downloadRefSeqGenome: Download RefSeq reference genome

Description Usage Arguments Value Stable release Note See Also Examples

View source: R/downloadRefSeqGenome.R

Description

Download RefSeq reference genome

Usage

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downloadRefSeqGenome(
  organism,
  taxonomicGroup = NULL,
  genomeBuild = NULL,
  outputDir = ".",
  cache = TRUE
)

Arguments

organism

character(1). Full Latin organism name (e.g. "Homo sapiens").

taxonomicGroup

character(1). Only applies to RefSeq. FTP server taxonomic group subdirectory path (e.g. "vertebrate_mammalian"). Defining this manually avoids having to query the FTP server.

genomeBuild

character(1). RefSeq genome build assembly name (e.g. "GCF_000001405.39_GRCh38.p12"). If set NULL, defauls to the most recent build available.

outputDir

character(1). Output directory path.

cache

logical(1). Cache URLs locally, using BiocFileCache internally.

Value

Invisible list.

Stable release

The latest assembly defined under the "release/" subdirectory is not considered "stable" by the RefSeq team. It is considered good practice to use a genome build one version behind as a stable release (e.g. "GCF_000001405.38_GRCh38.p12" instead of current "GCF_000001405.39_GRCh38.p13" build).

Note

Updated 2021-09-03.

See Also

Examples

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## This example is bandwidth intensive.
## > downloadRefSeqGenome(
## >     organism = "Homo sapiens",
## >     taxonomicGroup = "vertebrate_mammalian",
## >     genomeBuild = "GCF_000001405.39_GRCh38.p12",
## > )

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