makeProbePackage: Make a package with probe sequence related data for...
In AnnotationForge: Tools for building SQLite-based annotation data packages

Description Usage Arguments Details Examples

Make a package with probe sequence related data for microarrays

makeProbePackage(arraytype,
    importfun = "getProbeDataAffy",
    maintainer,
    version,
    species,
    pkgname = NULL,
    outdir  = ".",
    quiet = FALSE,
    check = TRUE, build = TRUE, unlink = TRUE, ...)

`arraytype`	Character. Name of array type (typically a vendor's name like "HG-U133A").
`importfun`	Character. Name of a function that can read the probe sequence data e.g. from a file. See `getProbeDataAffy` for an example.
`maintainer`	Character. Name and email address of the maintainer.
`version`	Character. Version number for the package.
`species`	Character. Species name in the format Genus\_species (e.g., Homo\_sapiens)
`pkgname`	Character. Name of the package. If missing, a name is created from `arraytype`.
`outdir`	Character. Path where the package is to be written.
`quiet`	Logical. If `TRUE` do not print statements on progress on the console
`check`	Logical. If `TRUE` call `R CMD check` on the package
`build`	Logical. If `TRUE` call `R CMD build` on the package
`unlink`	Logical. If `TRUE` unlink (remove) the `check` directory (only relevant if `check=TRUE`)
`...`	Further arguments that get passed along to `importfun`

See vignette.

Important note for Windows users: Building and checking packages requires some tools outside of R (e.g. a Perl interpreter). While these tools are standard with practically every Unix, they do not come with MS-Windows and need to be installed separately on your computer. See http://www.murdoch-sutherland.com/Rtools. If you just want to build probe packages, you will not need the compilers, and the "Windows help" stuff is optional.

filename <- system.file("extdata", "HG-U95Av2_probe_tab.gz", 
     package="AnnotationDbi")
outdir   <- tempdir()
me       <- "Wolfgang Huber <huber@ebi.ac.uk>"
makeProbePackage("HG-U95Av2",
                 datafile   = gzfile(filename, open="r"),
                 outdir     = outdir,
                 maintainer = me, 
                 version    = "0.0.1",
                 species    = "Homo_sapiens", 
                 check      = FALSE)
dir(outdir)