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Retrieve annotation *.gff files for metagenomes from NCBI Genbank

Source: R/getMetaGenomeAnnotations.R
getMetaGenomeAnnotations.Rd

Retrieve available annotation *.gff files for metagenomes from NCBI Genbank. NCBI Genbank allows users to download entire metagenomes and their annotations of several metagenome projects. This function downloads available metagenomes that can then be downloaded via getMetaGenomes.

Usage

getMetaGenomeAnnotations(
  name,
  path = file.path("_ncbi_downloads", "metagenome", "annotations"),
  metagenomes.members = dplyr::filter(getMetaGenomeSummary(), organism_name == name &
    total_gene_count > 0)
)

Arguments

name

metagenome name retrieved by listMetaGenomes.

path

a character string specifying the location (a folder) in which the corresponding metagenome annotations shall be stored. Default is path = file.path("_ncbi_downloads","metagenome","annotations").

metagenomes.members

a tibble with selected assemblies, default: dplyr::filter(getMetaGenomeSummary(), organism_name == name & total_gene_count > 0)). This is different to getMetaGenome since it requires a gff to exist, most genbank assemblies are .gbff files only, which are usually not useful.

See also

getMetaGenomes, listMetaGenomes, getGFF

Author

Hajk-Georg Drost

Examples

if (FALSE) { # \dontrun{
# Frist, retrieve a list of available metagenomes
listMetaGenomes()

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