popHUMANDB {AnnotationDbi}R Documentation

Populates an SQLite DB with and produces a schema definition

Description

Creates SQLite file useful for making a SQLite based annotation package. Also produces the schema file which details the schema for the database produced.

Usage

  popHUMANDB(prefix, chipSrc, metaDataSrc, outputDir, printSchema)

Arguments

prefix prefix is the first part of the eventual desired package name. (ie. "prefix.sqlite")
chipSrc The path and filename to the intermediate database containing the annotation data for the sqlite to build.
metaDataSrc Either a named character vector containing pertinent information about the metadata OR the path and filename to the intermediate database containing the metadata information for the package.
If this is a custom package, then it must be a named vector with the following fields:
metaDataSrc <- c( DBSCHEMA="the DB schema", ORGANISM="the organism", SPECIES="the species", MANUFACTURER="the manufacturer", CHIPNAME="the chipName", MANUFACTURERURL="the manufacturerUrl")
outputDir Where you would like the output files to be placed.
printSchema Boolean to indicate whether or not to produce an output of the schema (default is FALSE).

Examples

## Not run: 
  ##Set up the metadata
  my_metaDataSrc <- c( DBSCHEMA="the DB schema",
                    ORGANISM="the organism",
                    SPECIES="the species",
                    MANUFACTURER="the manufacturer",
                    CHIPNAME="the chipName",
                    MANUFACTURERURL="the manufacturerUrl")  

  ##Builds the org.Hs.eg sqlite:
  popHUMANDB(prefix="org.Hs.eg",
             chipSrc = "/mnt/cpb_anno/mcarlson/proj/sqliteGen/nli/annosrc/db/chipsrc_human.sqlite",
             metaDataSrc = my_metaDataSrc,
             printSchema=TRUE)

  ##Or if the package is a standard package (it probably isn't):
  ##Builds the org.Hs.eg sqlite:
  popHUMANDB(prefix="org.Hs.eg",
             chipSrc = "/mnt/cpb_anno/mcarlson/proj/sqliteGen/nli/annosrc/db/chipsrc_human.sqlite",
             metaDataSrc = "/mnt/cpb_anno/mcarlson/proj/sqliteGen/nli/annosrc/db/metadatasrc.sqlite",
             printSchema=TRUE)
## End(Not run)

[Package AnnotationDbi version 1.4.3 Index]