mapid: Mapping taxonomic names to NCBI identifiers

mapidR 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.

Methods (by class)

  • phyloseq: phyloseq dispatch

  • TreeSummarizedExperiment: TreeSummarizedExperiment dispatch


qpmnguyen/TaxaSetsUtils documentation built on April 30, 2022, 6:13 p.m.