downloadGencodeGenome: Download GENCODE reference genome

In acidgenomics/r-acidgenomes: Acid Genomics Genome Annotations

Download GENCODE reference genome

Description

Download GENCODE reference genome

Usage

downloadGencodeGenome(
  organism,
  genomeBuild = NULL,
  release = NULL,
  outputDir = getwd(),
  cache = FALSE
)

Arguments

organism	character(1). Full Latin organism name (e.g. "Homo sapiens").
genomeBuild	character(1). Ensembl genome build assembly name (e.g. "GRCh38"). If set NULL, defaults to the most recent build available. Note: don't pass in UCSC build IDs (e.g. "hg38").
release	integer(1). Ensembl release version (e.g. 100). We recommend setting this value if possible, for improved reproducibility. When left unset, the latest release available via AnnotationHub/ensembldb is used. Note that the latest version available can vary, depending on the versions of AnnotationHub and ensembldb in use.
outputDir	character(1). Output directory path.
cache	logical(1). Cache URLs locally, using BiocFileCache internally.

Value

Invisible list.

Note

Updated 2023-11-28.

Examples

## This example is bandwidth intensive.
## > downloadGencodeGenome(
## >     organism = "Homo sapiens",
## >     genomeBuild = "GRCh38",
## >     release = 44L,
## >     type = "transcriptome",
## >     annotation = "gtf"
## > )

acidgenomics/r-acidgenomes documentation built on Jan. 12, 2024, 4:06 a.m.