geneInfo: Get gene information
In YulongNiu/KEGGAPI: A package for providing KEGG databases API in R

Description Usage Arguments Details Value Author(s) Examples

KEGG Database API - Get gene information

getKEGGGeneInfo(KEGGGeneIDs, enforceURL = FALSE, n = 1)

doTenInfo(tenWebInfo)

ExtractLocus(locusStr)

ExtractMotif(motifStr)

`KEGGGeneIDs`	A vector of KEGG IDs. Seqences from different species could be combined together.
`enforceURL`	whether to enfoce get get url until the results returned. The default value is "FALSE".
`n`	The number of CPUs or processors, and the default value is 1.
`tenWebInfo`	return results from function getURL().
`locusStr`	named location strings whose names are gene names.
`motifStr`	named motif strings whole names are gene names

getKEGGGeneInfo(): Get gene information. This function supports multiple querys.

ExtractLocus(): Extract prokaryotic gene location.

ExtractMotif(): Extract protein motifs.

getKEGGGeneInfo(): A string vectors containing gene informations

ExtractLocus(): A matrix: 1st gene names, 2ed is genome, 3rd is start, 4th is end, and the 5th is the strand.

ExtractMotif(): A list: each element is a motif vector.

a list each contains the annotation items (for the case without annotation returns NULL).

Yulong Niu niuylscu@gmail.com

genes <- c('eco:b4600', 'ece:Z5100', 'eco:b3160', 'dra:DR_0001', 'dra:DR_A0001', 'dra:DR_B0001')
genesInfo <- getKEGGGeneInfo(genes, n = 2)
locusVec <- c('complement(join(1631002..1632285,1652755..1652838))', 'complement(4658240..4658986)',
'3303448..3304455', '1:complement(1..1182)', '2:653..1435', 'MP1:520..1296')
names(locusVec) <- c('eco:b4600', 'ece:Z5100',
'eco:b3160', 'dra:DR_0001', 'dra:DR_A0001', 'dra:DR_B0001')
ExtractLocus(locusVec)
motifVec <- c('Pfam: B_lectin S_locus_glycop',
'Pfam: VIT1 AlaDh_PNT_C DUF4168 PsbI',
'Pfam: BRF1 Coilin_N')
names(motifVec) <- c('ath:AT2G01780', 'ath:AT2G01770',
'ath:AT2G01800')
ExtractMotif(motifVec)