getIDsRank: Get taxonomy info for a list of taxa

In PhyloProfile: PhyloProfile

Description

Get NCBI taxonomy IDs, ranks and names for an input taxon list.

Usage

getIDsRank(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 3 dataframes: idList, rankList and reducedInfoList. The "rankList" contains taxon names and all taxonomy ranks of the input taxa including also the noranks from the input rank to the taxonomy root. The "idList" contains input taxon IDs, taxon names, all the ranks from current rank to the taxonomy root together with their IDs (with the format "id#rank"). The reducedInfoList is a subset of preProcessedTaxonomy.txt file, containing the NCBI IDs, taxon fullnames, their current rank and their direct parent ID.

Author(s)

Vinh Tran [e-mail]

Examples

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

PhyloProfile documentation built on March 27, 2021, 6:01 p.m.