popYEASTCHIPDB {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

  popYEASTCHIPDB(affy, prefix, fileName, chipSrc, metaDataSrc,
  outputDir, printSchema)

Arguments

affy Boolean to indicate if this is starting from an affy csv file or not. If it is, then that will be parsed to make the sqlite file, if not, then you can feed a tab delimited file with IDs as was done before with AnnBuilder.
prefix prefix is the first part of the eventual desired package name. (ie. "prefix.sqlite")
fileName The path and filename for the file to be parsed. This can either be an affy csv file or it can be a more classic file type.
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 ag sqlite:
  popYEASTCHIPDB(affy=TRUE,
                 fileName="/mnt/cpb_anno/mcarlson/proj/sqliteGen/srcFiles/yeast2/Yeast_2_annot.csv.070824",
                 prefix="yeast2",
                 chipSrc = "/mnt/cpb_anno/mcarlson/proj/sqliteGen/nli/annosrc/db/chipsrc_yeast.sqlite",
                 metaDataSrc = my_metaDataSrc,
                 printSchema=TRUE)

  ##Or if the package is a standard package (it probably isn't):
  popYEASTCHIPDB(affy=TRUE,
                 fileName="/mnt/cpb_anno/mcarlson/proj/sqliteGen/srcFiles/yeast2/Yeast_2_annot.csv.070824",
                 prefix="yeast2",
                 chipSrc = "/mnt/cpb_anno/mcarlson/proj/sqliteGen/nli/annosrc/db/chipsrc_yeast.sqlite",
                 metaDataSrc = "/mnt/cpb_anno/mcarlson/proj/sqliteGen/nli/annosrc/db/metadatasrc.sqlite",
                 printSchema=TRUE)
## End(Not run)

[Package AnnotationDbi version 1.6.1 Index]