processNcbiTaxonomy {PhyloProfile} | R Documentation

## Pre-processing NCBI taxonomy data

### Description

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.

### Usage

    processNcbiTaxonomy()

### Value

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.

### Author(s)

Vinh Tran tran@bio.uni-frankfurt.de

### Examples

    ?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)

[Package PhyloProfile version 1.2.8 Index]