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Get human GENCODE transcript dataset

Source: R/get_gencode.R
get_gencode.Rd

Downloads and returns a pre-processed dataset of GENCODE transcripts. The dataset comes as a list object, with two elements:

  • metadata - a data frame with metadata regarding annotation resources used

  • records - a list with two data frames of transcripts, one for grch37, and one for grch38 (see specific column format below)

The GENCODE datasets provided were established by parsing the GENCODE comprehensive gene annotation GTF file with the valr package, and also providing cross-references to RefSeq (through the use of the biomaRt package), and UniProt accessions/identifiers.

Usage

get_gencode(
  cache_dir = NA,
  force_download = FALSE,
  chromosomes_only = TRUE,
  ensembl_release = 111
)

Source

https://www.gencodegenes.org/

https://uniprot.org

https://www.ncbi.nlm.nih.gov/gene

https://apprisws.bioinfo.cnio.es/landing_page/

Arguments

cache_dir

Local directory for data download

force_download

Logical indicating if local cache should be overwritten (set to TRUE to re-download if file exists in cache)

chromosomes_only

Logical indicating if transcripts returned should belong to ordinary chromosomes only (scaffolds etc. should be ignored)

ensembl_release

version of Ensembl to use - this will dictate the version of GENCODE used for grch38

Value

metadata - A data frame with 3 rows and 6 columns:

  • source - gene annotation source

  • annotation_data - type of annotations used

  • url - URL of annotation resource

  • citation - publication to cite for annotation source (citation; PMID)

  • version - version used

  • abbreviation - abbreviation (e.g. used in column names of records)

records - A list with one data frame per assembly

  • chrom - chromosome

  • start - transcript start with 5kb padding (upstream)

  • end - transcript end with 5kb padding (downstream)

  • transcript_start - transcript start

  • transcript_end - transcript end

  • strand - strand

  • ensembl_gene_id - Ensembl gene identifier

  • ensembl_transcript_id - Ensembl transcript identifier

  • ensembl_transcript_id_full - Ensembl transcript identifier (with version)

  • ensembl_protein_id - Ensembl protein identifier

  • symbol - official gene symbol

  • hgnc_id - HGNC gene identifier

  • entrezgene - Entrez gene identifier

  • name - genename

  • gene_biotype - gene biotype (GENCODE)

  • transcript_biotype - transcript biotype (GENCODE))

  • tag - tag (GENCODE))

  • refseq_protein_id - RefSeq peptide identifier

  • refseq_transcript_id - RefSeq mRNA identifier

  • mane_select - MANE Select

  • mane_plus_clinical - MANE Plus Clinical

  • principal_isoform_flag - Principal isoform tag (APPRIS)

  • uniprot_acc - UniProtKB protein accession

  • uniprot_id - UniProtKB protein identifier

  • ensembl_version - Ensembl version

  • gencode_version - GENCODE version

  • uniprot_version - UniProtKB version

list object with GENCODE transcripts (records) and associated metadata (metadata)

Examples

if (FALSE) { # \dontrun{
library(geneOncoX)
transcripts_gencode <- get_gencode(cache_dir = tempdir())
} # }