speciesNorganism()
organism2species(organism)
organism2alias(organism)
getShortSciName(organism)
organism2taxID(organism)
taxID2organism(taxID)
.srcUrls(name)
getSrcUrl(src, organism = "")
getALLUrl(organism)
getSrcBuilt(src, organism = "")
getALLBuilt(organism)
getSrcSQUrl(src,organism)
getSrcSQBuilt(src,organism)
getSPUrl()
getTREMBLUrl()
getIPIUrl(organism)
getREFSEQUrl(organism)
getGOUrl()
getGOAUrl(organism)
getGENEINTUrl()
getINTACTUrl()
getMPPIUrl()
get3DIDUrl()
getDOMINEUrl()
getDBSUBLOCUrl()
getBACELLOUrl()
getINTERPROUrl()
getPFAMUrl()
getSCOPUrl()
getHOMOLOGENEUrl()
getINPARANOIDUrl(organism)
getPEPTIDEATLASUrl(organism)
getSYSPTMUrl()
getSYSBODYFLUIDUrl()
getSPSQUrl()
getTREMBLSQUrl()
getIPISQUrl(organism)
getREFSEQSQUrl(organism)
getSPBuilt()
getTREMBLBuilt()
getIPIBuilt(organism)
getREFSEQBuilt(organism)
getGOABuilt(organism)
getGENEINTBuilt()
getINTACTBuilt()
getMPPIBuilt()
get3DIDBuilt()
getDOMINEBuilt()
getDBSUBLOCBuilt()
getBACELLOBuilt()
getINTERPROBuilt()
getPFAMBuilt()
getSCOPBuilt()
getHOMOLOGENEBuilt()
getINPARANOIDBuilt()
getPEPTIDEATLASBuilt(organism)
getSYSPTMBuilt()
getSYSBODYFLUIDBuilt()
getSrcUrl
return a character string to indicate the url of
data file.getSrcBuilt
return a character string to indicate the release/
version of the database.
speciesNorganism
return a three-column matrix.
organism2species() and organism2alias() employ speciesNorganism()
to get organism and alias used in IPI database.
organism2species
use speciesNorganism() to convert organism to
their species name.
organism2alias
use speciesNorganism() to convert organism to
their alias name.
getShortSciName
get 3-character short name, eg: "Hsa".
organism2taxID
convert organism to taxID, eg: 9606 for
"Homo sapiens".
taxID2organism
convert taxID to organism, eg: "Homo sapiens"
for 9606.
Functions developped to get url and release information for data file:
.srcUrls
get basic web address for the given database.
getSrcUrl
get url for the data file based on .srcUrls().
getALLUrl
get all available urls in this package.
getSrcBuilt
get version/release information based on
.srcUrls
.
getALLBuilt
get release information for databases in
getALLUrl
.
getSrcSQUrl
get url for protein sequence files.
getSrcSQBuilt
get release information for
protein sequence files.
if(interactive()){
# Get urls of all related databases for "Homo sapiens".
getALLUrl("Homo sapiens")
# Get version/release information of all related databases for "Homo sapiens".
getALLBuilt ("Homo sapiens")
}
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