transPhyloCyc2NCBI: Get NCBI Taxonomy ID From BioCyc species ID

In YulongNiu/KEGG_BioCyc_API: A package for providing KEGG and BioCyc databases API in R

Description

BioCyc Database Additional API - Get the NCBI taxonomy ID from a given BioCyc ID

Usage

transPhyloCyc2NCBI(cycID, n = 4)

Arguments

cycID	The cyc species ID. The KEGG support multiple species ID, for example c('HUMAN', 'MOUSE', 'ECOLI').
n	The number of CPUs or processors, and the default value is 4.

Details

NCBI taxonomy ID is used as unique ID accoss cyc and BioCyc databases. This functions is used to get the corresponding NCBI Taxonomy ID from BioCyc.If BioCyc has no official NCBI taxonomy ID, it will return a character with length of 0 (it looks like "").

Value

The corresponding NCBI Taxonomy ID in character vector.

Author(s)

Yulong Niu [e-mail]

Examples

# get human, mouse, and Ecoli NCBI taxonomy ID with 2 threads
transPhyloCyc2NCBI(c('HUMAN', 'MOUSE', 'ECOLI'), n = 2)

## Not run: 
# transfer all BioCyc species ID to NCBI taxonomy ID
wBiocycSpe <- getCycPhylo(whole = TRUE)
wNCBISpe <- transPhyloCyc2NCBI(wBiocycSpe[, 1])

## End(Not run)

YulongNiu/KEGG_BioCyc_API documentation built on May 10, 2019, 1:13 a.m.