genomicGenes: Retrieve genomic genes

In YulongNiu/ProGenome: A package for processing prokaryotic genomes

Description

Retrieve genomic genes.

Usage

getGenomicGenes(KEGGSpe)

getGenesfGenomes(KEGGSpe)

getGenesfGeneids(KEGGSpe)

Arguments

KEGGSpe

A KEGG species ID

Details

Retrieve the whole genomic gene from a prokaryotic species. The function returns gene location in all genomes, including the cellular genoms and plasmids. For some gene, multiple location may return. If the genome has no gene featurs, "NULL" will be returned. getGenesfGenomes(): retrieve whole genomic genes from NCBI genomes. getGenesfGeneids(): retrieve whole genomic genes from NCBI gene IDs. getGenomicGenes(): a wrapped of these top two function, which trys getGenesfGeneids() at first and then getGenesfGenomes() if the genome is from GenBank.

Value

A list. Each element represents a genome, and the gene IDs are in KEGG format.

A list. Each element represents a genome, and the gene IDs are in KEGG format.

A list. Each element represents a genome, and the gene IDs are in KEGG format.

Author(s)

Yulong Niu [e-mail]

Yulong Niu [e-mail]

Yulong Niu [e-mail]

Yulong Niu [e-mail]

Examples

## no genomic genes
noGenes <- getGenomicGenes('csu')
## Not run: 
## from GenBank
## one genome with three plasmids
hxaGenes <- getGenomicGenes('hxa')

## from RefSeq
## two genomes with two plasmids
draGenes <- getGenomicGenes('dra')
## End(Not run)

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