downloadGencodeGenome: Download GENCODE reference genome

Description Usage Arguments Value Note Examples

View source: R/downloadGencodeGenome.R

Description

Download GENCODE reference genome

Usage

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downloadGencodeGenome(
  organism,
  genomeBuild = NULL,
  release = NULL,
  outputDir = ".",
  cache = TRUE
)

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. 90). 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 2021-08-03.

Examples

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## This example is bandwidth intensive.
## > downloadGencodeGenome(
## >     organism = "Homo sapiens",
## >     genomeBuild = "GRCh38",
## >     release = 36L,
## >     type = "transcriptome",
## >     annotation = "gtf"
## > )

acidgenomics/AcidGenomes documentation built on Sept. 16, 2021, 7:30 p.m.