build_lncrna_annots: A helper function to build lncRNA annotations.

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

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.

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