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PAnnBuilder (version 1.36.0)

writeData_DB: Parse and Write Data into R Data Packages

Description

These functions store data tables in the "*.sqlite" file in SQLite-based annotation package.

Usage

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)

Arguments

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")

Details

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.