getKEGGPhylo: Get species list from KEGG.

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

Description

KEGG Database API - Get species KEGG/NCBI ID.

Usage

getKEGGPhylo(speList, speType = "KEGG", whole = FALSE)

Arguments

speList	The species list that is a vector like 'c("hsa", "eco")'. The input 'speList' should be consistent with the parameter 'speType'.
speType	It supports five types: 'KEGG', 'Tnum', 'regexpr', and 'phylo'. KEGG type is a three or four letters, for exmaple 'hsa' is the KEGG ID for Homo sapiens, while the corresponding T number is 'T01001'. The 'regexpr' is used for regulare expression search with the Latin name ('Escherichia coli'), sub-species name ('K-12 MG1655'), and common name ('human'). The 'phylo' uses phylogentic orders for search, and it supports 'Domain' (either 'Eukaryotes' or 'Prokaryotes'), 'Kingdom' ('Animals'), 'phylum' ('Vertebrates'), and 'class' ('Mammals'). But it does not support mixed 'KEGG'. Attention: Mutiple KEGG species ID may correspond to one taxonomy ID, for exmaple 'lph' and 'lpo' to '91891'
whole	Whether or not get the whole KEGG species list, and the default value is FALSE.

Details

Get the phylogenetic information of given species. It supports both batch input and regular expression search.

Value

Matrix of species information.

Author(s)

Yulong Niu [e-mail]

Examples

# search species list from KEGG ID
getKEGGPhylo(c('hsa', 'eco'))
# search species whose names include 'Escherichia coli'
getKEGGPhylo('Escherichia coli', speType = 'regexpr')
# search species whose class is 'Mammals'
getKEGGPhylo('Mammals', speType = 'phylo')
# get whole KEGG species information table
getKEGGPhylo(whole = TRUE)

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