getMetaGenomes: Retrieve metagenomes from NCBI Genbank

In ropensci/biomartr: Genomic Data Retrieval

Retrieve metagenomes from NCBI Genbank

Description

Retrieve available metagenomes from NCBI Genbank. NCBI Genbank allows users to download entire metagenomes of several metagenome projects. This function downloads available metagenomes that can then be downloaded via getMetaGenomes.

Usage

getMetaGenomes(
  name,
  path = file.path("_ncbi_downloads", "metagenome"),
  metagenomes.members = dplyr::filter(getMetaGenomeSummary(), organism_name == name)
)

Arguments

name	metagenome name retrieved by listMetaGenomes.
path	a character string specifying the location (a folder) in which the corresponding metagenome shall be stored. Default is path = file.path("_ncbi_downloads","metagenome").
metagenomes.members	a tibble of metagenome assemblies, default: dplyr::filter(getMetaGenomeSummary(), organism_name == name)

Author(s)

Hajk-Georg Drost

See Also

getMetaGenomeAnnotations, listMetaGenomes

Examples

## Not run: 
# Frist, retrieve a list of available metagenomes
listMetaGenomes()

# Now, retrieve the 'human gut metagenome'
getMetaGenomes(name = "human gut metagenome")

## End(Not run)

ropensci/biomartr documentation built on Feb. 4, 2025, 3:37 p.m.