annotate_with_NCBI_taxid: Retrieve the taxonomic data for a given NCBI taxon ID using a...

In currocam/taxa2hmmer: Get more out of homologous sequence search with HMMER

Retrieve the taxonomic data for a given NCBI taxon ID using a local database or as remote data sources.

Description

Retrieve the taxonomic data for a given NCBI taxon ID using a local database or as remote data sources.

Usage

annotate_with_NCBI_taxid(taxid, rank_vc = NULL, mode = "remote")

Arguments

taxid	A character or numeric vector containing the target NCBI taxon ID.
rank_vc	A character vector containing the desired taxonomic ranks. If empty, all available taxonomic ranges will be retrieved.
mode	A character vector, if "local" will use a local database instead of remote resources. You will not have to download the database but it is slower.

Value

A DataFrame with columns taxid and taxonomic ranks.

Examples

annotate_with_NCBI_taxid(7955, "species")
## Not run: 
taxa <- annotate_with_NCBI_taxid(
        taxid = hits$taxid,
        mode = "local")

## End(Not run)

currocam/taxa2hmmer documentation built on April 10, 2022, 11:02 a.m.