writeData_DB {PAnnBuilder} | R Documentation |
These functions store data tables in the "*.sqlite" file in SQLite-based annotation package.
createEmptyDPkg(pkgName, pkgPath,folders = c("man", "R", "data"), force = TRUE) writeMeta_DB(db, repList) writeData_DB(type, srcUrls, db, organism="") writeSPData_DB(srcUrls, db, organism) writeIPIData_DB(srcUrls, db, organism) writeREFSEQData_DB(srcUrls, db, organism) writeSYSBODYFLUIDData_DB(srcUrls, db) writeGOAData_DB(srcUrls, db) writeHomoloGeneData_DB(srcUrls, db) writeInParanoidData_DB(srcUrls, db) writeGENEINTData_DB(srcUrls, db) writeINTACTData_DB(srcUrls, db) writeMPPIData_DB(srcUrls, db) write3DIDData_DB(srcUrls, db) writeDOMINEData_DB(srcUrls, db) writePeptideAtlasData_DB(srcUrls, db) writeSYSPTMData_DB(srcUrls, db) writeSCOPData_DB(srcUrls, db) writeBACELLOData_DB(srcUrls, db) writeDBSUBLOCData_DB(srcUrls, db) writeName_DB(type, srcUrls, db) writeGOName_DB(srcUrls, db) writeKEGGName_DB(srcUrls, db) writePFAMName_DB(srcUrls, db) writeINTERPROName_DB(srcUrls, db) writeTAXName_DB(srcUrls, db)
pkgName |
the name of the data package to be built. (e.g. "hsaSP") |
pkgPath |
a character string for the full path of an existing directory where the built backage will be stored. |
folders |
a string vector for the file folder of establish R package. |
force |
a boolean to indicate whether the existed homonymic folder will be removed. |
db |
a object that extends DBIConnection. |
repList |
a named list which will replace the symbols in template file. |
type |
character string, giving the name of concerned database. |
srcUrls |
a character string, giving the url of the source file. |
organism |
a character string for the name of the organism of concern. (eg: "Homo sapiens") |
These functions download and parse data from diverse databases. The result files are stored as tables in the "*.sqlite" file.
writeMeta_DB
writes information from "repList" into a table
called "metadata".
writeData_DB
download and parse source file, and write the result
files into tables.
Hong Li