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 1.2.2 Index]