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. 'mapCdfName' can bne
     loaded using 'data(mapCdfName)'.

_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")