writeData_DB: Parse and Write Data into R Data Packages

In PAnnBuilder: Protein annotation data package builder

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.

Author(s)

Hong Li

PAnnBuilder documentation built on May 2, 2018, 4:07 a.m.