taxonomyTableCreator: Align NCBI taxonomy IDs of list of taxa into a sorted rank...

In PhyloProfile: PhyloProfile

Description

Align NCBI taxonomy IDs of list of taxa into a sorted rank list.

Usage

taxonomyTableCreator(idListFile = NULL, rankListFile = NULL)

Arguments

idListFile	a text file whose each row is a rank+ID list of a taxon (see idListFile in example)
rankListFile	a text file whose each row is a rank list of a taxon (see rankListFile in example)

Value

An aligned taxonomy dataframe which contains all the available taxonomy ranks from the id and rank list file. This dataframe can be used for creating a well resolved taxonomy tree (see ?createRootedTree) and sorting taxa based on a selected reference taxon (see ?sortInputTaxa).

Author(s)

Vinh Tran [e-mail]

See Also

rankIndexing, createRootedTree, sortInputTaxa

Examples

idListFile <- system.file(
    "extdata", "data/idList.txt", package = "PhyloProfile", mustWork = TRUE
)
rankListFile <- system.file(
    "extdata", "data/rankList.txt", package = "PhyloProfile", mustWork = TRUE
)
taxonomyTableCreator(idListFile, rankListFile)

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