getCycPhylo: Get species from BioCyc

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

Description

BioCyc Database API - Get species information from BioCyc.

Usage

getCycPhylo(speList, speType = "BioCyc", whole = FALSE)

Arguments

speList	The species list that is a vector like 'c("HUMAN", "ECOLI", "ZMOB579138")'. The input speList should be consistent with the parameter 'speType'.
speType	It supports two types: 'BioCyc' and 'regexpr'. BioCyc type is the BioCyc species ID, for exmaple 'HUMAN' is the BioCyc ID for the Homo sapiens.The 'regexpr' is used for regulare expression search with the Latin name for example 'Escherichia coli'.
whole	Whether or not get the whole BioCyc species list, and the default value is FALSE.

Details

Get the BioCyc species information including the BioCyc species ID and the Latin name.

Value

Matrix of species information.

Author(s)

Yulong Niu [e-mail]

Examples

# search species list from BioCyc ID
getCycPhylo(c('HUMAN', 'ECOLI', 'ZMOB579138'), speType = 'BioCyc')

# search species whose names include 'Escherichia coli'
getCycPhylo('Escherichia coli', speType = 'regexpr')

## Not run: 
# get whole BioCyc species information table
getCycPhylo(whole = TRUE)
## End(Not run)

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