Description Usage Arguments Details Value Author(s) Examples
KEGG Database API - Get gene information
1 2 3 4 5 6 7 | 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
Yulong Niu niuylscu@gmail.com
Yulong Niu niuylscu@gmail.com
1 2 3 4 5 6 7 8 9 10 11 12 13 | 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)
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.