affy-options              package:affy              R Documentation

_O_p_t_i_o_n_s _f_o_r _t_h_e _a_f_f_y _p_a_c_k_a_g_e

_D_e_s_c_r_i_p_t_i_o_n:

     Description of the options for the affy package.

_N_o_t_e:

     The affy package options are contained in the Bioconductor
     options. The options are: \begin{itemize}

     *  'use.widgets': a logical used to decide on the default of
        widget use.

     *  'compress.cel': a logical

     *  'compress.cdf': a logical

     *  'probes.loc': a list. Each element of the list is it self a
        list with two elements {\it what} and {\it where}. When looking
        for the informations about the locations of the probes on the
        array, the elements in the list will be looked at one after the
        other. The first one for which {\it what} and {\it where} lead
        to the matching locations information is used. The element {\it
        what} can be one of {\it package}, {\it environment} or {\it
        file}. The element {\it where} depends on the corresponding
        element {\it what}. \begin{itemize}

     *  if {\it package}: location for the package (like it would be
        for the argument 'lib.loc' for the function 'library'.

     *  if {\it environment}: an 'environment' to look for the
        information (like the argument 'env' for the function 'get').

     *  if {\it file}: a 'character' with the path in which a CDF file
        can be found. \end{itemize} \end{itemize}

_E_x_a_m_p_l_e_s:

     ## get the options
     opt <- getOption("BioC")
     affy.opt <- opt$affy

     ## list their names
     names(affy.opt)

     ## set the option compress.cel
     affy.opt$compress.cel <- TRUE
     options(BioC=opt)