processNcbiTaxonomy {PhyloProfile} | R Documentation |
Download NCBI taxonomy database and parse information that are needed for PhyloProfile, including taxon IDs, their scientific names, systematic ranks, and parent (next higher) rank IDs.
processNcbiTaxonomy()
A dataframe contains NCBI taxon IDs, taxon names, taxon ranks and the next higher taxon IDs (parent's IDs) of all taxa in the NCBI taxonomy database.
Vinh Tran tran@bio.uni-frankfurt.de
?processNcbiTaxonomy ## Not run: preProcessedTaxonomy <- processNcbiTaxonomy() # save to text (tab-delimited) file write.table( preProcessedTaxonomy, file = "preProcessedTaxonomy.txt", col.names = TRUE, row.names = FALSE, quote = FALSE, sep = "\t" ) # save to rdata file save( preProcessedTaxonomy, file = "preProcessedTaxonomy.RData", compress='xz' ) ## End(Not run)