getTaxHierarchy: Get taxonomy hierarchy for a list of taxon IDs
In BIONF/PhyloProfile: PhyloProfile

getTaxHierarchy

R Documentation

Get taxonomy hierarchy for a list of taxon IDs

Description

Get NCBI taxonomy hierarchy and URLs for an input taxon list.

Usage

getTaxHierarchy(inputTaxa = NULL, currentNCBIinfo = NULL)

Arguments

`inputTaxa`	NCBI ID list of input taxa.
`currentNCBIinfo`	table/dataframe of the pre-processed NCBI taxonomy data (/PhyloProfile/data/preProcessedTaxonomy.txt)

Value

A list of dataframs containing taxonomy hierarchy and its URL to NCBI database for input taxon IDs

Author(s)

Vinh Tran tran@bio.uni-frankfurt.de

Examples

inputTaxa <- c("272557", "176299")
ncbiFilein <- system.file(
    "extdata", "data/preProcessedTaxonomy.txt",
    package = "PhyloProfile", mustWork = TRUE
)
currentNCBIinfo <- as.data.frame(data.table::fread(ncbiFilein))
PhyloProfile:::getTaxHierarchy(inputTaxa, currentNCBIinfo)

BIONF/PhyloProfile documentation built on April 14, 2024, 10:39 p.m.