taxonomyTableCreator {PhyloProfile} | R Documentation |
Align NCBI taxonomy IDs of list of taxa into a sorted rank list.
taxonomyTableCreator(idListFile = NULL, rankListFile = NULL)
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) |
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).
Vinh Tran tran@bio.uni-frankfurt.de
rankIndexing
, createRootedTree
,
sortInputTaxa
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)