make.cdf.package         package:makecdfenv         R Documentation

_C_D_F _E_n_v_i_r_o_n_m_e_n_t _P_a_c_k_a_g_e _M_a_k_e_r

_D_e_s_c_r_i_p_t_i_o_n:

     This function reads an Affymetrix chip description file (CDF) and
     creates an R package that when loaded has the CDF environment
     available for use.

_U_s_a_g_e:

     make.cdf.package(filename,
       packagename  = NULL,
       cdf.path     = getwd(),   
       package.path = getwd(),
       compress     = FALSE,
       author       = "The Bioconductor Project",
       maintainer   = "Biocore Data Team <biocannotation@lists.fhcrc.org>",
       version      = packageDescription("makecdfenv", field="Version"),
       species      = NULL,
       unlink       = FALSE,
       verbose      = TRUE)

_A_r_g_u_m_e_n_t_s:

filename: Character. Filename of the CDF file - *without* the path
          prefix!

packagename: Character. Name wanted for the package.

cdf.path: Character. Path to the CDF file.

package.path: Character. Path where the package will be created.

compress: Logical. If 'TRUE', CDF file is compressed.

  author: Character. What to put in the 'author' field of the package.

maintainer: Character. What to put in the 'maintainer' field of the
          package.

 version: Character. What to put in the version field. Should be a of
          the form 'x.x.x'.

 species: Character. Must be specified using the format e.g.,
          Homo_sapiens

  unlink: Logical. If 'TRUE', and a package directory exists already in
          'package.path', that is overwritten.

 verbose: Logical. If 'TRUE' messages are shown.

_D_e_t_a_i_l_s:

     The function is called for its side effect, creating a package. By
     default the package name will be the name of the CDF file made
     lower case and with special characters removed (i.e. only
     alpha-numeric). 

     In general one would want to use the name given in by
     'cleancdfname(abatch@cdfName)' with 'abatch' an 'AffyBatch' object
     obtained, for example, using 'ReadAffy'. This is the package name
     that the 'affy' package looks for by default.

     If the user has a CEL file, called 'filename', the recommended
     package name for the environment is
     'cleancdfname(whatcdf(filename))'. This usually coincides with the
     default.

     Please see the vignette for more details.

_V_a_l_u_e:

     If success, the function returns the name of the created package.

_A_u_t_h_o_r(_s):

     Rafael A. Irizarry, Wolfgang Huber

_S_e_e _A_l_s_o:

     'make.cdf.env'

_E_x_a_m_p_l_e_s:

       pkgpath <- tempdir()
       make.cdf.package("Hu6800.CDF.gz",
                cdf.path=system.file("extdata", package="makecdfenv"),
                compress=TRUE, species = "Homo_sapiens",
                package.path = pkgpath)
       dir(pkgpath)     

