Creates a sqlite database, and then makes an annotation package with it
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 BiocManager::install().
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)
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. |
## Not run:
##Build the hgu95av2.db package
makeDBPackage(
"HUMANCHIP_DB",
affy = TRUE,
prefix = "hgu95av2",
fileName = "~/proj/mcarlson/sqliteGen/srcFiles/hgu95av2/HG_U95Av2_annot.csv.070824",
otherSrc = c(
EA="~/proj/mcarlson/sqliteGen/srcFiles/hgu95av2/hgu95av2.EA.txt",
UMICH="~/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)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.