx_id` being the Ensembl transcript ID, `gene_id` being the Entrez ID coming from a mapping of gene symbol to Entrez ID, `symbol` being the gene_name from the GENCODE file, and the `type` being `[genome]_lncrna_gencode`.

[Package annotatr version 1.4.1 Index]