ncbit: retrieve and build NBCI taxonomic data

Description Usage Arguments Details Value References Examples

View source: R/ncbit.R

Description

making accessible the NCBI taxonomic data

Usage

1

Arguments

update

whether to update database or to use the locally installed version

...

additional arguments to be used if update=TRUE)

Details

This function will return a dataframe of the NCBI taxonomy, using either a freshly updated version (if update=TRUE) or a loaded version of the locally installed version. An internet connection must be functional and several utilities must be available and if updating the database: curl, gunzip, tar, perl, mv, and possibly rm. If any of the required utilities are unavailable, the function will issue an error. If updating the database, the database will be assembled in the data directory of the ncbit package and temporary files will be removed in the process. The removal of temporary files can be prevented with rm=FALSE in the call to ncbit.

Value

A dataframe of class 'taxdump' is returned with the following elements:

id

a unique integer associated with the node

node

a string descriptor of the node

unique

a string describing the node

type

the type of datum (e.g., scientific name, common name, synonym, etc.)

parent_id

a unique integer associated with the parent node

References

http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html

Sayers EW, T Barrett, DA Benson, SH Bryant, K Canese, V Chetvernin, DM Church, M DiCuccio, R Edgar, S Federhen, M Feolo, LY Geer, M Hlemberg, Y Kapustin, D Landsman, DJ Lipman, TL Madden, DR Maglott, V Miller, I Mizrachi, J Ostell, KD Pruitt, GD Schuler, E Sequeira, ST Sherry, M Shumway, K Sirotkin, A Souvorov, G Starchenko, TA Tatusova, L Wagner, E yaschenko, and J Ye. 2009. Database resources of the National Center for Biotechnology Information. Nucleic Acids Research 37:D5-15.

Benson DA, I Karsch-Mizrachi, DJ Lipman, J Ostell, and EW Sayers. 2009. GenBank. Nucleic Acids Research 37:D26-31.

Examples

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ncbit documentation built on May 2, 2019, 2:59 a.m.

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