KEGGMotifList: Get motif list from KEGG.
In YulongNiu/KEGG_BioCyc_API: A package for providing KEGG and BioCyc databases API in R
Description
Usage
Arguments
Details
Value
Author(s)
See Also
Examples
Description
KEGG Database Additional API - Get genes processing certain motif
Usage
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getKEGGMotifList(motifName)
getKEGGMotifList2(motifName)
Arguments
motifName
A single KEGG motif ID
Details
Get all the gene having certain motif.
Value
A matrix of KEGG genes and description
A vector of protein names including UniProt and SWISS-PROT. Not all these "protID" have KEGG IDs. KEGG uses UniProt and SWISS-PROT for gene UniProt annotation.
Author(s)
Yulong Niu niuylscu@gmail.com
Yulong Niu niuylscu@gmail.com
See Also
convKEGG
Examples
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## Not run:
getKEGGMotifList('pf:DUF3675')
## End(Not run)
pfUniprot <- getKEGGMotifList2('pf:DUF3675')
## Not run:
# convert uniprot ID to KEGG IDs
pfUniprot <- paste0('uniprot:', pfUniprot)
pfGeneID <- convKEGG('genes', pfUniprot, convertType = 'identity')
## End(Not run)
YulongNiu/KEGG_BioCyc_API documentation built on May 10, 2019, 1:13 a.m.
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Description Usage Arguments Details Value Author(s) See Also Examples
Description
KEGG Database Additional API - Get genes processing certain motif
Usage
1 2 3 | getKEGGMotifList(motifName)
getKEGGMotifList2(motifName)
|
Arguments
motifName |
A single KEGG motif ID |
Details
Get all the gene having certain motif.
Value
A matrix of KEGG genes and description
A vector of protein names including UniProt and SWISS-PROT. Not all these "protID" have KEGG IDs. KEGG uses UniProt and SWISS-PROT for gene UniProt annotation.
Author(s)
Yulong Niu niuylscu@gmail.com
Yulong Niu niuylscu@gmail.com
See Also
convKEGG
Examples
1 2 3 4 5 6 7 8 9 10 | ## Not run:
getKEGGMotifList('pf:DUF3675')
## End(Not run)
pfUniprot <- getKEGGMotifList2('pf:DUF3675')
## Not run:
# convert uniprot ID to KEGG IDs
pfUniprot <- paste0('uniprot:', pfUniprot)
pfGeneID <- convKEGG('genes', pfUniprot, convertType = 'identity')
## End(Not run)
|
R Package Documentation
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We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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