makeHUMANCHIP_DB {AnnotationDbi}R Documentation

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

  makeHUMANCHIP_DB(affy, prefix, fileName, otherSrc, chipMapSrc, chipSrc,
  baseMapType, outputDir, version, manufacturer, chipName,
  manufacturerUrl, author, maintainer)

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.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.
chipSrc The path and filename to the intermediate database containing the annotation data for the sqlite to build.
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.

Examples

## Not run: 
makeHUMANCHIP_DB(affy = TRUE,
                 prefix = "hgu95av2",
                 fileName = "/mnt/cpb_anno/mcarlson/proj/sqliteGen/srcFiles/hgu95av2/HG_U95Av2_annot.csv.070824",
                 otherSrc = c(
                   EA="/mnt/cpb_anno/mcarlson/proj/sqliteGen/srcFiles/hgu95av2/hgu95av2.EA.txt",
                   UMICH="/mnt/cpb_anno/mcarlson/proj/sqliteGen/srcFiles/hgu95av2/hgu95av2_UMICH.txt"),
                 chipMapSrc = "/mnt/cpb_anno/mcarlson/proj/sqliteGen/nli/annosrc/db/chipmapsrc_human.sqlite",
                 chipSrc = "/mnt/cpb_anno/mcarlson/proj/sqliteGen/nli/annosrc/db/chipsrc_human.sqlite",
                 baseMapType = "gbNRef",
                 version = "1.0.0",
                 manufacturer = "Affymetrix",
                 chipName = "hgu95av2",
                 manufacturerUrl = "http://www.affymetrix.com")
## End(Not run)

[Package AnnotationDbi version 1.6.1 Index]