processNcbiTaxonomy: Pre-processing NCBI taxonomy data

In PhyloProfile: PhyloProfile

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 [e-mail]

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)

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