createAnnObjs: Creates the AnnObj instances
In PAnnBuilder: Protein annotation data package builder

Description Usage Arguments Details Author(s)

These functions creates the AnnObj instances for the SQLite-based annotation data packages.

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createSeeds(type) 

createAnnObjs(type, prefix, datacache, dbconn)

`type`	character string, giving the name of concerned database. Possible values of type are : "sp", "trembl", "ipi", "refseq", "geneint", "intact", "mppi", "3DID", "DOMINE", "BaCelLo", "DBSubLoc", "SCOP", "HomoloGene", "InParanoid", "PeptideAtlas", "SysPTM", "SysBodyFluid", "GOA", "GO", "KEGGNAME", "PFAMNAME", "INTERPRONAME", "TAXNAME", "dName", "cross", "pSeq"
`prefix`	the prefix of the name of the data package to be built. (e.g. "hsaSP"). The name of builded package is prefix+".db".
`datacache`	a R environment, giving the name of "*.sqlite" database file, and a object which extends DBIConnection to the database.
`dbconn`	a connection object to the package.

Given the abbreviation of databases, createSeeds returns a list which describes the set of AnnObj objects.

createAnnObjs creates the AnnObj instances based on the values of createSeeds.

dbschema(x, file="", show.indices=FALSE): Print the schema definition of the SQLite DB. Also works if x is a DBIConnection object. The file argument must be a connection, or a character string naming the file to print to (see the file argument of the cat function for the details). The CREATE INDEX statements are not shown by default. Use show.indices=TRUE to get them.

Hong Li

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