build_lncrna_annots: A helper function to build lncRNA annotations.

Description Usage Arguments Value

View source: R/build_annotations.R

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

1
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 Oct. 19, 2018, 6:38 p.m.