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:

        *  '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 _what_ and _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 _what_ and _where_ lead
           to the matching locations information is used. The element
           _what_ can be one of _package_, _environment_ or _file_. The
           element _where_ depends on the corresponding element _what_.

           *  if _package_: location for the package (like it would be
              for the argument 'lib.loc' for the function 'library'.)

           *  if _environment_: an 'environment' to look for the
              information (like the argument 'env' for the function
              'get').

           *  if _file_: a 'character' with the path in which a CDF
              file can be found.


_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)

