makeProbePackage: Make a package with probe sequence related data for...

In Bioconductor/AnnotationForge: Tools for building SQLite-based annotation data packages

Make a package with probe sequence related data for microarrays

Description

Make a package with probe sequence related data for microarrays

Usage

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

Arguments

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

Details

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.

Examples

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

Bioconductor/AnnotationForge documentation built on Nov. 2, 2024, 6:30 a.m.