cleancdfname              package:affy              R Documentation

_C_l_e_a_n _A_f_f_y_m_e_t_r_i_x'_s _C_D_F _n_a_m_e

_D_e_s_c_r_i_p_t_i_o_n:

     This function converts Affymetrix's names for CDF files to the
     names used in the annotation pacakge and in all Bioconductor.

_U_s_a_g_e:

     cleancdfname(cdfname, addcdf = TRUE)

_A_r_g_u_m_e_n_t_s:

 cdfname: A 'character' denoting Affymetrix'x CDF file name 

  addcdf: A 'logical'. If 'TRUE' it adds the string "cdf" at the end of
          the cleaned CDF name. This is used to name the 'cdfenvs'
          packages.

_D_e_t_a_i_l_s:

     This function takes a CDF filename obtained from an Affymetrix
     file (from a CEL file for example) and convert it to a convention
     of ours: all small caps and only alphanumeric characters. The
     details of the rule can be seen in the code. We observed
     exceptions that made us create a set of special cases for mapping
     CEL to CDF. The object 'mapCdfName' holds information about these
     cases. It is a 'data.frame' of three elements: the first is the
     name as found in the CDF file, the second the name in the CEL file
     and the third the name in bioconductor. (note: 'mapCdfName' is
     created dynamically each time you attach the package by a call to
     the function 'library' from the information in the file
     'mapCdfName.tab' in the 'data' directory of your installation of
     the package)

_V_a_l_u_e:

     A 'character'

_E_x_a_m_p_l_e_s:

     cdf.tags <- c("HG_U95Av2", "HG-133A")
     for (i in cdf.tags)
       cat(i, "becomes", cleancdfname(i), "\n")

