makeProbePackage         package:matchprobes         R Documentation

_M_a_k_e _a _p_a_c_k_a_g_e _w_i_t_h _p_r_o_b_e _s_e_q_u_e_n_c_e _r_e_l_a_t_e_d _d_a_t_a _f_o_r _m_i_c_r_o_a_r_r_a_y_s

_D_e_s_c_r_i_p_t_i_o_n:

     Make a package with probe sequence related data for microarrays

_U_s_a_g_e:

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

_A_r_g_u_m_e_n_t_s:

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'

_D_e_t_a_i_l_s:

     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 <URL: 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.

_E_x_a_m_p_l_e_s:

     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)

