Make a package with probe sequence related data for microarrays
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
|
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 |
outdir |
Character. Path where the package is to be written. |
quiet |
Logical. If |
check |
Logical. If |
build |
Logical. If |
unlink |
Logical. If |
... |
Further arguments that get passed along to |
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)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.