mapid: Mapping taxonomic names to NCBI identifiers
In qpmnguyen/TaxaSetsUtils: Creating and manipulating taxonomic sets

mapid

R Documentation

Mapping taxonomic names to NCBI identifiers

Description

This function takes a data container object (type phyloseq, data.frame\tibble, TreeSummarizedExperiment) and returns NCBI identifiers.

Usage

mapid(obj, type, ..., rebuild_ncbi = FALSE, db = NULL)

## S4 method for signature 'phyloseq'
mapid(obj, type, ..., rebuild_ncbi = FALSE, db = NULL)

## S4 method for signature 'TreeSummarizedExperiment'
mapid(obj, type, ..., rebuild_ncbi = FALSE, db = NULL)

Arguments

`obj`	A `phyloseq` type object or a `TreeSummarizedExperiment` type object
`type`	Approach used to match names with identifiers. Can be either `db`, `path`, `name`.
`...`	Other arguments not currently used
`rebuild_ncbi`	(Logical). Indicate whether `taxizedb` should re-build the cached NCBI database.
`db`	(String). If type is `db`, this argument specifies which db to use. Defaults to NULL. Currently only supports `silva` and `metaphlan`

Details

The input is a data.frame, matrix, or typical microbiome container that has a taxonomic table specified. The schematic of a taxonomic table is a table where the left-most column indicates the highest level of the hierarchy (usually kingdom or superkingdom) and the right-most column specifies the lowest level of the taxonomic hierarchy (usually species, genus or strains). Given that format, the type argument determines how matching is done.

name: This matches using the name of the lowest rank in the taxonomic table to the NCBI database.
path_*: Uses a full path matching algorithm as defined in Balvociute and Huson 2017. (doi: 10.1186/s12864-017-3501-4)
db: Use directly from a database that has a cross-walk between NCBI Ids and the full name path. Currently only silva and metaphlan are supported. Future support might include RDP.