makeDBPackage: Creates a sqlite database, and then makes an annotation package with it

Description

This function 1st creates a SQLite file useful for making a SQLite based annotation package by using the correct popXXXCHIP\_DB function. Next, this function produces an annotation package featuring the sqlite database produced. All makeXXXXChip_DB functions REQUIRE that you previously have installed the appropriate XXXX.db0 package. Call the function available.db0pkgs() to see what your options are, and then install the appropriate package with biocLite().

Usage

makeDBPackage(schema, ...)
#  usage case with required arguments
#  makeDBPackage(schema, affy, prefix, fileName, baseMapType, version)
#  usage case with all arguments
#  makeDBPackage(schema, affy, prefix, fileName, otherSrc, chipMapSrc,
#  chipSrc, baseMapType, outputDir, version, manufacturer, chipName,
#  manufacturerUrl, author, maintainer)

Arguments

schema

String listing the schema that you want to use to make the DB. You can list schemas with available.dbschemas()

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.db")

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.

otherSrc

The path and filenames to any other lists of IDs which might add information about how a probe will map.

chipMapSrc

The path and filename to the intermediate database containing the mapping data for allowed ID types and how these IDs relate to each other. If not provided, then the appropriate source DB from the most current .db0 package will be used instead.

chipSrc

The path and filename to the intermediate database containing the annotation data for the sqlite to build. If not provided, then the appropriate source DB from the most current .db0 package will be used instead.

baseMapType

The type of ID that is used for the initial base mapping. If using a classic base mapping file, this should be the ID type present in the fileName. This can be any of the following values: "gb" = for genbank IDs "ug" = unigene IDs "eg" = Entrez Gene IDs "refseq" = refseq IDs "gbNRef" = mixture of genbank and refseq IDs

outputDir

Where you would like the output files to be placed.

version

What is the version number for the desired package.

manufacturer

Who made the chip being described.

chipName

What is the name of the chip.

manufacturerUrl

URL for manufacturers website.

author

List of authors involved in making the package.

maintainer

List of package maintainers with email addresses for contact purposes.

...

Just used so we can have a wrapper function. Ignore this argument.

Examples

Run this code

## Not run: 
# ##Build the hgu95av2.db package
# makeDBPackage("HUMANCHIP_DB",
#               affy = TRUE,
#               prefix = "hgu95av2",
#               fileName = "/mnt/cpb_anno/mcarlson/proj/mcarlson/sqliteGen/srcFiles/hgu95av2/HG_U95Av2_annot.csv.070824",
#               otherSrc = c(
#                 EA="/mnt/cpb_anno/mcarlson/proj/mcarlson/sqliteGen/srcFiles/hgu95av2/hgu95av2.EA.txt",
#                 UMICH="/mnt/cpb_anno/mcarlson/proj/mcarlson/sqliteGen/srcFiles/hgu95av2/hgu95av2_UMICH.txt"),
#               baseMapType = "gbNRef",
#               version = "1.0.0",
#               manufacturer = "Affymetrix",
#               chipName = "hgu95av2",
#               manufacturerUrl = "http://www.affymetrix.com")
# ## End(Not run)

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