makeProbePackage {matchprobes} | R Documentation

## 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  = ".",
        force = FALSE, 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.
`force` | Logical. If `TRUE` overrides possible warnings
`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="matchprobes")
    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,
                     force      = TRUE)
    dir(outdir)

[Package matchprobes version 1.12.1 Index]