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

Description Usage Arguments Details Examples

View source: R/makeProbePackage.R

Description

Make a package with probe sequence related data for microarrays

Usage

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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

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

AnnotationForge documentation built on May 2, 2018, 3:19 a.m.